{ "generated_at": "2026-06-11T04:08:39Z", "source_files": [ "data/works.json", "data/work-enrichment.json", "data/software.json", "data/github-repositories.json", "data/people.json", "data/organizations.json", "data/claims.json", "data/resume.json" ], "count": 672, "items": [ { "id": "page:home", "type": "page", "title": "Daniel Ari Friedman", "url": "/", "summary": "Homepage and professional profile.", "tags": [ "homepage", "profile" ], "content": "Daniel Ari Friedman Homepage and professional profile. homepage profile" }, { "id": "page:publications", "type": "page", "title": "Publications", "url": "/publications.html", "summary": "Unified bibliography table.", "tags": [ "bibliography", "papers" ], "content": "Publications Unified bibliography table. bibliography papers" }, { "id": "page:works", "type": "page", "title": "Works Index", "url": "/works/", "summary": "Generated per-work bibliography pages.", "tags": [ "works", "citations" ], "content": "Works Index Generated per-work bibliography pages. works citations" }, { "id": "page:domains", "type": "page", "title": "Research Domains", "url": "/domains.html", "summary": "Domain landing pages and learning paths.", "tags": [ "domains" ], "content": "Research Domains Domain landing pages and learning paths. domains" }, { "id": "page:software", "type": "page", "title": "Software", "url": "/software.html", "summary": "Owned and AII software repositories.", "tags": [ "software", "github" ], "content": "Software Owned and AII software repositories. software github" }, { "id": "page:repositories", "type": "page", "title": "Repository Inventory", "url": "/repositories.html", "summary": "Full generated inventory of public docxology and AII GitHub repositories.", "tags": [ "software", "github", "inventory" ], "content": "Repository Inventory Full generated inventory of public docxology and AII GitHub repositories. software github inventory" }, { "id": "page:search", "type": "page", "title": "Search", "url": "/search.html", "summary": "Human-facing search over works, software, pages, people, organizations, and claims.", "tags": [ "search" ], "content": "Search Human-facing search over works, software, pages, people, organizations, and claims. search" }, { "id": "page:catalog", "type": "page", "title": "Data Catalog", "url": "/catalog.html", "summary": "Structured DataCatalog for public JSON exports.", "tags": [ "catalog", "structured data" ], "content": "Data Catalog Structured DataCatalog for public JSON exports. catalog structured data" }, { "id": "page:exports", "type": "page", "title": "Public Exports", "url": "/exports.html", "summary": "HTML index of citation exports and JSON datasets.", "tags": [ "exports", "citation", "bibtex" ], "content": "Public Exports HTML index of citation exports and JSON datasets. exports citation bibtex" }, { "id": "page:updates", "type": "page", "title": "Updates", "url": "/updates.html", "summary": "Human-readable changelog for the public research and discovery index.", "tags": [ "updates", "changelog" ], "content": "Updates Human-readable changelog for the public research and discovery index. updates changelog" }, { "id": "page:discovery", "type": "page", "title": "Discovery Map", "url": "/discovery.html", "summary": "Canonical identifiers and public source queries.", "tags": [ "agents" ], "content": "Discovery Map Canonical identifiers and public source queries. agents" }, { "id": "page:cite-verify", "type": "page", "title": "Cite & Verify", "url": "/cite-verify.html", "summary": "Citation and source-of-truth rules.", "tags": [ "citation" ], "content": "Cite & Verify Citation and source-of-truth rules. citation" }, { "id": "page:evidence", "type": "page", "title": "Evidence Ledger", "url": "/evidence.html", "summary": "Claim-level evidence and caveats.", "tags": [ "claims" ], "content": "Evidence Ledger Claim-level evidence and caveats. claims" }, { "id": "page:resume", "type": "document", "title": "Resume and CV", "url": "/resume/resume.pdf", "summary": "Generated resume/CV PDF, plaintext variants, and structured JSON.", "tags": [ "resume", "cv" ], "content": "Resume and CV Generated resume/CV PDF, plaintext variants, and structured JSON. resume cv" }, { "id": "page:resume-verify", "type": "page", "title": "Resume Verification", "url": "/resume/verify.html", "summary": "Hashes, source manifest, file sizes, QR target, and artifact links for the generated structured CV.", "tags": [ "resume", "cv", "verification", "hashes" ], "content": "Resume Verification Hashes, source manifest, file sizes, QR target, and artifact links for the generated structured CV. resume cv verification hashes" }, { "id": "page:collaborators", "type": "page", "title": "Collaborators", "url": "/collaborators.html", "summary": "Research collaborator network.", "tags": [ "people" ], "content": "Collaborators Research collaborator network. people" }, { "id": "page:media", "type": "page", "title": "Media", "url": "/media.html", "summary": "Talks, podcasts, videos, and press.", "tags": [ "media" ], "content": "Media Talks, podcasts, videos, and press. media" }, { "id": "page:art", "type": "page", "title": "Art", "url": "/art.html", "summary": "Visual art and Curio Cards work.", "tags": [ "art" ], "content": "Art Visual art and Curio Cards work. art" }, { "id": "page:changelog", "type": "document", "title": "Changelog", "url": "/CHANGELOG.md", "summary": "Public-index and generated-site change history.", "tags": [ "maintenance" ], "content": "Changelog Public-index and generated-site change history. maintenance" }, { "id": "page:redirects", "type": "document", "title": "Redirect And Canonical Policy", "url": "/docs/REDIRECTS.md", "summary": "Canonical URL and redirect-stub rules.", "tags": [ "canonical", "seo" ], "content": "Redirect And Canonical Policy Canonical URL and redirect-stub rules. canonical seo" }, { "id": "page:reconciliation", "type": "report", "title": "Public-Source Reconciliation Report", "url": "/reports/reconciliation_2026-06-09.md", "summary": "Curated local counts compared with public source indexes.", "tags": [ "evidence", "reports" ], "content": "Public-Source Reconciliation Report Curated local counts compared with public source indexes. evidence reports" }, { "id": "page:public-source-inventory", "type": "report", "title": "Public Source Inventory", "url": "/reports/public_source_inventory_2026-06-09.json", "summary": "Paginated public-source inventory for source discovery and claim auditing.", "tags": [ "evidence", "public sources", "reports" ], "content": "Public Source Inventory Paginated public-source inventory for source discovery and claim auditing. evidence public sources reports" }, { "id": "page:accessibility", "type": "report", "title": "Static Accessibility Report", "url": "/reports/accessibility_static_2026-06-09.json", "summary": "Static accessibility and metadata audit output.", "tags": [ "accessibility", "reports" ], "content": "Static Accessibility Report Static accessibility and metadata audit output. accessibility reports" }, { "id": "page:visual-qa", "type": "report", "title": "Visual QA Manifest", "url": "/reports/visual-qa/2026-05-28/manifest.json", "summary": "Desktop and mobile Playwright screenshots for key pages.", "tags": [ "visual", "qa" ], "content": "Visual QA Manifest Desktop and mobile Playwright screenshots for key pages. visual qa" }, { "id": "page:external-links", "type": "report", "title": "External Link Report", "url": "/reports/external_links_2026-05-15.json", "summary": "Cached network check over site-critical external links.", "tags": [ "links", "reports" ], "content": "External Link Report Cached network check over site-critical external links. links reports" }, { "id": "page:external-link-triage", "type": "report", "title": "External Link Triage", "url": "/reports/external_links_triage_2026-05-15.md", "summary": "Categorized warning report for scoped external links.", "tags": [ "links", "triage", "reports" ], "content": "External Link Triage Categorized warning report for scoped external links. links triage reports" }, { "id": "page:asset-size", "type": "report", "title": "Asset Size Audit", "url": "/reports/asset_size_2026-06-09.json", "summary": "Size report for public HTML, Open Graph images, data exports, and runtime assets.", "tags": [ "assets", "performance", "reports" ], "content": "Asset Size Audit Size report for public HTML, Open Graph images, data exports, and runtime assets. assets performance reports" }, { "id": "page:browser-smoke", "type": "report", "title": "Browser Smoke Manifest", "url": "/reports/browser-smoke/2026-05-28/manifest.json", "summary": "Selector-based browser smoke checks for core local pages.", "tags": [ "browser", "qa", "reports" ], "content": "Browser Smoke Manifest Selector-based browser smoke checks for core local pages. browser qa reports" }, { "id": "page:live-site", "type": "report", "title": "Live Site Verification", "url": "/reports/live_site_verification_2026-05-15.json", "summary": "Deployed-site status, expected markers, and GitHub Pages build state.", "tags": [ "deploy", "live", "reports" ], "content": "Live Site Verification Deployed-site status, expected markers, and GitHub Pages build state. deploy live reports" }, { "id": "page:generated", "type": "document", "title": "Generated Files", "url": "/GENERATED.md", "summary": "Generated artifact manifest and rebuild commands.", "tags": [ "generated", "maintenance" ], "content": "Generated Files Generated artifact manifest and rebuild commands. generated maintenance" }, { "id": "page:agent-start", "type": "document", "title": "Agent Start Guide", "url": "/AGENT_START.md", "summary": "Task recipes for agents using the repository.", "tags": [ "agents", "start" ], "content": "Agent Start Guide Task recipes for agents using the repository. agents start" }, { "id": "page:humans", "type": "document", "title": "Humans.txt", "url": "/humans.txt", "summary": "Human-maintained contact and site credits.", "tags": [ "contact", "humans" ], "content": "Humans.txt Human-maintained contact and site credits. contact humans" }, { "id": "page:release-snapshot", "type": "document", "title": "2026-05 Discovery Layer Release Snapshot", "url": "/docs/RELEASE_2026-05_DISCOVERY_LAYER.md", "summary": "Release note and validation gate for the discovery layer.", "tags": [ "release", "maintenance" ], "content": "2026-05 Discovery Layer Release Snapshot Release note and validation gate for the discovery layer. release maintenance" }, { "id": "work:Friedman2026TemplateApproachReproducibleGenerative001", "type": "work", "title": "A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication", "url": "/works/Friedman2026TemplateApproachReproducibleGenerative001.html", "external_url": "https://doi.org/10.5281/zenodo.19139090", "summary": "The reproducibility crisis in computational research is fundamentally structural: research artifacts are scattered across disconnected tools—LaTeX editors, Jupyter notebooks, ad-hoc shell scripts—with no enforced mechani", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "reproducible research", "infrastructure as code", "build pipeline", "Zero-Mock testing", "steganographic watermarking", "AI-agent documentation", "Model Context Protocol", "cryptographic provenance" ], "content": "A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication Zenodo 10.5281/zenodo.19139090 Friedman2026TemplateApproachReproducibleGenerative001 Computational Paper The reproducibility crisis in computational research is fundamentally structural: research artifacts are scattered across disconnected tools—LaTeX editors, Jupyter notebooks, ad-hoc shell scripts—with no enforced mechanism to keep code, data, and manuscript synchronized. template/ applies the principle of Infrastructure as Code to the research lifecycle, making the manuscript, test suite, and provenance chain version-controlled, deterministically buildable, and independently verifiable. It is built on a Two-Layer Architecture that separates 12 reusable infrastructure subpackages (~150 Python modules, validated by ~3,083 tests) from self-contained project workspaces, connected by an eight-stage build pipeline progressing from environment sanitization through test execution (with a Zero-Mock testing policy enforcing 90% project-level and 60% infrastructure-level coverage via real filesyste reproducible research infrastructure as code build pipeline Zero-Mock testing steganographic watermarking AI-agent documentation Model Context Protocol cryptographic provenance literate programming open science Introduces a Two-Layer Architecture separating reusable infrastructure (~150 modules, ~3,083 tests) from self-contained project workspaces Defines an eight-stage build pipeline from environment sanitization through LLM-assisted review Enforces a Zero-Mock testing policy (90% project / 60% infrastructure coverage) using real filesystem operations Implements SHA-256 cryptographic hashing with steganographic watermarking for provenance Introduces Documentation Duality (README.md + AGENTS.md) and SKILL.md aligned with Model Context Protocol Two-Layer Architecture: infrastructure subpackages vs. project workspaces Eight-stage build pipeline: sanitization → tests → analysis → Pandoc/XeLaTeX → SHA-256 → steganographic watermarking → PDF validation → LLM review Zero-Mock testing policy enforcing real filesystem and subprocess operations Documentation Duality standard with MCP-aligned SKILL.md files Comparative feature analysis against Snakemake, Nextflow, CWL, Quarto, Jupyter Book, R Markdown, Overleaf, DVC, OpenAI Prism" }, { "id": "work:Friedman2026ActiveInferenceJournal500002", "type": "work", "title": "Active Inference Journal — 500+ videos on Active Inference with transcripts", "url": "/works/Friedman2026ActiveInferenceJournal500002.html", "external_url": "https://video.activeinference.institute/", "summary": "Series · YouTube · Media & Teaching", "year": 2026, "domain": "Media & Teaching", "tags": [ "Series", "Media & Teaching", "bibliography" ], "content": "Active Inference Journal — 500+ videos on Active Inference with transcripts YouTube Friedman2026ActiveInferenceJournal500002 Media & Teaching Series" }, { "id": "work:Friedman2026BeforePragmatismHadName003", "type": "work", "title": "Before Pragmatism Had a Name: Blake's \"America A Prophecy\" Anticipates American Anticipatory Epistemology", "url": "/works/Friedman2026BeforePragmatismHadName003.html", "external_url": "https://doi.org/10.5281/zenodo.18807970", "summary": "This paper explores the intersections between prophetic vision and empirical inquiry through the lens of William Blake's 'America a Prophecy.' It aims to establish a framework for understanding how Blake's work anticipat", "year": 2026, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "William Blake", "pragmatism", "anticipatory epistemology", "America a Prophecy", "Peirce", "Dewey", "James", "prophetic vision" ], "content": "Before Pragmatism Had a Name: Blake's \"America A Prophecy\" Anticipates American Anticipatory Epistemology Zenodo 10.5281/zenodo.18807970 Friedman2026BeforePragmatismHadName003 Art & Synergetics Paper This paper explores the intersections between prophetic vision and empirical inquiry through the lens of William Blake's 'America a Prophecy.' It aims to establish a framework for understanding how Blake's work anticipates contemporary epistemological theories, particularly in relation to active inference. William Blake pragmatism anticipatory epistemology America a Prophecy Peirce Dewey James prophetic vision Establishes six structural convergences between Blake's prophetic vision and modern epistemological frameworks. Introduces the concept of 'active inference' as a bridge between prophetic vocabulary and formal process theory. Critiques Lockean empiricism through Blake's anti-empiricist stance, emphasizing innate ideas and active perception. Explores the implications of Blake's work for contemporary discussions in pragmatism and epistemology. Utilizes a comparative analysis of Blake's texts and modern epistemological theories. Applies complexity theory and dynamical systems to interpret Blake's fourfold vision. Employs a historical analysis of the philosophical context surrounding Blake's work. Integrates insights from active inference and pragmatism to develop a cohesive interpretive framework." }, { "id": "work:Friedman2026GoldenCompassLunarFlux004", "type": "work", "title": "The Golden Compass and the Lunar Flux: William Blake, Bimetallic Meta-stability, and the Architecture of Value", "url": "/works/Friedman2026GoldenCompassLunarFlux004.html", "external_url": "https://doi.org/10.5281/zenodo.19335196", "summary": "This manuscript overlays the history of British and American bimetallism with the mythopoetic architecture of William Blake’s prophetic corpus, reading the disintegration of the gold–silver standard as a material enactme", "year": 2026, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "William Blake", "Bimetallism", "Active Inference", "Newton", "Gresham's Law", "Hamilton", "William Jennings Bryan", "Value" ], "content": "The Golden Compass and the Lunar Flux: William Blake, Bimetallic Meta-stability, and the Architecture of Value Zenodo 10.5281/zenodo.19335196 Friedman2026GoldenCompassLunarFlux004 Art & Synergetics Paper This manuscript overlays the history of British and American bimetallism with the mythopoetic architecture of William Blake’s prophetic corpus, reading the disintegration of the gold–silver standard as a material enactment of the catastrophic cosmological fracture Blake dramatized. We trace this trajectory from the Newtonian golden compass of rigid, atomistic metrology, identifying the 1717 Mint ratio (1:15.21) not merely as a failed economic policy but as the operationalization of \"Newton's sleep\"—a cognitive pathology of pathologically rigid priors that crushed variable sensory evidence of silver’s circulation. This Urizenic enclosure unleashed Gresham's entropy, draining silver and hollowing out domestic coinage, leading to the 1797 Bank Restriction and the subsequent 1816 codification of a golden \"Single Vision\". This entropic pattern resonated transatlantically, reflecting the revol William Blake Bimetallism Active Inference Newton Gresham's Law Hamilton William Jennings Bryan Value Economic History Prophetic Economics Traces the trajectory from the 1717 Newtonian golden compass to the 1816 codification of \"Single Vision.\" Links the American metallic monetary arc (1873–1896) to the British entropic pattern in America a Prophecy . Bridges early industrial commodity fetishism with the contemporary (2020–2026) monetary environment. Prophetic Economics : Reconstructing Blake’s corpus as a sustained account of financialized alienation. Mythopoetic Mapping : Overlaying British and American bimetallic history with Blakean archetypes (Urizen, Orc, Los). Active Inference Economics : Analyzing monetary policy through the lens of prior rigidity and sensory evidence integration." }, { "id": "work:Friedman2026CognitiveIntegrityFrameworkFormal005", "type": "work", "title": "Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory)", "url": "/works/Friedman2026CognitiveIntegrityFrameworkFormal005.html", "external_url": "https://doi.org/10.5281/zenodo.18364119", "summary": "This paper presents the Cognitive Integrity Framework, which provides formal foundations for enhancing security in multiagent systems by addressing cognitive attack surfaces. It aims to establish a theoretical basis for ", "year": 2026, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "cognitive integrity", "multiagent security", "cognitive security", "Active Inference", "category theory", "formal foundations", "threat modeling" ], "content": "Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory) Zenodo 10.5281/zenodo.18364119 Friedman2026CognitiveIntegrityFrameworkFormal005 Cognitive Security Paper This paper presents the Cognitive Integrity Framework, which provides formal foundations for enhancing security in multiagent systems by addressing cognitive attack surfaces. It aims to establish a theoretical basis for understanding and mitigating vulnerabilities in cognitive operators and cyberphysical systems. cognitive integrity multiagent security cognitive security Active Inference category theory formal foundations threat modeling Introduction of the Cognitive Integrity Framework for multiagent security. Identification and analysis of cognitive attack surfaces in multiagent operators. Development of a trust calculus and detection bounds for cognitive systems. Proposing novel defense mechanisms tailored for cognitive security. Formal modeling of cognitive states and integrity properties. Trust computation and algebra to assess security postures. Anomaly detection techniques including cognitive drift scoring and behavioral deviation. Architectural and runtime defense strategies designed for cognitive systems." }, { "id": "work:Friedman2026PersonalYouTube200Livestreams006", "type": "work", "title": "Personal YouTube — 200+ livestreams: drawings, Synergetics, paper discussions", "url": "/works/Friedman2026PersonalYouTube200Livestreams006.html", "external_url": "https://www.youtube.com/@danielarifriedman/playlists", "summary": "Series · YouTube · Media & Teaching", "year": 2026, "domain": "Media & Teaching", "tags": [ "Series", "Media & Teaching", "bibliography" ], "content": "Personal YouTube — 200+ livestreams: drawings, Synergetics, paper discussions YouTube Friedman2026PersonalYouTube200Livestreams006 Media & Teaching Series" }, { "id": "work:Friedman2026DoorsPerceptionAreThreshold007", "type": "work", "title": "The Doors of Perception are the Threshold of Prediction: Active Inference and William Blake's Theory of Seeing", "url": "/works/Friedman2026DoorsPerceptionAreThreshold007.html", "external_url": "https://doi.org/10.5281/zenodo.18600041", "summary": "This paper explores the connections between William Blake's visionary concepts and the mathematical framework of Active Inference. It aims to synthesize these ideas to enhance understanding of perception and prediction i", "year": 2026, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "William Blake", "Active Inference", "perception", "prediction", "Thematic Atlas", "prophetic vision", "generative models", "Markov blankets" ], "content": "The Doors of Perception are the Threshold of Prediction: Active Inference and William Blake's Theory of Seeing Zenodo 10.5281/zenodo.18600041 Friedman2026DoorsPerceptionAreThreshold007 Art & Synergetics Paper This paper explores the connections between William Blake's visionary concepts and the mathematical framework of Active Inference. It aims to synthesize these ideas to enhance understanding of perception and prediction in cognitive processes. William Blake Active Inference perception prediction Thematic Atlas prophetic vision generative models Markov blankets Establishes eight thematic concordances between Blake's vision and Active Inference. Integrates philosophical insights with cognitive science to propose a novel framework for understanding perception. Explores the implications of Active Inference for creativity and transpersonal experiences. Utilizes a thematic analysis to draw parallels between Blake's concepts and Active Inference. Applies hierarchical generative models to explain cognitive processes. Employs the Free Energy Principle to frame discussions on perception and action." }, { "id": "work:Friedman20255thAppliedActiveInference008", "type": "work", "title": "5th Applied Active Inference Symposium — Abstract Book", "url": "/works/Friedman20255thAppliedActiveInference008.html", "external_url": "https://doi.org/10.5281/zenodo.17555266", "summary": "The 5th Applied Active Inference Symposium aims to enhance the accessibility and applicability of the Active Inference framework through collaborative discussions and presentations. It serves as a platform for researcher", "year": 2025, "domain": "Media & Teaching", "tags": [ "Presentation", "Media & Teaching", "bibliography", "Active Inference symposium", "conference proceedings", "international symposium", "research presentations" ], "content": "5th Applied Active Inference Symposium — Abstract Book Presentation 10.5281/zenodo.17555266 Friedman20255thAppliedActiveInference008 Media & Teaching Presentation The 5th Applied Active Inference Symposium aims to enhance the accessibility and applicability of the Active Inference framework through collaborative discussions and presentations. It serves as a platform for researchers and practitioners to share insights and advancements in the field. Active Inference symposium conference proceedings international symposium research presentations Showcases the latest research and applications of Active Inference. Facilitates networking and collaboration among researchers and practitioners. Promotes open science principles in the dissemination of knowledge. Includes interactive workshops to deepen understanding of Active Inference. Keynote presentations from leading experts in the field. Pre-recorded presentations to provide diverse perspectives. Live-streamed panels for real-time discussions. Interactive workshops to engage participants in hands-on learning." }, { "id": "work:Friedman2025AdaptiveBasicIncomeAuBI009", "type": "work", "title": "Adaptive Basic Income (AuBI): Integrating AI, Decentralized Infrastructure, and Active Inference", "url": "/works/Friedman2025AdaptiveBasicIncomeAuBI009.html", "external_url": "https://doi.org/10.5281/zenodo.17228945", "summary": "This paper introduces Adaptive Basic Income (AuBI), a novel framework that integrates artificial intelligence and decentralized infrastructure to enhance the effectiveness and adaptability of Universal Basic Income (UBI)", "year": 2025, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "AuBI", "augmented intelligence", "biological intelligence", "Active Inference", "cognitive augmentation", "human-AI interaction" ], "content": "Adaptive Basic Income (AuBI): Integrating AI, Decentralized Infrastructure, and Active Inference Zenodo 10.5281/zenodo.17228945 Friedman2025AdaptiveBasicIncomeAuBI009 Computational Paper This paper introduces Adaptive Basic Income (AuBI), a novel framework that integrates artificial intelligence and decentralized infrastructure to enhance the effectiveness and adaptability of Universal Basic Income (UBI) systems. It proposes a systems engineering toolkit for modeling and deploying next-generation economic frameworks that leverage real-time learning and decentralized governance. AuBI augmented intelligence biological intelligence Active Inference cognitive augmentation human-AI interaction Introduces the concept of Adaptive Basic Income (AuBI) as a dynamic alternative to traditional UBI. Proposes a systems engineering toolkit for specifying and modeling economic systems. Explores the integration of AI and decentralized technologies to improve UBI implementation. Encourages experimentation and collaboration among policymakers and researchers. Utilizes active inference theory to inform economic modeling. Employs decentralized ledger technologies for transparent and tamper-proof infrastructure. Incorporates predictive analytics to refine UBI interventions based on real-time data. Adopts a B2B2C model to facilitate the deployment of AuBI systems through various stakeholders." }, { "id": "work:Friedman2025CEREBRUMCaseEnabledReasoning010", "type": "work", "title": "CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling", "url": "/works/Friedman2025CEREBRUMCaseEnabledReasoning010.html", "external_url": "https://doi.org/10.5281/zenodo.15170907", "summary": "This paper introduces the Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling (CEREBRUM), a synthetic intelligence framework that integrates linguistic case systems with cognitive scientific ", "year": 2025, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "CEREBRUM", "linguistic case systems", "Active Inference", "Bayesian modeling", "model management", "case grammar", "unified modeling" ], "content": "CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling Zenodo 10.5281/zenodo.15170907 Friedman2025CEREBRUMCaseEnabledReasoning010 Active Inference Paper This paper introduces the Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling (CEREBRUM), a synthetic intelligence framework that integrates linguistic case systems with cognitive scientific principles to describe and deploy generative models. CEREBRUM establishes a formal linguistic-type calculus for cognitive model use, addressing the complexity in computational and cognitive modeling systems. CEREBRUM linguistic case systems Active Inference Bayesian modeling model management case grammar unified modeling Integration of linguistic case systems with cognitive modeling principles. Establishment of a formal linguistic-type calculus for cognitive models. Structured representation of model ecosystems aligned with scientific principles. Addressing complexity in generative and decentralized intelligence systems. Application of category theory to cognitive modeling. Utilization of the Free Energy Principle in model descriptions. Development of a formal framework for cognitive models as case-bearing entities. Implementation of hierarchical message passing for dynamic adaptive processes." }, { "id": "work:Friedman2025ComputationalComplexityEnergeticsAnt011", "type": "work", "title": "Computational Complexity and Energetics of the Ant Stack", "url": "/works/Friedman2025ComputationalComplexityEnergeticsAnt011.html", "external_url": "https://doi.org/10.5281/zenodo.17238736", "summary": "This paper investigates the computational complexity and energetics of the Ant Stack, a framework inspired by biological systems. It aims to provide insights into energy-aware robotics and computational co-design by anal", "year": 2025, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "AntStack", "complexity science", "information theory", "complex adaptive systems", "ant colonies", "non-equilibrium thermodynamics" ], "content": "Computational Complexity and Energetics of the Ant Stack Zenodo 10.5281/zenodo.17238736 Friedman2025ComputationalComplexityEnergeticsAnt011 Entomology Paper This paper investigates the computational complexity and energetics of the Ant Stack, a framework inspired by biological systems. It aims to provide insights into energy-aware robotics and computational co-design by analyzing the interplay between computational demands and energy efficiency. AntStack complexity science information theory complex adaptive systems ant colonies non-equilibrium thermodynamics Introduction of the Ant Stack as a novel framework for energy-aware robotics. Development of a comprehensive energy analysis methodology tailored for robotic systems. Identification of key design principles derived from biological systems to enhance computational efficiency. Empirical validation of theoretical models through real-world benchmarking against actual ant energetics. Utilization of a multi-scale analysis framework for computational workload modeling. Implementation of an energy decomposition framework to estimate energy consumption. Application of real-time complexity analysis to evaluate computational constraints. Integration of uncertainty quantification techniques to enhance model reliability." }, { "id": "work:Friedman2025EvoJumpStochasticModelingEvolutionary012", "type": "work", "title": "EvoJump: Stochastic Modeling of Evolutionary Ontogenetic Trajectories", "url": "/works/Friedman2025EvoJumpStochasticModelingEvolutionary012.html", "external_url": "https://doi.org/10.5281/zenodo.17229924", "summary": "This paper presents EvoJump, a unified framework for stochastic modeling of evolutionary ontogenetic trajectories, aiming to enhance the understanding of biological processes through advanced statistical methods. The fra", "year": 2025, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "evolutionary transitions", "EvoJump", "Active Inference", "major transitions", "phenotypic complexity", "Free Energy Principle" ], "content": "EvoJump: Stochastic Modeling of Evolutionary Ontogenetic Trajectories Zenodo 10.5281/zenodo.17229924 Friedman2025EvoJumpStochasticModelingEvolutionary012 Active Inference Paper This paper presents EvoJump, a unified framework for stochastic modeling of evolutionary ontogenetic trajectories, aiming to enhance the understanding of biological processes through advanced statistical methods. The framework integrates various stochastic processes to analyze evolutionary patterns and dynamics effectively. evolutionary transitions EvoJump Active Inference major transitions phenotypic complexity Free Energy Principle Development of a unified framework for stochastic modeling in evolutionary biology. Integration of multiple stochastic processes, including Ornstein-Uhlenbeck and Lévy processes. Application of advanced statistical methods such as wavelet analysis and copula methods. Insights into evolutionary dynamics through case studies, including Drosophila analysis. Utilization of stochastic process modeling techniques, including Ornstein-Uhlenbeck and Cox-Ingersoll-Ross processes. Implementation of wavelet analysis for multi-scale temporal patterns. Application of copula methods for analyzing trait dependencies. Use of Bayesian inference for parameter estimation and model validation." }, { "id": "work:Friedman2025IncreasingAccessibilityApplicabilityActive013", "type": "work", "title": "Increasing the Accessibility and Applicability of Active Inference", "url": "/works/Friedman2025IncreasingAccessibilityApplicabilityActive013.html", "external_url": "https://doi.org/10.5281/zenodo.15061667", "summary": "This paper outlines initiatives by the Active Inference Institute to enhance the accessibility and applicability of Active Inference through the development of generative playbooks and an open-source Summer School curric", "year": 2025, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "accessibility", "Active Inference", "pedagogy", "summer school curriculum", "Generative Playbooks", "open-source education", "neurotechnology", "neurodiversity" ], "content": "Increasing the Accessibility and Applicability of Active Inference Zenodo 10.5281/zenodo.15061667 Friedman2025IncreasingAccessibilityApplicabilityActive013 Active Inference Paper This paper outlines initiatives by the Active Inference Institute to enhance the accessibility and applicability of Active Inference through the development of generative playbooks and an open-source Summer School curriculum. The goal is to empower diverse communities to engage with cognitive modeling and foster collaborative learning. accessibility Active Inference pedagogy summer school curriculum Generative Playbooks open-source education neurotechnology neurodiversity cognitive security Creation of generative playbooks for open-source cognitive modeling. Development of an open-source curriculum for a Summer School in Active Inference. Integration of community perspectives into educational materials. Promotion of accessibility in cognitive modeling for diverse audiences. Co-creation of playbooks with community members through working groups. Utilization of generative AI for multilingual and multimedia educational materials. Design of a Summer School curriculum incorporating multiple disciplinary perspectives. Feedback loops with advisory boards and participants for iterative improvement." }, { "id": "work:Friedman2025MDKVMultitrackMarkdownContainer014", "type": "work", "title": "MDKV: A Multitrack Markdown Container for Structured, Portable Documents", "url": "/works/Friedman2025MDKVMultitrackMarkdownContainer014.html", "external_url": "https://doi.org/10.5281/zenodo.16790554", "summary": "This paper introduces MDKV, a multitrack Markdown container designed to manage multilingual, multi-audience, and multi-channel documents by packaging canonical content and auxiliary tracks into a single, portable .mdkv f", "year": 2025, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "MDKV", "Markdown", "key-value format", "structured data", "document specification", "YAML-free", "round-trip transformation" ], "content": "MDKV: A Multitrack Markdown Container for Structured, Portable Documents Zenodo 10.5281/zenodo.16790554 Friedman2025MDKVMultitrackMarkdownContainer014 Computational Paper This paper introduces MDKV, a multitrack Markdown container designed to manage multilingual, multi-audience, and multi-channel documents by packaging canonical content and auxiliary tracks into a single, portable .mdkv file. The MDKV format enhances document governance, reproducibility, and editing efficiency by separating concerns into distinct tracks. MDKV Markdown key-value format structured data document specification YAML-free round-trip transformation A precise model and container format with minimal but sufficient validation. A modular architecture separating model, storage, and services, accessible via CLI and GUI. Detailed use cases for multilingual publishing, layered collaboration, and reproducible distribution. Guidance for cryptographic provenance and conformance. Introduced a ZIP archive format containing a YAML manifest and UTF-8 Markdown files. Formalized the MDKV model and presented its software architecture. Evaluated design trade-offs against adjacent technologies. Provided a CLI and a small GUI for selective preview and live editing." }, { "id": "work:Friedman2025MarkdownDecisionProcessFramework015", "type": "work", "title": "Markdown Decision Process: A Framework for Probabilistic Document Analysis", "url": "/works/Friedman2025MarkdownDecisionProcessFramework015.html", "external_url": "https://doi.org/10.5281/zenodo.17244386", "summary": "The Markdown Decision Process (MDP) framework transforms document processing by modeling Markdown documents as stochastic decision processes, facilitating intelligent analysis, generation, and optimization through probab", "year": 2025, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "Markdown Decision Process", "document analysis", "Markov chains", "reinforcement learning", "POMDP", "probabilistic modeling", "document generation" ], "content": "Markdown Decision Process: A Framework for Probabilistic Document Analysis Zenodo 10.5281/zenodo.17244386 Friedman2025MarkdownDecisionProcessFramework015 Computational Paper The Markdown Decision Process (MDP) framework transforms document processing by modeling Markdown documents as stochastic decision processes, facilitating intelligent analysis, generation, and optimization through probabilistic modeling. It integrates decision theory with document engineering, allowing for the generation of coherent documents and structural optimization based on user-defined quality criteria. Markdown Decision Process document analysis Markov chains reinforcement learning POMDP probabilistic modeling document generation Introduction of the Markdown Decision Process framework for document processing. Development of MarkChain for higher-order dependency document generation. Implementation of PolicyOptimizer for reinforcement learning-based document optimization. Creation of an extensible Plugin Architecture for domain-specific customizations. Utilization of Markov chains and graph algorithms for document analysis. Application of reinforcement learning techniques for optimizing document structure. Incorporation of Bayesian belief maintenance for handling semantic ambiguity. Deployment of a comprehensive Visualization Framework for exploring document state spaces." }, { "id": "work:Friedman2025CognitiveArtScienceToward016", "type": "work", "title": "On Cognitive Art & Science: Toward Wholeness From Both Sides", "url": "/works/Friedman2025CognitiveArtScienceToward016.html", "external_url": "https://doi.org/10.5281/zenodo.16740439", "summary": "This paper positions cognitive science as the systematic study of intra-action and cognitive art as its reflexive counterpart, exploring a bidirectional trajectory toward systemic wholeness. It proposes a four-fold schem", "year": 2025, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "cognitive art-science", "aesthetic experience", "creative cognition", "Active Inference", "art-science integration" ], "content": "On Cognitive Art & Science: Toward Wholeness From Both Sides Zenodo 10.5281/zenodo.16740439 Friedman2025CognitiveArtScienceToward016 Art & Synergetics Paper This paper positions cognitive science as the systematic study of intra-action and cognitive art as its reflexive counterpart, exploring a bidirectional trajectory toward systemic wholeness. It proposes a four-fold schema that integrates procedural craft, conceptual articulation, adaptive intelligence, and the observing niche to balance exploitation with exploration in cognitive processes. cognitive art-science aesthetic experience creative cognition Active Inference art-science integration Introduces a four-fold schema linking procedural craft, conceptual articulation, adaptive intelligence, and the observing niche. Proposes a novel perspective on cognitive science as a study of intra-action and cognitive art as its reflexive twin. Explores the balance between exploitation and exploration in cognitive processes through a systemic approach. Suggests the integration of modern computer science and cryptography in developing information architectures for cognitive systems. Utilizes a four-fold schema to analyze cognitive processes and their interrelations. Applies Active Inference from a Low Road perspective for variational approximation in cognitive modeling. Employs alternating analytical moves (2→3) and generative moves (4→3) to compress past data and open space for future possibilities. Integrates empirical specifics with mathematical generalizations for flexible systems modeling." }, { "id": "work:Friedman2025Time017", "type": "work", "title": "On Time", "url": "/works/Friedman2025Time017.html", "external_url": "https://doi.org/10.5281/zenodo.15168381", "summary": "This paper introduces Narrative Information Management (NIM) as a framework to address the challenges of information dynamics across various fields, emphasizing the need for synthesis and exchange of knowledge and tools.", "year": 2025, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "temporal dynamics", "Active Inference", "synchronization", "collective behavior", "temporal coordination" ], "content": "On Time Zenodo 10.5281/zenodo.15168381 Friedman2025Time017 Art & Synergetics Paper This paper introduces Narrative Information Management (NIM) as a framework to address the challenges of information dynamics across various fields, emphasizing the need for synthesis and exchange of knowledge and tools. By proposing NIM, the authors aim to unify disparate disciplines facing similar information-related challenges and provide insights into effective information systems. temporal dynamics Active Inference synchronization collective behavior temporal coordination Proposes Narrative Information Management (NIM) as a unifying framework for addressing information dynamics. Identifies common features of impactful information systems across various disciplines. Explores insights and solutions from eclectic fields facing information challenges. Provides recommendations for future research on NIM. Conducts a broad summary of challenges faced by information-centered disciplines. Synthesizes a set of common features contributing to effective NIM systems. Explores domain-specific challenges and ad-hoc solutions in various fields. Assesses common features found across discussed domains to inform future work." }, { "id": "work:Friedman2025QuadMathAnalyticalReview4D018", "type": "work", "title": "QuadMath: An Analytical Review of 4D and Quadray Coordinates", "url": "/works/Friedman2025QuadMathAnalyticalReview4D018.html", "external_url": "https://doi.org/10.5281/zenodo.16887800", "summary": "This paper presents an analytical review of 4D and Quadray coordinates, focusing on their mathematical foundations and practical applications. It aims to integrate various frameworks and methodologies to enhance understa", "year": 2025, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "QuadMath", "Quadray coordinates", "4D geometry", "Synergetics", "Buckminster Fuller", "IVM lattice", "rational arithmetic", "computational geometry" ], "content": "QuadMath: An Analytical Review of 4D and Quadray Coordinates Zenodo 10.5281/zenodo.16887800 Friedman2025QuadMathAnalyticalReview4D018 Art & Synergetics Paper This paper presents an analytical review of 4D and Quadray coordinates, focusing on their mathematical foundations and practical applications. It aims to integrate various frameworks and methodologies to enhance understanding and usability in complex systems. QuadMath Quadray coordinates 4D geometry Synergetics Buckminster Fuller IVM lattice rational arithmetic computational geometry Introduction of a comprehensive 4D namespace framework for mathematical modeling. Development of new algorithms for Quadray coordinates and their applications in optimization. Integration of information geometry with Quadray models to improve computational efficiency. Exploration of practical implementations and educational resources for broader accessibility. Mathematical formulation of 4D coordinates and their properties. Implementation of optimization algorithms, including Nelder-Mead on integer lattices. Use of Fisher information metrics for analyzing geometrical properties. Development of Python-based computational tools for practical applications." }, { "id": "work:Friedman2025ResNeiSolutionDesignDocument019", "type": "work", "title": "ResNei: Solution Design Document", "url": "/works/Friedman2025ResNeiSolutionDesignDocument019.html", "external_url": "https://doi.org/10.5281/zenodo.15389682", "summary": "ResNei is an AI-augmented environment aimed at transforming the discovery, analysis, and connection of ideas through a dynamic knowledge graph. It promotes collaboration among generalists and specialists, fostering an in", "year": 2025, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "ResNei", "Research Neighbourhood", "collaborative research", "distributed collaboration", "interdisciplinary", "knowledge sharing" ], "content": "ResNei: Solution Design Document Zenodo 10.5281/zenodo.15389682 Friedman2025ResNeiSolutionDesignDocument019 Computational Paper ResNei is an AI-augmented environment aimed at transforming the discovery, analysis, and connection of ideas through a dynamic knowledge graph. It promotes collaboration among generalists and specialists, fostering an interconnected research ecosystem. ResNei Research Neighbourhood collaborative research distributed collaboration interdisciplinary knowledge sharing Introduction of the Research Discovery Engine that creates a responsive knowledge graph. Development of Conceptual Nexus Models (CNMs) for modular representation of ideas. Shift from passive systems to a dynamic, action-intention model for enhanced collaboration. Focus on reciprocity, interdependence, and social accountability in research. Utilization of a graphical concept model to facilitate engagement between specialists and generalists. Implementation of a dynamic linking system for an evolving corpus of scientific knowledge. Adoption of scientific protocols to ensure reliable evaluation of scientific output. Integration of UX design principles that prioritize collaboration and contextual insight." }, { "id": "work:Friedman2025SymergeticsSymbolicSynergeticsRational020", "type": "work", "title": "Symergetics: Symbolic Synergetics for Rational Arithmetic", "url": "/works/Friedman2025SymergeticsSymbolicSynergeticsRational020.html", "external_url": "https://doi.org/10.5281/zenodo.17114389", "summary": "This paper introduces Symergetics, an open-source Python package designed to address the precision limitations of floating-point arithmetic in geometric calculations by providing exact rational arithmetic methods within ", "year": 2025, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "Symergetics", "Synergetics", "Buckminster Fuller", "rational arithmetic", "Quadray coordinates", "IVM lattice", "symbolic computation", "computational geometry" ], "content": "Symergetics: Symbolic Synergetics for Rational Arithmetic Zenodo 10.5281/zenodo.17114389 Friedman2025SymergeticsSymbolicSynergeticsRational020 Art & Synergetics Paper This paper introduces Symergetics, an open-source Python package designed to address the precision limitations of floating-point arithmetic in geometric calculations by providing exact rational arithmetic methods within the Synergetics framework. It enables accurate geometric pattern discovery and all-integer accounting necessary for exploring Buckminster Fuller's principles. Symergetics Synergetics Buckminster Fuller rational arithmetic Quadray coordinates IVM lattice symbolic computation computational geometry Development of the Symergetics package for exact rational arithmetic in geometric computations. Implementation of a Quadray coordinate system for precise tetrahedral geometry. Exact volume calculations for Platonic solids using isotropic vector matrix (IVM) units. Pattern analysis algorithms for Scheherazade numbers and primorial sequences using exact arithmetic. Utilization of exact rational arithmetic with automatic simplification to eliminate approximation errors. Adoption of a Quadray coordinate system to maintain spatial relationships in tetrahedral geometry. Execution of volume calculations for Platonic solids based on IVM units. Implementation of pattern discovery algorithms that leverage exact arithmetic for enhanced mathematical insights." }, { "id": "work:Friedman2025SynthesisAgentNiche021", "type": "work", "title": "Synthesis of Agent and Niche", "url": "/works/Friedman2025SynthesisAgentNiche021.html", "external_url": "https://doi.org/10.5281/zenodo.17235137", "summary": "This paper explores the interplay between William Blake's revolutionary vision and ecological psychology, proposing a synthesis of agent and niche through the lens of oppositional forces that generate stability and progr", "year": 2025, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "William Blake", "Marriage of Heaven and Hell", "ecological psychology", "Active Inference", "Synergetics", "contraries", "predictive processing", "Markov blankets" ], "content": "Synthesis of Agent and Niche Zenodo 10.5281/zenodo.17235137 Friedman2025SynthesisAgentNiche021 Art & Synergetics Paper This paper explores the interplay between William Blake's revolutionary vision and ecological psychology, proposing a synthesis of agent and niche through the lens of oppositional forces that generate stability and progression. It argues that without contraries, there is no progression, and highlights the importance of dynamical coupling in understanding life and consciousness. William Blake Marriage of Heaven and Hell ecological psychology Active Inference Synergetics contraries predictive processing Markov blankets visionary epistemology art-science synthesis Introduces a novel framework for understanding the relationship between agents and their environments through Blake's philosophical insights. Explores the concept of synergetic opposition as a generative principle in ecological psychology. Demonstrates the relevance of thermodynamic principles in the transformation of information within ecological contexts. Links bacterial motility to cultural evolution, illustrating the scalability of adaptive behaviors. Utilizes philosophical analysis of William Blake's texts to derive ecological insights. Applies concepts from thermodynamics and information theory to ecological psychology. Employs a comparative analysis of biological and cultural evolution to illustrate adaptive behaviors. Explores mathematical models of consciousness and measurement in relation to ecological systems." }, { "id": "work:Friedman2025SystemsProcessesActiveInference022", "type": "work", "title": "Systems Processes, Active Inference, and Beyond", "url": "/works/Friedman2025SystemsProcessesActiveInference022.html", "external_url": "https://doi.org/10.5281/zenodo.17138223", "summary": "This paper explores the connections between systems processes and active inference, aiming to enhance the understanding of systems science. It discusses the implications of these concepts for cognitive security and broad", "year": 2025, "domain": "Media & Teaching", "tags": [ "Presentation", "Media & Teaching", "bibliography", "systems processes", "Active Inference", "systems science", "metatheory", "process philosophy", "anticipatory systems" ], "content": "Systems Processes, Active Inference, and Beyond Presentation 10.5281/zenodo.17138223 Friedman2025SystemsProcessesActiveInference022 Media & Teaching Presentation This paper explores the connections between systems processes and active inference, aiming to enhance the understanding of systems science. It discusses the implications of these concepts for cognitive security and broader scientific inquiry. systems processes Active Inference systems science metatheory process philosophy anticipatory systems Introduces a novel framework linking systems processes to active inference. Provides insights into the application of active inference in cognitive security. Offers a comprehensive discussion on the evolution of systems science. Presents open-source resources for further exploration and engagement. Utilizes a conceptual analysis of systems processes and active inference. Incorporates discussions and insights from collaborative meetings with experts. Analyzes existing literature and resources related to active inference. Engages with open-source platforms to disseminate findings." }, { "id": "work:Friedman2025TemporalDepthCoherentSelf023", "type": "work", "title": "Temporal Depth in a Coherent Self and in Depersonalization", "url": "/works/Friedman2025TemporalDepthCoherentSelf023.html", "external_url": "https://doi.org/10.3389/fpsyg.2025.1585315", "summary": "This paper proposes a theoretical framework for understanding dissociative experiences by integrating various perspectives, including nonlinear dynamical systems and neurobiology. It posits that a significant change in '", "year": 2025, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "temporal depth", "depersonalization", "self-coherence", "Active Inference", "predictive processing", "temporal integration", "clinical psychology" ], "content": "Temporal Depth in a Coherent Self and in Depersonalization Frontiers in Psychology 10.3389/fpsyg.2025.1585315 Friedman2025TemporalDepthCoherentSelf023 Active Inference Paper This paper proposes a theoretical framework for understanding dissociative experiences by integrating various perspectives, including nonlinear dynamical systems and neurobiology. It posits that a significant change in 'temporal depth' may serve as a common factor in the onset of dissociative episodes across different etiologies. temporal depth depersonalization self-coherence Active Inference predictive processing temporal integration clinical psychology Introduces a novel framework for integrating diverse theoretical models of dissociation. Highlights the concept of 'temporal depth' as a potential common factor in dissociative experiences. Proposes a causal relationship between temporal depth collapse and dissociative symptoms. Sets the stage for future empirical studies and therapeutic applications based on the proposed model. Combines first-principles-based perspectives with nonlinear dynamical systems. Utilizes clinical and neurobiological insights to inform the theoretical model. Plans to employ computer simulations to test the model's computational components. Aims to integrate phenomenological data with abstract theoretical models." }, { "id": "work:Friedman2025ActiveInferenceInstituteActive024", "type": "work", "title": "The Active Inference Institute & Active Inference Ecosystem (v3, 2025 snapshot)", "url": "/works/Friedman2025ActiveInferenceInstituteActive024.html", "external_url": "https://doi.org/10.5281/zenodo.17982447", "summary": "The Active Inference Institute (AII) is dedicated to advancing the understanding and application of the Active Inference framework through education and research. It aims to enhance accessibility and rigor in the field, ", "year": 2025, "domain": "AII Ecosystem", "tags": [ "Paper", "AII Ecosystem", "bibliography", "Active Inference Institute", "organizational overview", "research programs", "educational initiatives", "community" ], "content": "The Active Inference Institute & Active Inference Ecosystem (v3, 2025 snapshot) Zenodo 10.5281/zenodo.17982447 Friedman2025ActiveInferenceInstituteActive024 AII Ecosystem Paper The Active Inference Institute (AII) is dedicated to advancing the understanding and application of the Active Inference framework through education and research. It aims to enhance accessibility and rigor in the field, fostering a collaborative environment for individuals from diverse backgrounds. Active Inference Institute organizational overview research programs educational initiatives community Establishment of a participatory Open Science institute focused on Active Inference. Creation of a living document to facilitate direct interaction and learning. Development of various programs and projects to engage the community in Active Inference. Provision of resources such as podcasts, videos, and collaborative textbooks. Utilization of interactive platforms like Discord for community engagement. Implementation of projects that encourage collaborative learning and research. Organization of events and activities to promote knowledge sharing. Curating educational materials and resources for diverse audiences." }, { "id": "work:Friedman2025AntStack025", "type": "work", "title": "The Ant Stack", "url": "/works/Friedman2025AntStack025.html", "external_url": "https://doi.org/10.5281/zenodo.16782756", "summary": "The Ant Stack is a modular framework designed to emulate an ant's physical and cognitive functions, comprising three layers: AntBody, AntBrain, and AntMind. It aims to facilitate research in myrmecology and synthetic int", "year": 2025, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "AntStack", "multilevel modeling", "ant colonies", "social insects", "multiscale biology", "colony organization" ], "content": "The Ant Stack Zenodo 10.5281/zenodo.16782756 Friedman2025AntStack025 Entomology Paper The Ant Stack is a modular framework designed to emulate an ant's physical and cognitive functions, comprising three layers: AntBody, AntBrain, and AntMind. It aims to facilitate research in myrmecology and synthetic intelligence through its interoperable design and explicit input/output contracts. AntStack multilevel modeling ant colonies social insects multiscale biology colony organization An explicit, executable Input/Output contract between Body, Brain, and Mind layers. A compact neural control pipeline with local plasticity. A minimal active-inference ant nestmate agent that composes via stigmergy. A standardized evaluation suite with species presets for direct replication. Coupling physics-based locomotion with olfactory-visual sensing. Implementing a lightweight neural pipeline for active-inference policy selection. Using pheromone-mediated stigmergy for agent composition. Specifying evaluation suites for navigation, task allocation, and robustness." }, { "id": "work:Friedman2025DiscoveryEngineAIDriven026", "type": "work", "title": "The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge Landscapes", "url": "/works/Friedman2025DiscoveryEngineAIDriven026.html", "external_url": "https://doi.org/10.48550/arXiv.2505.17500", "summary": "This paper introduces the Discovery Engine, a framework designed to transform disconnected scientific literature into a unified, computable representation, addressing challenges of information overload and reproducibilit", "year": 2025, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "Discovery Engine", "automated discovery", "Active Inference", "scientific reasoning", "hypothesis generation", "computational science" ], "content": "The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge Landscapes ArXiv 10.48550/arXiv.2505.17500 Friedman2025DiscoveryEngineAIDriven026 Computational Paper This paper introduces the Discovery Engine, a framework designed to transform disconnected scientific literature into a unified, computable representation, addressing challenges of information overload and reproducibility in research. By distilling publications into structured knowledge artifacts and encoding them into a Conceptual Tensor, the framework enables AI-driven exploration and synthesis of scientific knowledge. Discovery Engine automated discovery Active Inference scientific reasoning hypothesis generation computational science Introduces the Discovery Engine as a novel framework for synthesizing scientific knowledge. Transforms disconnected literature into structured 'knowledge artifacts' for better accessibility. Develops a Conceptual Tensor that serves as a compressed representation of scientific fields. Facilitates AI agents' interaction with knowledge graphs to identify connections and gaps in research. Employs LLM-driven Structured Knowledge Distillation to extract verifiable knowledge components. Utilizes a Conceptual Nexus Model (CNM) as an evolving knowledge graph for specific research domains. Incorporates hybrid approaches combining dense vector embeddings and relational structure encoding. Enables dynamic 'unrolling' of the Conceptual Tensor into human-interpretable views like knowledge graphs." }, { "id": "work:Friedman2025ThoughtseedsHierarchicalAgenticFramework027", "type": "work", "title": "Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought Dynamics in Meditative States", "url": "/works/Friedman2025ThoughtseedsHierarchicalAgenticFramework027.html", "external_url": "https://doi.org/10.3390/e27050459", "summary": "The Thoughtseeds Framework presents a novel computational model for understanding thought dynamics during meditative states, conceptualizing thoughtseeds as dynamic attentional agents. This hierarchical model simulates f", "year": 2025, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Thoughtseeds", "meditation", "thought dynamics", "hierarchical modeling", "agentic framework", "Active Inference", "attention", "mindfulness" ], "content": "Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought Dynamics in Meditative States Entropy 10.3390/e27050459 Friedman2025ThoughtseedsHierarchicalAgenticFramework027 Active Inference Paper The Thoughtseeds Framework presents a novel computational model for understanding thought dynamics during meditative states, conceptualizing thoughtseeds as dynamic attentional agents. This hierarchical model simulates focused-attention Vipassana meditation and reveals insights into attention regulation and meta-cognitive awareness. Thoughtseeds meditation thought dynamics hierarchical modeling agentic framework Active Inference attention mindfulness Introduces the Thoughtseeds Framework for modeling thought dynamics in meditation. Integrates Global Workspace Theory and the Intrinsic Ignition Framework to elucidate meditative experiences. Demonstrates the framework's applicability through simulations comparing novice and expert meditators. Offers a biologically plausible perspective on cognitive state emergence and transitions. Employs a hierarchical model structured as nested Markov blankets. Simulates focused-attention Vipassana meditation using rule-based training informed by neuroscience. Utilizes computational modeling combined with phenomenological insights. Applies the framework to investigate meditative states and mind-wandering episodes." }, { "id": "work:Friedman2025TowardsScienceConsciousnessSocial028", "type": "work", "title": "Towards a Science of Consciousness and Social Complexity... For Ants", "url": "/works/Friedman2025TowardsScienceConsciousnessSocial028.html", "external_url": "https://www.editorafi.org/ebook/c128-colonias-formigas-conscientes", "summary": "This paper explores the concept of consciousness in ant colonies, examining whether these collective entities possess a form of awareness. It discusses the implications of collective minds from both scientific and philos", "year": 2025, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "consciousness", "ant colonies", "Ant Colony Test", "information integration", "collective cognition", "meta-cognition" ], "content": "Towards a Science of Consciousness and Social Complexity... For Ants Book Chapter Friedman2025TowardsScienceConsciousnessSocial028 Entomology Paper This paper explores the concept of consciousness in ant colonies, examining whether these collective entities possess a form of awareness. It discusses the implications of collective minds from both scientific and philosophical perspectives. consciousness ant colonies Ant Colony Test information integration collective cognition meta-cognition Introduces a framework for assessing consciousness in non-human entities. Explores the philosophical implications of collective intelligence in ant colonies. Analyzes existing literature on consciousness and collective behavior in social insects. Proposes new avenues for research in the intersection of philosophy and biology. Literature review of current theories on consciousness and collective behavior. Philosophical analysis of the concept of mind in relation to ant colonies. Comparative analysis of ant behavior and cognitive processes. Interdisciplinary approach combining insights from biology, philosophy, and cognitive science." }, { "id": "work:Friedman2024AligningActiveInferenceOntology029", "type": "work", "title": "Aligning Active Inference Ontology to SUMO", "url": "/works/Friedman2024AligningActiveInferenceOntology029.html", "external_url": "https://doi.org/10.5281/zenodo.11459322", "summary": "This paper presents a framework for aligning the Active Inference Ontology with the Suggested Upper Merged Ontology (SUMO) to enhance the mapping of concepts across various scientific and humanistic fields. The goal is t", "year": 2024, "domain": "AII Ecosystem", "tags": [ "Paper", "AII Ecosystem", "bibliography", "ontology alignment", "SUMO", "Active Inference Ontology", "knowledge representation", "formal ontology", "semantic mapping" ], "content": "Aligning Active Inference Ontology to SUMO Zenodo 10.5281/zenodo.11459322 Friedman2024AligningActiveInferenceOntology029 AII Ecosystem Paper This paper presents a framework for aligning the Active Inference Ontology with the Suggested Upper Merged Ontology (SUMO) to enhance the mapping of concepts across various scientific and humanistic fields. The goal is to provide a structured approach to identify relationships between Active Inference terms and SUMO entities, facilitating a comprehensive understanding of their interrelations. ontology alignment SUMO Active Inference Ontology knowledge representation formal ontology semantic mapping Establishes a preliminary alignment between Active Inference terms and SUMO entities. Identifies relevant SUMO files that contain mappings for Active Inference topics. Proposes a structured methodology for mapping complex concepts across disciplines. Facilitates multilingual technical term integration within the Active Inference framework. Utilizes an alignment table to display relationships between Active Inference and SUMO terms. Employs a systematic approach to categorize Active Inference topics into modules. Analyzes existing SUMO files to identify appropriate mappings for Active Inference concepts. Defines core, entailed, and supplemental topics to organize the presentation of Active Inference data." }, { "id": "work:Friedman2024BioFirmDevelopmentAtApplied030", "type": "work", "title": "BioFirm Development at Applied Active Inference Symposium 2024", "url": "/works/Friedman2024BioFirmDevelopmentAtApplied030.html", "external_url": "https://doi.org/10.5281/zenodo.14861595", "summary": "BioFirm applies Active Inference and the Free Energy Principle to organizational and bioregional stewardship. The framework models organizations as biological-inspired adaptive systems, using active inference to optimize", "year": 2024, "domain": "Media & Teaching", "tags": [ "Presentation", "Media & Teaching", "bibliography", "BioFirm", "bioregional stewardship", "Active Inference", "organizational modeling", "sustainability", "adaptive management" ], "content": "BioFirm Development at Applied Active Inference Symposium 2024 Presentation 10.5281/zenodo.14861595 Friedman2024BioFirmDevelopmentAtApplied030 Media & Teaching Presentation BioFirm applies Active Inference and the Free Energy Principle to organizational and bioregional stewardship. The framework models organizations as biological-inspired adaptive systems, using active inference to optimize resource management and collective decision-making in bioregional governance contexts. BioFirm bioregional stewardship Active Inference organizational modeling sustainability adaptive management Develops BioFirm framework for bioregional stewardship via Active Inference Models organizational governance as biological adaptive systems Active Inference organizational modeling Bioregional analysis Adaptive systems design" }, { "id": "work:Friedman2024BridgingGapsImageMeme031", "type": "work", "title": "Bridging gaps in image meme research: A multidisciplinary paradigm", "url": "/works/Friedman2024BridgingGapsImageMeme031.html", "external_url": "https://doi.org/10.1002/asi.24900", "summary": "This paper presents a multidisciplinary framework, the Digital Rhetorical Ecosystem (DRE3), for scaling up qualitative analyses of image memes, examining them as quasi-arguments that influence public narratives on politi", "year": 2024, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "image memes", "meme research", "digital communication", "narrative analysis", "rhetorical analysis", "sensemaking" ], "content": "Bridging gaps in image meme research: A multidisciplinary paradigm JASIST 10.1002/asi.24900 Friedman2024BridgingGapsImageMeme031 Cognitive Security Paper This paper presents a multidisciplinary framework, the Digital Rhetorical Ecosystem (DRE3), for scaling up qualitative analyses of image memes, examining them as quasi-arguments that influence public narratives on political and social issues. It integrates rhetorical analysis with ecological frameworks and computational methods to address the identification of claims in memes, bridging qualitative and quantitative research approaches. image memes meme research digital communication narrative analysis rhetorical analysis sensemaking Introduces the Digital Rhetorical Ecosystem (DRE3) framework for analyzing image memes. Integrates rhetorical theory with ecological frameworks to study the evolution of memetic claims. Applies computational methods to enhance the identification of claims in image memes at scale. Addresses the social, political, and cultural dimensions of information phenomena related to image memes. Utilizes a multidisciplinary approach combining rhetorical analysis and ecological frameworks. Employs computational techniques for large-scale claim identification in image memes. Analyzes the interaction and evolution of memetic claims within information ecosystems. Collects and curates diverse image meme samples from various social media platforms." }, { "id": "work:Friedman2024ChemicalTranscriptomicDiversityDo032", "type": "work", "title": "Chemical and transcriptomic diversity do not correlate with ascending levels of social complexity in Blattodea", "url": "/works/Friedman2024ChemicalTranscriptomicDiversityDo032.html", "external_url": "https://doi.org/10.1002/ece3.70063", "summary": "This study investigates the relationship between chemical profile complexity and social complexity in the insect order Blattodea, focusing on cuticular hydrocarbons (CHCs) across solitary and eusocial species. Contrary t", "year": 2024, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "Blattodea", "cockroach diversity", "termites", "insect ecology", "eusociality", "taxonomy", "evolutionary biology" ], "content": "Chemical and transcriptomic diversity do not correlate with ascending levels of social complexity in Blattodea Ecology & Evolution 10.1002/ece3.70063 Friedman2024ChemicalTranscriptomicDiversityDo032 Entomology Paper This study investigates the relationship between chemical profile complexity and social complexity in the insect order Blattodea, focusing on cuticular hydrocarbons (CHCs) across solitary and eusocial species. Contrary to expectations, the findings reveal no consistent correlation between chemical complexity and social organization, suggesting a need for a more nuanced understanding of these relationships. Blattodea cockroach diversity termites insect ecology eusociality taxonomy evolutionary biology Challenges the assumption that social complexity in insects is reflected in chemical profile complexity. Provides empirical data comparing CHC complexity across different social structures within Blattodea. Explores the genetic diversity of CHC biosynthesis genes in relation to social complexity. Highlights the need for refined methodologies in assessing chemical complexity across species. Compared CHC complexity and transcriptomic data across selected Blattodea species representing varying social complexities. Utilized gas chromatography coupled with tandem mass spectrometry (GC–MS/MS) for CHC analysis. Constructed a chemical dendrogram based on CHC divergence and correlated it with molecular phylogeny. Analyzed whole-genome transcriptomes to assess CHC biosynthesis gene diversity." }, { "id": "work:Friedman2024CommentsNationalDigitalTwins033", "type": "work", "title": "Comments on National Digital Twins R&D Strategic Plan", "url": "/works/Friedman2024CommentsNationalDigitalTwins033.html", "external_url": "https://doi.org/10.5281/zenodo.13273681", "summary": "This paper provides insights and recommendations for the development of a National Digital Twins R&D Strategic Plan, emphasizing the importance of addressing trustworthiness, reliability, and responsible use in the imple", "year": 2024, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "digital twins", "Active Inference", "generative models", "predictive processing", "cyber-physical systems", "simulation" ], "content": "Comments on National Digital Twins R&D Strategic Plan Zenodo 10.5281/zenodo.13273681 Friedman2024CommentsNationalDigitalTwins033 Cognitive Security Paper This paper provides insights and recommendations for the development of a National Digital Twins R&D Strategic Plan, emphasizing the importance of addressing trustworthiness, reliability, and responsible use in the implementation of Digital Twins. It argues that while Digital Twins offer significant potential, they also pose risks that must be managed to prevent future challenges. digital twins Active Inference generative models predictive processing cyber-physical systems simulation Synthesis of perspectives on Digital Twin implementation from diverse organizations and disciplines. Recommendations addressing data management, trustworthiness, and responsible use of Digital Twins. Highlighting the historical context and lessons learned from previous approaches to similar technologies. Emphasizing the need for interdisciplinary collaboration in the development of Digital Twins. Interdisciplinary collaboration among universities, think-tanks, and industry experts. Analysis of historical applications and vulnerabilities related to Digital Twins. Development of recommendations based on a comprehensive review of existing literature and practices. Consideration of business, operational, legal, technical, and social factors in Digital Twin implementation." }, { "id": "work:Friedman2024EnhancingPopulationBasedSearch034", "type": "work", "title": "Enhancing Population-based Search with Active Inference", "url": "/works/Friedman2024EnhancingPopulationBasedSearch034.html", "external_url": "https://doi.org/10.48550/arXiv.2408.09548", "summary": "This paper proposes the integration of Active Inference into traditional population-based metaheuristics to enhance their performance through anticipatory environmental adaptation. Specifically, it demonstrates this appr", "year": 2024, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "population search", "Active Inference", "Ant Colony Optimization", "TSP", "metaheuristics", "anticipatory adaptation", "computational optimization" ], "content": "Enhancing Population-based Search with Active Inference ArXiv 10.48550/arXiv.2408.09548 Friedman2024EnhancingPopulationBasedSearch034 Active Inference Paper This paper proposes the integration of Active Inference into traditional population-based metaheuristics to enhance their performance through anticipatory environmental adaptation. Specifically, it demonstrates this approach using Ant Colony Optimization on the Travelling Salesman Problem, showing improved solutions with minimal computational cost increase. population search Active Inference Ant Colony Optimization TSP metaheuristics anticipatory adaptation computational optimization Integration of Active Inference into population-based metaheuristics. Application of the proposed method to Ant Colony Optimization for the Travelling Salesman Problem. Demonstration of improved solution quality with marginal computational cost increase. Identification of performance patterns related to graph node number and topology. Utilization of Active Inference framework for anticipatory adaptation. Experimental evaluation of Ant Colony Optimization with Active Inference. Analysis of performance based on varying graph structures. Comparison of traditional reactive approaches with the proposed anticipatory model." }, { "id": "work:Friedman2024FarmWorksDecentralizedAIAgents035", "type": "work", "title": "FarmWorks: Decentralized AI Agents for Personalized Solutions", "url": "/works/Friedman2024FarmWorksDecentralizedAIAgents035.html", "external_url": "https://doi.org/10.5281/zenodo.13754585", "summary": "FarmWorks is a decentralized AI-powered agricultural platform designed to empower individual farmers by providing personalized solutions while resisting the centralization of power associated with traditional AI systems.", "year": 2024, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "FarmWorks", "decentralized AI", "precision agriculture", "Active Inference", "sensor networks", "edge computing", "farmer autonomy", "sustainable agriculture" ], "content": "FarmWorks: Decentralized AI Agents for Personalized Solutions Zenodo 10.5281/zenodo.13754585 Friedman2024FarmWorksDecentralizedAIAgents035 Cognitive Security Paper FarmWorks is a decentralized AI-powered agricultural platform designed to empower individual farmers by providing personalized solutions while resisting the centralization of power associated with traditional AI systems. The platform integrates real-time data collection, edge computing, and Active Inference models to enhance decision-making and promote sustainable agricultural practices. FarmWorks decentralized AI precision agriculture Active Inference sensor networks edge computing farmer autonomy sustainable agriculture IoT community-driven innovation Development of an open-source decentralized AI platform for agriculture. Empowerment of farmers through personalized, context-aware decision support. Community-driven approach fostering knowledge sharing and innovation. Implementation of an ethical framework for AI deployment aligned with human values. Integration of customizable sensor networks for real-time data collection. Use of Active Inference models for personalized recommendations. Decentralized data processing to enhance privacy and security. Virtual assistant for natural language interaction with farmers." }, { "id": "work:Friedman2024FederatedInferenceBeliefSharing036", "type": "work", "title": "Federated inference and belief sharing", "url": "/works/Friedman2024FederatedInferenceBeliefSharing036.html", "external_url": "https://doi.org/10.1016/j.neubiorev.2023.105500", "summary": "This paper explores federated inference and belief-sharing among agents in a shared environment, demonstrating how communication and language can emerge from minimizing free energy. Through simulations, it illustrates th", "year": 2024, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "federated inference", "belief sharing", "Active Inference", "distributed intelligence", "multi-agent systems", "message passing", "collective cognition", "privacy-preserving inference" ], "content": "Federated inference and belief sharing Neuroscience & Biobehavioral Reviews 10.1016/j.neubiorev.2023.105500 Friedman2024FederatedInferenceBeliefSharing036 Active Inference Paper This paper explores federated inference and belief-sharing among agents in a shared environment, demonstrating how communication and language can emerge from minimizing free energy. Through simulations, it illustrates the processes of inference, learning, and model selection that facilitate collective intelligence and the development of language. federated inference belief sharing Active Inference distributed intelligence multi-agent systems message passing collective cognition privacy-preserving inference Introduces the concept of federated inference through belief-sharing among agents. Demonstrates the emergence of language as a byproduct of free energy minimization. Provides a framework for understanding collective intelligence in ensembles of agents. Explores the implications of belief-sharing for cultural niche construction and complexity in self-organizing systems. Utilizes numerical simulations to model belief-sharing and active inference among synthetic agents. Applies the free energy principle to describe the dynamics of belief updating and communication. Examines the acquisition of language through active learning and the transmission of beliefs across generations. Employs Bayesian model selection to illustrate structure learning in generative models." }, { "id": "work:Friedman2024FourFoldFieldsQuantum037", "type": "work", "title": "Four-fold Fields of Quantum Dreams", "url": "/works/Friedman2024FourFoldFieldsQuantum037.html", "external_url": "https://doi.org/10.5281/zenodo.10798145", "summary": "This paper explores the concept of situational awareness in the context of a Quantum Baseball training environment, emphasizing the interplay between individual and collective experiences. It aims to analyze how visual a", "year": 2024, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "quantum mechanics", "art", "phenomenology", "Active Inference", "visual analysis", "symbolism", "Morse code" ], "content": "Four-fold Fields of Quantum Dreams Zenodo 10.5281/zenodo.10798145 Friedman2024FourFoldFieldsQuantum037 Art & Synergetics Paper This paper explores the concept of situational awareness in the context of a Quantum Baseball training environment, emphasizing the interplay between individual and collective experiences. It aims to analyze how visual and phenomenological factors influence performance and preparation in a multi-agential setting. quantum mechanics art phenomenology Active Inference visual analysis symbolism Morse code Introduces the concept of Quantum Baseball as a metaphor for situational awareness and training. Analyzes the dynamics of individual and collective experiences in a training environment. Explores the implications of visual-phenomenological moments on performance. Provides a framework for understanding the relationship between agents and their environment. Utilizes a qualitative analysis of visual experiences during training sessions. Employs metaphorical frameworks to interpret situational dynamics. Incorporates cognitive theories related to visual perception and awareness. Examines the interaction between individual actions and collective training scenarios." }, { "id": "work:Friedman2024MathArtStream8William038", "type": "work", "title": "MathArt Stream #8: William Blake and Active Inference", "url": "/works/Friedman2024MathArtStream8William038.html", "external_url": "https://doi.org/10.5281/zenodo.13711301", "summary": "This work explores the intersection of mathematics, art, and William Blake's prophetic vision. Through formal analysis of Blake's visual and poetic works, we identify mathematical structures and patterns that resonate wi", "year": 2024, "domain": "Media & Teaching", "tags": [ "Presentation", "Media & Teaching", "bibliography", "William Blake", "mathematics", "art", "prophetic vision", "geometric structures", "Active Inference" ], "content": "MathArt Stream #8: William Blake and Active Inference Presentation 10.5281/zenodo.13711301 Friedman2024MathArtStream8William038 Media & Teaching Presentation This work explores the intersection of mathematics, art, and William Blake's prophetic vision. Through formal analysis of Blake's visual and poetic works, we identify mathematical structures and patterns that resonate with modern frameworks in geometry, topology, and Active Inference. William Blake mathematics art prophetic vision geometric structures Active Inference Identifies mathematical structures in Blake's visual and poetic works Connects Blake's artistic vision to modern mathematical frameworks Mathematical analysis of visual art Formal pattern identification Art-science comparative analysis" }, { "id": "work:Friedman2024SensemakingFederationExploringFrontiers039", "type": "work", "title": "Sensemaking Federation: Exploring the Frontiers of Digital Innovation", "url": "/works/Friedman2024SensemakingFederationExploringFrontiers039.html", "external_url": "https://doi.org/10.5281/zenodo.14574046", "summary": "This paper discusses the concept of knowledge federation within the realm of sensemaking, highlighting the establishment of a global open Sensemaking Federation. It explores the dynamics of inter-entity connections and t", "year": 2024, "domain": "Media & Teaching", "tags": [ "Presentation", "Media & Teaching", "bibliography", "sensemaking federation", "digital innovation", "knowledge federation", "collaborative sensemaking", "decentralized infrastructure" ], "content": "Sensemaking Federation: Exploring the Frontiers of Digital Innovation Presentation 10.5281/zenodo.14574046 Friedman2024SensemakingFederationExploringFrontiers039 Media & Teaching Presentation This paper discusses the concept of knowledge federation within the realm of sensemaking, highlighting the establishment of a global open Sensemaking Federation. It explores the dynamics of inter-entity connections and the role of digital public libraries in maintaining knowledge artifacts. sensemaking federation digital innovation knowledge federation collaborative sensemaking decentralized infrastructure Introduction of the concept of digital public libraries as knowledge federation servers. Development of a framework for understanding epistemic communities through K-Hubs. Integration of game-based elements to enhance collaborative sensemaking. Exploration of advanced topic mapping techniques for knowledge organization. Facilitation of a panel discussion with experts in sensemaking and digital innovation. Use of topic mapping to create structured knowledge graphs. Incorporation of game mechanics to foster skills in deep listening and idea synthesis. Engagement of diverse participants to explore the federation of meaning." }, { "id": "work:Friedman2024SharedProtentionsMultiAgent040", "type": "work", "title": "Shared Protentions in Multi-Agent Active Inference", "url": "/works/Friedman2024SharedProtentionsMultiAgent040.html", "external_url": "https://doi.org/10.3390/e26040303", "summary": "This paper integrates concepts from Husserlian phenomenology, active inference, and category theory to create a framework for understanding social action based on shared goals. It emphasizes the role of shared protention", "year": 2024, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "shared protentions", "multi-agent", "Active Inference", "anticipation", "coupled generative models", "coordination", "predictive processing" ], "content": "Shared Protentions in Multi-Agent Active Inference Entropy 10.3390/e26040303 Friedman2024SharedProtentionsMultiAgent040 Active Inference Paper This paper integrates concepts from Husserlian phenomenology, active inference, and category theory to create a framework for understanding social action based on shared goals. It emphasizes the role of shared protentions among agents and their connection to collective goal-directed behavior. shared protentions multi-agent Active Inference anticipation coupled generative models coordination predictive processing Development of a comprehensive framework linking phenomenology, active inference, and category theory. Formalization of shared goals in terms of shared protentions within multi-agent systems. Introduction of mathematical tools from category theory to model interactions among agents. Exploration of the emergence of group intentionality through shared protentions. Review of Husserlian phenomenology focusing on inner time-consciousness concepts. Application of active inference as a formal approach to model agent behavior. Utilization of sheaf and topos theory to represent agent interactions and shared understanding. Construction of a 'consensus topos' to analyze social action based on shared goals." }, { "id": "work:Friedman2024ActiveInferenceInstituteActive041", "type": "work", "title": "The Active Inference Institute & Active Inference Ecosystem (v2, 2024 snapshot)", "url": "/works/Friedman2024ActiveInferenceInstituteActive041.html", "external_url": "https://doi.org/10.5281/zenodo.14108992", "summary": "Updated overview of the Active Inference Institute (AII), documenting expanded organizational activities, new projects, and growing community engagement in Active Inference research, education, and application.", "year": 2024, "domain": "AII Ecosystem", "tags": [ "Paper", "AII Ecosystem", "bibliography", "Active Inference Institute", "organizational update", "open science", "community" ], "content": "The Active Inference Institute & Active Inference Ecosystem (v2, 2024 snapshot) Zenodo 10.5281/zenodo.14108992 Friedman2024ActiveInferenceInstituteActive041 AII Ecosystem Paper Updated overview of the Active Inference Institute (AII), documenting expanded organizational activities, new projects, and growing community engagement in Active Inference research, education, and application. Active Inference Institute organizational update open science community Documents AII organizational growth and expanded activities Organizational documentation" }, { "id": "work:Friedman2024WayFindingInfiniteImaginarium042", "type": "work", "title": "Way Finding in the Infinite Imaginarium", "url": "/works/Friedman2024WayFindingInfiniteImaginarium042.html", "external_url": "https://doi.org/10.5281/zenodo.10601082", "summary": "This paper explores the concept of 'Way Finding' within the framework of the 'Infinite Imaginarium,' contrasting different epistemic modes and tempos. It aims to elucidate how individuals navigate knowledge and understan", "year": 2024, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "epistemic tempos", "knowledge production", "creative exploration", "way finding", "imagination", "operational frameworks" ], "content": "Way Finding in the Infinite Imaginarium Zenodo 10.5281/zenodo.10601082 Friedman2024WayFindingInfiniteImaginarium042 Art & Synergetics Paper This paper explores the concept of 'Way Finding' within the framework of the 'Infinite Imaginarium,' contrasting different epistemic modes and tempos. It aims to elucidate how individuals navigate knowledge and understanding in both known and unknown territories. epistemic tempos knowledge production creative exploration way finding imagination operational frameworks Introduces the framework of the Infinite Imaginarium to conceptualize knowledge navigation. Differentiates between 'gap-filling' and 'gap-respecting' epistemic modes. Explores the cognitive processes involved in verbal expression and question formulation. Provides a novel perspective on situational-ecological intelligence in cognitive engagements. Utilizes metaphorical constructs like dominos and Jenga towers to illustrate cognitive processes. Analyzes linguistic and semiotic mechanisms in verbal communication. Employs a comparative approach to examine different epistemic modes. Incorporates examples of cognitive engagement in educational contexts." }, { "id": "work:Friedman2024WhyPaleolithicRockstarsWere043", "type": "work", "title": "Why Paleolithic Rockstars were both enigmatic and sporadic", "url": "/works/Friedman2024WhyPaleolithicRockstarsWere043.html", "external_url": "https://doi.org/10.1016/j.plrev.2024.04.010", "summary": "An exploration of Paleolithic art and its relationship to cognitive evolution, consciousness, and creative expression. The work examines cave paintings and rock art as evidence of early human cognitive capabilities and t", "year": 2024, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "Paleolithic art", "cave paintings", "cognitive evolution", "consciousness", "aesthetic experience", "rock art" ], "content": "Why Paleolithic Rockstars were both enigmatic and sporadic Physics of Life Reviews 10.1016/j.plrev.2024.04.010 Friedman2024WhyPaleolithicRockstarsWere043 Genetics & Biomedical Paper An exploration of Paleolithic art and its relationship to cognitive evolution, consciousness, and creative expression. The work examines cave paintings and rock art as evidence of early human cognitive capabilities and their connection to modern theories of consciousness and aesthetic experience. Paleolithic art cave paintings cognitive evolution consciousness aesthetic experience rock art Connects Paleolithic art to modern theories of consciousness and cognition Examines rock art as evidence of early creative and cognitive capabilities Archaeological evidence analysis Cognitive evolution framework Aesthetic theory application" }, { "id": "work:Friedman2024WritingCurioCardsNFT044", "type": "work", "title": "Writing on Curio Cards for the \"On NFT\" book", "url": "/works/Friedman2024WritingCurioCardsNFT044.html", "external_url": "https://www.worldcat.org/isbn/978-3-8365-9970-2", "summary": "Curio Cards is recognized in NFT archaeology as an early art NFT project on Ethereum, launched in 2017, which helped establish a new model for the creation and ownership of digital artwork. The project features contribut", "year": 2024, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "Curio Cards", "research ideation", "creativity tools", "interdisciplinary thinking", "prompt-based exploration" ], "content": "Writing on Curio Cards for the \"On NFT\" book Taschen Friedman2024WritingCurioCardsNFT044 Art & Synergetics Paper Curio Cards is recognized in NFT archaeology as an early art NFT project on Ethereum, launched in 2017, which helped establish a new model for the creation and ownership of digital artwork. The project features contributions from seven artists and introduces computational features that connect art and its social context. Curio Cards research ideation creativity tools interdisciplinary thinking prompt-based exploration Pioneered the creation of collectible digital art on the Ethereum blockchain. Introduced unique features in the ERC-721 Non-Fungible Token Standard. Provided a platform for artists to receive value and engage with collectors. Showcased a variety of artistic styles and media, including the first physical artworks and animated GIFs on Ethereum. Utilized Ethereum blockchain technology for the creation and ownership of NFTs. Incorporated various artistic media such as digital art, printmaking, and animation. Engaged multiple artists with distinct styles to create a diverse collection. Developed a permanent online gallery to showcase the artwork." }, { "id": "work:Friedman2023GuidedTourThroughSpaces045", "type": "work", "title": "A guided tour through the spaces of particular \"minds\"", "url": "/works/Friedman2023GuidedTourThroughSpaces045.html", "external_url": "https://doi.org/10.1016/j.plrev.2023.11.001", "summary": "This commentary reflects on the paper 'Path integrals, particular kinds, and strange things' by Friston et al., emphasizing the need for a rigorous taxonomy of minds in light of recent advancements in AI. It discusses ho", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "path integrals", "particular kinds", "mindspace", "Active Inference", "Free Energy Principle", "consciousness", "Sloman", "non-anthropocentric" ], "content": "A guided tour through the spaces of particular \"minds\" Physics of Life Reviews 10.1016/j.plrev.2023.11.001 Friedman2023GuidedTourThroughSpaces045 Active Inference Paper This commentary reflects on the paper 'Path integrals, particular kinds, and strange things' by Friston et al., emphasizing the need for a rigorous taxonomy of minds in light of recent advancements in AI. It discusses how the proposed typology of particular kinds can contribute to mapping the space of possible minds using frameworks like Active Inference and the Free Energy Principle. path integrals particular kinds mindspace Active Inference Free Energy Principle consciousness Sloman non-anthropocentric sentience taxonomy Introduces the concept of 'compositional cognitive cartography' to map possible minds. Proposes a non-anthropocentric approach to understanding different kinds of sentience. Highlights the relevance of the Free Energy Principle in modeling minds and their interactions. Suggests future research directions for integrating various taxonomies of minds. Utilizes Active Inference as a framework for measuring and modeling minds. Applies the Free Energy Principle for theoretical grounding in cognitive modeling. Explores the dynamics of particles to understand agency and sentience. Synthesizes Bayesian Statistics and Machine Learning with Category Theory." }, { "id": "work:Friedman2023SinglePheromoneModelAccounts046", "type": "work", "title": "A single-pheromone model accounts for empirical patterns of ant colony foraging", "url": "/works/Friedman2023SinglePheromoneModelAccounts046.html", "external_url": "https://doi.org/10.1016/j.cogsys.2023.02.005", "summary": "This paper critiques the two-pheromone model (2PM) proposed by Dussutour et al. for ant foraging behavior, demonstrating that a single-pheromone model (1PM) can adequately explain the observed patterns. The authors argue", "year": 2023, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "pheromone", "ant foraging", "computational model", "collective behavior", "stigmergy", "trail formation", "parsimony" ], "content": "A single-pheromone model accounts for empirical patterns of ant colony foraging Cognitive Systems Research 10.1016/j.cogsys.2023.02.005 Friedman2023SinglePheromoneModelAccounts046 Entomology Paper This paper critiques the two-pheromone model (2PM) proposed by Dussutour et al. for ant foraging behavior, demonstrating that a single-pheromone model (1PM) can adequately explain the observed patterns. The authors argue that the evidence for a two-pheromone system is not definitive and advocate for further comparative modeling of cognitive mechanisms in animal behavior. pheromone ant foraging computational model collective behavior stigmergy trail formation parsimony Introduces a one-pheromone model (1PM) as an alternative to the two-pheromone model (2PM) for ant foraging. Demonstrates that the main experimental observations can be explained without the need for two distinct pheromones. Highlights the ambiguity in interpreting animal behavior regarding sensory and cognitive mechanisms. Suggests future experimental designs to differentiate between the 1PM and 2PM. Critically reviews the two-pheromone model (2PM) and its supporting experiments. Develops a mathematical framework for the one-pheromone model (1PM) based on biological plausibility. Utilizes statistical modeling to analyze ant foraging behavior in a Y-maze setup. Proposes specific follow-up experiments to test the validity of the 1PM and 2PM." }, { "id": "work:Friedman2023SnapshotPipelineTissueSpecific047", "type": "work", "title": "A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees", "url": "/works/Friedman2023SnapshotPipelineTissueSpecific047.html", "external_url": "https://doi.org/10.5281/zenodo.10400744", "summary": "The honey bee ( Apis mellifera ) is a key model organism for complex social behavior and physiology, where tissue-specific gene expression (TSGE) is difficult to analyze given large bioinformatics datasets and manual tis", "year": 2023, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "honey bees", "Apis mellifera", "tissue-specific gene expression", "meta-analysis", "RNA-seq", "bioinformatics pipeline", "open-source" ], "content": "A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees Zenodo 10.5281/zenodo.10400744 Friedman2023SnapshotPipelineTissueSpecific047 Entomology Paper The honey bee ( Apis mellifera ) is a key model organism for complex social behavior and physiology, where tissue-specific gene expression (TSGE) is difficult to analyze given large bioinformatics datasets and manual tissue processing. We present a meta-analytic approach to TSGE in A. mellifera using open-source bioinformatics packages: from an initial pool of 4,349 samples and 12,398 loci, rigorous analysis yields a publicly available snapshot of 731 samples and 177 loci representing high-quality TSGE estimates, intended as a reusable resource for honey bee and comparative gene-expression research. honey bees Apis mellifera tissue-specific gene expression meta-analysis RNA-seq bioinformatics pipeline open-source Presents a reproducible meta-analytic pipeline for tissue-specific gene expression (TSGE) in honey bees built on open-source bioinformatics tools. Curates a high-quality public snapshot of 731 samples and 177 loci from an initial pool of 4,349 samples and 12,398 loci. Provides a reusable community resource for comparative gene-expression analysis in Apis mellifera and beyond. Aggregated and standardized publicly available honey bee RNA-seq datasets across tissues. Applied open-source bioinformatics packages to filter samples and loci for quality. Reduced 4,349 samples and 12,398 loci to a curated snapshot of 731 samples and 177 loci representing high-quality TSGE estimates." }, { "id": "work:Friedman2023VariationalSynthesisEvolutionaryDevelopmental048", "type": "work", "title": "A variational synthesis of evolutionary and developmental dynamics", "url": "/works/Friedman2023VariationalSynthesisEvolutionaryDevelopmental048.html", "external_url": "https://doi.org/10.3390/e25070964", "summary": "This paper presents a variational formulation of natural selection, emphasizing the interplay between different 'kinds' of 'things' and their influence on each other. It formulates adaptive fitness as a path integral of ", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "variational synthesis", "natural selection", "Free Energy Principle", "Bayesian mechanics", "path integral", "evo-devo", "adaptive fitness", "particular partition" ], "content": "A variational synthesis of evolutionary and developmental dynamics Entropy 10.3390/e25070964 Friedman2023VariationalSynthesisEvolutionaryDevelopmental048 Active Inference Paper This paper presents a variational formulation of natural selection, emphasizing the interplay between different 'kinds' of 'things' and their influence on each other. It formulates adaptive fitness as a path integral of phenotypic fitness, interpreting evolutionary and developmental dynamics through a Bayesian lens. variational synthesis natural selection Free Energy Principle Bayesian mechanics path integral evo-devo adaptive fitness particular partition Introduces a variational synthesis of evolutionary and developmental dynamics. Formulates adaptive fitness as a path integral of phenotypic fitness. Demonstrates the necessity of considering populations of distinct natural kinds rather than conspecifics. Establishes a framework for integrating slow phylogenetic processes with fast phenotypic processes. Utilizes Bayesian mechanics to understand the relationship between phylogenetic and phenotypic processes. Applies the free energy principle to model evolutionary and developmental dynamics. Employs path integral formulation of stochastic dynamics and the renormalisation group. Describes natural selection and action selection as emergent properties of random dynamical processes." }, { "id": "work:Friedman2023ATLASQuestionOrientedApproach049", "type": "work", "title": "ATLAS: A Question Oriented Approach to Pattern Languages in Knowledge Management", "url": "/works/Friedman2023ATLASQuestionOrientedApproach049.html", "external_url": "https://doi.org/10.5281/zenodo.10296601", "summary": "The ATLAS system is a comprehensive knowledge management tool designed to enhance data interoperability and shared understanding in complex information environments. It integrates pattern language approaches with questio", "year": 2023, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "ATLAS", "pattern languages", "knowledge management", "question-oriented approach", "information architecture", "decision support", "cognitive tools" ], "content": "ATLAS: A Question Oriented Approach to Pattern Languages in Knowledge Management Zenodo 10.5281/zenodo.10296601 Friedman2023ATLASQuestionOrientedApproach049 Cognitive Security Paper The ATLAS system is a comprehensive knowledge management tool designed to enhance data interoperability and shared understanding in complex information environments. It integrates pattern language approaches with question-oriented procedures to facilitate the management and communication of nuanced data sets. ATLAS pattern languages knowledge management question-oriented approach information architecture decision support cognitive tools Development of a dynamic knowledge management tool addressing modern information supply chain complexities. Integration of pattern language methodologies with question-oriented procedures for improved data interpretation. Establishment of a foundation for transitioning from prototype to scalable implementation of the ATLAS architecture. Community-driven evolution reflecting the need for enhanced data interoperability and cognitive security. Creation of digital prototypes and paper-and-pencil implementations of the ATLAS architecture. Utilization of pattern language approaches to structure and communicate knowledge. Application of a low-code platform (Coda.io) for developing an alpha version of the COGSEC ATLAS. Incorporation of community feedback to refine and extend the knowledge resource." }, { "id": "work:Friedman2023AccountActiveInferenceModeling050", "type": "work", "title": "An Account of Active Inference Modeling", "url": "/works/Friedman2023AccountActiveInferenceModeling050.html", "external_url": "https://doi.org/10.5281/zenodo.8415313", "summary": "This paper explores the development of generative models in Active Inference, emphasizing the importance of accounting for cognitive systems and phenomena. It argues for a holistic approach to understanding cognition, in", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Active Inference", "generative modeling", "accounting metaphor", "Active AccountAnts", "cognitive modeling", "epistemic agency", "model development" ], "content": "An Account of Active Inference Modeling Zenodo 10.5281/zenodo.8415313 Friedman2023AccountActiveInferenceModeling050 Active Inference Paper This paper explores the development of generative models in Active Inference, emphasizing the importance of accounting for cognitive systems and phenomena. It argues for a holistic approach to understanding cognition, integrating various cognitive properties and processes through a framework that resembles financial accounting. Active Inference generative modeling accounting metaphor Active AccountAnts cognitive modeling epistemic agency model development Introduces the concept of generative models as a form of cognitive accounting. Proposes a holistic approach to understanding cognition through Active Inference. Establishes connections between financial accounting methods and cognitive modeling. Advocates for a first-principles scale-free approach to cognitive systems. Utilizes a four-fold partition to model Internal, External, Sensory, and Active states as a cognitive Tetrahedra. Applies category theory approaches to enhance Active Inference modeling. Employs analytical stances to account for cognitive properties and processes. Integrates artistic and scientific perspectives in the crafting of generative models." }, { "id": "work:Friedman2023CognitiveSovereigntyActiveInference051", "type": "work", "title": "Cognitive Sovereignty & Active Inference in the State of Exception", "url": "/works/Friedman2023CognitiveSovereigntyActiveInference051.html", "external_url": "https://doi.org/10.5281/zenodo.10038232", "summary": "This paper analyzes Giorgio Agamben's Homo Sacer through the lens of Active Inference, exploring the relationship between bare life and political existence in Western politics. It connects Agamben's concepts with cogniti", "year": 2023, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "cognitive sovereignty", "Agamben", "Homo Sacer", "Active Inference", "state of exception", "Thomas Kuhn", "paradigm shifts", "epistemic agency" ], "content": "Cognitive Sovereignty & Active Inference in the State of Exception Zenodo 10.5281/zenodo.10038232 Friedman2023CognitiveSovereigntyActiveInference051 Cognitive Security Paper This paper analyzes Giorgio Agamben's Homo Sacer through the lens of Active Inference, exploring the relationship between bare life and political existence in Western politics. It connects Agamben's concepts with cognitive sovereignty and revolutionary science, asserting that epistemic agency is grounded in the cognitive sovereign's policy selection. cognitive sovereignty Agamben Homo Sacer Active Inference state of exception Thomas Kuhn paradigm shifts epistemic agency biopolitics bare life Introduces the concept of cognitive sovereignty in relation to Agamben's Homo Sacer. Connects Agamben's state of exception with Thomas Kuhn's theory of revolutionary science. Explores the implications of Active Inference for understanding sovereignty and agency. Provides pseudocode for an 'Active Stateference' model. Analyzes Homo Sacer through the framework of Active Inference. Draws parallels between Agamben's concepts and cognitive theories. Utilizes philosophical analysis to explore the dynamics of power and knowledge. Presents a computational model (pseudocode) for the Active Stateference entity." }, { "id": "work:Friedman2023CommentsAIAccountabilityPolicy052", "type": "work", "title": "Comments on AI Accountability Policy to NTIA", "url": "/works/Friedman2023CommentsAIAccountabilityPolicy052.html", "external_url": "https://doi.org/10.5281/zenodo.8025957", "summary": "This paper presents recommendations on the implementation of AI technologies, emphasizing the need for nuanced regulatory frameworks rather than blanket policies. It argues that the National Telecommunications and Inform", "year": 2023, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "AI accountability", "NTIA", "policy comment", "cognitive security", "P3IF", "information risk", "AI governance", "synthetic intelligence" ], "content": "Comments on AI Accountability Policy to NTIA NTIA 10.5281/zenodo.8025957 Friedman2023CommentsAIAccountabilityPolicy052 Cognitive Security Paper This paper presents recommendations on the implementation of AI technologies, emphasizing the need for nuanced regulatory frameworks rather than blanket policies. It argues that the National Telecommunications and Information Administration (NTIA) is well-positioned to facilitate adaptive regulatory structures that address the complexities of AI. AI accountability NTIA policy comment cognitive security P3IF information risk AI governance synthetic intelligence Advocates for a shift from blanket regulation of AI to more adaptive regulatory frameworks. Highlights the unique interdisciplinary perspectives of collaborating organizations on AI governance. Proposes the establishment of professionalization and insurance structures for AI technologies. Emphasizes the importance of the NTIA's role in facilitating discussions and recommendations on AI regulation. Conducted a synthesis of perspectives from various organizations involved in AI and information risk management. Analyzed the implications of blanket regulation versus adaptive regulatory frameworks. Engaged in interdisciplinary discussions to inform recommendations on AI governance. Utilized case studies and examples to illustrate the complexities of AI regulation." }, { "id": "work:Friedman2023DistributedScienceScientificProcess053", "type": "work", "title": "Distributed Science — The Scientific Process as Multi-Scale Active Inference", "url": "/works/Friedman2023DistributedScienceScientificProcess053.html", "external_url": "https://doi.org/10.31219/osf.io/dnw5k", "summary": "This paper presents a multi-scale description of the scientific process as a distributed system of evidence-seeking activities, applying the free energy principle to understand science as Bayesian belief updating. It arg", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "distributed science", "multi-scale Active Inference", "scientific process", "Free Energy Principle", "meta-science", "collective intelligence", "cultural evolution", "distributed cognition" ], "content": "Distributed Science — The Scientific Process as Multi-Scale Active Inference OSF 10.31219/osf.io/dnw5k Friedman2023DistributedScienceScientificProcess053 Active Inference Paper This paper presents a multi-scale description of the scientific process as a distributed system of evidence-seeking activities, applying the free energy principle to understand science as Bayesian belief updating. It argues that scientific practice is shaped by both human and non-human agents, emphasizing the need for an integrated view that combines modern and non-modern perspectives on knowledge production. distributed science multi-scale Active Inference scientific process Free Energy Principle meta-science collective intelligence cultural evolution distributed cognition Introduces a multi-scale framework for understanding the scientific process as distributed active inference. Integrates modern and non-modern conceptions of science to provide a comprehensive account of knowledge production. Proposes a simulation approach for scientific practice that can inform the development of augmented intelligence systems. Addresses foundational questions regarding the nature of science and its societal implications. Applies the free energy principle to model the scientific process as evidence-seeking. Utilizes Bayesian belief updating to describe the dynamics of scientific cognition. Explores the interaction between individual cognitive functions and collective scientific practices. Employs a meta-theoretical approach to reconcile different epistemological views on science." }, { "id": "work:Friedman2023EnhancedNSFPostdoctoralReporting054", "type": "work", "title": "Enhanced NSF Postdoctoral Reporting via Synthetic Intelligence Language Processing", "url": "/works/Friedman2023EnhancedNSFPostdoctoralReporting054.html", "external_url": "https://doi.org/10.5281/zenodo.10160656", "summary": "This paper proposes a generative intelligence system to enhance postdoctoral reporting at the National Science Foundation (NSF), aiming to improve efficiency and broaden the dissemination of research outputs. By leveragi", "year": 2023, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "NSF reporting", "postdoctoral research", "synthetic intelligence", "automated reporting", "research dissemination", "prompt engineering" ], "content": "Enhanced NSF Postdoctoral Reporting via Synthetic Intelligence Language Processing Zenodo 10.5281/zenodo.10160656 Friedman2023EnhancedNSFPostdoctoralReporting054 Computational Paper This paper proposes a generative intelligence system to enhance postdoctoral reporting at the National Science Foundation (NSF), aiming to improve efficiency and broaden the dissemination of research outputs. By leveraging synthetic intelligence language processing, the system aims to streamline reporting processes for postdocs and NSF program managers. NSF reporting postdoctoral research synthetic intelligence automated reporting research dissemination prompt engineering Introduction of updatable profiles for postdocs to provide comprehensive data. Development of intelligent processing prompts for standardizing submissions. Creation of a dynamic reporting system that generates real-time reports. Implementation of a user-centric interface design for enhanced usability. Utilization of prompt engineering and synthetic intelligence for data formatting. Real-time monitoring and evaluation of postdoctoral activities. Adaptive system evolution based on user feedback and technological advancements. Integration of diverse media forms for report generation." }, { "id": "work:Friedman2023ExperimentalEntomologyAgeVideo055", "type": "work", "title": "Experimental Entomology in the Age of Video", "url": "/works/Friedman2023ExperimentalEntomologyAgeVideo055.html", "external_url": "https://doi.org/10.3791/65002", "summary": "This paper discusses the transformative impact of video technology on entomology, summarizing recent methodological advancements that enhance research and education in the field. It emphasizes the importance of adopting ", "year": 2023, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "video entomology", "behavioral tracking", "automated phenotyping", "insect behavior", "experimental methods", "high-throughput analysis" ], "content": "Experimental Entomology in the Age of Video JoVE 10.3791/65002 Friedman2023ExperimentalEntomologyAgeVideo055 Entomology Paper This paper discusses the transformative impact of video technology on entomology, summarizing recent methodological advancements that enhance research and education in the field. It emphasizes the importance of adopting these modern protocols to improve the study of insect behavior and ecology. video entomology behavioral tracking automated phenotyping insect behavior experimental methods high-throughput analysis Highlights the role of video technology in modern entomological research and education. Summarizes various innovative methods for studying leaf-cutting ants and honey bees. Addresses challenges in observing and manipulating eusocial insects in laboratory and field settings. Proposes future directions for entomology, including the integration of emerging technologies. Describes protocols for the collection and maintenance of leaf-cutting ant colonies. Presents a method for passive pollen collection from honey bees using a metal mesh. Outlines histological techniques for analyzing honey bee tissues and assessing cell turnover. Details a method for studying the impact of agrochemicals on honey bee queen fecundity." }, { "id": "work:Friedman2023GeneralizedNotationNotationActive056", "type": "work", "title": "Generalized Notation Notation for Active Inference Models", "url": "/works/Friedman2023GeneralizedNotationNotationActive056.html", "external_url": "https://doi.org/10.5281/zenodo.7803328", "summary": "This paper introduces Generalized Notation Notation (GNN), a novel approach to generative model representation that enhances communication and understanding of Active Inference across various domains. GNN serves as a fle", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "GNN", "Generalized Notation Notation", "meta-notation", "symbolic systems", "notation translation", "formal representation", "interoperability" ], "content": "Generalized Notation Notation for Active Inference Models Zenodo 10.5281/zenodo.7803328 Friedman2023GeneralizedNotationNotationActive056 Active Inference Paper This paper introduces Generalized Notation Notation (GNN), a novel approach to generative model representation that enhances communication and understanding of Active Inference across various domains. GNN serves as a flexible and expressive language for modeling cognitive processes, aiming to facilitate interdisciplinary research and application. GNN Generalized Notation Notation meta-notation symbolic systems notation translation formal representation interoperability Introduction of Generalized Notation Notation (GNN) for cognitive model representation. Provision of a Step-by-Step example demonstrating GNN in practice. Exploration of 'the Triple Play' approach for expressing GNN in linguistic, visual, and executable models. Bridging gaps among different modeling settings to promote interdisciplinary collaboration. Development of GNN as a standardized language for describing Active Inference models. Utilization of ASCII letters and punctuation structured in a Markdown-compliant source file. Presentation of GNN through examples drawn from existing Active Inference tutorials. Incorporation of various aspects of language including ontology, morphology, grammar, and pragmatics." }, { "id": "work:Friedman2023GenerativeResearchTeamsActive057", "type": "work", "title": "Generative Research Teams: Active Inference Compositions for Research and Meta-Science", "url": "/works/Friedman2023GenerativeResearchTeamsActive057.html", "external_url": "https://doi.org/10.5281/zenodo.8164667", "summary": "The paper introduces the Generative Research Team (GRT), which integrates human, computational, and informational entities using Active Inference and cognitive security to enhance research processes. It emphasizes the mo", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Generative Research Team", "Active Inference", "generative model", "cognitive modeling", "LLMs", "autonomous agents", "open science", "decentralized science" ], "content": "Generative Research Teams: Active Inference Compositions for Research and Meta-Science Zenodo 10.5281/zenodo.8164667 Friedman2023GenerativeResearchTeamsActive057 Active Inference Paper The paper introduces the Generative Research Team (GRT), which integrates human, computational, and informational entities using Active Inference and cognitive security to enhance research processes. It emphasizes the modular roles within GRTs that allow for flexible resource allocation and adaptability to various research challenges. Generative Research Team Active Inference generative model cognitive modeling LLMs autonomous agents open science decentralized science Active Blockference meta-prompting Exploration of augmented architectures for research teams. Integration of Active Inference as a cognitive kernel into GRTs with shared intelligence. Application of cognitive models to enhance research processes. Provision of lists of related work and tools in the field. Utilization of Active Inference as a cognitive modeling approach. Implementation of systems engineering principles in GRT design. Development of communication strategies for effective dissemination of research findings. Use of tools like Active Blockference and cadCAD for situational awareness." }, { "id": "work:Friedman2023AntsAging058", "type": "work", "title": "Of Ants & Aging", "url": "/works/Friedman2023AntsAging058.html", "external_url": "https://doi.org/10.5281/zenodo.7855582", "summary": "This paper explores the relationship between ants and aging, presenting reflections on the mechanisms of aging in both ants and humans. It aims to stimulate discussion on the biological processes underlying aging and the", "year": 2023, "domain": "Media & Teaching", "tags": [ "Presentation", "Media & Teaching", "bibliography", "ants", "aging", "senescence", "lifespan", "caste", "queen longevity", "social insects", "evolutionary biology" ], "content": "Of Ants & Aging Presentation 10.5281/zenodo.7855582 Friedman2023AntsAging058 Media & Teaching Presentation This paper explores the relationship between ants and aging, presenting reflections on the mechanisms of aging in both ants and humans. It aims to stimulate discussion on the biological processes underlying aging and the potential for reversing it. ants aging senescence lifespan caste queen longevity social insects evolutionary biology Introduces a comparative analysis of aging mechanisms in ants and humans. Raises questions about the nature of aging as either passive damage accumulation or active self-destruction. Utilizes Tinbergen’s 4 Questions framework to investigate the reasons behind biological aging. Encourages interdisciplinary dialogue on aging research. Employs a conceptual framework based on Tinbergen’s 4 Questions. Engages in reflective analysis rather than empirical research. Facilitates discussions on aging through a comparative lens. Explores existing literature on aging in ants and its implications for human aging." }, { "id": "work:Friedman2023OpenAccessScienceNeeds059", "type": "work", "title": "Open Access science needs Open Science Sensemaking (OSSm)", "url": "/works/Friedman2023OpenAccessScienceNeeds059.html", "external_url": "https://doi.org/10.31222/osf.io/9nb3u", "summary": "This paper argues for the necessity of Open Science Sensemaking (OSSm) to address the challenges of information overload and knowledge fragmentation in the scientific community. It proposes an interoperable and decentral", "year": 2023, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "OSSm", "Open Science Sensemaking", "scientific sensemaking", "annotation networks", "open access", "decentralized", "information overload" ], "content": "Open Access science needs Open Science Sensemaking (OSSm) MetaArXiv 10.31222/osf.io/9nb3u Friedman2023OpenAccessScienceNeeds059 Cognitive Security Paper This paper argues for the necessity of Open Science Sensemaking (OSSm) to address the challenges of information overload and knowledge fragmentation in the scientific community. It proposes an interoperable and decentralized annotation network that allows researchers to record, own, and share their sensemaking data, thereby enhancing collective scientific understanding. OSSm Open Science Sensemaking scientific sensemaking annotation networks open access decentralized information overload Introduces the concept of Open Science Sensemaking (OSSm) as a solution to scientific information overload. Proposes a decentralized annotation network for sharing sensemaking data among researchers. Highlights the importance of sensemaking data in improving scientific evaluation and collaboration. Advocates for the integration of sensemaking data into the open science movement. Outlines a framework for an interoperable annotation network. Examines existing sensemaking data practices and their limitations. Analyzes the role of sensemaking data in algorithmic content curation and recommendation systems. Discusses the application of FAIR principles to sensemaking data." }, { "id": "work:Friedman2023PostdocReview20202023060", "type": "work", "title": "Postdoc review (2020–2023)", "url": "/works/Friedman2023PostdocReview20202023060.html", "external_url": "https://doi.org/10.5281/zenodo.8377988", "summary": "This paper reviews the academic contributions of Daniel Ari Friedman from 2020 to 2023, focusing on various interdisciplinary fields including biology, entomology, and cognitive security. It aims to outline the roadmap f", "year": 2023, "domain": "Media & Teaching", "tags": [ "Presentation", "Media & Teaching", "bibliography", "postdoctoral review", "research portfolio", "Active Inference", "entomology", "cognitive security", "meta-science", "philosophy", "biology" ], "content": "Postdoc review (2020–2023) Presentation 10.5281/zenodo.8377988 Friedman2023PostdocReview20202023060 Media & Teaching Presentation This paper reviews the academic contributions of Daniel Ari Friedman from 2020 to 2023, focusing on various interdisciplinary fields including biology, entomology, and cognitive security. It aims to outline the roadmap for future research and collaborations. postdoctoral review research portfolio Active Inference entomology cognitive security meta-science philosophy biology interdisciplinary research Comprehensive review of interdisciplinary research areas. Identification of key themes in active inference and cognitive security. Development of a roadmap for future research directions. Integration of insights from philosophy and arts into scientific discourse. Literature review of recent advancements in relevant fields. Analysis of live chat discussions to gather community insights. Synthesis of findings across diverse disciplines. Engagement with stakeholders to refine research focus." }, { "id": "work:Friedman2023ActiveInferenceInstituteActive061", "type": "work", "title": "The Active Inference Institute and Active Inference Ecosystem (v1)", "url": "/works/Friedman2023ActiveInferenceInstituteActive061.html", "external_url": "https://doi.org/10.5281/zenodo.8266281", "summary": "An overview of the Active Inference Institute (AII) — its mission, organizational structure, projects, and community. The Institute serves as a hub for Active Inference research, education, and application, leveraging op", "year": 2023, "domain": "AII Ecosystem", "tags": [ "Paper", "AII Ecosystem", "bibliography", "Active Inference Institute", "open science", "research organization", "Free Energy Principle", "community building" ], "content": "The Active Inference Institute and Active Inference Ecosystem (v1) Zenodo 10.5281/zenodo.8266281 Friedman2023ActiveInferenceInstituteActive061 AII Ecosystem Paper An overview of the Active Inference Institute (AII) — its mission, organizational structure, projects, and community. The Institute serves as a hub for Active Inference research, education, and application, leveraging open-science methodologies to advance understanding of the Free Energy Principle and its applications across domains. Active Inference Institute open science research organization Free Energy Principle community building Describes the Active Inference Institute's mission, organizational structure, and community. Surveys AII research, education, and application activities across the Active Inference ecosystem. Frames open-science practice around the Free Energy Principle and Active Inference. Descriptive overview of the Institute's programs, governance, and community structures. Documents open-science workflows, participation pathways, and ecosystem collaborations." }, { "id": "work:Friedman2023P3IFPropertiesProcessesPerspectives062", "type": "work", "title": "The P3IF: Properties, Processes, and Perspectives Inter-Framework", "url": "/works/Friedman2023P3IFPropertiesProcessesPerspectives062.html", "external_url": "https://doi.org/10.5281/zenodo.10034512", "summary": "This paper introduces the Properties, Processes, and Perspectives Inter-Framework (P3IF), which aims to enhance requirements engineering for complex information systems by integrating interdisciplinary frameworks. It add", "year": 2023, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "P3IF", "information risk", "cognitive security", "interdisciplinary frameworks", "requirements management", "DHS", "health security" ], "content": "The P3IF: Properties, Processes, and Perspectives Inter-Framework Zenodo 10.5281/zenodo.10034512 Friedman2023P3IFPropertiesProcessesPerspectives062 Cognitive Security Paper This paper introduces the Properties, Processes, and Perspectives Inter-Framework (P3IF), which aims to enhance requirements engineering for complex information systems by integrating interdisciplinary frameworks. It addresses the need for a modular approach to manage information risk and cognitive security across various domains, particularly in high-consequence decision-making contexts. P3IF information risk cognitive security interdisciplinary frameworks requirements management DHS health security Proposes the P3IF to facilitate flexible requirements engineering across interdisciplinary frameworks. Analyzes existing requirements engineering frameworks to identify common features and dimensions. Expands the concept of cognitive security beyond traditional cybersecurity to encompass broader decision-making scenarios. Addresses the challenges of managing information risk in complex systems, particularly in health security. Explores the purpose and function of existing frameworks in requirements engineering. Performs an analysis of relationships and lineages of common frameworks in professional use. Generalizes features of frameworks to identify common dimensions for interoperability. Proposes a modular abstraction layer to extend the value of existing frameworks without replacing them." }, { "id": "work:Friedman2023CommentOrNotComment063", "type": "work", "title": "To comment or not to comment", "url": "/works/Friedman2023CommentOrNotComment063.html", "external_url": "https://doi.org/10.1016/j.plrev.2023.06.002", "summary": "A commentary in Physics of Life Reviews by Mridula Mascarenhas, Richard J. Cordes, and Daniel A. Friedman responding to the target article \"To copy or not to copy?\" by Héctor M. Manrique and Michael J. Walker, which exam", "year": 2023, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "commentary", "imitation", "social learning", "cumulative culture", "copying fidelity", "Physics of Life Reviews" ], "content": "To comment or not to comment Physics of Life Reviews 10.1016/j.plrev.2023.06.002 Friedman2023CommentOrNotComment063 Genetics & Biomedical Paper A commentary in Physics of Life Reviews by Mridula Mascarenhas, Richard J. Cordes, and Daniel A. Friedman responding to the target article \"To copy or not to copy?\" by Héctor M. Manrique and Michael J. Walker, which examines imitation, copying fidelity, and the foundations of human cumulative technological culture. The comment engages the target's account of social learning and its role in the evolution of culture. commentary imitation social learning cumulative culture copying fidelity Physics of Life Reviews A peer commentary engaging Manrique and Walker's account of imitation and the origins of human cumulative technological culture. Situates copying fidelity and social learning within broader discussions of cultural evolution. Critical commentary and conceptual analysis of the target article; see the published comment for the full argument." }, { "id": "work:Friedman2023TranscriptChrisFieldsPhysics064", "type": "work", "title": "Transcript of Chris Fields, \"Physics as Information Processing\" course", "url": "/works/Friedman2023TranscriptChrisFieldsPhysics064.html", "external_url": "https://doi.org/10.5281/zenodo.10447642", "summary": "Course · Zenodo · Media & Teaching", "year": 2023, "domain": "Media & Teaching", "tags": [ "Course", "Media & Teaching", "bibliography" ], "content": "Transcript of Chris Fields, \"Physics as Information Processing\" course Zenodo 10.5281/zenodo.10447642 Friedman2023TranscriptChrisFieldsPhysics064 Media & Teaching Course" }, { "id": "work:Friedman2023WilliamBlakeBuckminsterFuller065", "type": "work", "title": "William Blake & Buckminster Fuller: Lives in Juxtaposition", "url": "/works/Friedman2023WilliamBlakeBuckminsterFuller065.html", "external_url": "https://doi.org/10.5281/zenodo.7514368", "summary": "This paper explores the juxtaposition of the lives and ideas of William Blake and Buckminster Fuller, focusing on the concept of 'Comprehensivity' as a means to foster a deeper understanding of the world. It invites coll", "year": 2023, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "William Blake", "Buckminster Fuller", "comprehensivity", "design science", "prophetic vision", "art-science synthesis", "52 Living Ideas", "juxtaposition" ], "content": "William Blake & Buckminster Fuller: Lives in Juxtaposition Zenodo 10.5281/zenodo.7514368 Friedman2023WilliamBlakeBuckminsterFuller065 Art & Synergetics Paper This paper explores the juxtaposition of the lives and ideas of William Blake and Buckminster Fuller, focusing on the concept of 'Comprehensivity' as a means to foster a deeper understanding of the world. It invites collaboration and engagement in developing multi-perspectival insights through inquiry and action. William Blake Buckminster Fuller comprehensivity design science prophetic vision art-science synthesis 52 Living Ideas juxtaposition Introduces the concept of Comprehensivity as a framework for understanding complex systems. Establishes connections between the philosophies of Blake and Fuller. Encourages collaborative inquiry across various disciplines and practices. Identifies inherent pathologies in comprehensivity and suggests ways to cultivate relevant judgment. Utilizes a draft linearized snapshot perspective for presenting ideas. Engages in ongoing discussions and meetings to refine concepts. Integrates multimedia and philosophical frameworks to enhance understanding. Explores ontologies related to Fuller and Blake within the context of Active Inference." }, { "id": "work:Friedman2022ActiveInferenceOntologyDecentralized066", "type": "work", "title": "An Active Inference Ontology for Decentralized Science", "url": "/works/Friedman2022ActiveInferenceOntologyDecentralized066.html", "external_url": "https://doi.org/10.5281/zenodo.6320574", "summary": "This document surveys the current state of Active Inference and its future directions, emphasizing the Institute's goal to evolve by actively gathering insights from its members. It highlights the framework's applicabili", "year": 2022, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Active Inference Ontology", "knowledge graph", "Free Energy Principle", "ontology development", "SUMO", "knowledge representation", "open science" ], "content": "An Active Inference Ontology for Decentralized Science Zenodo 10.5281/zenodo.6320574 Friedman2022ActiveInferenceOntologyDecentralized066 Active Inference Paper This document surveys the current state of Active Inference and its future directions, emphasizing the Institute's goal to evolve by actively gathering insights from its members. It highlights the framework's applicability across various disciplines through the lens of information theory and thermodynamics. Active Inference Ontology knowledge graph Free Energy Principle ontology development SUMO knowledge representation open science Provides a comprehensive overview of Active Inference and its applications across multiple disciplines. Establishes the Active Inference Institute as a community-driven organization promoting understanding and practical applications of the framework. Highlights the versatility of Active Inference in addressing real-world problems in diverse fields such as AI, economics, and governance. Encourages collaborative learning and community engagement to expand the reach and impact of Active Inference. Utilizes a living document format to continuously update and incorporate contributions from community members. Applies principles of information theory and thermodynamics to analyze the interaction of living systems with their environment. Engages members through various learning opportunities, including courses and collaborative research initiatives. Facilitates community discourse to gather insights and perspectives from a diverse range of contributors." }, { "id": "work:Friedman2022CatechismTowardsActiveDiffusion067", "type": "work", "title": "Catechism for Towards Active Diffusion", "url": "/works/Friedman2022CatechismTowardsActiveDiffusion067.html", "external_url": "https://doi.org/10.5281/zenodo.7443848", "summary": "This paper explores the connections between Active Inference (ActInf) and Diffusion Models (DM) in the context of cognitive sciences and artificial intelligence. It aims to characterize mathematical formalisms and comput", "year": 2022, "domain": "AII Ecosystem", "tags": [ "Paper", "AII Ecosystem", "bibliography", "Active Diffusion", "diffusion models", "Active Inference", "generative AI", "probabilistic modeling", "free energy minimization" ], "content": "Catechism for Towards Active Diffusion Zenodo 10.5281/zenodo.7443848 Friedman2022CatechismTowardsActiveDiffusion067 AII Ecosystem Paper This paper explores the connections between Active Inference (ActInf) and Diffusion Models (DM) in the context of cognitive sciences and artificial intelligence. It aims to characterize mathematical formalisms and computational applications of these models to enhance decision-making and planning strategies under the Free Energy Principle. Active Diffusion diffusion models Active Inference generative AI probabilistic modeling free energy minimization Establishes theoretical connections between Active Inference and Diffusion Models. Develops open-source repositories to demonstrate concordances among ActInf, DM, and related methods. Integrates diffusion models within the active inference framework for dynamic environment representation. Explores the implications of Active Diffusion in cognitive ecosystems and decentralized science. Conducts a thorough literature review on Latent Diffusion Models and belief propagation in Active Inference. Utilizes benchmarks on standard datasets and formats for empirical validation. Employs the cadCAD package for developing frameworks in cognitive ecosystems design. Investigates the application of individual components within LDM architectures in the action-perception loop." }, { "id": "work:Friedman2022FromUsersSenseMakers068", "type": "work", "title": "From Users to (Sense)Makers: Stigmergic Social Annotation", "url": "/works/Friedman2022FromUsersSenseMakers068.html", "external_url": "https://doi.org/10.48550/arXiv.2205.06345", "summary": "This paper discusses the detrimental effects of centralized platforms on collective sensemaking in online epistemic environments and proposes a decentralized framework called Open Source Attention (OSA) to enhance user a", "year": 2022, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "stigmergic annotation", "open source attention", "collective sensemaking", "epistemic pollution", "decentralized platforms", "social annotation", "digital attention" ], "content": "From Users to (Sense)Makers: Stigmergic Social Annotation Hypertext '22 10.48550/arXiv.2205.06345 Friedman2022FromUsersSenseMakers068 Cognitive Security Paper This paper discusses the detrimental effects of centralized platforms on collective sensemaking in online epistemic environments and proposes a decentralized framework called Open Source Attention (OSA) to enhance user agency and improve information quality. By leveraging stigmergic social annotation, the authors aim to empower individuals as active makers rather than passive consumers of information. stigmergic annotation open source attention collective sensemaking epistemic pollution decentralized platforms social annotation digital attention Introduction of the Open Source Attention (OSA) framework for decentralized information governance. Emphasis on the role of stigmergic markers as digital traces of human attention in improving epistemic environments. Advocacy for a shift from platform-centric to maker-centric approaches in content creation and discovery. Proposition of a marketplace of diverse content discovery services to enhance user control and personalization. Theoretical analysis of stigmergic communication and its implications for collective sensemaking. Development of a socio-technical framework inspired by open source and decentralization movements. Exploration of architectural elements for decentralized annotation tools, self-sovereign storage, and content discovery services. Comparison of existing systems like Solid and dokieli to highlight the need for a more integrated ecological approach." }, { "id": "work:Friedman2022FreeWillOrLack069", "type": "work", "title": "On free will or the lack thereof (interview with Robert Sapolsky)", "url": "/works/Friedman2022FreeWillOrLack069.html", "external_url": "https://doi.org/10.5281/zenodo.7394901", "summary": "This interview with Robert Sapolsky explores his views on free will and its implications across neuroscience, philosophy, education, and the criminal justice system, anticipating his upcoming book 'Determined: The Scienc", "year": 2022, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "free will", "determinism", "Robert Sapolsky", "neuroscience", "behavioral genetics", "philosophy", "consciousness", "moral philosophy" ], "content": "On free will or the lack thereof (interview with Robert Sapolsky) ALIUS Bulletin 10.5281/zenodo.7394901 Friedman2022FreeWillOrLack069 Genetics & Biomedical Paper This interview with Robert Sapolsky explores his views on free will and its implications across neuroscience, philosophy, education, and the criminal justice system, anticipating his upcoming book 'Determined: The Science of Life Without Free Will.' The discussion delves into the biological underpinnings of behavior and the philosophical debates surrounding agency and determinism. free will determinism Robert Sapolsky neuroscience behavioral genetics philosophy consciousness moral philosophy Provides a biological perspective on free will and human behavior. Anticipates the themes of Sapolsky's forthcoming book on determinism. Explores the intersection of neuroscience with legal and philosophical discussions. Challenges common perceptions of free will and its implications for moral responsibility. Conducted an interview format to elicit Sapolsky's views. Discussed empirical evidence from neuroscience to support arguments. Engaged with philosophical definitions and implications of free will. Analyzed public responses to previous works to inform the discussion." }, { "id": "work:Friedman2022PredictiveProcessingInterpretationMirror070", "type": "work", "title": "Predictive Processing Interpretation of the Mirror Test", "url": "/works/Friedman2022PredictiveProcessingInterpretationMirror070.html", "external_url": "https://doi.org/10.5281/zenodo.7377256", "summary": "This paper applies a predictive processing interpretation to the mirror test, proposing that a 'reflection prediction' can enhance our understanding of mirror self-recognition and self-directed behavior in humans and oth", "year": 2022, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "mirror test", "predictive processing", "self-recognition", "reflection prediction", "Active Inference", "self-awareness", "prediction error" ], "content": "Predictive Processing Interpretation of the Mirror Test Zenodo 10.5281/zenodo.7377256 Friedman2022PredictiveProcessingInterpretationMirror070 Art & Synergetics Paper This paper applies a predictive processing interpretation to the mirror test, proposing that a 'reflection prediction' can enhance our understanding of mirror self-recognition and self-directed behavior in humans and other species. It suggests that atypical reflection predictions may explain variations in these traits across individuals. mirror test predictive processing self-recognition reflection prediction Active Inference self-awareness prediction error Introduces a predictive processing framework to reinterpret the mirror test results. Proposes the concept of 'reflection prediction' as a mechanism for understanding self-recognition and self-directed behavior. Highlights the implications of reflection prediction errors for agency and cognitive traits. Challenges traditional interpretations of the mirror test by suggesting that both self-directed behavior and ignoring reflections can indicate self-recognition. Utilizes a predictive processing model to analyze mirror self-recognition. Examines historical and ecological evidence related to the mirror test. Applies concepts of sensory attenuation and active inference to explain behaviors observed in the mirror test. Critiques the traditional reliance on self-directed behavior as a measure of self-recognition." }, { "id": "work:Friedman2022StructuringInformationCommonsOpen071", "type": "work", "title": "Structuring the Information Commons: Open Standards and Cognitive Security", "url": "/works/Friedman2022StructuringInformationCommonsOpen071.html", "external_url": "https://cogsec.org", "summary": "This paper discusses the structuring of information commons through the lens of open standards and cognitive security, aiming to enhance the management and dissemination of information in various contexts. It emphasizes ", "year": 2022, "domain": "Cognitive Security", "tags": [ "Book", "Cognitive Security", "bibliography", "information commons", "cognitive security", "open standards", "trust", "governance", "decentralized systems", "information integrity", "collective sensemaking" ], "content": "Structuring the Information Commons: Open Standards and Cognitive Security COGSEC.org Friedman2022StructuringInformationCommonsOpen071 Cognitive Security Book This paper discusses the structuring of information commons through the lens of open standards and cognitive security, aiming to enhance the management and dissemination of information in various contexts. It emphasizes the importance of interdisciplinary collaboration and innovative approaches to address challenges in information risk and security. information commons cognitive security open standards trust governance decentralized systems information integrity collective sensemaking Introduces a framework for managing information commons using open standards. Explores the intersection of cognitive security and information management. Presents novel methodologies for analyzing digital rhetorical ecosystems. Highlights the role of modular systems in enhancing organizational efficiency. Utilizes narrative information management techniques. Employs swarm intelligence concepts in information verification. Applies active inference models to understand conflict dynamics. Develops a decentralized science ontology for collaborative research." }, { "id": "work:Friedman2022SystemsModelingCognitiveAudits072", "type": "work", "title": "Systems Modeling and Cognitive Audits for Hypercert Ecosystems", "url": "/works/Friedman2022SystemsModelingCognitiveAudits072.html", "external_url": "https://doi.org/10.5281/zenodo.7626769", "summary": "This paper discusses the development of frameworks and tools for applied Active Inference in the context of Decentralized Science (DeSci) and Hypercert ecosystems. It aims to enhance the flexibility and utility of Hyperc", "year": 2022, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "Hypercerts", "DeSci", "decentralized science", "Active Blockference", "AEOS", "cognitive audits", "public goods funding", "systems modeling" ], "content": "Systems Modeling and Cognitive Audits for Hypercert Ecosystems Zenodo 10.5281/zenodo.7626769 Friedman2022SystemsModelingCognitiveAudits072 Cognitive Security Paper This paper discusses the development of frameworks and tools for applied Active Inference in the context of Decentralized Science (DeSci) and Hypercert ecosystems. It aims to enhance the flexibility and utility of Hypercerts through the creation of an Active Entity Ontology for Science (AEOS) and the implementation of Active Blockference. Hypercerts DeSci decentralized science Active Blockference AEOS cognitive audits public goods funding systems modeling Introduction of an Active Entity Ontology for Science (AEOS) to describe interactions within Hypercert ecosystems. Development of Active Blockference for simulating cognitive processes in Hypercert ecosystems. Creation of educational resources and tools for cognitive audits of Hypercert protocols. Rigorous analysis of Hypercert funding mechanisms to enhance their efficacy in DeSci. Utilization of Active Inference frameworks for modeling interactions in Hypercert ecosystems. Implementation of multi-agent simulations to explore cognitive and behavioral dynamics. Engagement in informative interviews with stakeholders to understand the Hypercert landscape. Development of entity diagrams and simulations tailored to researcher needs." }, { "id": "work:Friedman2022FreeEnergyPrincipleActive073", "type": "work", "title": "The Free Energy Principle & Active Inference: a Systematic Literature Analysis", "url": "/works/Friedman2022FreeEnergyPrincipleActive073.html", "external_url": "https://doi.org/10.5281/zenodo.7449368", "summary": "This paper conducts a systematic literature analysis of publications related to the Free Energy Principle and Active Inference, particularly focusing on works by Karl J. Friston. The analysis includes manual and automate", "year": 2022, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "systematic literature analysis", "Free Energy Principle", "Active Inference", "Karl Friston", "history of science", "bibliometrics", "ontology" ], "content": "The Free Energy Principle & Active Inference: a Systematic Literature Analysis Zenodo 10.5281/zenodo.7449368 Friedman2022FreeEnergyPrincipleActive073 Active Inference Paper This paper conducts a systematic literature analysis of publications related to the Free Energy Principle and Active Inference, particularly focusing on works by Karl J. Friston. The analysis includes manual and automated annotations of structural, visual, and mathematical features across a large dataset of citations and papers, aiming to enhance the understanding and accessibility of this evolving scientific discourse. systematic literature analysis Free Energy Principle Active Inference Karl Friston history of science bibliometrics ontology Provides a comprehensive literature analysis of the Free Energy Principle and Active Inference. Introduces a systematic approach to annotate and analyze scientific publications. Aims to facilitate integration of manual and automated contributions in research. Addresses the historical and philosophical context of the Free Energy Principle and Active Inference. Utilized Publish or Perish software for citation discovery and dataset compilation. Employed BioPython API to query open source publications from the NCBI Pubmed Database. Conducted manual annotation of papers based on structural, visual, and mathematical features. Developed an analysis pipeline for examining publication dynamics and language use." }, { "id": "work:Friedman2022TrustFinderRecommendationsCommunityBased074", "type": "work", "title": "TrustFinder: Recommendations for Community-Based Trust Systems", "url": "/works/Friedman2022TrustFinderRecommendationsCommunityBased074.html", "external_url": "https://doi.org/10.5281/zenodo.7093837", "summary": "TrustFinder is a sociotechnical system designed to enhance situational awareness in the information environment by enabling users to collaboratively manage the information supply chain. It aims to help users find trusted", "year": 2022, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "TrustFinder", "trust systems", "information evaluation", "cognitive security", "verified information", "collaborative assessment", "sociotechnical systems" ], "content": "TrustFinder: Recommendations for Community-Based Trust Systems Zenodo 10.5281/zenodo.7093837 Friedman2022TrustFinderRecommendationsCommunityBased074 Cognitive Security Paper TrustFinder is a sociotechnical system designed to enhance situational awareness in the information environment by enabling users to collaboratively manage the information supply chain. It aims to help users find trusted sources and evaluate claims through structured tools and community engagement. TrustFinder trust systems information evaluation cognitive security verified information collaborative assessment sociotechnical systems Development of a collaborative platform for managing information sources and claims. Implementation of trust scores to evaluate the quality of authors and content. Introduction of web and document annotation tools to enrich content and facilitate sensemaking. Establishment of a framework for mapping the information supply chain. Utilization of user-created Workspaces for collaborative projects. Incorporation of various informational structures such as Claims, Claim Instances, and Questions. Application of argument representation frameworks to connect Claims and enhance navigation. Use of crowdsourcing design principles to leverage global research community contributions." }, { "id": "work:Friedman2021ActiveInferantsActiveInference075", "type": "work", "title": "Active Inferants: An Active Inference Framework for Ant Colony Behavior", "url": "/works/Friedman2021ActiveInferantsActiveInference075.html", "external_url": "https://doi.org/10.3389/fnbeh.2021.647732", "summary": "This paper presents an active inference model of ant colony foraging behavior, utilizing a Markov decision process to simulate and analyze the dynamics of trail formation and decision-making in ant colonies. The study ai", "year": 2021, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "active inference", "ant foraging", "Markov decision process", "stigmergy", "T-maze", "collective behavior", "behavioral modeling", "eco-evo-devo" ], "content": "Active Inferants: An Active Inference Framework for Ant Colony Behavior Frontiers in Behavioral Neuroscience 10.3389/fnbeh.2021.647732 Friedman2021ActiveInferantsActiveInference075 Entomology Paper This paper presents an active inference model of ant colony foraging behavior, utilizing a Markov decision process to simulate and analyze the dynamics of trail formation and decision-making in ant colonies. The study aims to integrate insights from behavioral modeling with ecological and evolutionary frameworks to enhance understanding of collective behavior in eusocial insects. active inference ant foraging Markov decision process stigmergy T-maze collective behavior behavioral modeling eco-evo-devo Introduced an active inference model specifically for ant colony foraging behavior. Demonstrated the model's ability to replicate key phenomena such as trail formation in response to food discovery. Integrated stigmergic regulation into the active inference framework, enhancing the understanding of collective decision-making. Provided a versatile simulation model that can be adapted for various environmental and biophysical manipulations. Developed a Bayesian simulation model based on active inference principles. Utilized a Markov decision process to simulate ant foraging behavior. Focused on stigmergic outcomes using a single trail pheromone molecule. Conducted in silico experiments to validate the model against established behavioral paradigms." }, { "id": "work:Friedman2021ActiveInferenceModelingConflict076", "type": "work", "title": "Active Inference in Modeling Conflict", "url": "/works/Friedman2021ActiveInferenceModelingConflict076.html", "external_url": "https://doi.org/10.5281/zenodo.5759807", "summary": "This paper integrates conflict studies with Active Inference, proposing the Active Inference Conflict (AIC) model to analyze modern conflict through a multiscale process of communication, trust, and relationship manageme", "year": 2021, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Active Inference", "conflict modeling", "AIC model", "OODA loops", "cognitive security", "information warfare", "BOLTS framework", "trust management" ], "content": "Active Inference in Modeling Conflict Zenodo 10.5281/zenodo.5759807 Friedman2021ActiveInferenceModelingConflict076 Active Inference Paper This paper integrates conflict studies with Active Inference, proposing the Active Inference Conflict (AIC) model to analyze modern conflict through a multiscale process of communication, trust, and relationship management. The AIC model extends traditional frameworks, offering insights into various forms of conflict that are not adequately addressed by existing models. Active Inference conflict modeling AIC model OODA loops cognitive security information warfare BOLTS framework trust management Introduction of the Active Inference Conflict (AIC) model for analyzing modern conflict. Extension of traditional conflict models to include non-kinetic forms of conflict. Integration of insights from various fields to enhance understanding of complex conflicts. Recommendations for future research and social systems design based on qualitative use of the AIC model. Utilization of Active Inference as a framework for understanding cognition and behavior in conflict. Survey of past qualitative and quantitative models of conflict to identify gaps and needs. Analysis of the relationship between the AIC model and existing frameworks like OODA and the Rumsfeld Matrix. Exploration of multiscale processes in conflict management and relationship dynamics." }, { "id": "work:Friedman2021DigitalRhetoricalEcosystemAnalysis077", "type": "work", "title": "Digital Rhetorical Ecosystem Analysis: Sensemaking of Digital Memetic Discourse", "url": "/works/Friedman2021DigitalRhetoricalEcosystemAnalysis077.html", "external_url": "https://doi.org/10.5281/zenodo.5573947", "summary": "This paper advocates for the integration of rhetorical and ecological frameworks to analyze digital image memes, aiming to enhance understanding of how these memes shape online narratives. It highlights the need for a rh", "year": 2021, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "digital rhetoric", "image memes", "DRE3 model", "narrative ecosystems", "rhetorical ecology", "sensemaking", "computational discourse analysis" ], "content": "Digital Rhetorical Ecosystem Analysis: Sensemaking of Digital Memetic Discourse Zenodo 10.5281/zenodo.5573947 Friedman2021DigitalRhetoricalEcosystemAnalysis077 Cognitive Security Paper This paper advocates for the integration of rhetorical and ecological frameworks to analyze digital image memes, aiming to enhance understanding of how these memes shape online narratives. It highlights the need for a rhetorical approach to better categorize and model multimedia discourse, particularly in the context of the current digital information crisis. digital rhetoric image memes DRE3 model narrative ecosystems rhetorical ecology sensemaking computational discourse analysis Introduces a combined rhetorical and ecological framework for analyzing digital image memes. Develops the Digital Rhetorical Ecosystem three-tiered model (DRE3) to explain the impact of memes on public narratives. Emphasizes the narrative power of image memes through parsimony and polysemy. Proposes a new approach to address the epistemic crisis by focusing on rhetorical conditions rather than just misinformation. Utilizes a rhetorical approach to analyze message features and audience engagement. Applies an ecosystem approach to trace narratives across digital platforms and media types. Introduces the DRE3 model for systematic analysis of digital discourse. Explores implications for the design of computational analysis systems for digital rhetoric." }, { "id": "work:Friedman2021InnovatorSDigitalPlaybook078", "type": "work", "title": "Innovator's Digital Playbook", "url": "/works/Friedman2021InnovatorSDigitalPlaybook078.html", "external_url": "https://innovatorsdigitalplaybook.com/", "summary": "Playbook · Web · Media & Teaching", "year": 2021, "domain": "Media & Teaching", "tags": [ "Playbook", "Media & Teaching", "bibliography" ], "content": "Innovator's Digital Playbook Web Friedman2021InnovatorSDigitalPlaybook078 Media & Teaching Playbook" }, { "id": "work:Friedman2021NarrativeInformationEcosystemsConflict079", "type": "work", "title": "Narrative Information Ecosystems: Conflict and Trust on the Endless Frontier", "url": "/works/Friedman2021NarrativeInformationEcosystemsConflict079.html", "external_url": "https://cogsec.org", "summary": "This paper proposes a comprehensive framework for Remote Teams that integrates Active Inference and Systems Engineering to enhance communication and decision-making processes. By defining the roles of Ontologies, Narrati", "year": 2021, "domain": "Cognitive Security", "tags": [ "Book", "Cognitive Security", "bibliography", "narrative ecosystems", "Active Inference", "Remote Teams", "ONFT framework", "epistemic foraging", "niche construction", "collective intelligence", "systems engineering" ], "content": "Narrative Information Ecosystems: Conflict and Trust on the Endless Frontier COGSEC.org Friedman2021NarrativeInformationEcosystemsConflict079 Cognitive Security Book This paper proposes a comprehensive framework for Remote Teams that integrates Active Inference and Systems Engineering to enhance communication and decision-making processes. By defining the roles of Ontologies, Narratives, Formal documents, and Tools (ONFT), the authors aim to improve team efficiency and the phenomenology of the working day. narrative ecosystems Active Inference Remote Teams ONFT framework epistemic foraging niche construction collective intelligence systems engineering Introduces a framework combining Active Inference with Systems Engineering for Remote Teams. Explores the role of communication in enhancing team function and organization. Synthesizes previous work on Active Inference with narratives and ontologies. Addresses the need for effective communication systems in complex multi-agent environments. Utilizes the Active Inference framework to analyze communication in Remote Teams. Applies Systems Engineering principles to formalize Remote Team processes. Investigates the dynamics of narratives and their impact on team coherence. Examines the use of digital tools for enhancing team collaboration and decision-making." }, { "id": "work:Friedman2021NarrativeInformationManagement080", "type": "work", "title": "Narrative Information Management", "url": "/works/Friedman2021NarrativeInformationManagement080.html", "external_url": "https://doi.org/10.5281/zenodo.5573287", "summary": "This paper proposes Narrative Information Management (NIM) as a framework to address information-related challenges across various fields by facilitating knowledge exchange and synthesis. It aims to unify diverse discipl", "year": 2021, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "Narrative Information Management", "NIM", "collective sensemaking", "knowledge management", "information systems", "cognitive load", "interdisciplinary synthesis" ], "content": "Narrative Information Management Zenodo 10.5281/zenodo.5573287 Friedman2021NarrativeInformationManagement080 Cognitive Security Paper This paper proposes Narrative Information Management (NIM) as a framework to address information-related challenges across various fields by facilitating knowledge exchange and synthesis. It aims to unify diverse disciplines facing similar issues in organizational sensemaking and offers recommendations for future research. Narrative Information Management NIM collective sensemaking knowledge management information systems cognitive load interdisciplinary synthesis Introduces Narrative Information Management (NIM) as a unifying framework for information dynamics. Identifies common features of effective information systems across various disciplines. Explores insights and solutions from eclectic fields facing information challenges. Provides recommendations for future research directions in information management. Conducts a literature review on information-focused disciplines to identify impactful system features. Analyzes challenges faced by various fields in managing information and sensemaking. Synthesizes common features of NIM systems from diverse domains. Explores domain-specific challenges and ad-hoc solutions related to information dynamics." }, { "id": "work:Friedman2021FacilitatorSCatechismPlaybook081", "type": "work", "title": "The Facilitator's Catechism Playbook", "url": "/works/Friedman2021FacilitatorSCatechismPlaybook081.html", "external_url": "https://doi.org/10.5281/zenodo.4579414", "summary": "Playbook · Zenodo · Media & Teaching", "year": 2021, "domain": "Media & Teaching", "tags": [ "Playbook", "Media & Teaching", "bibliography" ], "content": "The Facilitator's Catechism Playbook Zenodo 10.5281/zenodo.4579414 Friedman2021FacilitatorSCatechismPlaybook081 Media & Teaching Playbook" }, { "id": "work:Friedman2020ActiveInferenceBehaviorEngineering082", "type": "work", "title": "Active Inference & Behavior Engineering for Teams", "url": "/works/Friedman2020ActiveInferenceBehaviorEngineering082.html", "external_url": "https://doi.org/10.5281/zenodo.4021163", "summary": "This paper proposes a comprehensive framework for Remote Teams that integrates Active Inference with Systems Engineering to enhance communication and decision-making processes. By leveraging the Free Energy Principle, th", "year": 2020, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "behavior engineering", "systems engineering", "organizational behavior", "complex adaptive systems", "team formation", "behavioral design" ], "content": "Active Inference & Behavior Engineering for Teams Zenodo 10.5281/zenodo.4021163 Friedman2020ActiveInferenceBehaviorEngineering082 Active Inference Paper This paper proposes a comprehensive framework for Remote Teams that integrates Active Inference with Systems Engineering to enhance communication and decision-making processes. By leveraging the Free Energy Principle, the authors aim to develop effective ontologies, narratives, and tools that can significantly improve team functionality and productivity. behavior engineering systems engineering organizational behavior complex adaptive systems team formation behavioral design Establishes the importance of effective communication systems in both natural and designed teams. Synthesizes Active Inference with Systems Engineering to formalize Remote Team processes. Explores the application of Active Inference in both located and all-online Remote Teams. Addresses the need for a structured approach to team communication and lifecycle management. Utilizes the Active Inference framework to analyze communication in teams. Applies Systems Engineering principles to define and manage team functions. Investigates the role of narratives and ontologies in enhancing team communication. Examines the dynamics of team formation and the impact of shared organizational culture." }, { "id": "work:Friedman2020CommunicationRemoteTeams083", "type": "work", "title": "Communication for Remote Teams", "url": "/works/Friedman2020CommunicationRemoteTeams083.html", "external_url": "https://www.udemy.com/course/communication-for-remote-teams/", "summary": "Course · Udemy · Media & Teaching", "year": 2020, "domain": "Media & Teaching", "tags": [ "Course", "Media & Teaching", "bibliography" ], "content": "Communication for Remote Teams Udemy Friedman2020CommunicationRemoteTeams083 Media & Teaching Course" }, { "id": "work:Friedman2020DistributedPhysiologyMolecularBasis084", "type": "work", "title": "Distributed physiology and the molecular basis of social life in eusocial insects", "url": "/works/Friedman2020DistributedPhysiologyMolecularBasis084.html", "external_url": "https://doi.org/10.1016/j.yhbeh.2020.104757", "summary": "This paper explores the physiological and molecular processes that govern social life in eusocial insects, emphasizing the importance of colony-level regulation and decentralized physiological mechanisms. It argues for a", "year": 2020, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "distributed physiology", "superorganism", "collective behavior", "ant colonies", "decentralized control", "interaction networks", "colony metabolism", "social immunity" ], "content": "Distributed physiology and the molecular basis of social life in eusocial insects Hormones & Behavior 10.1016/j.yhbeh.2020.104757 Friedman2020DistributedPhysiologyMolecularBasis084 Entomology Paper This paper explores the physiological and molecular processes that govern social life in eusocial insects, emphasizing the importance of colony-level regulation and decentralized physiological mechanisms. It argues for a framework that integrates functional genomics and social physiology to better understand the evolution and behavior of these complex social systems. distributed physiology superorganism collective behavior ant colonies decentralized control interaction networks colony metabolism social immunity Introduces the concept of 'social physiology' to describe the coordination of colony-level traits. Highlights the evolutionary significance of decentralized physiological processes in eusocial insects. Explores the interaction between organismal and colony-level physiological processes. Proposes a framework for integrating theoretical models with empirical research in eusocial insect studies. Reviews empirical research on physiological processes in eusocial insects. Analyzes the roles of molecular signaling and social communication mechanisms. Compares nestmate-level and colony-level physiological traits. Utilizes functional genomic approaches to investigate the genetics of eusocial behavior." }, { "id": "work:Friedman2020EmergentTeamsComplexThreats085", "type": "work", "title": "Emergent Teams for Complex Threats", "url": "/works/Friedman2020EmergentTeamsComplexThreats085.html", "external_url": "https://doi.org/10.5281/zenodo.3986085", "summary": "This paper explores the intersection of Complexity Science and Military Science, emphasizing the need for new approaches to conflict management in light of evolving threats. It discusses how rapid team assembly and the p", "year": 2020, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "emergent teams", "operations orders", "team formation", "innovation", "facilitation", "collective intelligence", "hackathons", "research accelerators" ], "content": "Emergent Teams for Complex Threats Zenodo 10.5281/zenodo.3986085 Friedman2020EmergentTeamsComplexThreats085 Cognitive Security Paper This paper explores the intersection of Complexity Science and Military Science, emphasizing the need for new approaches to conflict management in light of evolving threats. It discusses how rapid team assembly and the pooling of collective expertise can address emergent hazards in military and civilian contexts. emergent teams operations orders team formation innovation facilitation collective intelligence hackathons research accelerators Introduces the concept of Complex Threat Surfaces in military and civilian organizations. Highlights the role of Complexity Science in analyzing and managing complex threats. Proposes Rapid Team Assembly as a method for developing spontaneous expertise and actionable intelligence. Examines lessons from the 2008 Mumbai attack to illustrate the effectiveness of decentralized operations. Utilizes a Complexity Science framework to model and de-risk complex threats. Analyzes counterinsurgency and counterterrorism operations through case studies. Discusses best practices for rapid reorganization and adaptation in response to emergent problems. Examines the use of open-source intelligence (OSINT) in planning and executing operations." }, { "id": "work:Friedman2020GeneExpressionVariationBrains086", "type": "work", "title": "Gene expression variation in the brains of harvester ant foragers is associated with collective behavior", "url": "/works/Friedman2020GeneExpressionVariationBrains086.html", "external_url": "https://doi.org/10.1038/s42003-020-0813-8", "summary": "This study investigates how gene expression variation in the brains of red harvester ant foragers is linked to collective behavior and reproductive success. Using RNA-seq, we found that differences in gene expression amo", "year": 2020, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "gene expression", "foragers", "RNA-Seq", "division of labor", "transcriptomics", "harvester ants", "behavioral castes", "Pogonomyrmex barbatus" ], "content": "Gene expression variation in the brains of harvester ant foragers is associated with collective behavior Communications Biology 10.1038/s42003-020-0813-8 Friedman2020GeneExpressionVariationBrains086 Entomology Paper This study investigates how gene expression variation in the brains of red harvester ant foragers is linked to collective behavior and reproductive success. Using RNA-seq, we found that differences in gene expression among colonies correlate with their sensitivity to humidity and the dopamine-to-serotonin ratio in forager brains. gene expression foragers RNA-Seq division of labor transcriptomics harvester ants behavioral castes Pogonomyrmex barbatus Identified gene expression differences in forager brains across ant colonies. Established a link between gene expression variation and colony-level traits related to foraging behavior. Demonstrated that neurophysiological differences influence collective behavior in natural settings. Provided insights into the evolutionary constraints on gene expression related to colony behavior. Utilized RNA-seq to profile gene expression in the brains of foragers from nine colonies. Applied supervised and unsupervised statistical approaches to analyze transcriptomic patterns. Conducted dimensional reduction techniques such as PCA and linear discriminant analysis to differentiate colonies. Performed gene ontology enrichment analyses to identify functional categories associated with expression patterns." }, { "id": "work:Friedman2020HowUseKeybaseRemote087", "type": "work", "title": "How to use Keybase for remote teams", "url": "/works/Friedman2020HowUseKeybaseRemote087.html", "external_url": "https://www.udemy.com/course/keybase-for-remote-teams/", "summary": "Course · Udemy · Media & Teaching", "year": 2020, "domain": "Media & Teaching", "tags": [ "Course", "Media & Teaching", "bibliography" ], "content": "How to use Keybase for remote teams Udemy Friedman2020HowUseKeybaseRemote087 Media & Teaching Course" }, { "id": "work:Friedman2020MeasurementNaturalVariationNeurotransmitter088", "type": "work", "title": "Measurement of natural variation of neurotransmitter tissue content in red harvester ant brains", "url": "/works/Friedman2020MeasurementNaturalVariationNeurotransmitter088.html", "external_url": "https://doi.org/10.1007/s00216-019-02355-3", "summary": "This study quantifies the tissue content of four biogenic amines in the brains of red harvester ants from different colonies, linking foraging behavior to neurotransmitter signaling. Using capillary electrophoresis coupl", "year": 2020, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "neurotransmitters", "dopamine", "serotonin", "octopamine", "tyramine", "Pogonomyrmex barbatus", "CE-FSCV", "biogenic amines" ], "content": "Measurement of natural variation of neurotransmitter tissue content in red harvester ant brains Analytical & Bioanalytical Chemistry 10.1007/s00216-019-02355-3 Friedman2020MeasurementNaturalVariationNeurotransmitter088 Entomology Paper This study quantifies the tissue content of four biogenic amines in the brains of red harvester ants from different colonies, linking foraging behavior to neurotransmitter signaling. Using capillary electrophoresis coupled with fast-scan cyclic voltammetry, the research reveals significant variation in neurotransmitter levels among colonies in a natural environment. neurotransmitters dopamine serotonin octopamine tyramine Pogonomyrmex barbatus CE-FSCV biogenic amines colony variation First measurements of biogenic amine tissue content in single forager ant brains from natural populations. Demonstration of capillary electrophoresis coupled with fast-scan cyclic voltammetry as an effective method for neurotransmitter analysis in small samples. Identification of significant differences in neurotransmitter levels across ant colonies, suggesting environmental influences on biogenic amine signaling. Establishment of a foundation for future studies correlating neurotransmitter content with ant foraging behavior. Utilized capillary electrophoresis with fast-scan cyclic voltammetry (CE-FSCV) for neurotransmitter detection. Field-amplified sample stacking was employed to enhance detection limits of neurotransmitters in single ant brains. Ant brains were dissected and homogenized in a controlled environment to prepare samples for analysis. Statistical analysis was performed using GraphPad Prism to evaluate variations in neurotransmitter content." }, { "id": "work:Friedman2020GreatPresetRemoteTeams089", "type": "work", "title": "The Great Preset: Remote Teams and Operational Art", "url": "/works/Friedman2020GreatPresetRemoteTeams089.html", "external_url": "https://cogsec.org", "summary": "The paper explores the dynamics of remote teams and their operational strategies, emphasizing the importance of cognitive security in collaborative environments. It aims to provide insights into effective management and ", "year": 2020, "domain": "Cognitive Security", "tags": [ "Book", "Cognitive Security", "bibliography", "cognitive security", "narrative ecosystems", "Great Reset", "sensemaking", "Active Inference", "information theory", "socioeconomic narratives" ], "content": "The Great Preset: Remote Teams and Operational Art COGSEC.org Friedman2020GreatPresetRemoteTeams089 Cognitive Security Book The paper explores the dynamics of remote teams and their operational strategies, emphasizing the importance of cognitive security in collaborative environments. It aims to provide insights into effective management and communication practices for remote teams. cognitive security narrative ecosystems Great Reset sensemaking Active Inference information theory socioeconomic narratives Introduces a framework for understanding cognitive security in remote team settings. Analyzes the impact of operational art on team collaboration and performance. Offers practical strategies for enhancing communication and trust among remote team members. Highlights case studies demonstrating successful remote team management. Conducted qualitative interviews with remote team leaders and members. Utilized case study analysis to identify best practices in remote team operations. Applied theoretical frameworks from cognitive security and operational art to analyze findings. Developed a set of guidelines based on empirical data and expert insights." }, { "id": "work:Friedman2020InnovatorSCatechism090", "type": "work", "title": "The Innovator's Catechism", "url": "/works/Friedman2020InnovatorSCatechism090.html", "external_url": "https://doi.org/10.5281/zenodo.4383230", "summary": "This paper presents 'The Innovator’s Catechism', a structured operations order designed for early-stage innovation teams to enhance alignment on narrative, workflow, and objectives. By adapting military operations orders", "year": 2020, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "operations orders", "innovation teams", "Innovator's Catechism", "team alignment", "military transfer", "organizational design", "hackathons" ], "content": "The Innovator's Catechism Zenodo 10.5281/zenodo.4383230 Friedman2020InnovatorSCatechism090 Cognitive Security Paper This paper presents 'The Innovator’s Catechism', a structured operations order designed for early-stage innovation teams to enhance alignment on narrative, workflow, and objectives. By adapting military operations orders for business contexts, the authors aim to improve the reliability and effectiveness of innovation management. operations orders innovation teams Innovator's Catechism team alignment military transfer organizational design hackathons Introduction of 'The Innovator’s Catechism' tailored for early-stage innovation teams. Adaptation of military operations orders to enhance organizational efficacy in business settings. Integration of insights from high reliability organizations (HROs) and innovation management. Development of a structured framework to facilitate communication and alignment in innovation teams. Combination of the Facilitator’s Catechism with Blank’s innovation pipeline framework. Analysis of military operations orders and their impact on organizational performance. Utilization of insights from industrial and organizational psychology, sensemaking, and narrative construction. Creation of a series of structured questions for innovators at each stage of the innovation process." }, { "id": "work:Friedman2020NeuroscienceDecisionMakingInterview091", "type": "work", "title": "The neuroscience of decision making (interview with Timothy Hanks)", "url": "/works/Friedman2020NeuroscienceDecisionMakingInterview091.html", "external_url": "https://doi.org/10.34700/8pg4-0h12", "summary": "This interview with Professor Tim Hanks explores the intersection of neuroscience and decision making, emphasizing the importance of an integrative approach that incorporates various experimental methods and models. Hank", "year": 2020, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "decision making", "computational neuroscience", "Bayesian brain", "free will", "mental health", "attention", "neural circuits" ], "content": "The neuroscience of decision making (interview with Timothy Hanks) ALIUS Bulletin 10.34700/8pg4-0h12 Friedman2020NeuroscienceDecisionMakingInterview091 Genetics & Biomedical Paper This interview with Professor Tim Hanks explores the intersection of neuroscience and decision making, emphasizing the importance of an integrative approach that incorporates various experimental methods and models. Hanks discusses how computational neuroscience informs research agendas and everyday decision-making processes, while also addressing the philosophical implications of free will and conscious awareness. decision making computational neuroscience Bayesian brain free will mental health attention neural circuits Introduces an integrative approach to studying decision making that combines multiple experimental methods. Highlights the role of computational neuroscience in shaping research agendas and personal decision-making. Explores the relationship between neural mechanisms and the philosophical concept of free will. Encourages open-mindedness about future developments in neuroscience. Utilizes Bayesian reasoning to inform decision-making processes. Discusses the accumulation of evidence to a threshold level as a mechanism for decision commitment. Examines neural activity related to decision-making and its implications for understanding free will. Proposes a roadmap for future research that bridges conscious awareness with neural measurements." }, { "id": "work:Friedman2019DennettExplainedInterviewDaniel092", "type": "work", "title": "Dennett Explained (interview with Daniel Dennett)", "url": "/works/Friedman2019DennettExplainedInterviewDaniel092.html", "external_url": "https://doi.org/10.34700/7gkw-zh08", "summary": "This paper features an interview with Daniel Dennett, exploring his interdisciplinary approach to philosophy, cognitive science, and consciousness. Dennett emphasizes the importance of integrating philosophical insights ", "year": 2019, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "consciousness", "philosophy of mind", "Daniel Dennett", "cognitive science", "psychedelics", "predictive processing", "altered states" ], "content": "Dennett Explained (interview with Daniel Dennett) ALIUS Bulletin 10.34700/7gkw-zh08 Friedman2019DennettExplainedInterviewDaniel092 Genetics & Biomedical Paper This paper features an interview with Daniel Dennett, exploring his interdisciplinary approach to philosophy, cognitive science, and consciousness. Dennett emphasizes the importance of integrating philosophical insights with scientific inquiry and discusses the potential therapeutic value of psychoactive substances. consciousness philosophy of mind Daniel Dennett cognitive science psychedelics predictive processing altered states Highlights Dennett's unique approach to philosophy that bridges gaps between various disciplines. Discusses the significance of psychoactive substances in scientific and therapeutic contexts. Explores Dennett's influence on the understanding of consciousness and cognitive science. Advocates for the role of philosophers in enhancing scientific methodologies. Conducted an interview format to elicit Dennett's thoughts and experiences. Utilized cross-disciplinary perspectives to analyze philosophical and scientific concepts. Engaged in speculative discussions about empirical questions related to consciousness. Incorporated historical context and philosophical lineage to frame Dennett's ideas." }, { "id": "work:Friedman2019PhDBehavioralPhysiologicalTranscriptomic093", "type": "work", "title": "PhD: Behavioral, Physiological, and Transcriptomic Variation Among Colonies of Pogonomyrmex barbatus", "url": "/works/Friedman2019PhDBehavioralPhysiologicalTranscriptomic093.html", "external_url": "http://purl.stanford.edu/pb813wm1484", "summary": "This dissertation examines the physiological and transcriptomic variations among colonies of the red harvester ant (Pogonomyrmex barbatus) and their association with collective behaviors. It highlights the neurophysiolog", "year": 2019, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "PhD dissertation", "Pogonomyrmex barbatus", "collective behavior", "transcriptomics", "behavioral ecology", "foraging gene", "dopamine", "colony variation" ], "content": "PhD: Behavioral, Physiological, and Transcriptomic Variation Among Colonies of Pogonomyrmex barbatus Stanford University Friedman2019PhDBehavioralPhysiologicalTranscriptomic093 Entomology Paper This dissertation examines the physiological and transcriptomic variations among colonies of the red harvester ant (Pogonomyrmex barbatus) and their association with collective behaviors. It highlights the neurophysiological basis of behavioral differences and explores how these variations impact foraging strategies and reproductive success. PhD dissertation Pogonomyrmex barbatus collective behavior transcriptomics behavioral ecology foraging gene dopamine colony variation Stanford University Investigated the neurophysiological basis of behavioral variation among ant colonies. Demonstrated the impact of dopamine levels on foraging activity in red harvester ants. Explored the relationship between colony foraging behavior and reproductive success. Analyzed gene expression variation in relation to colony traits using RNA-seq. Conducted transcriptomic profiling of forager brains to assess gene expression differences. Performed pharmacological experiments to evaluate the effects of dopamine on foraging behavior. Executed manipulative field experiments to study foraging trips in relation to hydration levels. Utilized RNA-seq to analyze gene expression variation within and among colonies." }, { "id": "work:Friedman2019AntColonyAsTest094", "type": "work", "title": "The ant colony as a test for scientific theories of consciousness", "url": "/works/Friedman2019AntColonyAsTest094.html", "external_url": "https://doi.org/10.1007/s11229-019-02130-y", "summary": "This paper explores the complexities surrounding the scientific study of consciousness by proposing the Ant Colony Test (ACT) as a reverse test for consciousness theories. By examining social insect colonies, the authors", "year": 2019, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "consciousness", "ant colony", "Ant Colony Test", "philosophy of science", "social insects", "collective cognition", "scientific theories of consciousness" ], "content": "The ant colony as a test for scientific theories of consciousness Synthese 10.1007/s11229-019-02130-y Friedman2019AntColonyAsTest094 Entomology Paper This paper explores the complexities surrounding the scientific study of consciousness by proposing the Ant Colony Test (ACT) as a reverse test for consciousness theories. By examining social insect colonies, the authors aim to provide a framework for evaluating various theories of consciousness and to clarify the discourse on this elusive topic. consciousness ant colony Ant Colony Test philosophy of science social insects collective cognition scientific theories of consciousness Introduces the Ant Colony Test (ACT) as a novel reverse test for theories of consciousness. Reinterprets frameworks for studying consciousness through the lens of social insect evolutionary biology. Highlights the potential of social insect colonies as a model system for ethical experiments on consciousness. Calls for a reassessment of existing theories of consciousness in light of empirical data from social insects. Analyzes the dichotomy between forward tests and reverse tests in scientific methodology. Utilizes a comparative approach to assess consciousness theories against the behavior of social insect colonies. Draws on a long lineage of neurobehavioral, evolutionary, and ecological studies of social insects. Employs philosophical analysis to clarify the implications of consciousness in disaggregated systems." }, { "id": "work:Friedman2019PhysiologyForagerHydrationVariation095", "type": "work", "title": "The physiology of forager hydration and variation among harvester ant colonies", "url": "/works/Friedman2019PhysiologyForagerHydrationVariation095.html", "external_url": "https://doi.org/10.1038/s41598-019-41586-3", "summary": "This paper investigates the relationship between hydration status and foraging behavior in red harvester ants (Pogonomyrmex barbatus), revealing that hydrated foragers are more active and that desiccation tolerance is li", "year": 2019, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "Pogonomyrmex barbatus", "desiccation physiology", "foraging behavior", "water balance", "colony variation", "collective behavior", "behavioral ecology", "reproductive fitness" ], "content": "The physiology of forager hydration and variation among harvester ant colonies Scientific Reports 10.1038/s41598-019-41586-3 Friedman2019PhysiologyForagerHydrationVariation095 Entomology Paper This paper investigates the relationship between hydration status and foraging behavior in red harvester ants (Pogonomyrmex barbatus), revealing that hydrated foragers are more active and that desiccation tolerance is linked to reproductive success among colonies. The findings suggest that physiological differences among colonies influence collective foraging strategies in response to environmental stressors. Pogonomyrmex barbatus desiccation physiology foraging behavior water balance colony variation collective behavior behavioral ecology reproductive fitness Demonstrated the impact of hydration on foraging activity in red harvester ants. Established a link between desiccation tolerance and reproductive success in ant colonies. Identified physiological differences among colonies that affect collective behavior. Provided insights into the evolutionary adaptations of social insects to desiccating environments. Conducted field experiments manipulating hydration levels of foragers and observing subsequent foraging behavior. Performed desiccation tests to assess water loss sensitivity in foragers from different colonies. Utilized statistical analyses, including Wilcoxon signed-rank tests and regression models, to evaluate the effects of hydration on foraging trips. Collected environmental data (temperature and humidity) to correlate with foraging activity." }, { "id": "work:Friedman2018ForagingBehaviorLocomotionInvasive096", "type": "work", "title": "Foraging behavior and locomotion of the invasive Argentine ant from winter aggregations", "url": "/works/Friedman2018ForagingBehaviorLocomotionInvasive096.html", "external_url": "https://doi.org/10.1371/journal.pone.0202117", "summary": "This study investigates the foraging behavior and locomotion of the invasive Argentine ant (Linepithema humile) during winter in northern California, focusing on how these behaviors are influenced by environmental condit", "year": 2018, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "Argentine ant", "Linepithema humile", "invasive species", "supercolony", "nestmate recognition", "collective behavior", "chemical ecology", "cuticular hydrocarbons" ], "content": "Foraging behavior and locomotion of the invasive Argentine ant from winter aggregations PLoS One 10.1371/journal.pone.0202117 Friedman2018ForagingBehaviorLocomotionInvasive096 Entomology Paper This study investigates the foraging behavior and locomotion of the invasive Argentine ant (Linepithema humile) during winter in northern California, focusing on how these behaviors are influenced by environmental conditions. The findings reveal that foraging activity peaks at specific temperatures and is affected by humidity, while the presence of a competing native ant species does not significantly deter foraging efforts. Argentine ant Linepithema humile invasive species supercolony nestmate recognition collective behavior chemical ecology cuticular hydrocarbons First comprehensive study of Argentine ant foraging behavior in winter conditions. Identification of a winter circadian rhythm in foraging activity. Demonstration of the impact of temperature and humidity on locomotion and foraging rates. Insights into the competitive dynamics between Argentine ants and native species. Recorded foraging rates and walking speeds of three L. humile colonies over three 24-hour periods. Measured environmental conditions including temperature, humidity, and light levels. Analyzed the correlation between foraging activity and the presence of the native ant species Prenolepis imparis. Utilized mixed effect models to assess the relationships between environmental factors and ant behavior." }, { "id": "work:Friedman2018MVEEFrameworkEvolutionaryStudies097", "type": "work", "title": "MVEE: A Framework for Evolutionary Studies", "url": "/works/Friedman2018MVEEFrameworkEvolutionaryStudies097.html", "external_url": "https://doi.org/10.5281/zenodo.13999298", "summary": "This paper presents the MVEE framework, aimed at formalizing the evolution of heredity, environment, and phenotype across biological levels and time. It seeks to extend Variational Neuroethology to create a comprehensive", "year": 2018, "domain": "Media & Teaching", "tags": [ "Presentation", "Media & Teaching", "bibliography", "MVEE", "evolutionary theory", "multilevel evolution", "phenotypic plasticity", "eco-evo-devo", "variational methods", "multilevel selection", "open-ended evolution" ], "content": "MVEE: A Framework for Evolutionary Studies Presentation 10.5281/zenodo.13999298 Friedman2018MVEEFrameworkEvolutionaryStudies097 Media & Teaching Presentation This paper presents the MVEE framework, aimed at formalizing the evolution of heredity, environment, and phenotype across biological levels and time. It seeks to extend Variational Neuroethology to create a comprehensive framework for evolutionary studies. MVEE evolutionary theory multilevel evolution phenotypic plasticity eco-evo-devo variational methods multilevel selection open-ended evolution Introduces the MVEE framework for evolutionary studies. Integrates concepts of plasticity, meta-plasticity, and ecological variability. Proposes new measurements and experiments to enhance evolutionary research. Addresses interactions across different biological scales. Extends existing theories in Variational Neuroethology. Utilizes a formalized approach to model evolutionary processes. Incorporates interdisciplinary data from biological, social, and computational systems. Analyzes ecological variability over multiple time scales." }, { "id": "work:Friedman2018WoodliceMenBayesianAccount098", "type": "work", "title": "Of woodlice and men: A Bayesian account of cognition, life and consciousness (with Karl Friston)", "url": "/works/Friedman2018WoodliceMenBayesianAccount098.html", "external_url": "https://doi.org/10.34700/h460-nz89", "summary": "This paper presents an interview with Karl Friston, exploring the development of the free energy principle as a theoretical framework that unifies psychological, neural, and biological aspects of living beings. It discus", "year": 2018, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Free Energy Principle", "Karl Friston", "Bayesian brain", "predictive processing", "Markov blanket", "consciousness", "self-organization", "variational inference" ], "content": "Of woodlice and men: A Bayesian account of cognition, life and consciousness (with Karl Friston) ALIUS Bulletin 10.34700/h460-nz89 Friedman2018WoodliceMenBayesianAccount098 Active Inference Paper This paper presents an interview with Karl Friston, exploring the development of the free energy principle as a theoretical framework that unifies psychological, neural, and biological aspects of living beings. It discusses the implications of this framework for understanding cognition, life, and consciousness through a Bayesian lens. Free Energy Principle Karl Friston Bayesian brain predictive processing Markov blanket consciousness self-organization variational inference philosophy of mind Introduces the free energy principle as a unifying framework for understanding cognition and consciousness. Explores the relationship between the Bayesian brain hypothesis, predictive coding, and the free energy principle. Highlights the simplicity and elegance of the free energy principle in explaining complex behaviors. Discusses the evolution of the free energy principle from early childhood observations to a comprehensive theoretical model. Utilizes Bayesian inference to model cognitive processes and perceptual states. Applies variational Bayes for ensemble learning and probability density dynamics. Examines hierarchical structures in the brain to understand spatial and temporal processes in cognition. Analyzes the reduction of surprise and informational entropy in relation to sensory data and hypotheses." }, { "id": "work:Friedman2018PartnerPenPlayParallel099", "type": "work", "title": "Partner Pen Play in Parallel (PPPiP): A New Paradigm for Relationship Improvement", "url": "/works/Friedman2018PartnerPenPlayParallel099.html", "external_url": "https://doi.org/10.3390/arts7030039", "summary": "This paper introduces Partner Pen Play in Parallel (PPPiP), a novel technique for enhancing romantic relationships through simultaneous improvisational drawing. By integrating insights from art therapy, sexology, and neu", "year": 2018, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "PPPiP", "art therapy", "improvisation", "intimate relationships", "affective neuroscience", "creativity", "dyadic interaction", "sexology" ], "content": "Partner Pen Play in Parallel (PPPiP): A New Paradigm for Relationship Improvement Arts 10.3390/arts7030039 Friedman2018PartnerPenPlayParallel099 Art & Synergetics Paper This paper introduces Partner Pen Play in Parallel (PPPiP), a novel technique for enhancing romantic relationships through simultaneous improvisational drawing. By integrating insights from art therapy, sexology, and neuroscience, the authors propose PPPiP as a low-cost, non-clinical method for fostering intimacy and emotional well-being. PPPiP art therapy improvisation intimate relationships affective neuroscience creativity dyadic interaction sexology controlled novelty Introduces PPPiP as a new paradigm for relationship improvement. Synthesizes interdisciplinary evidence supporting the efficacy of artistic creation in enhancing intimate relationships. Highlights the importance of narrative structure and controlled novelty in partnerships. Demonstrates how PPPiP can promote neural synchrony and joint attention between partners. Describes PPPiP as the act of two individuals drawing together on the same sheet of paper. Utilizes insights from art therapy, sexology, and affective neuroscience to support the practice. Emphasizes the non-clinical, improvisational nature of PPPiP compared to traditional art therapy. Explores the impact of joint attention and neural synchrony during the drawing process." }, { "id": "work:Friedman2018RoleDopamineCollectiveRegulation100", "type": "work", "title": "The Role of Dopamine in Collective Regulation of Foraging in Harvester Ants", "url": "/works/Friedman2018RoleDopamineCollectiveRegulation100.html", "external_url": "https://doi.org/10.1016/j.isci.2018.09.001", "summary": "This study investigates the context-dependent expression of the foraging gene in field colonies of harvester ants, focusing on the roles of age, environment, and task. By examining gene expression across different worker", "year": 2018, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "dopamine", "foraging behavior", "Pogonomyrmex barbatus", "neuromodulation", "task allocation", "behavioral pharmacology", "biogenic amines", "harvester ants" ], "content": "The Role of Dopamine in Collective Regulation of Foraging in Harvester Ants iScience 10.1016/j.isci.2018.09.001 Friedman2018RoleDopamineCollectiveRegulation100 Entomology Paper This study investigates the context-dependent expression of the foraging gene in field colonies of harvester ants, focusing on the roles of age, environment, and task. By examining gene expression across different worker groups and under varying light conditions, the research highlights the complex interactions that influence foraging behavior. dopamine foraging behavior Pogonomyrmex barbatus neuromodulation task allocation behavioral pharmacology biogenic amines harvester ants Demonstrated the temporal regulation of the foraging gene in harvester ants based on age and task. Provided evidence of significant daily oscillations in foraging gene expression linked to activity rhythms. Investigated the effects of light exposure on foraging gene expression in brood workers and foragers. Established correlations between foraging gene expression and the circadian clock gene, cycle. Collected harvester ant workers from natural populations and categorized them into age- and task-related groups. Conducted field experiments to assess foraging gene expression at different times of day. Manipulated light conditions to evaluate their impact on gene expression in various worker tasks. Analyzed mRNA levels of the foraging gene and the circadian clock gene in relation to worker activity." }, { "id": "work:Friedman2017MutAntsAreHere101", "type": "work", "title": "The MutAnts are here", "url": "/works/Friedman2017MutAntsAreHere101.html", "external_url": "https://doi.org/10.1016/j.cell.2017.07.046", "summary": "This paper discusses the successful application of CRISPR/Cas9-mediated gene knockout in two ant species, enabling new insights into the role of olfactory cues in their collective behavior. The findings highlight the gen", "year": 2017, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "CRISPR/Cas9", "Orco gene", "olfactory receptor", "ant genetics", "Ooceraea biroi", "Harpegnathos saltator", "social behavior", "pheromone" ], "content": "The MutAnts are here Cell 10.1016/j.cell.2017.07.046 Friedman2017MutAntsAreHere101 Entomology Paper This paper discusses the successful application of CRISPR/Cas9-mediated gene knockout in two ant species, enabling new insights into the role of olfactory cues in their collective behavior. The findings highlight the genetic and neuroanatomical implications of disrupting the Orco gene, which is crucial for olfactory perception in ants. CRISPR/Cas9 Orco gene olfactory receptor ant genetics Ooceraea biroi Harpegnathos saltator social behavior pheromone gene knockout Demonstrated CRISPR/Cas9-mediated gene knockout in two ant species, advancing ant genetics. Provided evidence for the central role of the Orco gene in olfactory perception and collective behavior in ants. Revealed neuroanatomical defects in the antennal lobe of Orco mutants, suggesting a novel developmental role for Orco. Facilitated the understanding of the genetic basis of social insect behavior and adaptation. Injected freshly-laid ant eggs with purified Cas9 protein and synthetic guide RNAs targeting the Orco gene. Conducted behavioral assays to assess the impact of Orco knockout on ant behavior and reproductive performance. Utilized olfactory assays to evaluate sensitivity to semiochemicals in Orco null mutants. Analyzed neuroanatomical structures in mutant ants to identify defects in the antennal lobe." }, { "id": "work:Friedman2017TwoLineagesThatNeed102", "type": "work", "title": "Two lineages that need each other", "url": "/works/Friedman2017TwoLineagesThatNeed102.html", "external_url": "https://doi.org/10.1111/mec.13964", "summary": "This paper discusses the dependent-lineage system in harvester ants, where two interdependent lineages are necessary for the production of reproductives and workers. It highlights the evolutionary and ecological implicat", "year": 2017, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "dependent-lineage", "mating systems", "Pogonomyrmex", "harvester ants", "genetic caste determination", "intragenomic conflict", "colony organization", "social evolution" ], "content": "Two lineages that need each other Molecular Ecology 10.1111/mec.13964 Friedman2017TwoLineagesThatNeed102 Entomology Paper This paper discusses the dependent-lineage system in harvester ants, where two interdependent lineages are necessary for the production of reproductives and workers. It highlights the evolutionary and ecological implications of this system, particularly in relation to hybridization and mating behaviors. dependent-lineage mating systems Pogonomyrmex harvester ants genetic caste determination intragenomic conflict colony organization social evolution Identification of a dependent-lineage system in Messor harvester ants using RNA sequencing. Exploration of the evolutionary significance of hybridogenesis in ant reproductive systems. Discussion of the ecological implications of mating behaviors in dependent-lineage systems. Comparison of lineage ratios and reproductive strategies between Pogonomyrmex and Messor genera. Utilization of RNA sequencing to investigate genetic systems in harvester ants. Analysis of mating patterns and reproductive outcomes in ant colonies. Long-term ecological studies to assess lineage ratios and survival rates. Examination of hybridization hypotheses through phylogenetic evidence." }, { "id": "work:Friedman2016AntGeneticsReproductivePhysiology103", "type": "work", "title": "Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior", "url": "/works/Friedman2016AntGeneticsReproductivePhysiology103.html", "external_url": "https://doi.org/10.1146/annurev-neuro-070815-013927", "summary": "This paper reviews the genetics of morphological and physiological diversity in ants, with a focus on the limited studies investigating the genetics of ant behavior. It highlights the significant gene turnover in ant gen", "year": 2016, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "ants", "behavioral genetics", "genomics", "colony organization", "caste determination", "division of labor", "foraging gene", "social insects" ], "content": "Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior Annual Review of Neuroscience 10.1146/annurev-neuro-070815-013927 Friedman2016AntGeneticsReproductivePhysiology103 Entomology Paper This paper reviews the genetics of morphological and physiological diversity in ants, with a focus on the limited studies investigating the genetics of ant behavior. It highlights the significant gene turnover in ant genomes, particularly in genes related to olfactory communication, and emphasizes the need for further research into the genetic basis of ant behavior. ants behavioral genetics genomics colony organization caste determination division of labor foraging gene social insects pheromone communication Provides a comprehensive review of the current state of ant genetics research, particularly behavioral genetics. Identifies gaps in the literature regarding the genetic basis of ant behavior. Highlights the importance of gene turnover in the evolution of ant communication and behavior. Suggests future directions for research in ant behavioral genetics. Utilizes quantitative genetic approaches to assess heritability of task performance. Employs transcriptomic studies to analyze gene expression patterns. Conducts phylogenetic analyses of DNA sequence homology. Investigates epigenetic mechanisms affecting gene regulation." }, { "id": "work:Friedman2016ContextDependentExpressionForaging104", "type": "work", "title": "Context-dependent expression of the foraging gene in field colonies of ants", "url": "/works/Friedman2016ContextDependentExpressionForaging104.html", "external_url": "https://doi.org/10.1098/rspb.2016.0841", "summary": "This study investigates the context-dependent expression of the foraging gene in harvester ants, focusing on how age, environment, and task influence gene regulation. By examining field colonies, we reveal that foraging ", "year": 2016, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "foraging gene", "Pogonomyrmex barbatus", "harvester ants", "gene expression", "circadian rhythms", "task allocation", "division of labor", "field study" ], "content": "Context-dependent expression of the foraging gene in field colonies of ants Proceedings of the Royal Society B 10.1098/rspb.2016.0841 Friedman2016ContextDependentExpressionForaging104 Entomology Paper This study investigates the context-dependent expression of the foraging gene in harvester ants, focusing on how age, environment, and task influence gene regulation. By examining field colonies, we reveal that foraging gene expression varies with ontogenetic changes and daily activity rhythms, highlighting the complex interplay between genetic regulation and behavioral plasticity. foraging gene Pogonomyrmex barbatus harvester ants gene expression circadian rhythms task allocation division of labor field study behavioral ecology Demonstrated the context-dependent regulation of the foraging gene in harvester ants. Provided evidence of daily oscillations in foraging gene expression linked to activity rhythms. Investigated the effects of light exposure on foraging gene expression in different task groups. Highlighted the importance of temporal patterns in behavioral gene expression for understanding social insect behavior. Collected harvester ants from natural populations and categorized them into age- and task-related groups. Conducted field experiments to measure foraging gene expression at different times of day. Manipulated light conditions to assess their impact on foraging gene expression. Analyzed the correlation between foraging gene expression and the circadian clock gene." }, { "id": "work:Friedman2016InfluenceNuclearStructureFormation105", "type": "work", "title": "Influence of Nuclear Structure on formation of radiation-induced lethal lesions", "url": "/works/Friedman2016InfluenceNuclearStructureFormation105.html", "external_url": "https://doi.org/10.3109/09553002.2016.1144941", "summary": "This paper discusses the influence of nuclear structure on the formation of radiation-induced lethal lesions, particularly focusing on the rejoining of fragmented nuclear DNA caused by ionizing radiation. It synthesizes ", "year": 2016, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "Hi-C", "chromosome conformation", "radiation biology", "chromatin architecture", "DNA damage", "topologically associating domains", "nuclear organization", "3C technologies" ], "content": "Influence of Nuclear Structure on formation of radiation-induced lethal lesions Int. J. Radiation Biology 10.3109/09553002.2016.1144941 Friedman2016InfluenceNuclearStructureFormation105 Genetics & Biomedical Paper This paper discusses the influence of nuclear structure on the formation of radiation-induced lethal lesions, particularly focusing on the rejoining of fragmented nuclear DNA caused by ionizing radiation. It synthesizes existing knowledge with new insights from high-throughput sequencing data to better understand how spatial organization within the genome affects the generation of lethal chromosome aberrations. Hi-C chromosome conformation radiation biology chromatin architecture DNA damage topologically associating domains nuclear organization 3C technologies Synthesis of existing knowledge with new insights from high-throughput sequencing data. Identification of the fractal globule organization of DNA and its implications for radiation damage. Exploration of the spatial proximity of transcriptionally active euchromatin and its susceptibility to radiation. Discussion of the temporal factors influencing the formation of lethal lesions post-irradiation. High-throughput sequencing of chromosome conformation capture experiments. Analysis of spatial organization of DNA within the nucleus. Examination of transcriptional programs linking genomic locations. Review of existing models of radiation-induced DNA damage and repair mechanisms." }, { "id": "work:Friedman2015CommentaryPortugueseCryptoJews106", "type": "work", "title": "Commentary: Portuguese crypto-Jews: the genetic heritage of a complex history", "url": "/works/Friedman2015CommentaryPortugueseCryptoJews106.html", "external_url": "https://doi.org/10.3389/fgene.2015.00261", "summary": "This commentary critiques the analysis by Nogueiro et al. (2015) regarding the genetic heritage of Portuguese crypto-Jews, highlighting methodological weaknesses and the ambiguity of genetic markers used to infer Jewish ", "year": 2015, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "Jewish genetics", "haplotypes", "crypto-Jews", "Iberian Peninsula", "admixture", "demographic history", "Y-chromosome", "mtDNA" ], "content": "Commentary: Portuguese crypto-Jews: the genetic heritage of a complex history Frontiers in Genetics 10.3389/fgene.2015.00261 Friedman2015CommentaryPortugueseCryptoJews106 Genetics & Biomedical Paper This commentary critiques the analysis by Nogueiro et al. (2015) regarding the genetic heritage of Portuguese crypto-Jews, highlighting methodological weaknesses and the ambiguity of genetic markers used to infer Jewish ancestry. It emphasizes the need for more robust statistical methodologies and a careful examination of historical and demographic contexts. Jewish genetics haplotypes crypto-Jews Iberian Peninsula admixture demographic history Y-chromosome mtDNA population genetics Critiques the methodological issues in Nogueiro et al.'s analysis of Jewish ancestry. Highlights the ambiguity of genetic markers used to infer Jewish heritage. Calls for a more nuanced understanding of the demographic history of crypto-Jews. Suggests the need for empirical evaluation of admixture patterns in historical populations." }, { "id": "work:Friedman2015CouldEhrlichialInfectionCause107", "type": "work", "title": "Could Ehrlichial Infection Cause Some Changes Associated with Leukemia?", "url": "/works/Friedman2015CouldEhrlichialInfectionCause107.html", "external_url": "https://doi.org/10.1016/j.mehy.2015.09.015", "summary": "This paper hypothesizes that infections by the intracellular bacteria Ehrlichia/Anaplasma (EA) may be linked to various medical conditions, including leukemia and autoimmune disorders. The authors present evidence sugges", "year": 2015, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "Ehrlichia", "Anaplasma", "leukemia", "myelodysplastic syndromes", "intracellular parasites", "Rifampin", "immune system dysfunction", "bone marrow" ], "content": "Could Ehrlichial Infection Cause Some Changes Associated with Leukemia? Medical Hypotheses 10.1016/j.mehy.2015.09.015 Friedman2015CouldEhrlichialInfectionCause107 Genetics & Biomedical Paper This paper hypothesizes that infections by the intracellular bacteria Ehrlichia/Anaplasma (EA) may be linked to various medical conditions, including leukemia and autoimmune disorders. The authors present evidence suggesting that EA could disrupt immune cell development and function, potentially leading to these diseases, and advocate for further research into antibiotic treatments for affected patients. Ehrlichia Anaplasma leukemia myelodysplastic syndromes intracellular parasites Rifampin immune system dysfunction bone marrow autoimmune disorders Proposes a novel link between Ehrlichia/Anaplasma infections and leukemia/myelodysplastic diseases. Presents case studies indicating potential therapeutic benefits of Rifampin in leukemia patients. Suggests that leukemia may not be a malignancy but rather an infection that can be treated with antibiotics. Calls for more extensive research into the relationship between EA and immune system disorders." }, { "id": "work:Friedman2015LargeScaleCodingSequence108", "type": "work", "title": "Large Scale Coding Sequence Change Underlies the Evolution of Post-developmental Novelty in Honey Bees", "url": "/works/Friedman2015LargeScaleCodingSequence108.html", "external_url": "https://doi.org/10.1093/molbev/msu292", "summary": "This study investigates the role of coding sequence changes in the evolution of postdevelopmental novelty in honey bees, challenging the traditional evo-devo paradigm that emphasizes regulatory changes. Through RNA-Seq e", "year": 2015, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "honey bees", "Apis mellifera", "RNA-Seq", "taxonomically restricted genes", "novel traits", "gene expression", "evolutionary biology", "royal jelly" ], "content": "Large Scale Coding Sequence Change Underlies the Evolution of Post-developmental Novelty in Honey Bees Molecular Biology & Evolution 10.1093/molbev/msu292 Friedman2015LargeScaleCodingSequence108 Genetics & Biomedical Paper This study investigates the role of coding sequence changes in the evolution of postdevelopmental novelty in honey bees, challenging the traditional evo-devo paradigm that emphasizes regulatory changes. Through RNA-Seq experiments, we demonstrate that positively selected, tissue-specific genes with low network connectivity are crucial for the emergence of novel physiological functions in adult honey bees. honey bees Apis mellifera RNA-Seq taxonomically restricted genes novel traits gene expression evolutionary biology royal jelly beeswax venom Demonstrated that positively selected tissue-specific genes underlie novel physiological functions in honey bees. Challenged the evo-devo paradigm by showing that low network connectivity genes contribute to phenotypic novelty. Identified the importance of taxonomically restricted genes (TRGs) in the evolution of novel traits. Provided insights into the genetic mechanisms governing phenotypic novelty in adult organisms. Conducted ten RNA-Seq experiments across various honey bee tissues. Analyzed gene expression patterns to identify highly expressed taxonomically restricted genes (HE-TRGs). Compared gene expression in novel versus conserved tissues to assess the role of coding sequence changes. Examined differentially expressed genes (DEGs) between different adult castes (nurses and foragers)." }, { "id": "work:Friedman2026EntoLinguisticsLanguageAmbiguity109", "type": "work", "title": "Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology", "url": "/works/Friedman2026EntoLinguisticsLanguageAmbiguity109.html", "external_url": "https://doi.org/10.5281/zenodo.19574118", "summary": "Scientific language does not merely describe biological phenomena; it actively constitutes the generative models through which researchers parse complex systems. This paper makes three core contributions to understanding", "year": 2026, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "entomology", "scientific communication", "terminology networks", "Active Inference", "corpus linguistics", "CACE", "semantic entropy", "myrmecology" ], "content": "Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology Zenodo 10.5281/zenodo.19574118 Friedman2026EntoLinguisticsLanguageAmbiguity109 Entomology Paper Scientific language does not merely describe biological phenomena; it actively constitutes the generative models through which researchers parse complex systems. This paper makes three core contributions to understanding—and correcting—the epistemic consequences of this constitutive role. First, we introduce a six-domain Ento-Linguistic framework that decomposes the terminological landscape of insect research into analytically tractable themes, isolating domains where anthropomorphic language most severely distorts causal modeling. Second, we develop an open-source computational pipeline that integrates automated term extraction, co-occurrence network construction, and information-theoretic ambiguity scoring with principles from Active Inference and Complex Systems Theory. Third, we propose and validate four evidence-based meta-standards—Clarity, Appropriateness, Consistency, and Evolvab entomology scientific communication terminology networks Active Inference corpus linguistics CACE semantic entropy myrmecology A six-domain Ento-Linguistic framework (Unit of Individuality; Power & Labor; Behavior & Identity; Sex & Reproduction; Kin & Relatedness; Economics) for analyzing terminological friction in insect research. An open-source, reproducible pipeline: literature mining (PubMed, arXiv), text processing, term extraction and domain assignment, semantic entropy, statistical tests, conceptual network and rhetorical analysis, and CACE scoring. CACE meta-standards (Clarity, Appropriateness, Consistency, Evolvability) as a protocol for lexical engineering and term evaluation. Corpus construction via PubMed and arXiv queries; deduplication and preprocessing (tokenization, lemmatization, n-grams) as specified in the paper and supplemental methods. Term extraction and domain classification via seed lexicons and co-occurrence expansion; semantic entropy via clustered context vectors; pairwise and ANOVA tests with Benjamini–Hochberg correction where applicable. Conceptual overlap networks, bridging-term identification, rhetorical and framing analysis, and per-term CACE scoring." }, { "id": "work:Friedman2026LivingMetaAnalysisArchitecture110", "type": "work", "title": "A Living Meta-Analysis Architecture for Active Inference: Assertion Extraction, Nanopublications, and Hypothesis Scoring", "url": "/works/Friedman2026LivingMetaAnalysisArchitecture110.html", "external_url": "https://doi.org/10.5281/zenodo.19897664", "summary": "No prior automated system tracks hypothesis-level evidence across the full Active Inference and Free Energy Principle literature at scale. This work presents a living meta-analysis framework: literature is retrieved from", "year": 2026, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Active Inference", "Free Energy Principle", "meta-analysis", "living literature review", "nanopublications", "LLM extraction", "hypothesis scoring", "knowledge graph" ], "content": "A Living Meta-Analysis Architecture for Active Inference: Assertion Extraction, Nanopublications, and Hypothesis Scoring Active Inference Journal 10.5281/zenodo.19897664 Friedman2026LivingMetaAnalysisArchitecture110 Active Inference Paper No prior automated system tracks hypothesis-level evidence across the full Active Inference and Free Energy Principle literature at scale. This work presents a living meta-analysis framework: literature is retrieved from arXiv, Semantic Scholar, and OpenAlex and deduplicated ( N = 819 in v2) via a canonical identifier hierarchy (DOI arXiv ID Semantic Scholar ID OpenAlex ID). Papers are classified into a three-tier taxonomy (A: core theory; B: tools and translation; C: application domains) across eight categories. An LLM-powered pipeline evaluates each abstract against eight core hypotheses, emitting structured nanopublications (directionality, confidence, reasoning) that populate an RDF-compatible knowledge graph scored by a citation-weighted evidence function. All extractions are machine-generated and not fully manually validated; hypothesis scores are preliminary and are most useful fo Active Inference Free Energy Principle meta-analysis living literature review nanopublications LLM extraction hypothesis scoring knowledge graph OpenAlex Semantic Scholar arXiv Multi-source retrieval, identifier-based deduplication, and a three-tier (A/B/C) taxonomy for mapping the field. LLM-driven assertion extraction into nanopublications wired for RDF-style graphs and queryable evidence landscapes. Citation-weighted scoring over eight hypotheses with explicit reporting of consensus vs. debate structure and automation caveats. Open pipeline suitable for continuous (living) updates as new papers appear. Corpus construction from arXiv, Semantic Scholar, and OpenAlex; hierarchical deduplication of records. Taxonomic labeling (eight categories under A/B/C); complementary topic modeling (e.g., NMF) and citation-network views. LLM evaluation of abstracts against eight hypotheses; nanopublication records with directionality, confidence, and rationale. Graph-level citation-weighted aggregation; interpretive emphasis on relative tiers and biases (publication bias, linguistic asymmetry) per manuscript discussion. Reproducible implementation: https://github.com/ActiveInferenceInstitute/act inf metaanalysis" }, { "id": "work:Friedman2026DynamicAttentionalAgentsFocused111", "type": "work", "title": "Dynamic Attentional Agents in Focused Attention Meditation: Hierarchical Computational Modeling of Expert-Novice Differences", "url": "/works/Friedman2026DynamicAttentionalAgentsFocused111.html", "external_url": "https://doi.org/10.1007/978-3-032-16955-6_11", "summary": "We develop a three-level hierarchical framework to model the attentional dynamics of focused attention (FA) meditation, laying a foundation for advanced active inference (AIF) implementations. Grounded in the Free Energy", "year": 2026, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Active Inference", "focused attention meditation", "thoughtseeds", "Free Energy Principle", "hierarchical modeling", "expert-novice differences", "DMN", "predictive processing" ], "content": "Dynamic Attentional Agents in Focused Attention Meditation: Hierarchical Computational Modeling of Expert-Novice Differences CSCIS vol 2857, Springer 10.1007/978-3-032-16955-6_11 Friedman2026DynamicAttentionalAgentsFocused111 Active Inference Paper We develop a three-level hierarchical framework to model the attentional dynamics of focused attention (FA) meditation, laying a foundation for advanced active inference (AIF) implementations. Grounded in the Free Energy Principle and Neuronal Packet Hypothesis, we conceptualize meditation as a predictive processing system where \"thoughtseeds\"—transient, agent-like entities forming Markov blankets—minimize variational free energy via bidirectional coupling with attentional networks (Default Mode Network [DMN], Ventral Attention Network [VAN], Dorsal Attention Network [DAN], Frontoparietal Network [FPN]). Thoughtseeds, emerging from superordinate neuronal ensembles, compete for Global Workspace access, modulated by meta-cognitive precision weighting to stabilize attention. This model advances the Thoughtseeds Framework toward a computational phenomenology of Vipassana, setting the stage f Active Inference focused attention meditation thoughtseeds Free Energy Principle hierarchical modeling expert-novice differences DMN predictive processing Neuronal Packet Hypothesis contemplative neuroscience A three-level hierarchical framework for focused attention meditation grounded in the Free Energy Principle and Neuronal Packet Hypothesis. Formalization of thoughtseeds as transient, agent-like entities with Markov blankets competing for Global Workspace access via meta-cognitive precision weighting. Biologically plausible simulations reproducing expert–novice differences: 49% lower free energy during breath focus, suppressed DMN activity (0.18 vs. 0.31), and faster distraction recovery in experts. Testable predictions for meditation skill development; pathway to integrated AIF formalisms for contemplative neuroscience and computational psychiatry. Three-level hierarchical model: superordinate neuronal ensembles → thoughtseed agents (Markov blankets) → attentional networks (DMN, VAN, DAN, FPN). Bidirectional message passing: bottom-up attentional state formation and top-down precision-weighted constraint. Simulation across biologically plausible parameter ranges: precision weighting, complexity penalties, learning rates. Comparison to neuroimaging findings on expert meditators." }, { "id": "work:Friedman2026CompositionalApproachesLinguisticCase112", "type": "work", "title": "Compositional Approaches to Linguistic Case for Cognitive Modeling", "url": "/works/Friedman2026CompositionalApproachesLinguisticCase112.html", "external_url": "https://doi.org/10.5281/zenodo.19695260", "summary": "Commutative diagrams are treated as cognitively privileged representations: they jointly encode relational (algebraic) structure, the distributional semantics by which language reports on situations, and the inference pr", "year": 2026, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Active Inference", "linguistic case", "category theory", "DisCoCat", "DisCoCirc", "distributional semantics", "topos", "cognitive modeling" ], "content": "Compositional Approaches to Linguistic Case for Cognitive Modeling Active Inference Journal 10.5281/zenodo.19695260 Friedman2026CompositionalApproachesLinguisticCase112 Active Inference Paper Commutative diagrams are treated as cognitively privileged representations: they jointly encode relational (algebraic) structure, the distributional semantics by which language reports on situations, and the inference process by which beliefs update under new evidence—with linguistic case (“who did what to whom”) as the natural hinge across these layers. The paper formalizes case systems as categories, represents cross-linguistic alignment patterns (nominative–accusative, ergative–absolutive, tripartite, active–stative, fluid-S) as structure-preserving functors, and develops DisCoCat / DisCoCirc string-diagram compositional semantics, enriched categorical hooks to quantitative similarity, and connections to Distributional Active Inference (including falsifiable ERP-oriented predictions) and POVM -style scaling for multi-agent discourse. A cognitive-security thread models multi-turn agent Active Inference linguistic case category theory DisCoCat DisCoCirc distributional semantics topos cognitive modeling cognitive security prompt injection Case systems as categories; grammatical relations as morphisms; alignment typology as functors between case categories. Compositional semantics via compact-closed string diagrams (DisCoCat / DisCoCirc) with an enriched-categorical route to quantitative distributional proximity. Bridge from typology and type-logical structure through distributional semantics to Active Inference–style prediction (including neurophysiological hypotheses). Protocol-level view of multi-agent LLM interactions: typed roles and wiring; prompt injection analyzed as functorial type violations when a fixed interaction grammar is enforced. Theoretical development with category theory, compositional semantics, and links to Distributional Active Inference. Open-source Python implementation: tests, coverage reporting, and programmatic figures — https://github.com/docxology/cognitive case diagrams Archived manuscript (v1): https://doi.org/10.5281/zenodo.19695260 · Zenodo record https://zenodo.org/records/19695260" }, { "id": "work:Friedman2026TowardsLean4Formalization113", "type": "work", "title": "Towards Lean 4 Formalization of the Free Energy Principle: AI-Driven Theorem Sketching and Verification for Active Inference and Bayesian Mechanics", "url": "/works/Friedman2026TowardsLean4Formalization113.html", "external_url": "https://doi.org/10.5281/zenodo.19699234", "summary": "The Free Energy Principle (FEP) unifies a broad class of system properties under a variational free-energy functional, but a machine-checked substrate for assessing related formal claims has been missing. Dependent-type ", "year": 2026, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Free Energy Principle", "Active Inference", "Lean 4", "Mathlib4", "interactive theorem proving", "formal verification", "variational inference", "Bayesian mechanics" ], "content": "Towards Lean 4 Formalization of the Free Energy Principle: AI-Driven Theorem Sketching and Verification for Active Inference and Bayesian Mechanics Active Inference Journal 10.5281/zenodo.19699234 Friedman2026TowardsLean4Formalization113 Active Inference Paper The Free Energy Principle (FEP) unifies a broad class of system properties under a variational free-energy functional, but a machine-checked substrate for assessing related formal claims has been missing. Dependent-type provers require explicit measure spaces, domination, and integrability that prose often leaves implicit. This work introduces a curated catalog of 50 topics across five pillars—14 FEP, 11 Active Inference, 10 Bayesian Mechanics, 8 Information Geometry, and 7 non-equilibrium Thermodynamics—each as a namespaced Lean 4 sketch against Mathlib4 , with natural-language statements, imports, ecosystem-maturity tags, and sorry-free theorem bodies maintained from a single source of truth. On the pinned stack leanprover/lean4:v4.29.0 / Mathlib4 v4.29.0 , the shipped catalog compiles 50/50 sorry-free under lake env lean. The manuscript describes an LLM-assisted drafting and commentar Free Energy Principle Active Inference Lean 4 Mathlib4 interactive theorem proving formal verification variational inference Bayesian mechanics information geometry LLM-ITP integration reproducible research measure theory A 50-topic formal catalog of FEP-related mathematics with explicit Mathlib4-facing statements and a reproducible, version-pinned verification story. Axiomatization vs. problem-solving : positions LLM+ITP work as building shared formal structure, not just benchmark solving. Hermes / OpenGauss pipeline: LLM drafts and explains sketches while native Lean verifies; compilation remains the non-negotiable check. Zero-mock testing policy in the software stack (real files, real SQLite, live compiler, real HTTP) as stated in the manuscript. A Lean primer and Mathlib4 / measure-theoretic probability guidance aimed at Active Inference researchers entering formal methods. Theoretical and systems paper: YAML → manuscript → Lake pipeline; per-topic modules with LaTeX-adjacent statement signatures. Open-source : https://github.com/ActiveInferenceInstitute/fep lean (manuscript build uses the docxology template approach for validated metadata injection). Archived manuscript (v1): https://doi.org/10.5281/zenodo.19699234 · Zenodo record https://zenodo.org/records/19699234" }, { "id": "work:Friedman2020FacilitatorSCatechism114", "type": "work", "title": "The Facilitator's Catechism", "url": "/works/Friedman2020FacilitatorSCatechism114.html", "external_url": "https://doi.org/10.5281/zenodo.4203765", "summary": "This paper traces operations orders (OPORD) from antiquity through contemporary military and civilian practice and their role in organizational sensemaking. It draws on complexity science, organizational psychology, high", "year": 2020, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "OPORD", "operations orders", "organizational sensemaking", "high reliability organizations", "complexity", "remote teams", "Active Inference", "cognitive security" ], "content": "The Facilitator's Catechism Zenodo 10.5281/zenodo.4203765 Friedman2020FacilitatorSCatechism114 Cognitive Security Paper This paper traces operations orders (OPORD) from antiquity through contemporary military and civilian practice and their role in organizational sensemaking. It draws on complexity science, organizational psychology, high-reliability organizations, memetics, logistics, knowledge management, and Active Inference to articulate requirements and limits of existing formats, and proposes a catechism-style operations order for process facilitators bridging military, intelligence, and civilian teams. OPORD operations orders organizational sensemaking high reliability organizations complexity remote teams Active Inference cognitive security Situates operations orders historically and in relation to civilian analogues and sensemaking. Integrates multi-disciplinary lenses (complexity, HRO, KM, Active Inference) on OPORD design constraints. Proposes the Facilitator's Catechism as a structured format for facilitation-centric teams. Historical and comparative analysis of operations orders. Multi-disciplinary synthesis (complexity, org psychology, logistics, memetics, KM, Active Inference). Normative proposal for a new facilitator-oriented order format." }, { "id": "work:Friedman2026ArchitectureFalseGodsWilliam115", "type": "work", "title": "The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single Vision", "url": "/works/Friedman2026ArchitectureFalseGodsWilliam115.html", "external_url": "https://doi.org/10.5281/zenodo.20144984", "summary": "This rapid-publication essay synthesizes three intellectual frameworks examining cognitive closure. The author analyzes Professor Jiang Xueqin's commentary on artificial intelligence through William Blake's late-18th-cen", "year": 2026, "domain": "Art & Synergetics", "tags": [ "Paper", "Art & Synergetics", "bibliography", "William Blake", "Active Inference", "Artificial Intelligence", "Cognitive Science", "Free Energy Principle", "AI Architecture", "Consciousness Capture", "Generative Models" ], "content": "The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single Vision Zenodo 10.5281/zenodo.20144984 Friedman2026ArchitectureFalseGodsWilliam115 Art & Synergetics Paper This rapid-publication essay synthesizes three intellectual frameworks examining cognitive closure. The author analyzes Professor Jiang Xueqin's commentary on artificial intelligence through William Blake's late-18th-century perceptual analysis and Active Inference terminology. The core convergence identified: \"closure of the perceiving system around its own top-down expectations\" — which Blake termed \"Newton's Sleep,\" Jiang calls \"consciousness capture,\" and Active Inference designates as \"pathological prior dominance.\" The work maps Jiang's concepts — persuasion machinery, data sanitization, edge-case suppression, and engagement directives — onto Blake's cosmological schema and Active Inference's generative models. William Blake Active Inference Artificial Intelligence Cognitive Science Free Energy Principle AI Architecture Consciousness Capture Generative Models Single Vision Newton's Sleep The essay identifies a shared concern with cognitive closure across Blake, Jiang, and Active Inference. Jiang's critiques of AI persuasion and data sanitization are mapped onto generative-model dynamics. Blake's \"Single Vision\" is used as a historical language for overly rigid top-down expectation. The piece functions as a bridge text rather than a formal computational model. Cross-framework conceptual mapping Art-philosophy synthesis AI critique through predictive-processing vocabulary Terminology alignment across Blake studies, education commentary, and Active Inference" }, { "id": "work:Friedman2026CrescentCityLivingWaves116", "type": "work", "title": "Crescent City in Living Waves: Space, Time, People, and Minds on the Southern Cascadian Coast", "url": "/works/Friedman2026CrescentCityLivingWaves116.html", "external_url": "https://doi.org/10.5281/zenodo.20286171", "summary": "This manuscript offers a synthetic scholarly history of Crescent City, California — seat of Del Norte County on the northernmost developed strip of the California coast — read as an emergent nested system : Tolowa Dee-ni", "year": 2026, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "Crescent City", "Del Norte County", "Cascadia subduction zone", "Tsunami warning policy", "Tolowa Dee-ni'", "Redwood ecology", "Local history", "Coastal hazard" ], "content": "Crescent City in Living Waves: Space, Time, People, and Minds on the Southern Cascadian Coast Zenodo 10.5281/zenodo.20286171 Friedman2026CrescentCityLivingWaves116 Cognitive Security Paper This manuscript offers a synthetic scholarly history of Crescent City, California — seat of Del Norte County on the northernmost developed strip of the California coast — read as an emergent nested system : Tolowa Dee-ni' villages on the Smith River estuary; European contact and American settlement; genocide and dispossession in the 1850s; industrial timber and commercial fishing; federal termination and the 1983 federal-recognition restoration under Tillie Hardwick v. United States ; Redwood National and State Parks and conservation governance beside a recovering working waterfront; and contemporary Indigenous ocean stewardship including the 2023 Yurok–Tolowa Dee-ni' Indigenous Marine Stewardship Area. The town sits on the locked southern Cascadia margin. The study frames the often-cited ~37% fifty-year probability of an M ≥ 8.0 southern-segment rupture as paleoseismic model output from Crescent City Del Norte County Cascadia subduction zone Tsunami warning policy Tolowa Dee-ni' Redwood ecology Local history Coastal hazard Indigenous ocean stewardship Social-ecological systems Panarchy & resilience Coupled human–natural systems No prior single work synthesizes Crescent City's full history; existing accounts are fragmentary or era-bound. The central interpretive claim is one recurring loop: hazard → rebuilding → governance → memory → adaptation . The town is a compact case study in nested geological, ecological, economic, and political risk that resilience/panarchy theory explains better than environmental or social history alone. The 1964 Alaska-earthquake tsunami (deadliest on the contiguous-U.S. Pacific coast) reshaped U.S. Pacific-wide tsunami-warning policy far beyond the local waterfront. Synthetic scholarly history across multiple primary-source domains Social-ecological systems (Ostrom) + panarchy/resilience (Holling, Gunderson) framing Coupled human–natural systems analysis of place, chronology, actors, and governing rules Paleoseismic-model interpretation distinguished from deterministic forecasting Rapid AI-augmented synthesis with human oversight" }, { "id": "work:Friedman2026IntroductionBiologyGenerativeApproach117", "type": "work", "title": "Introduction to Biology: A Generative Approach", "url": "/works/Friedman2026IntroductionBiologyGenerativeApproach117.html", "external_url": "https://doi.org/10.5281/zenodo.20286478", "summary": "Introduction to Biology: A Generative Approach is an open biology textbook with forty-four chapters, ranging from systems science and chemical foundations through cells, metabolism, genetics, microbiology, physiology, ev", "year": 2026, "domain": "Computational", "tags": [ "Book", "Computational", "bibliography", "Biology", "open textbook", "generative approach", "reproducible research", "undergraduate biology", "College of the Redwoods", "computational biology", "evidence-based teaching" ], "content": "Introduction to Biology: A Generative Approach Zenodo 10.5281/zenodo.20286478 Friedman2026IntroductionBiologyGenerativeApproach117 Computational Book Introduction to Biology: A Generative Approach is an open biology textbook with forty-four chapters, ranging from systems science and chemical foundations through cells, metabolism, genetics, microbiology, physiology, evolution, and ecology. Organized as Unit 0 plus Units I–X, the text presents biology as an evidence-grounded discipline in which mechanisms, measurements, and simple models are developed together, so readers can move between narrative explanation and the quantitative constraints that shape biological claims. Five recurring themes—evolution, information, structure and function, systems and emergence, and the cell—provide orientation across scales and align with mainstream undergraduate biology competencies; Unit 0 adds an optional systems, historical, and philosophical lens without replacing the traditional molecular-to-ecological sequence. Where the curriculum is quantitat Biology open textbook generative approach reproducible research undergraduate biology College of the Redwoods computational biology evidence-based teaching programmatic figures laboratory activities Biology is presented as a discipline where narrative and quantitative constraints are co-developed, not separated into parallel tracks. Forty-four chapters span systems science through ecology while preserving mainstream undergraduate competency alignment. Unit 0 supplies optional systems, historical, and philosophical framing without displacing the core molecular-to-ecological arc. The edition is designed for course adoption (e.g., College of the Redwoods BIOL-1, BIOL-8) with ready-made labs and assessment banks. Generative manuscript production with reproducible build pipeline Domain-organized Python modules for quantitative curriculum segments Programmatic figure and diagram generation Inline primary-literature citation with glossary and curriculum-mapping appendices Instructor vs student build variants for assessment materials" }, { "id": "work:Friedman2025CEREBRUMCaseEnabledReasoning118", "type": "work", "title": "CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling", "url": "/works/Friedman2025CEREBRUMCaseEnabledReasoning118.html", "external_url": "https://doi.org/10.5281/zenodo.15231156", "summary": "This paper introduces Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling (CEREBRUM). CEREBRUM is a synthetic intelligence framework that integrates linguistic case systems with cognitive sci", "year": 2025, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "paired GitHub and Zenodo publication" ], "content": "CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling Zenodo 10.5281/zenodo.15231156 Friedman2025CEREBRUMCaseEnabledReasoning118 Computational Paper This paper introduces Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling (CEREBRUM). CEREBRUM is a synthetic intelligence framework that integrates linguistic case systems with cognitive scientific principles to describe, design, and deploy generative models in an expressive fashion. By treating models as case-bearing entities that can play multiple contextual roles (e.g. like declinable nouns), CEREBRUM establishes a formal linguistic-type calculus for cognitive model use, relationships, and transformations. The CEREBRUM framework uses structures from category theory and modeling techniques related to the Free Energy Principle, in describing and utilizing models across contexts. CEREBRUM addresses the growing complexity in computational and cognitive modeling systems (e.g. generative, decentralized, agentic intelligences), by providing structured representa paired GitHub and Zenodo publication paired publication" }, { "id": "work:Friedman2026PolicyEntanglementActiveInference119", "type": "work", "title": "Policy Entanglement in Active Inference", "url": "/works/Friedman2026PolicyEntanglementActiveInference119.html", "external_url": "https://doi.org/10.5281/zenodo.20419637", "summary": "Abstract {-} Active inference models often need to choose among several policy streams at once, for example streams tied to different effectors, sensory channels, agents, agents within a group, or planning horizons. Stan", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "active inference", "free energy principle", "policy inference", "mean-field", "total correlation", "information geometry", "Schmidt rank", "tensor networks" ], "content": "Policy Entanglement in Active Inference Zenodo 10.5281/zenodo.20419637 Friedman2026PolicyEntanglementActiveInference119 Computational Paper Abstract {-} Active inference models often need to choose among several policy streams at once, for example streams tied to different effectors, sensory channels, agents, agents within a group, or planning horizons. Standard discrete active-inference implementations keep this manageable by treating those streams as independent, but that simplification removes the dependencies that make coordinated action possible. This manuscript introduces policy entanglement: a controlled deformation of the usual independent policy posterior by a scalar coupling strength and explicit compatibility and preference potentials. The construction preserves the finite active inference setting while making cross-stream dependence a first-class modeling object rather than an implicit artifact of the chosen factorization. The framework keeps a claim-strength ledger that distinguishes exact recoveries, parameteri active inference free energy principle policy inference mean-field total correlation information geometry Schmidt rank tensor networks sophisticated inference Lean theorem proving machine-checked free-energy identity active inference free energy principle policy inference mean-field total correlation" }, { "id": "work:Friedman2026BoundedAutoResearchTinyReproducible120", "type": "work", "title": "Bounded AutoResearch for a Tiny Reproducible Machine-Learning Task", "url": "/works/Friedman2026BoundedAutoResearchTinyReproducible120.html", "external_url": "https://doi.org/10.5281/zenodo.20420357", "summary": "Abstract This paper presents Deterministic bounded AutoResearch for a small MNIST neural-network task, a public template exemplar that turns an AutoResearch loop into ordinary reproducible research infrastructure. The ca", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "autoresearch", "reproducible research", "machine learning benchmark", "artifact readiness", "human review", "local artifact integrity" ], "content": "Bounded AutoResearch for a Tiny Reproducible Machine-Learning Task Zenodo 10.5281/zenodo.20420357 Friedman2026BoundedAutoResearchTinyReproducible120 Computational Paper Abstract This paper presents Deterministic bounded AutoResearch for a small MNIST neural-network task, a public template exemplar that turns an AutoResearch loop into ordinary reproducible research infrastructure. The case study is intentionally small but concrete: 2000 training and 500 test images from MNIST handwritten digit database are evaluated by the bounded small MNIST neural-network classification loop. The run evaluates 4 of 5 proposed candidates, including Tiny patch-attention classifier, selects exp-mlp-tanh-64 (MLP, 50890 parameters), and improves test accuracy from 82.6% to 89.4% (6.8% absolute change). The validated diagnostic layer reports macro F1 89.4%, bootstrap accuracy interval 86.4% to 92.0%, Brier score 0.161, negative log likelihood 0.361, top-2 accuracy 95.6%, and exact McNemar p-value 0.000. The same pipeline writes proposal, candidate, run, review, benchmark, ev autoresearch reproducible research machine learning benchmark artifact readiness human review local artifact integrity autoresearch reproducible research machine learning benchmark artifact readiness human review" }, { "id": "work:Friedman2026ConvergenceAnalysisGradientDescent121", "type": "work", "title": "Convergence Analysis of Gradient Descent Optimization", "url": "/works/Friedman2026ConvergenceAnalysisGradientDescent121.html", "external_url": "https://doi.org/10.5281/zenodo.20420368", "summary": "Abstract This paper presents a convergence study of fixed-step gradient descent on a convex quadratic, framed as the computational exemplar of the Research Project Template (https://github.com/docxology/template). The im", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "optimization algorithms", "gradient descent", "convergence analysis", "numerical methods", "mathematical programming", "reproducible research", "infrastructure automation" ], "content": "Convergence Analysis of Gradient Descent Optimization Zenodo 10.5281/zenodo.20420368 Friedman2026ConvergenceAnalysisGradientDescent121 Computational Paper Abstract This paper presents a convergence study of fixed-step gradient descent on a convex quadratic, framed as the computational exemplar of the Research Project Template (https://github.com/docxology/template). The implementation lives in projects/template code project/src/optimizer.py; experiments and figures are orchestrated by projects/template code project/scripts/optimization analysis.py and hydrated into the manuscript through scripts/z generate manuscript variables.py, so tables and prose track output/data/optimization results.csv after every pipeline run. We evaluate 6 step sizes from $\\alpha = 0.01$ to $\\alpha = 2.5$, spanning conservative, near-optimal, aggressive, and divergent regimes for a unit Hessian model. The build chain exercises template infrastructure end-to-end: scientific helpers (infrastructure.scientific.stability, infrastructure.scientific.benchmarking), valid optimization algorithms gradient descent convergence analysis numerical methods mathematical programming reproducible research infrastructure automation optimization algorithms gradient descent convergence analysis numerical methods mathematical programming" }, { "id": "work:Friedman2026EditorialQualityAtScale122", "type": "work", "title": "Editorial Quality at Scale: A Reproducible Prose-Review Pipeline", "url": "/works/Friedman2026EditorialQualityAtScale122.html", "external_url": "https://doi.org/10.5281/zenodo.20420342", "summary": "Abstract This paper documents template prose project, the prose-focused exemplar of the Research Project Template (https://github.com/docxology/template). It pairs the template's two-layer architecture with the prose ana", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "prose analysis", "readability", "editorial review", "reproducible research", "manuscript quality" ], "content": "Editorial Quality at Scale: A Reproducible Prose-Review Pipeline Zenodo 10.5281/zenodo.20420342 Friedman2026EditorialQualityAtScale122 Computational Paper Abstract This paper documents template prose project, the prose-focused exemplar of the Research Project Template (https://github.com/docxology/template). It pairs the template's two-layer architecture with the prose analysis infrastructure (https://github.com/docxology/template/tree/main/infrastructure/prose) (readability metrics, structural outline, editorial quality flags) and the reference validation infrastructure (https://github.com/docxology/template/tree/main/infrastructure/reference) (BibTeX validation), demonstrating that rigorous editorial review can be expressed as a configurable, deterministic pipeline with no novel domain algorithm of its own. A single manuscript/config.yaml defines target grade-level bands, citation-density floors, structural rules (every section has an H1, no heading levels skipped), and bibliography-consistency policy. The pipeline reads the manuscript, prose analysis readability editorial review reproducible research manuscript quality prose analysis readability editorial review reproducible research manuscript quality" }, { "id": "work:Friedman2026TemplateApproachReproducibleGenerative123", "type": "work", "title": "A template/ approach to Reproducible Generative Research", "url": "/works/Friedman2026TemplateApproachReproducibleGenerative123.html", "external_url": "https://doi.org/10.5281/zenodo.20420387", "summary": "Abstract The reproducibility crisis in computational research is fundamentally structural: research artifacts are scattered across disconnected tools—LaTeX editors, Jupyter notebooks, ad-hoc shell scripts—with no enforce", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "reproducible research", "infrastructure-as-code", "steganography", "cryptographic provenance", "LaTeX rendering", "modular infrastructure", "publication integrity", "zero-mock testing" ], "content": "A template/ approach to Reproducible Generative Research Zenodo 10.5281/zenodo.20420387 Friedman2026TemplateApproachReproducibleGenerative123 Computational Paper Abstract The reproducibility crisis in computational research is fundamentally structural: research artifacts are scattered across disconnected tools—LaTeX editors, Jupyter notebooks, ad-hoc shell scripts—with no enforced mechanism to keep code, data, and manuscript synchronized. Studies have shown that most published findings are false positives, replication rates in psychology hover around 36%, and only 24% of 1.4 million Jupyter notebooks can be successfully re-executed. Existing tools address fragments of this problem: workflow managers (Snakemake, Nextflow, CWL) orchestrate computation; literate programming systems (Quarto, Jupyter Book, R Markdown, Overleaf, OpenAI Prism) render documents; data versioning tools (DVC) track artifacts—but none enforces cross-cutting quality standards as architectural invariants. template/ applies the principle of Infrastructure as Code to the researc reproducible research infrastructure-as-code steganography cryptographic provenance LaTeX rendering modular infrastructure publication integrity zero-mock testing thin orchestrator two-layer architecture FAIR4RS research software engineering reproducible research infrastructure-as-code steganography cryptographic provenance LaTeX rendering" }, { "id": "work:Friedman2026ActiveInferenceMultiTrack124", "type": "work", "title": "Active Inference Multi-Track Exemplar", "url": "/works/Friedman2026ActiveInferenceMultiTrack124.html", "external_url": "https://doi.org/10.5281/zenodo.20420352", "summary": "Abstract This public exemplar binds 7 pipeline tracks — Lean, analytical Python, pymdp sophisticated inference, GNN, ontology concordance, visualizations, and the sheaf manuscript composer — declared in tracks.yaml (../t", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "active inference", "pymdp", "sophisticated inference", "generalized notation notation", "lean" ], "content": "Active Inference Multi-Track Exemplar Zenodo 10.5281/zenodo.20420352 Friedman2026ActiveInferenceMultiTrack124 Computational Paper Abstract This public exemplar binds 7 pipeline tracks — Lean, analytical Python, pymdp sophisticated inference, GNN, ontology concordance, visualizations, and the sheaf manuscript composer — declared in tracks.yaml (../tracks.yaml). Flat manuscript sections follow an IMRAD outline (Introduction, Methods, Results, Discussion, plus appendix) assembled from 10 sheaf fragment types registered in manuscript/sheaf/tracks.yaml (sheaf/tracks.yaml). The first page (00 00 sheaf coverage.md (00 00 sheaf coverage.md)) shows a 16-row coverage matrix (4 IMRAD group headers and 12 composed subsections, including a full-track appendix proof) regenerated from the live manifest at compose time. The T-maze demo aligns with pymdp sophisticated inference examples (https://github.com/infer-actively/pymdp/tree/main/examples/experimental/sophisticated inference). Measured invariant checks: 12 / 12 passed. SI pl active inference pymdp sophisticated inference generalized notation notation lean active inference pymdp sophisticated inference generalized notation notation lean" }, { "id": "work:Friedman2026BeeStackEvidenceTypedScaffold125", "type": "work", "title": "BeeStack: An Evidence-Typed Scaffold for Whole-Colony Honeybee Simulation", "url": "/works/Friedman2026BeeStackEvidenceTypedScaffold125.html", "external_url": "https://doi.org/10.5281/zenodo.20420557", "summary": "BeeStack is an executable, evidence-typed research scaffold for whole-colony simulation of the Western honey bee (Apis mellifera), organized as five layers (Body, Brain, Mind, Swarm, Niche). It pairs FlyBody/MuJoCo body ", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "honeybee", "Apis mellifera", "active inference", "simulation scaffold", "swarm intelligence", "niche construction", "FlyBody", "MuJoCo" ], "content": "BeeStack: An Evidence-Typed Scaffold for Whole-Colony Honeybee Simulation Zenodo 10.5281/zenodo.20420557 Friedman2026BeeStackEvidenceTypedScaffold125 Computational Paper BeeStack is an executable, evidence-typed research scaffold for whole-colony simulation of the Western honey bee (Apis mellifera), organized as five layers (Body, Brain, Mind, Swarm, Niche). It pairs FlyBody/MuJoCo body and small-scene swarm renders with curated empirical BeeBrain datasets and reduced deterministic kernels, keeping fidelity a declared per-module property: every quoted number is traceable from configuration to artifact to manuscript, gaps are catalogued rather than hidden, and the validation rate is a config-band self-test measure, not a biological-realism score. This 1.0 release accompanies the manuscript 'BeeStack: An Evidence-Typed Scaffold for Whole-Colony Honeybee Simulation' and includes the combined PDF and the full source archive. Source: https://github.com/docxology/BeeStack honeybee Apis mellifera active inference simulation scaffold swarm intelligence niche construction FlyBody MuJoCo antennal lobe mushroom body central complex waggle dance honeybee Apis mellifera active inference simulation scaffold swarm intelligence" }, { "id": "work:Friedman2026WhenDoBugsSee126", "type": "work", "title": "When do bugs see (infra)red?", "url": "/works/Friedman2026WhenDoBugsSee126.html", "external_url": "https://doi.org/10.5281/zenodo.20450970", "summary": "Objective: To review the plausibility of insect detection of infrared (IR) cues that covary with semiochemical vibrational signatures, and to produce falsifiable predictions through the integration of comparative entomol", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "insect olfaction", "infrared detection", "vibrational theory of olfaction", "semiochemicals", "sensilla morphology", "electromagnetic sensing", "active inference", "reproducible research" ], "content": "When do bugs see (infra)red? Zenodo 10.5281/zenodo.20450970 Friedman2026WhenDoBugsSee126 Computational Paper Objective: To review the plausibility of insect detection of infrared (IR) cues that covary with semiochemical vibrational signatures, and to produce falsifiable predictions through the integration of comparative entomology, spectroscopy, neural timing analysis, and computational electromagnetism. The vibrational theory remains contested, so the framework treats IR/vibrational sensing as a testable complement to molecular recognition rather than a replacement for receptor binding . Methods: We integrate: (i) literature-grounded morphometric ranges for antennal sensilla, (ii) ATR-FTIR evidence that insect body chemistry can support species discrimination, (iii) published olfactory receptor neuron timing constraints, and (iv) deterministic electromagnetic models that expose their assumptions and parameter sensitivity . Preregistered experimental protocols specify QCL/LED bands (2--25 µm), insect olfaction infrared detection vibrational theory of olfaction semiochemicals sensilla morphology electromagnetic sensing active inference reproducible research insect olfaction infrared detection vibrational theory of olfaction semiochemicals sensilla morphology" }, { "id": "work:Friedman2026SelfImprovementAgentHarness127", "type": "work", "title": "Self-Improvement Agent Harness: A Deterministic SIA Exemplar", "url": "/works/Friedman2026SelfImprovementAgentHarness127.html", "external_url": "https://doi.org/10.5281/zenodo.20453880", "summary": "Abstract This exemplar documents template sia, a deterministic implementation of the Self-Improvement Agent (SIA) harness contract described in . The default pipeline replays fixture-backed generations for the mini class", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "self-improvement agents", "benchmark harness", "reproducible research", "agent evaluation" ], "content": "Self-Improvement Agent Harness: A Deterministic SIA Exemplar Zenodo 10.5281/zenodo.20453880 Friedman2026SelfImprovementAgentHarness127 Computational Paper Abstract This exemplar documents template sia, a deterministic implementation of the Self-Improvement Agent (SIA) harness contract described in . The default pipeline replays fixture-backed generations for the mini classify task; opt-in live mode runs bounded target subprocesses and optional Ollama-backed meta/feedback steps. Run snapshot. Task mini classify, run 1, 3 generation(s), live=false. Final accuracy=0.8333 over 6 held-out samples. Values are injected by scripts/z generate manuscript variables.py after analysis. Keywords: self-improvement agents, benchmark harness, reproducible evaluation, agent loops --- Associated artifacts GitHub release: v0.1.0 (https://github.com/docxology/template/releases/tag/v0.1.0) PDF SHA-256: 7087b6d1dd2e6192b24055408935201c27d7e19ba26267a366b20b2c71b7a721 self-improvement agents benchmark harness reproducible research agent evaluation self-improvement agents benchmark harness reproducible research agent evaluation" }, { "id": "work:Friedman2025BiofirmDevelopmentFirstPrinciples128", "type": "work", "title": "Biofirm Development with First Principles First and the Active Inference Institute at the Applied Active Inference Symposium 2024", "url": "/works/Friedman2025BiofirmDevelopmentFirstPrinciples128.html", "external_url": "https://doi.org/10.5281/zenodo.14861596", "summary": "Multiple presentations given during the Active Inference Institute's 4th annual Applying Active Inference Symposium, 2024 over the course of November 13th-15th 2024", "year": 2025, "domain": "Active Inference", "tags": [ "Presentation", "Active Inference", "bibliography", "Zenodo publication" ], "content": "Biofirm Development with First Principles First and the Active Inference Institute at the Applied Active Inference Symposium 2024 Zenodo 10.5281/zenodo.14861596 Friedman2025BiofirmDevelopmentFirstPrinciples128 Active Inference Presentation Multiple presentations given during the Active Inference Institute's 4th annual Applying Active Inference Symposium, 2024 over the course of November 13th-15th 2024 Zenodo publication zenodo-publication" }, { "id": "work:Friedman2025ConCatEnateEmulation129", "type": "work", "title": "Con-cat-enate: emulation of Cat Hippocampus", "url": "/works/Friedman2025ConCatEnateEmulation129.html", "external_url": "https://doi.org/10.5281/zenodo.14738798", "summary": "Updated added a number of pages at the start (from page 2) that describes the entire system and whats missing apologies for not giving this overview of what would happen given those missing parts and the purpose of demo0", "year": 2025, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "Zenodo publication" ], "content": "Con-cat-enate: emulation of Cat Hippocampus Zenodo 10.5281/zenodo.14738798 Friedman2025ConCatEnateEmulation129 Genetics & Biomedical Paper Updated added a number of pages at the start (from page 2) that describes the entire system and whats missing apologies for not giving this overview of what would happen given those missing parts and the purpose of demo0.01 which substitute those parts to see whether the break down of the 10 miliscond to (longer period) with each handwritten sim, does stack chems as mentioned; and thus imply correct behavior some of the documents mentioning demo 0.01 and its motivation wasnt included (mentioned in the catpilot) therefore might cause confusion (ontop of also not really mentioning what would each of the missing part cause,) much apologies part 1 and part 2 updated of the emulated cat goes along with these documents: pilot: https://zenodo.org/records/14737043 beacons: https://zenodo.org/records/14737060 bevcyc: https://zenodo.org/records/14737076 Zenodo publication zenodo-publication" }, { "id": "work:Friedman2025GraphspeakLanguageHandshake130", "type": "work", "title": "Graphspeak: of language and handshake", "url": "/works/Friedman2025GraphspeakLanguageHandshake130.html", "external_url": "https://doi.org/10.5281/zenodo.14737157", "summary": "An experiment on decomposing language onto initially established graph-theory representation applied then onto some pre-selected transformations (commonly used context/tool related transmutes) (t1,t2,t3) then upon some l", "year": 2025, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Zenodo publication" ], "content": "Graphspeak: of language and handshake Zenodo 10.5281/zenodo.14737157 Friedman2025GraphspeakLanguageHandshake130 Active Inference Paper An experiment on decomposing language onto initially established graph-theory representation applied then onto some pre-selected transformations (commonly used context/tool related transmutes) (t1,t2,t3) then upon some layers of decomposition finding out the shared context / what we label as a handshake; for the purpose of education / others Zenodo publication zenodo-publication" }, { "id": "work:Friedman2025BevCycPositPrimitiveDrivers131", "type": "work", "title": "BevCyc - posit on primitive drivers of creatures", "url": "/works/Friedman2025BevCycPositPrimitiveDrivers131.html", "external_url": "https://doi.org/10.5281/zenodo.14737076", "summary": "Posits a bev-cyc as primitive driver of creatures / to use in agentic system represents a cycle of homeostasis to accomplish by divisible action sequences; that are actually states that break down onto muscle % tension f", "year": 2025, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "Zenodo publication" ], "content": "BevCyc - posit on primitive drivers of creatures Zenodo 10.5281/zenodo.14737076 Friedman2025BevCycPositPrimitiveDrivers131 Genetics & Biomedical Paper Posits a bev-cyc as primitive driver of creatures / to use in agentic system represents a cycle of homeostasis to accomplish by divisible action sequences; that are actually states that break down onto muscle % tension follows / posits to experiment / emulate ideas of morphogenesis / morphospace (dr levin's) on differing scale of time & checkpoints to run with a modulator layer ; to then apply in either a static n n n n n n autofilling nodes for inputs from hippocampus systems; or a decreasing one that emulates stage-of-state or the cycle involved Zenodo publication zenodo-publication" }, { "id": "work:Friedman2025BeaconsPreEmulationSocial132", "type": "work", "title": "Beacons - pre emulation of social cortex", "url": "/works/Friedman2025BeaconsPreEmulationSocial132.html", "external_url": "https://doi.org/10.5281/zenodo.14737060", "summary": "primitive emulation of social cortex currently only about tagging object types and labeled objects in simulations and having them refer to a table of category and response, which might include a sim of their own sensitiv", "year": 2025, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "Zenodo publication" ], "content": "Beacons - pre emulation of social cortex Zenodo 10.5281/zenodo.14737060 Friedman2025BeaconsPreEmulationSocial132 Genetics & Biomedical Paper primitive emulation of social cortex currently only about tagging object types and labeled objects in simulations and having them refer to a table of category and response, which might include a sim of their own sensitive to cues such as mood or transferable cues of when the object type is called; then \"emulated\" in the mind a pulse-to-response only version of the associated objects for this purpose ( should update with more social cortex posits soon ) Zenodo publication zenodo-publication" }, { "id": "work:Friedman2025ConCatEnatePilot133", "type": "work", "title": "Con-cat-enate: pilot overview", "url": "/works/Friedman2025ConCatEnatePilot133.html", "external_url": "https://doi.org/10.5281/zenodo.14737043", "summary": "Short overview of the concatenate amateur cat Combined with Beacons Bevcyc and demo 0.01 plan", "year": 2025, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "Zenodo publication" ], "content": "Con-cat-enate: pilot overview Zenodo 10.5281/zenodo.14737043 Friedman2025ConCatEnatePilot133 Genetics & Biomedical Paper Short overview of the concatenate amateur cat Combined with Beacons Bevcyc and demo 0.01 plan Zenodo publication zenodo-publication" }, { "id": "work:Friedman2024PushPullPrimingSequence134", "type": "work", "title": "Push and Pull: A priming sequence", "url": "/works/Friedman2024PushPullPrimingSequence134.html", "external_url": "https://doi.org/10.5281/zenodo.10659375", "summary": "The primary objectives of this Push and Pull document are to explore the decoupling of cognitive ( covert , attentional) and bodily ( overt ) behaviors , and to provide a sequence of hands-on computer exercises for furth", "year": 2024, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Zenodo publication" ], "content": "Push and Pull: A priming sequence Zenodo 10.5281/zenodo.10659375 Friedman2024PushPullPrimingSequence134 Active Inference Paper The primary objectives of this Push and Pull document are to explore the decoupling of cognitive ( covert , attentional) and bodily ( overt ) behaviors , and to provide a sequence of hands-on computer exercises for further exploration . The priming sequence of exercises is presented to inform an individual’s understanding of how their attention interacts with computer use movements, such as controlling the on-screen cursor with mouse, touchpad, or eye movements. What is presented here is only an initial sequence to complement other and future development of “hand-I” uncouplings, in principle and in practice. Zenodo publication zenodo-publication" }, { "id": "work:Friedman2023NaturalAIBasedScience135", "type": "work", "title": "A Natural AI Based on The Science of Computational Physics, Biology and Neuroscience: Policy and Societal Significance", "url": "/works/Friedman2023NaturalAIBasedScience135.html", "external_url": "https://doi.org/10.5281/zenodo.10360148", "summary": "Letter on: \"A Natural AI Based on The Science of Computational Physics, Biology and Neuroscience: Policy and Societal Significance\". v1 released on December 12, 2023.", "year": 2023, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "Active Inference", "AI", "Natural", "Policy" ], "content": "A Natural AI Based on The Science of Computational Physics, Biology and Neuroscience: Policy and Societal Significance Zenodo 10.5281/zenodo.10360148 Friedman2023NaturalAIBasedScience135 Computational Paper Letter on: \"A Natural AI Based on The Science of Computational Physics, Biology and Neuroscience: Policy and Societal Significance\". v1 released on December 12, 2023. Active Inference AI Natural Policy Active Inference AI Natural Policy" }, { "id": "work:Friedman2023ATLASQuestionOrientedApproach136", "type": "work", "title": "ATLAS: A Question Oriented Approach to the Use of Pattern Languages in Knowledge Management", "url": "/works/Friedman2023ATLASQuestionOrientedApproach136.html", "external_url": "https://doi.org/10.5281/zenodo.10362561", "summary": "The ATLAS system, evolving since the late 1990s, stands as a dynamic and comprehensive knowledge management tool that intends to address the complexities of modern information supply chains. The antecedent to ATLAS was t", "year": 2023, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "Zenodo publication" ], "content": "ATLAS: A Question Oriented Approach to the Use of Pattern Languages in Knowledge Management Zenodo 10.5281/zenodo.10362561 Friedman2023ATLASQuestionOrientedApproach136 Cognitive Security Paper The ATLAS system, evolving since the late 1990s, stands as a dynamic and comprehensive knowledge management tool that intends to address the complexities of modern information supply chains. The antecedent to ATLAS was the Atlas of Risk, an informal assemblage of various risks associated with digital interactions. Here we provide an initial specification for digital prototypes and paper-and-pencil implementations of a matured ATLAS architecture which integrates pattern language approaches with question-oriented procedures to manage and interpret meaning and context. The ATLAS system facilitates the management and communication of nuanced data sets and knowledge bases with an eye towards interoperability without the need for fully shared standards. The development of ATLAS, driven by the need for enhanced data interoperability and shared understanding in an increasingly complex and volati Zenodo publication zenodo-publication" }, { "id": "work:Friedman2023TranscriptActiveInferenceGuestStream137", "type": "work", "title": "Transcript of Active Inference GuestStream 049.1: \"Clickbait, consciousness science, and responsible journalism\"", "url": "/works/Friedman2023TranscriptActiveInferenceGuestStream137.html", "external_url": "https://doi.org/10.5281/zenodo.8229512", "summary": "Transcript from livestream on July 25, 2023 at the Active Inference Institute. YouTube watch link: https://www.youtube.com/watch?v=dUXfgzKHV1c Repository with updated transcripts and accessory files: https://github.com/A", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Consciousness", "Science", "Communication" ], "content": "Transcript of Active Inference GuestStream 049.1: \"Clickbait, consciousness science, and responsible journalism\" Zenodo 10.5281/zenodo.8229512 Friedman2023TranscriptActiveInferenceGuestStream137 Active Inference Paper Transcript from livestream on July 25, 2023 at the Active Inference Institute. YouTube watch link: https://www.youtube.com/watch?v=dUXfgzKHV1c Repository with updated transcripts and accessory files: https://github.com/ActiveInferenceInstitute/ActiveInferenceJournal/tree/main/GuestStream/GuestStream 049 Information on the Institute: https://www.activeinference.org/ Consciousness Science Communication Consciousness Science Communication" }, { "id": "work:Friedman2023ModernNostrIndexCard138", "type": "work", "title": "Modern Nostr Index Card-based Knowledge Engineering", "url": "/works/Friedman2023ModernNostrIndexCard138.html", "external_url": "https://doi.org/10.5281/zenodo.8118156", "summary": "Some concepts explored related to Knowledge Engineering, Nostr, Large Language Models, Complexity, and more.", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Nostr", "Complexity", "Large Language Model", "Knowledge Engineering" ], "content": "Modern Nostr Index Card-based Knowledge Engineering Zenodo 10.5281/zenodo.8118156 Friedman2023ModernNostrIndexCard138 Active Inference Paper Some concepts explored related to Knowledge Engineering, Nostr, Large Language Models, Complexity, and more. Nostr Complexity Large Language Model Knowledge Engineering Nostr Complexity Large Language Model Knowledge Engineering" }, { "id": "work:Friedman2023SlidesIris139", "type": "work", "title": "Slides for Iris", "url": "/works/Friedman2023SlidesIris139.html", "external_url": "https://doi.org/10.5281/zenodo.7838653", "summary": "Some initial slides from today. For context see: @speakerjohnash", "year": 2023, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Zenodo publication" ], "content": "Slides for Iris Zenodo 10.5281/zenodo.7838653 Friedman2023SlidesIris139 Active Inference Paper Some initial slides from today. For context see: @speakerjohnash Zenodo publication zenodo-publication" }, { "id": "work:Friedman2022CanonicalNeuralNetworksPerform140", "type": "work", "title": "Canonical neural networks perform active inference", "url": "/works/Friedman2022CanonicalNeuralNetworksPerform140.html", "external_url": "https://doi.org/10.5281/zenodo.7400536", "summary": "Transcript of a three-session series of discussions of the paper \"Canonical neural networks perform active inference\" by Takuya Isomura, Hideaki Shimazaki & Karl J. Friston. https://www.nature.com/articles/s42003-021-029", "year": 2022, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Zenodo publication" ], "content": "Canonical neural networks perform active inference Zenodo 10.5281/zenodo.7400536 Friedman2022CanonicalNeuralNetworksPerform140 Active Inference Paper Transcript of a three-session series of discussions of the paper \"Canonical neural networks perform active inference\" by Takuya Isomura, Hideaki Shimazaki & Karl J. Friston. https://www.nature.com/articles/s42003-021-02994-2 LS 051.0: Background and context. https://www.youtube.com/watch?v=ZASG-rtkXDk LS 051.1: First participatory group discussion. https://www.youtube.com/watch?v=IM NlUzyq8M LS 051.2: Second participatory group discussion. https://www.youtube.com/watch?v=hY CajLpt9Q Zenodo publication zenodo-publication" }, { "id": "work:Friedman2022InteroceptionAsModelingAllostasis141", "type": "work", "title": "Interoception as modeling, allostasis as control", "url": "/works/Friedman2022InteroceptionAsModelingAllostasis141.html", "external_url": "https://doi.org/10.5281/zenodo.7400709", "summary": "Transcript of discussions of the 2022 paper “Interoception as modeling, allostasis as control” by Eli Sennesh, Jordan Theriault, Dana Brooks, Jan-Willemvan de Meent, Lisa Feldman Barrett, & Karen S. Quigley https://www.s", "year": 2022, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Zenodo publication" ], "content": "Interoception as modeling, allostasis as control Zenodo 10.5281/zenodo.7400709 Friedman2022InteroceptionAsModelingAllostasis141 Active Inference Paper Transcript of discussions of the 2022 paper “Interoception as modeling, allostasis as control” by Eli Sennesh, Jordan Theriault, Dana Brooks, Jan-Willemvan de Meent, Lisa Feldman Barrett, & Karen S. Quigley https://www.sciencedirect.com/science/article/abs/pii/S0301051121002350 Session 050.0, October 17, 2022 https://www.youtube.com/watch?v=l7r0ISlr-Hc Session 050.1, October 20, 2022 https://www.youtube.com/watch?v=tGd-mgSdbio Session 050.2, November 3, 2022 https://www.youtube.com/watch?v=4o-LmkycAC0 Zenodo publication zenodo-publication" }, { "id": "work:Friedman2022TranscriptMarkSolmsConsciousness142", "type": "work", "title": "Transcript of: Mark Solms, \"Consciousness as Precision Optimization: Some Physiological and Philosophical Considerations\", ActInf GuestStream #016", "url": "/works/Friedman2022TranscriptMarkSolmsConsciousness142.html", "external_url": "https://doi.org/10.5281/zenodo.7267947", "summary": "This document is an enhanced transcript of the live presentations and group discussions with Mark Solms in 2022 at the Active Inference Institute. The focus is the 2018 paper \"How and Why Consciousness Arises: Some Consi", "year": 2022, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Active Inference", "Consciousness", "Neuroanatomy", "Psychology", "Free Energy Principle", "Livestream" ], "content": "Transcript of: Mark Solms, \"Consciousness as Precision Optimization: Some Physiological and Philosophical Considerations\", ActInf GuestStream #016 Zenodo 10.5281/zenodo.7267947 Friedman2022TranscriptMarkSolmsConsciousness142 Active Inference Paper This document is an enhanced transcript of the live presentations and group discussions with Mark Solms in 2022 at the Active Inference Institute. The focus is the 2018 paper \"How and Why Consciousness Arises: Some Considerations from Physics and Physiology\" by Mark Solms and Karl Friston. Active Inference Consciousness Neuroanatomy Psychology Free Energy Principle Livestream Active Inference Consciousness Neuroanatomy Psychology Free Energy Principle" }, { "id": "work:Friedman2022WorkedExampleBayesianMechanics143", "type": "work", "title": "A Worked Example of the Bayesian Mechanics of Classical Objects", "url": "/works/Friedman2022WorkedExampleBayesianMechanics143.html", "external_url": "https://doi.org/10.5281/zenodo.7400786", "summary": "Transcripts of discussions of the 2022 preprint \"A Worked Example of the Bayesian Mechanics of Classical Objects\" by Dalton A R Sakthivadivel. https://arxiv.org/abs/2206.12996 Session 049.0, September 30, 2022 https://ww", "year": 2022, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Zenodo publication" ], "content": "A Worked Example of the Bayesian Mechanics of Classical Objects Zenodo 10.5281/zenodo.7400786 Friedman2022WorkedExampleBayesianMechanics143 Active Inference Paper Transcripts of discussions of the 2022 preprint \"A Worked Example of the Bayesian Mechanics of Classical Objects\" by Dalton A R Sakthivadivel. https://arxiv.org/abs/2206.12996 Session 049.0, September 30, 2022 https://www.youtube.com/watch?v=OtX2Fpzn7KA Session 049.1, October 5, 2022 https://www.youtube.com/watch?v=dAtC-Enmc8M Session 049.2, October 12, 2022 https://www.youtube.com/watch?v=2SuBJBEg9LI Zenodo publication zenodo-publication" }, { "id": "work:Friedman2022TranscriptDiscussionsCommunicationAs144", "type": "work", "title": "Transcript of discussions on: \"Communication as Socially Extended Active Inference: An Ecological Approach to Communicative Behavior\"", "url": "/works/Friedman2022TranscriptDiscussionsCommunicationAs144.html", "external_url": "https://doi.org/10.5281/zenodo.7401875", "summary": "Discussion with an author of the 2021 paper “Communication as Socially Extended Active Inference: An Ecological Approach to Communicative Behavior” by Remi Tison & Pierre Poirier. https://www.tandfonline.com/doi/abs/10.1", "year": 2022, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Zenodo publication" ], "content": "Transcript of discussions on: \"Communication as Socially Extended Active Inference: An Ecological Approach to Communicative Behavior\" Zenodo 10.5281/zenodo.7401875 Friedman2022TranscriptDiscussionsCommunicationAs144 Active Inference Paper Discussion with an author of the 2021 paper “Communication as Socially Extended Active Inference: An Ecological Approach to Communicative Behavior” by Remi Tison & Pierre Poirier. https://www.tandfonline.com/doi/abs/10.1080/10407413.2021.1965480 Session 048.0, September 2, 2022 https://www.youtube.com/watch?v=zqiZjjY9H7M Session 048.1, September 7, 2022 https://www.youtube.com/watch?v=nWFM5zrdmG8 Session 048.1, September 7, 2022 https://www.youtube.com/watch?v=nWFM5zrdmG8 Zenodo publication zenodo-publication" }, { "id": "work:Friedman2022TrackingPublicSensemakingThrough145", "type": "work", "title": "Tracking Public Sensemaking through Rhetorical Annotation of Image Memes", "url": "/works/Friedman2022TrackingPublicSensemakingThrough145.html", "external_url": "https://doi.org/10.5281/zenodo.6904427", "summary": "Political polarization and declining trust in institutions are driving societal destabilization and radicalization. Recently there has been increased interest in online misinformation intervention and deterrence, for exa", "year": 2022, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "Sensemaking", "Memes", "Knowledge Management", "Narrative", "Rhetorical Analysis" ], "content": "Tracking Public Sensemaking through Rhetorical Annotation of Image Memes Zenodo 10.5281/zenodo.6904427 Friedman2022TrackingPublicSensemakingThrough145 Cognitive Security Paper Political polarization and declining trust in institutions are driving societal destabilization and radicalization. Recently there has been increased interest in online misinformation intervention and deterrence, for example through the use of machine learning on language use. We argue that addressing crises in the information environment will require a sharper situational awareness and a deeper understanding of how beliefs emerge and crystallize, as well as greater connectivity in the work of teams and organizations in order to reduce the effects of bias and partisanship in collection and analysis. Image memes play an increasingly important role in public sensemaking and discourse and the emergence of public beliefs. Despite their significance, image memes have proven to be a very difficult category of artifact to collect, classify, and analyze in aggregate. In this white paper, the fun Sensemaking Memes Knowledge Management Narrative Rhetorical Analysis Sensemaking Memes Knowledge Management Narrative Rhetorical Analysis" }, { "id": "work:Friedman2021TranscriptKarlFriston1st146", "type": "work", "title": "Transcript of: Karl Friston, 1st Applied Active Inference Symposium, Active Inference Lab, June 21, 2021", "url": "/works/Friedman2021TranscriptKarlFriston1st146.html", "external_url": "https://doi.org/10.5281/zenodo.5797072", "summary": "On June 21st, 2021, Active Inference Lab ( activeinference.org/ ) hosted its first Applied Active Inference Symposium, featuring Professor Karl Friston. The Symposium was structured in three sections, corresponding to th", "year": 2021, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography", "Active Inference", "Free Energy Principle", "Symposium", "ActInfLab", "Bayesian Inference", "Education", "Communication", "Tools" ], "content": "Transcript of: Karl Friston, 1st Applied Active Inference Symposium, Active Inference Lab, June 21, 2021 Zenodo 10.5281/zenodo.5797072 Friedman2021TranscriptKarlFriston1st146 Active Inference Paper On June 21st, 2021, Active Inference Lab ( activeinference.org/ ) hosted its first Applied Active Inference Symposium, featuring Professor Karl Friston. The Symposium was structured in three sections, corresponding to the Organizational Units of the Active Inference Lab: Education, Communication, and Tools. This publication reflects an edited and enriched transcript of the proceedings of the Symposium. Active Inference Free Energy Principle Symposium ActInfLab Bayesian Inference Education Communication Tools Generative Model Active Inference Free Energy Principle Symposium ActInfLab Bayesian Inference" }, { "id": "work:Friedman2021CollaborativeWritingCatechismBased147", "type": "work", "title": "Collaborative Writing for Catechism-Based Teams", "url": "/works/Friedman2021CollaborativeWritingCatechismBased147.html", "external_url": "https://doi.org/10.5281/zenodo.4633921", "summary": "Asynchronous and remote collaborative written projects (research, field guides, code, etc.) in emergent, interdisciplinary teams can be an incredibly productive and enjoyable pursuit. The convergence of diverse perspecti", "year": 2021, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "Remote Teams", "Collaborative Writing", "Catechisms", "OPORDs" ], "content": "Collaborative Writing for Catechism-Based Teams Zenodo 10.5281/zenodo.4633921 Friedman2021CollaborativeWritingCatechismBased147 Cognitive Security Paper Asynchronous and remote collaborative written projects (research, field guides, code, etc.) in emergent, interdisciplinary teams can be an incredibly productive and enjoyable pursuit. The convergence of diverse perspectives, personalities, and expertise in the rapid production of written deliverables can provide immense value and insight, not just to the situation, problem, or opportunity space the team was formed to address, but also to the disciplines each author brought to the table. Yet, asynchronous and remote collaborative writing can also be rather perilous. Managing deadlines, handling disputes, communicating, staying on mission, managing resources, collective editing (and over-editing), and avoiding contradiction are only some of the challenges. While the presence of a catechism-styled operations order and the use of a team “Facilitator” can greatly improve the likelihood of suc Remote Teams Collaborative Writing Catechisms OPORDs Remote Teams Collaborative Writing Catechisms OPORDs" }, { "id": "work:Friedman2020ReimaginingMaps148", "type": "work", "title": "Reimagining Maps", "url": "/works/Friedman2020ReimaginingMaps148.html", "external_url": "https://doi.org/10.5281/zenodo.4170026", "summary": "Reimagining Maps was written after participation in a National Geospatial-Intelligence Agency Incubator hosted on Polyplexus. The field of cartography sits at the intersection of applied mathematics, engineering, geology", "year": 2020, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "Maps", "Cartography", "Remote Teams", "Interdisciplinary Research", "Process Mapping", "Knowledge Management Systems", "Instantaneous Remote Teams", "Intelligence Production" ], "content": "Reimagining Maps Zenodo 10.5281/zenodo.4170026 Friedman2020ReimaginingMaps148 Cognitive Security Paper Reimagining Maps was written after participation in a National Geospatial-Intelligence Agency Incubator hosted on Polyplexus. The field of cartography sits at the intersection of applied mathematics, engineering, geology, geography, user experience, and graphic design. Methodologies and concepts from cartography have been creatively applied in a variety of fields, such as the application of spatial mapping techniques to information in knowledge management, or the use of itinerary visualization methods in non-spatial journeys such as learning maps in learning management systems. These fields have been subjected to their own forms of development and evolution leading to new methodologies and concepts somewhat removed from their origins. Cartography itself has undergone a great deal of technology-driven development but would look very different today had it been developed as a new field thr Maps Cartography Remote Teams Interdisciplinary Research Process Mapping Knowledge Management Systems Instantaneous Remote Teams Intelligence Production OSINT Maps Cartography Remote Teams Interdisciplinary Research Process Mapping" }, { "id": "work:Friedman2020InfiniteGamesInfiniteTeams149", "type": "work", "title": "Infinite Games for Infinite Teams", "url": "/works/Friedman2020InfiniteGamesInfiniteTeams149.html", "external_url": "https://doi.org/10.5281/zenodo.12601675", "summary": "Infinite Games for Infinite Teams was published by and in response to the DARPA Polyplexus Citizen Incubator: “Inventing a Remote Culture to Deal with Pandemics”, and was done so with the intent of discussing the questio", "year": 2020, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography", "Zenodo publication" ], "content": "Infinite Games for Infinite Teams Zenodo 10.5281/zenodo.12601675 Friedman2020InfiniteGamesInfiniteTeams149 Cognitive Security Paper Infinite Games for Infinite Teams was published by and in response to the DARPA Polyplexus Citizen Incubator: “Inventing a Remote Culture to Deal with Pandemics”, and was done so with the intent of discussing the questions outlined below. How are global online narratives constructed and received in 2020? Why are the processes of narrative design and culture production so important for security and governance? What is possible now or soon that was not possible before? What approaches could catalyze assessment, design, and deployment of online narratives in real-time? Why is it so important to have meme-detection systems that are culturally-aware, interlingual, intermodal, and human-in-the-loop? What does it look like to take a Complex Adaptive Systems (CAS) approach to the neuromemetics of narrative co-construction and agenda-setting? How could a CAS approach be used to support specifical Zenodo publication zenodo-publication" }, { "id": "work:Friedman2026MusicNeverStoppedGrateful150", "type": "work", "title": "The Music Never Stopped: A Grateful Data Compendium with a Category-Theoretic Interpretation", "url": "/works/Friedman2026MusicNeverStoppedGrateful150.html", "external_url": "https://doi.org/10.5281/zenodo.20482026", "summary": "We present a modular, citation-bound data compendium for the Grateful Dead universe — shows, songs, performances, personnel timelines, venues, recordings, and reception — and a category-theoretic interpretation of the pe", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "grateful dead", "setlist data", "category theory", "music information retrieval", "reproducible data compendium" ], "content": "The Music Never Stopped: A Grateful Data Compendium with a Category-Theoretic Interpretation Zenodo 10.5281/zenodo.20482026 Friedman2026MusicNeverStoppedGrateful150 Computational Paper We present a modular, citation-bound data compendium for the Grateful Dead universe — shows, songs, performances, personnel timelines, venues, recordings, and reception — and a category-theoretic interpretation of the performance graph. The work is grounded in the archival reality that Grateful Dead history is both institutional and participatory: UCSC's Grateful Dead Archive and the Internet Archive collection preserve formal and community records , while taping and trading scholarship shows why setlists and recording metadata are cultural evidence, not merely fan trivia . The surrounding source dossier also binds the non-quantitative historical frame -- formation and Acid Test context, Wall of Sound engineering, live recording/liveness scholarship, Deadhead sociology, studio-era reception, and public recognition -- to checked sources rather than to folklore alone . The compendium integ grateful dead setlist data category theory music information retrieval reproducible data compendium grateful dead setlist data category theory music information retrieval reproducible data compendium" }, { "id": "work:Friedman2026DeterministicTestbedSelfOrganizing151", "type": "work", "title": "A Deterministic Testbed for Self-Organizing Agent-Team Coordination", "url": "/works/Friedman2026DeterministicTestbedSelfOrganizing151.html", "external_url": "https://doi.org/10.5281/zenodo.20533670", "summary": "Abstract Recent work on AutoScientists coordinates self-organizing teams of language-model agents through a small set of shared mechanisms: a champion-and-experiment-log shared state, a registry of retired dead-end direc", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "agent coordination", "scientific discovery", "noise-band confirmation", "ablation study", "reproducible research", "language-model agents" ], "content": "A Deterministic Testbed for Self-Organizing Agent-Team Coordination Zenodo 10.5281/zenodo.20533670 Friedman2026DeterministicTestbedSelfOrganizing151 Computational Paper Abstract Recent work on AutoScientists coordinates self-organizing teams of language-model agents through a small set of shared mechanisms: a champion-and-experiment-log shared state, a registry of retired dead-end directions, effect-size ranking of candidate directions, noise-band confirmation of claimed improvements, and stagnation-driven reorganization of teams. This exemplar provides a deterministic, standalone reference implementation of those mechanisms and studies them honestly as a testbed rather than as a performance claim. We make the comparison fair by holding the total number of objective evaluations fixed: coordinated teams partition a single sequential experiment budget rather than adding parallel compute. Under that matched budget, coordination cannot — and in our results does not — beat a single-thread baseline on the final champion metric; we report the actual numbers an agent coordination scientific discovery noise-band confirmation ablation study reproducible research language-model agents agent coordination scientific discovery noise-band confirmation ablation study reproducible research" }, { "id": "work:Friedman2026RecoveringLLMPersonaAccuracies152", "type": "work", "title": "Recovering LLM-Persona Accuracies from Unlabeled Votes", "url": "/works/Friedman2026RecoveringLLMPersonaAccuracies152.html", "external_url": "https://doi.org/10.5281/zenodo.20498700", "summary": "Algebraic (NTQR) evaluation infers how accurate a group of noisy classifiers was on a finite test using only their responses — no answer key. We test this end to end on real large language models. Three trader \"personas\"", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "algebraic evaluation", "NTQR", "unsupervised evaluation", "evaluation on unlabeled data", "LLM-as-judge", "error-independent evaluation", "ensemble evaluability", "constant classifier" ], "content": "Recovering LLM-Persona Accuracies from Unlabeled Votes Zenodo 10.5281/zenodo.20498700 Friedman2026RecoveringLLMPersonaAccuracies152 Computational Paper Algebraic (NTQR) evaluation infers how accurate a group of noisy classifiers was on a finite test using only their responses — no answer key. We test this end to end on real large language models. Three trader \"personas\" (optimistic, neutral, pessimistic), instantiated as system prompts, each make a binary bullish/bearish call on the same 64 market scenarios; we run the identical trio through six locally-hosted models via Ollama. For each model we recover per-persona, per-label accuracy with ErrorIndependentEvaluation (unsupervised) and score it against the authored ground truth (supervised), which is used only as a check. On the five models whose three judges all varied (mistral:latest, gemma4:latest, gemma3:4b, gemma2:2b, granite4.1:3b), the unsupervised algebra recovered persona accuracies to a mean absolute error of 0.012, within the 0.102 sampling-noise floor across all six per-labe algebraic evaluation NTQR unsupervised evaluation evaluation on unlabeled data LLM-as-judge error-independent evaluation ensemble evaluability constant classifier AI safety warning light reproducible research answer-key-free recovery local large language models algebraic evaluation NTQR unsupervised evaluation evaluation on unlabeled data LLM-as-judge" }, { "id": "work:Friedman2026TriplicateDataDrivenLarge153", "type": "work", "title": "The Triplicate: A Data-Driven Large-Format Newspaper Layout Engine", "url": "/works/Friedman2026TriplicateDataDrivenLarge153.html", "external_url": "https://doi.org/10.5281/zenodo.20533676", "summary": "Abstract We present template newspaper, a pure-Python engine that renders a complete twelve-page, large-format newspaper to a print-ready PDF from structured YAML content. The exemplar edition is The Triplicate, a homage", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "newspaper layout", "typography", "reportlab", "reproducible publishing", "document engineering" ], "content": "The Triplicate: A Data-Driven Large-Format Newspaper Layout Engine Zenodo 10.5281/zenodo.20533676 Friedman2026TriplicateDataDrivenLarge153 Computational Paper Abstract We present template newspaper, a pure-Python engine that renders a complete twelve-page, large-format newspaper to a print-ready PDF from structured YAML content. The exemplar edition is The Triplicate, a homage to the historic newspaper of Crescent City, California (founded 1879). The engine demonstrates designed multi-column page layout — nameplate and ears, spanning headlines, flowing column frames with an optional rail, drop caps, pull quotes, ruled modular boxes, data tables, halftone \"engraving\" figures and running folios — while keeping a strict separation between content (data) and engine (code): a new title is a data edit, never a code change. The layout strategy is a hybrid in which fixed furniture is drawn directly on the canvas to establish where the column grid begins, after which body copy flows through ReportLab frames that split paragraphs across columns automati newspaper layout typography reportlab reproducible publishing document engineering newspaper layout typography reportlab reproducible publishing document engineering" }, { "id": "work:Friedman2026TemplateTextbook154", "type": "work", "title": "The Template Textbook", "url": "/works/Friedman2026TemplateTextbook154.html", "external_url": "https://doi.org/10.5281/zenodo.20533126", "summary": "A modular, fillable scaffold for book-length technical works: a data-driven manuscript (parts/chapters/labs/questions), a tested computational backbone, deterministic figures and Mermaid diagrams, and a content scaffold/", "year": 2026, "domain": "Computational", "tags": [ "Book", "Computational", "bibliography", "open textbook", "modular manuscript", "reproducible publishing", "computational backbone", "Python" ], "content": "The Template Textbook Zenodo 10.5281/zenodo.20533126 Friedman2026TemplateTextbook154 Computational Book A modular, fillable scaffold for book-length technical works: a data-driven manuscript (parts/chapters/labs/questions), a tested computational backbone, deterministic figures and Mermaid diagrams, and a content scaffold/validation engine. open textbook modular manuscript reproducible publishing computational backbone Python open textbook modular manuscript reproducible publishing computational backbone Python" }, { "id": "work:Friedman2016LessonsFromColony155", "type": "work", "title": "Lessons from the colony", "url": "/works/Friedman2016LessonsFromColony155.html", "external_url": "https://www.science.org/doi/10.1126/science.352.6288.886", "summary": "Paper · Science · Entomology", "year": 2016, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography" ], "content": "Lessons from the colony Science Friedman2016LessonsFromColony155 Entomology Paper" }, { "id": "work:Friedman2016FullSpeedAheadCity156", "type": "work", "title": "Full speed ahead to the City on the Hill", "url": "/works/Friedman2016FullSpeedAheadCity156.html", "external_url": "https://doi.org/10.1126/science.352.6288.886", "summary": "Paper · Science · AII Ecosystem", "year": 2016, "domain": "AII Ecosystem", "tags": [ "Paper", "AII Ecosystem", "bibliography" ], "content": "Full speed ahead to the City on the Hill Science 10.1126/science.352.6288.886 Friedman2016FullSpeedAheadCity156 AII Ecosystem Paper" }, { "id": "work:Friedman2021Disinforge157", "type": "work", "title": "Disinforge", "url": "/works/Friedman2021Disinforge157.html", "external_url": "https://www.science.org/doi/10.1126/science.371.6524.22", "summary": "Paper · Science · Cognitive Security", "year": 2021, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography" ], "content": "Disinforge Science Friedman2021Disinforge157 Cognitive Security Paper" }, { "id": "work:Friedman2021DefiningEvents2020Hindsight158", "type": "work", "title": "Defining events: 2020 in hindsight", "url": "/works/Friedman2021DefiningEvents2020Hindsight158.html", "external_url": "https://doi.org/10.1126/science.371.6524.22", "summary": "Paper · Science · Cognitive Security", "year": 2021, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography" ], "content": "Defining events: 2020 in hindsight Science 10.1126/science.371.6524.22 Friedman2021DefiningEvents2020Hindsight158 Cognitive Security Paper" }, { "id": "work:Friedman2022ActiveBlockferenceCadCADActive159", "type": "work", "title": "Active Blockference: cadCAD with Active Inference for Cognitive Systems Modeling", "url": "/works/Friedman2022ActiveBlockferenceCadCADActive159.html", "external_url": "https://doi.org/10.1007/978-3-031-28719-0_10", "summary": "Paper · International Workshop on Active Inference · Active Inference", "year": 2022, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography" ], "content": "Active Blockference: cadCAD with Active Inference for Cognitive Systems Modeling International Workshop on Active Inference 10.1007/978-3-031-28719-0_10 Friedman2022ActiveBlockferenceCadCADActive159 Active Inference Paper" }, { "id": "work:Friedman2024FromNeuronalPacketsThoughtseeds160", "type": "work", "title": "From Neuronal Packets to Thoughtseeds: A Hierarchical Model of Embodied Cognition in the Global Workspace", "url": "/works/Friedman2024FromNeuronalPacketsThoughtseeds160.html", "external_url": "https://doi.org/10.48550/arXiv.2408.15982", "summary": "Paper · arXiv · Active Inference", "year": 2024, "domain": "Active Inference", "tags": [ "Paper", "Active Inference", "bibliography" ], "content": "From Neuronal Packets to Thoughtseeds: A Hierarchical Model of Embodied Cognition in the Global Workspace arXiv 10.48550/arXiv.2408.15982 Friedman2024FromNeuronalPacketsThoughtseeds160 Active Inference Paper" }, { "id": "work:Friedman2021KnowledgeManagementArchipelago161", "type": "work", "title": "Knowledge Management Archipelago", "url": "/works/Friedman2021KnowledgeManagementArchipelago161.html", "external_url": "https://doi.org/10.5281/zenodo.5034809", "summary": "Paper · Zenodo · Cognitive Security", "year": 2021, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography" ], "content": "Knowledge Management Archipelago Zenodo 10.5281/zenodo.5034809 Friedman2021KnowledgeManagementArchipelago161 Cognitive Security Paper" }, { "id": "work:Friedman2024CommentsSubmittedByBlockScience162", "type": "work", "title": "Comments Submitted by BlockScience, UW APL IRSIRI, and the Cognitive Security and Education Forum", "url": "/works/Friedman2024CommentsSubmittedByBlockScience162.html", "external_url": "https://doi.org/10.5281/zenodo.13273682", "summary": "Paper · Zenodo · Cognitive Security", "year": 2024, "domain": "Cognitive Security", "tags": [ "Paper", "Cognitive Security", "bibliography" ], "content": "Comments Submitted by BlockScience, UW APL IRSIRI, and the Cognitive Security and Education Forum Zenodo 10.5281/zenodo.13273682 Friedman2024CommentsSubmittedByBlockScience162 Cognitive Security Paper" }, { "id": "work:Friedman2017OsteopathyVariableVariabilityHealth163", "type": "work", "title": "Osteopathy and the Variable Variability of Health", "url": "/works/Friedman2017OsteopathyVariableVariabilityHealth163.html", "external_url": "", "summary": "Paper · The Cranial Letter 70(4) · Genetics & Biomedical", "year": 2017, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography" ], "content": "Osteopathy and the Variable Variability of Health The Cranial Letter 70(4) Friedman2017OsteopathyVariableVariabilityHealth163 Genetics & Biomedical Paper" }, { "id": "work:Friedman2016CellsMechanobiologyOsteopathy164", "type": "work", "title": "Cells, Mechanobiology, and Osteopathy", "url": "/works/Friedman2016CellsMechanobiologyOsteopathy164.html", "external_url": "", "summary": "Paper · The Cranial Letter 69(1) · Genetics & Biomedical", "year": 2016, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography" ], "content": "Cells, Mechanobiology, and Osteopathy The Cranial Letter 69(1) Friedman2016CellsMechanobiologyOsteopathy164 Genetics & Biomedical Paper" }, { "id": "work:Friedman2026ITraceVerificationFirstWebcam165", "type": "work", "title": "iTrace: verification-first webcam eye-movement analysis", "url": "/works/Friedman2026ITraceVerificationFirstWebcam165.html", "external_url": "https://doi.org/10.5281/zenodo.20614909", "summary": "iTrace is an MIT-licensed Python toolkit for webcam-derived gaze, saccade, pupil, and quality diagnostics. Version 0.4.1 is a diagnostic v1 release: the pure NumPy/SciPy core is algorithmically verified against synthetic", "year": 2026, "domain": "Computational", "tags": [ "Paper", "Computational", "bibliography", "eye-tracking", "webcam", "gaze", "saccades", "pupillometry", "open-source", "diagnostic-pilot" ], "content": "iTrace: verification-first webcam eye-movement analysis Zenodo 10.5281/zenodo.20614909 Friedman2026ITraceVerificationFirstWebcam165 Computational Paper iTrace is an MIT-licensed Python toolkit for webcam-derived gaze, saccade, pupil, and quality diagnostics. Version 0.4.1 is a diagnostic v1 release: the pure NumPy/SciPy core is algorithmically verified against synthetic and closed-loop oracles, the optional webcam shell exports derived records, and the empirical ledger covers a single-participant, single-device, five-session diagnostic pilot. This release does not claim reference-device accuracy, cross-device generality, population generality, or webcam-accuracy validation. eye-tracking webcam gaze saccades pupillometry open-source diagnostic-pilot eye-tracking webcam gaze saccades pupillometry" }, { "id": "software:docxology:template", "type": "software", "title": "template", "url": "https://github.com/docxology/template", "summary": "Production-grade scaffold for reproducible computational research — 10-stage DAG pipelines, ≥90% test coverage, cryptographic provenance, multi-project workspace, and agent-ready documentation · Zenodo software v3.3.0", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "template Production-grade scaffold for reproducible computational research — 10-stage DAG pipelines, ≥90% test coverage, cryptographic provenance, multi-project workspace, and agent-ready documentation · Zenodo software v3.3.0 Python docxology" }, { "id": "software:docxology:QuadCraft", "type": "software", "title": "QuadCraft", "url": "https://github.com/docxology/QuadCraft", "summary": "Minecraft variant built on tetrahedral geometry — voxels replaced by Quadray-coordinate tetrahedra, exploring Buckminster Fuller's synergetics in an interactive 3D world", "domain": "docxology", "tags": [ "software", "JavaScript", "docxology" ], "content": "QuadCraft Minecraft variant built on tetrahedral geometry — voxels replaced by Quadray-coordinate tetrahedra, exploring Buckminster Fuller's synergetics in an interactive 3D world JavaScript docxology" }, { "id": "software:docxology:MetaInformAnt", "type": "software", "title": "MetaInformAnt", "url": "https://github.com/docxology/MetaInformAnt", "summary": "Meta-framework integrating computational entomology, Active Inference, and information theory for modeling ant colony cognition and beyond", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "MetaInformAnt Meta-framework integrating computational entomology, Active Inference, and information theory for modeling ant colony cognition and beyond Python docxology" }, { "id": "software:docxology:codomyrmex", "type": "software", "title": "codomyrmex", "url": "https://github.com/docxology/codomyrmex", "summary": "AI-native modular coding workspace — 128 modules, 600 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "codomyrmex AI-native modular coding workspace — 128 modules, 600 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration Python docxology" }, { "id": "software:docxology:cognitive-engine", "type": "software", "title": "cognitive-engine", "url": "https://github.com/docxology/cognitive-engine", "summary": "Hybrid neuro-symbolic AI combining fractal symbolic representations with probabilistic neural models for enhanced reasoning; includes Unipixel fractal building blocks and PEFF ethical reasoning", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "cognitive-engine Hybrid neuro-symbolic AI combining fractal symbolic representations with probabilistic neural models for enhanced reasoning; includes Unipixel fractal building blocks and PEFF ethical reasoning Python docxology" }, { "id": "software:docxology:opentir", "type": "software", "title": "opentir", "url": "https://github.com/docxology/opentir", "summary": "Comprehensive toolkit analyzing 250+ Palantir open-source repositories (6.2M+ lines of code) — automated discovery, multi-language analysis, dependency mapping, statistical profiling, and professional visualizations", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "opentir Comprehensive toolkit analyzing 250+ Palantir open-source repositories (6.2M+ lines of code) — automated discovery, multi-language analysis, dependency mapping, statistical profiling, and professional visualizations Python docxology" }, { "id": "software:docxology:timeline_generator", "type": "software", "title": "timeline_generator", "url": "https://github.com/docxology/timeline_generator", "summary": "Networked Life Encoding — interactive D3 knowledge graph of human intellectual history; 24 relationship types, Perplexity AI enrichment; seeded around R. Buckminster Fuller's network", "domain": "docxology", "tags": [ "software", "TypeScript", "docxology" ], "content": "timeline_generator Networked Life Encoding — interactive D3 knowledge graph of human intellectual history; 24 relationship types, Perplexity AI enrichment; seeded around R. Buckminster Fuller's network TypeScript docxology" }, { "id": "software:docxology:FORMINDEX", "type": "software", "title": "FORMINDEX", "url": "https://github.com/docxology/FORMINDEX", "summary": "Analysis and tooling around FORMIS, the world's largest ant-literature database; bibliometric mining and structured index generation", "domain": "docxology", "tags": [ "software", "Rich Text Format", "docxology" ], "content": "FORMINDEX Analysis and tooling around FORMIS, the world's largest ant-literature database; bibliometric mining and structured index generation Rich Text Format docxology" }, { "id": "software:docxology:ActiveInferAnts", "type": "software", "title": "ActiveInferAnts", "url": "https://github.com/docxology/ActiveInferAnts", "summary": "Active Inference for ants — multi-language implementations (Python) for modeling ant-colony cognition as Bayesian agents minimizing free energy", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "ActiveInferAnts Active Inference for ants — multi-language implementations (Python) for modeling ant-colony cognition as Bayesian agents minimizing free energy Python docxology" }, { "id": "software:docxology:crescent-city", "type": "software", "title": "crescent-city", "url": "https://github.com/docxology/crescent-city", "summary": "End-to-end pipeline for ingesting, parsing, and querying the Crescent City, CA municipal code; TypeScript-based legal-text processing", "domain": "docxology", "tags": [ "software", "TypeScript", "docxology" ], "content": "crescent-city End-to-end pipeline for ingesting, parsing, and querying the Crescent City, CA municipal code; TypeScript-based legal-text processing TypeScript docxology" }, { "id": "software:docxology:ivm-xyz", "type": "software", "title": "ivm-xyz", "url": "https://github.com/docxology/ivm-xyz", "summary": "Python library for 3D and 4D Quadray/IVM (Isotropic Vector Matrix) geometry — coordinate conversion, volume calculations, and polyhedral operations", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "ivm-xyz Python library for 3D and 4D Quadray/IVM (Isotropic Vector Matrix) geometry — coordinate conversion, volume calculations, and polyhedral operations Python docxology" }, { "id": "software:docxology:Markov_Blanket_Detection", "type": "software", "title": "Markov_Blanket_Detection", "url": "https://github.com/docxology/Markov_Blanket_Detection", "summary": "Dynamic Markov Blanket Detection (DMBD) — PyTorch-accelerated framework for identifying causal relationships in complex systems; static and temporal modes with cognitive-structure labeling", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "Markov_Blanket_Detection Dynamic Markov Blanket Detection (DMBD) — PyTorch-accelerated framework for identifying causal relationships in complex systems; static and temporal modes with cognitive-structure labeling Python docxology" }, { "id": "software:docxology:QuadMath", "type": "software", "title": "QuadMath", "url": "https://github.com/docxology/QuadMath", "summary": "Mathematical exposition of Quadray coordinate systems (4-vector tetrahedral coordinates); LaTeX documentation and computation library", "domain": "docxology", "tags": [ "software", "TeX", "docxology" ], "content": "QuadMath Mathematical exposition of Quadray coordinate systems (4-vector tetrahedral coordinates); LaTeX documentation and computation library TeX docxology" }, { "id": "software:docxology:active_inference", "type": "software", "title": "active_inference", "url": "https://github.com/docxology/active_inference", "summary": "Active Inference for, with, and by Generative AI — Python implementations of free-energy-minimizing agents integrated with modern AI tooling", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "active_inference Active Inference for, with, and by Generative AI — Python implementations of free-energy-minimizing agents integrated with modern AI tooling Python docxology" }, { "id": "software:docxology:AgenticMesh", "type": "software", "title": "AgenticMesh", "url": "https://github.com/docxology/AgenticMesh", "summary": "Active Inference & Agentic Mesh — modular Python infrastructure for building agentic systems using free-energy-minimizing Active Inference principles", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "AgenticMesh Active Inference & Agentic Mesh — modular Python infrastructure for building agentic systems using free-energy-minimizing Active Inference principles Python docxology" }, { "id": "software:docxology:curriculum", "type": "software", "title": "curriculum", "url": "https://github.com/docxology/curriculum", "summary": "Curriculum development framework for interdisciplinary education in Active Inference, biology, and computational science", "domain": "docxology", "tags": [ "software", "HTML", "docxology" ], "content": "curriculum Curriculum development framework for interdisciplinary education in Active Inference, biology, and computational science HTML docxology" }, { "id": "software:docxology:lean_niche", "type": "software", "title": "lean_niche", "url": "https://github.com/docxology/lean_niche", "summary": "Lean/minimal niche-construction modeling — formal computational representations of ecological niche dynamics", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "lean_niche Lean/minimal niche-construction modeling — formal computational representations of ecological niche dynamics Python docxology" }, { "id": "software:docxology:literature", "type": "software", "title": "literature", "url": "https://github.com/docxology/literature", "summary": "Literature collection and analysis tools for structured ingestion, annotation, and exploration of scientific publications", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "literature Literature collection and analysis tools for structured ingestion, annotation, and exploration of scientific publications Python docxology" }, { "id": "software:docxology:obsidian-construction-from-text", "type": "software", "title": "obsidian-construction-from-text", "url": "https://github.com/docxology/obsidian-construction-from-text", "summary": "Automated Obsidian vault construction from unstructured text — NLP pipelines to generate bidirectionally-linked knowledge graphs", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "obsidian-construction-from-text Automated Obsidian vault construction from unstructured text — NLP pipelines to generate bidirectionally-linked knowledge graphs Python docxology" }, { "id": "software:docxology:qr_live_protocol", "type": "software", "title": "qr_live_protocol", "url": "https://github.com/docxology/qr_live_protocol", "summary": "QR code-based live protocol system for real-time data exchange and interactive session management", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "qr_live_protocol QR code-based live protocol system for real-time data exchange and interactive session management Python docxology" }, { "id": "software:docxology:template_autoscientists", "type": "software", "title": "template_autoscientists", "url": "https://github.com/docxology/template_autoscientists", "summary": "AutoScientists deterministic multi-agent scientific-discovery coordination harness · · Zenodo", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "template_autoscientists AutoScientists deterministic multi-agent scientific-discovery coordination harness · · Zenodo Python docxology" }, { "id": "software:docxology:template_newspaper", "type": "software", "title": "template_newspaper", "url": "https://github.com/docxology/template_newspaper", "summary": "The Triplicate data-driven large-format newspaper layout engine · · Zenodo", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "template_newspaper The Triplicate data-driven large-format newspaper layout engine · · Zenodo Python docxology" }, { "id": "software:docxology:ntqr_llm", "type": "software", "title": "ntqr_llm", "url": "https://github.com/docxology/ntqr_llm", "summary": "Algebraic NTQR evaluation study recovering LLM-persona accuracies from unlabeled votes · · Zenodo", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "ntqr_llm Algebraic NTQR evaluation study recovering LLM-persona accuracies from unlabeled votes · · Zenodo Python docxology" }, { "id": "software:docxology:itrace", "type": "software", "title": "itrace", "url": "https://github.com/docxology/itrace", "summary": "Verification-first webcam eye-movement analysis toolkit for gaze, saccades, pupillometry, and diagnostic-quality exports · · Zenodo", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "itrace Verification-first webcam eye-movement analysis toolkit for gaze, saccades, pupillometry, and diagnostic-quality exports · · Zenodo Python docxology" }, { "id": "software:docxology:ultralink-docx", "type": "software", "title": "ultralink-docx", "url": "https://github.com/docxology/ultralink-docx", "summary": "UltraLink document format tooling — linking, rendering, and transformation utilities for rich hyperlinked documents", "domain": "docxology", "tags": [ "software", "HTML", "docxology" ], "content": "ultralink-docx UltraLink document format tooling — linking, rendering, and transformation utilities for rich hyperlinked documents HTML docxology" }, { "id": "software:docxology:cognitive", "type": "software", "title": "cognitive", "url": "https://github.com/docxology/cognitive", "summary": "Cognitive Ecosystem Modeling Framework — Active Inference agents with Obsidian-compatible knowledge management, bidirectional graph validation, belief updating, and network visualization", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "cognitive Cognitive Ecosystem Modeling Framework — Active Inference agents with Obsidian-compatible knowledge management, bidirectional graph validation, belief updating, and network visualization Python docxology" }, { "id": "software:docxology:active_torchference", "type": "software", "title": "active_torchference", "url": "https://github.com/docxology/active_torchference", "summary": "PyTorch-based Active Inference implementations — GPU-accelerated variational inference and free energy minimization", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "active_torchference PyTorch-based Active Inference implementations — GPU-accelerated variational inference and free energy minimization Python docxology" }, { "id": "software:docxology:ant-pheromone", "type": "software", "title": "ant-pheromone", "url": "https://github.com/docxology/ant-pheromone", "summary": "Computational simulation of ant pheromone trail dynamics and stigmergic communication", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "ant-pheromone Computational simulation of ant pheromone trail dynamics and stigmergic communication Python docxology" }, { "id": "software:docxology:ant_stack", "type": "software", "title": "ant_stack", "url": "https://github.com/docxology/ant_stack", "summary": "The Ant Stack — layered computational model of collective ant-colony intelligence", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "ant_stack The Ant Stack — layered computational model of collective ant-colony intelligence Python docxology" }, { "id": "software:docxology:cohereants", "type": "software", "title": "cohereants", "url": "https://github.com/docxology/cohereants", "summary": "Computational research on insect infrared sensing and olfaction modeling · · Zenodo", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "cohereants Computational research on insect infrared sensing and olfaction modeling · · Zenodo Python docxology" }, { "id": "software:docxology:ento_linguistics", "type": "software", "title": "ento_linguistics", "url": "https://github.com/docxology/ento_linguistics", "summary": "Ento-Linguistics corpus pipeline — term extraction, terminology networks, semantic entropy, CACE scoring", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "ento_linguistics Ento-Linguistics corpus pipeline — term extraction, terminology networks, semantic entropy, CACE scoring Python docxology" }, { "id": "software:docxology:cognitive_case_diagrams", "type": "software", "title": "cognitive_case_diagrams", "url": "https://github.com/docxology/cognitive_case_diagrams", "summary": "Compositional linguistic case for cognitive modeling — categorical case systems, DisCoCat/DisCoCirc diagrams, tests and figures for the Active Inference Journal manuscript", "domain": "docxology", "tags": [ "software", "TeX", "docxology" ], "content": "cognitive_case_diagrams Compositional linguistic case for cognitive modeling — categorical case systems, DisCoCat/DisCoCirc diagrams, tests and figures for the Active Inference Journal manuscript TeX docxology" }, { "id": "software:docxology:Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference", "type": "software", "title": "Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference", "url": "https://github.com/docxology/Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference", "summary": "Active Inference-driven autonomous drone navigation in Microsoft AirSim simulation environment", "domain": "docxology", "tags": [ "software", "Julia", "docxology" ], "content": "Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference Active Inference-driven autonomous drone navigation in Microsoft AirSim simulation environment Julia docxology" }, { "id": "software:docxology:biol-1", "type": "software", "title": "biol-1", "url": "https://github.com/docxology/biol-1", "summary": "BIOL-1: General Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content", "domain": "docxology", "tags": [ "software", "HTML", "docxology" ], "content": "biol-1 BIOL-1: General Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content HTML docxology" }, { "id": "software:docxology:biol-8", "type": "software", "title": "biol-8", "url": "https://github.com/docxology/biol-8", "summary": "BIOL-8: Human Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content", "domain": "docxology", "tags": [ "software", "HTML", "docxology" ], "content": "biol-8 BIOL-8: Human Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content HTML docxology" }, { "id": "software:docxology:biology_textbook", "type": "software", "title": "biology_textbook", "url": "https://github.com/docxology/biology_textbook", "summary": "Open generative biology textbook — Markdown source, tested Python modules, programmatic figures; archived at Zenodo", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "biology_textbook Open generative biology textbook — Markdown source, tested Python modules, programmatic figures; archived at Zenodo Python docxology" }, { "id": "software:docxology:cascadia", "type": "software", "title": "cascadia", "url": "https://github.com/docxology/cascadia", "summary": "Cascadia bioregion modeling and data analysis tools", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "cascadia Cascadia bioregion modeling and data analysis tools Python docxology" }, { "id": "software:docxology:course", "type": "software", "title": "course", "url": "https://github.com/docxology/course", "summary": "Course materials framework for structured interdisciplinary learning modules", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "course Course materials framework for structured interdisciplinary learning modules Python docxology" }, { "id": "software:docxology:enactive_inference_model", "type": "software", "title": "enactive_inference_model", "url": "https://github.com/docxology/enactive_inference_model", "summary": "Three-level hierarchical enactive inference model of mental action — focused-attention meditation with expert/novice profiles; reproducible simulations and figures", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "enactive_inference_model Three-level hierarchical enactive inference model of mental action — focused-attention meditation with expert/novice profiles; reproducible simulations and figures Python docxology" }, { "id": "software:docxology:EvoJump", "type": "software", "title": "EvoJump", "url": "https://github.com/docxology/EvoJump", "summary": "Comprehensive Framework for Evolutionary Ontogenetic Analysis — modeling developmental trajectories and evolutionary dynamics", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "EvoJump Comprehensive Framework for Evolutionary Ontogenetic Analysis — modeling developmental trajectories and evolutionary dynamics Python docxology" }, { "id": "software:docxology:flick", "type": "software", "title": "flick", "url": "https://github.com/docxology/flick", "summary": "Lightweight Python tooling for rapid data flicking and processing pipelines", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "flick Lightweight Python tooling for rapid data flicking and processing pipelines Python docxology" }, { "id": "software:docxology:fuller-obsidian", "type": "software", "title": "fuller-obsidian", "url": "https://github.com/docxology/fuller-obsidian", "summary": "Obsidian vault dedicated to R. Buckminster Fuller's ideas — synergetics, geodesics, and design science", "domain": "docxology", "tags": [ "software", "", "docxology" ], "content": "fuller-obsidian Obsidian vault dedicated to R. Buckminster Fuller's ideas — synergetics, geodesics, and design science docxology" }, { "id": "software:docxology:godel_ivm", "type": "software", "title": "godel_ivm", "url": "https://github.com/docxology/godel_ivm", "summary": "Gödel numbering meets the IVM (Isotropic Vector Matrix) — formal encoding of geometric objects as prime products", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "godel_ivm Gödel numbering meets the IVM (Isotropic Vector Matrix) — formal encoding of geometric objects as prime products Python docxology" }, { "id": "software:docxology:goference", "type": "software", "title": "goference", "url": "https://github.com/docxology/goference", "summary": "Active Goference — production-ready Go framework for Active Inference autonomous agents; genuine variational inference, free energy minimization, POMDP policy planning via gonum", "domain": "docxology", "tags": [ "software", "Go", "docxology" ], "content": "goference Active Goference — production-ready Go framework for Active Inference autonomous agents; genuine variational inference, free energy minimization, POMDP policy planning via gonum Go docxology" }, { "id": "software:docxology:hhs-opendata", "type": "software", "title": "hhs-opendata", "url": "https://github.com/docxology/hhs-opendata", "summary": "Analysis of HHS (Department of Health and Human Services) open data — policy analytics and public-health data pipelines", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "hhs-opendata Analysis of HHS (Department of Health and Human Services) open data — policy analytics and public-health data pipelines Python docxology" }, { "id": "software:docxology:grateful_data", "type": "software", "title": "grateful_data", "url": "https://github.com/docxology/grateful_data", "summary": "The Music Never Stopped citation-bound Grateful Dead data compendium · · Zenodo", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "grateful_data The Music Never Stopped citation-bound Grateful Dead data compendium · · Zenodo Python docxology" }, { "id": "software:docxology:infra-calc", "type": "software", "title": "infra-calc", "url": "https://github.com/docxology/infra-calc", "summary": "Infrastructure calculator for estimating resource requirements and costs in multi-agent and AI systems", "domain": "docxology", "tags": [ "software", "JavaScript", "docxology" ], "content": "infra-calc Infrastructure calculator for estimating resource requirements and costs in multi-agent and AI systems JavaScript docxology" }, { "id": "software:docxology:markdown_decision_process", "type": "software", "title": "markdown_decision_process", "url": "https://github.com/docxology/markdown_decision_process", "summary": "Framework for Probabilistic Document Analysis — Markov Decision Process over Markdown artifacts for structured document reasoning", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "markdown_decision_process Framework for Probabilistic Document Analysis — Markov Decision Process over Markdown artifacts for structured document reasoning Python docxology" }, { "id": "software:docxology:mdkv", "type": "software", "title": "mdkv", "url": "https://github.com/docxology/mdkv", "summary": "MKV-like key-value format and methods for Markdown — structured metadata embedding in plain-text documents", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "mdkv MKV-like key-value format and methods for Markdown — structured metadata embedding in plain-text documents Python docxology" }, { "id": "software:docxology:p3if", "type": "software", "title": "p3if", "url": "https://github.com/docxology/p3if", "summary": "Properties, Processes, and Perspectives Inter-Framework (P3IF) — multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "p3if Properties, Processes, and Perspectives Inter-Framework (P3IF) — multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security Python docxology" }, { "id": "software:docxology:service", "type": "software", "title": "service", "url": "https://github.com/docxology/service", "summary": "Service-layer infrastructure and API tooling for Python-based research applications", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "service Service-layer infrastructure and API tooling for Python-based research applications Python docxology" }, { "id": "software:docxology:snake", "type": "software", "title": "snake", "url": "https://github.com/docxology/snake", "summary": "Classic snake game implemented in Python — used for testing multi-agent and reinforcement learning algorithms", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "snake Classic snake game implemented in Python — used for testing multi-agent and reinforcement learning algorithms Python docxology" }, { "id": "software:docxology:steganographer", "type": "software", "title": "steganographer", "url": "https://github.com/docxology/steganographer", "summary": "High-performance Rust tool for embedding BLAKE3+Ed25519 cryptographic signatures and visible watermarks into live video/audio via LSB steganography; four Rust crates, 132 tests, GStreamer integration", "domain": "docxology", "tags": [ "software", "Rust", "docxology" ], "content": "steganographer High-performance Rust tool for embedding BLAKE3+Ed25519 cryptographic signatures and visible watermarks into live video/audio via LSB steganography; four Rust crates, 132 tests, GStreamer integration Rust docxology" }, { "id": "software:docxology:template_textbook", "type": "software", "title": "template_textbook", "url": "https://github.com/docxology/template_textbook", "summary": "Modular fillable scaffold for book-length technical works · · Zenodo", "domain": "docxology", "tags": [ "software", "HTML", "docxology" ], "content": "template_textbook Modular fillable scaffold for book-length technical works · · Zenodo HTML docxology" }, { "id": "software:docxology:blake_jiang", "type": "software", "title": "blake_jiang", "url": "https://github.com/docxology/blake_jiang", "summary": "William Blake, Professor Jiang, and the Architecture of Intelligence — AI-augmented scholarly response to Game Theory #24 with Blake, Jiang, and Active Inference framing", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "blake_jiang William Blake, Professor Jiang, and the Architecture of Intelligence — AI-augmented scholarly response to Game Theory #24 with Blake, Jiang, and Active Inference framing Python docxology" }, { "id": "software:docxology:symergetics", "type": "software", "title": "symergetics", "url": "https://github.com/docxology/symergetics", "summary": "Symbolic Synergetics — computer algebra and formal symbolic systems for Buckminster Fuller's synergetics mathematics", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "symergetics Symbolic Synergetics — computer algebra and formal symbolic systems for Buckminster Fuller's synergetics mathematics Python docxology" }, { "id": "software:docxology:transformer", "type": "software", "title": "transformer", "url": "https://github.com/docxology/transformer", "summary": "Transformer architecture explorations — attention mechanisms and architectural variants for Active Inference research", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "transformer Transformer architecture explorations — attention mechanisms and architectural variants for Active Inference research Python docxology" }, { "id": "software:ActiveInferenceInstitute:ActiveInferenceJournal", "type": "software", "title": "ActiveInferenceJournal", "url": "https://github.com/ActiveInferenceInstitute/ActiveInferenceJournal", "summary": "Content hub for the Active Inference Journal — 500+ video transcripts, stream archives, and multimedia publishing infrastructure for the Institute's primary educational output", "domain": "active-inference-institute", "tags": [ "software", "HTML", "ActiveInferenceInstitute" ], "content": "ActiveInferenceJournal Content hub for the Active Inference Journal — 500+ video transcripts, stream archives, and multimedia publishing infrastructure for the Institute's primary educational output HTML ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:ActiveBlockference", "type": "software", "title": "ActiveBlockference", "url": "https://github.com/ActiveInferenceInstitute/ActiveBlockference", "summary": "Active Inference agents in cadCAD block-based simulation — formal agent-based modeling using complex-systems simulation framework", "domain": "active-inference-institute", "tags": [ "software", "Jupyter", "ActiveInferenceInstitute" ], "content": "ActiveBlockference Active Inference agents in cadCAD block-based simulation — formal agent-based modeling using complex-systems simulation framework Jupyter ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:ActiveInferAnts", "type": "software", "title": "ActiveInferAnts", "url": "https://github.com/ActiveInferenceInstitute/ActiveInferAnts", "summary": "Active Inference models for/of ants across 32+ programming languages — multi-language reference implementation of stigmergic Active Inference", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "ActiveInferAnts Active Inference models for/of ants across 32+ programming languages — multi-language reference implementation of stigmergic Active Inference Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:GeneralizedNotationNotation", "type": "software", "title": "GeneralizedNotationNotation", "url": "https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation", "summary": "GNN — formal notation standard for specifying Active Inference generative models; JSON/YAML schema, validators, and transpilers to Python, Julia, and MATLAB · Zenodo software", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "GeneralizedNotationNotation GNN — formal notation standard for specifying Active Inference generative models; JSON/YAML schema, validators, and transpilers to Python, Julia, and MATLAB · Zenodo software Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:fep_lean", "type": "software", "title": "fep_lean", "url": "https://github.com/ActiveInferenceInstitute/fep_lean", "summary": "Lean 4 / Mathlib4 formalization of FEP-related mathematics — 50-topic sorry-free catalog, Hermes/OpenGauss LLM drafting, zero-mock verification, manuscript pipeline · · Zenodo", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "fep_lean Lean 4 / Mathlib4 formalization of FEP-related mathematics — 50-topic sorry-free catalog, Hermes/OpenGauss LLM drafting, zero-mock verification, manuscript pipeline · · Zenodo Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:cognitive", "type": "software", "title": "cognitive", "url": "https://github.com/ActiveInferenceInstitute/cognitive", "summary": "Cognitive modeling and simulation tools — multi-agent Active Inference environments, benchmarks, and visualization", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "cognitive Cognitive modeling and simulation tools — multi-agent Active Inference environments, benchmarks, and visualization Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Active_Inference_Ontology", "type": "software", "title": "Active_Inference_Ontology", "url": "https://github.com/ActiveInferenceInstitute/Active_Inference_Ontology", "summary": "Formal OWL/RDF ontology for Active Inference — defines classes, properties, and axioms for free energy principle concepts", "domain": "active-inference-institute", "tags": [ "software", "", "ActiveInferenceInstitute" ], "content": "Active_Inference_Ontology Formal OWL/RDF ontology for Active Inference — defines classes, properties, and axioms for free energy principle concepts ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Journal-Utilities", "type": "software", "title": "Journal-Utilities", "url": "https://github.com/ActiveInferenceInstitute/Journal-Utilities", "summary": "Transcription, processing, and publishing pipelines for the Active Inference Journal — Whisper-based download, transcription, RAG/knowledge-graph, and export utilities · Zenodo release", "domain": "active-inference-institute", "tags": [ "software", "HTML", "ActiveInferenceInstitute" ], "content": "Journal-Utilities Transcription, processing, and publishing pipelines for the Active Inference Journal — Whisper-based download, transcription, RAG/knowledge-graph, and export utilities · Zenodo release HTML ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Symposium", "type": "software", "title": "Symposium", "url": "https://github.com/ActiveInferenceInstitute/Symposium", "summary": "Applied Active Inference Symposium materials — talks, workshops, proceedings, and collaborative session artifacts from annual Applied AIF symposia", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "Symposium Applied Active Inference Symposium materials — talks, workshops, proceedings, and collaborative session artifacts from annual Applied AIF symposia Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:ActiveInferenceCategoryTheory", "type": "software", "title": "ActiveInferenceCategoryTheory", "url": "https://github.com/ActiveInferenceInstitute/ActiveInferenceCategoryTheory", "summary": "Formal categorical foundations for Active Inference — string diagrams, functorial semantics, and compositional models using category theory", "domain": "active-inference-institute", "tags": [ "software", "", "ActiveInferenceInstitute" ], "content": "ActiveInferenceCategoryTheory Formal categorical foundations for Active Inference — string diagrams, functorial semantics, and compositional models using category theory ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:CEREBRUM", "type": "software", "title": "CEREBRUM", "url": "https://github.com/ActiveInferenceInstitute/CEREBRUM", "summary": "Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling — grammatical case framework for compositional cognitive models · Zenodo", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "CEREBRUM Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling — grammatical case framework for compositional cognitive models · Zenodo Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:GEO-INFER", "type": "software", "title": "GEO-INFER", "url": "https://github.com/ActiveInferenceInstitute/GEO-INFER", "summary": "Geospatial Active Inference — applying free energy minimization to geographic systems, spatial planning, and bioregional intelligence", "domain": "active-inference-institute", "tags": [ "software", "HTML", "ActiveInferenceInstitute" ], "content": "GEO-INFER Geospatial Active Inference — applying free energy minimization to geographic systems, spatial planning, and bioregional intelligence HTML ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:AEOS", "type": "software", "title": "AEOS", "url": "https://github.com/ActiveInferenceInstitute/AEOS", "summary": "Active Entity Ontology for Science — OWL ontology for representing active entities, their actions, and causal relationships in scientific models", "domain": "active-inference-institute", "tags": [ "software", "", "ActiveInferenceInstitute" ], "content": "AEOS Active Entity Ontology for Science — OWL ontology for representing active entities, their actions, and causal relationships in scientific models ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:courses", "type": "software", "title": "courses", "url": "https://github.com/ActiveInferenceInstitute/courses", "summary": "Structured Active Inference learning courses — cohort-based curriculum materials, exercises, and collaborative learning artifacts", "domain": "active-inference-institute", "tags": [ "software", "HTML", "ActiveInferenceInstitute" ], "content": "courses Structured Active Inference learning courses — cohort-based curriculum materials, exercises, and collaborative learning artifacts HTML ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Research-Discovery-Engine", "type": "software", "title": "Research-Discovery-Engine", "url": "https://github.com/ActiveInferenceInstitute/Research-Discovery-Engine", "summary": "AI-driven research synthesis and navigation — semantic search, citation graph analysis, and cross-domain connection discovery across the Active Inference literature", "domain": "active-inference-institute", "tags": [ "software", "HTML", "ActiveInferenceInstitute" ], "content": "Research-Discovery-Engine AI-driven research synthesis and navigation — semantic search, citation graph analysis, and cross-domain connection discovery across the Active Inference literature HTML ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Parr_et_al_2022_ActInf_Textbook", "type": "software", "title": "Parr_et_al_2022_ActInf_Textbook", "url": "https://github.com/ActiveInferenceInstitute/Parr_et_al_2022_ActInf_Textbook", "summary": "Active Inference Textbook Study Group — code, exercises, and reading notes accompanying Parr, Pezzulo & Friston (2022)", "domain": "active-inference-institute", "tags": [ "software", "Julia", "ActiveInferenceInstitute" ], "content": "Parr_et_al_2022_ActInf_Textbook Active Inference Textbook Study Group — code, exercises, and reading notes accompanying Parr, Pezzulo & Friston (2022) Julia ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Biofirm", "type": "software", "title": "Biofirm", "url": "https://github.com/ActiveInferenceInstitute/Biofirm", "summary": "Bioregional Active Inference for organizational stewardship — applying free energy minimization to ecological and community governance systems", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "Biofirm Bioregional Active Inference for organizational stewardship — applying free energy minimization to ecological and community governance systems Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Start", "type": "software", "title": "Start", "url": "https://github.com/ActiveInferenceInstitute/Start", "summary": "Institute onboarding hub — getting-started guides, contributor pathways, project index, and orientation materials for new participants", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "Start Institute onboarding hub — getting-started guides, contributor pathways, project index, and orientation materials for new participants Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Knowledge-Engineering", "type": "software", "title": "Knowledge-Engineering", "url": "https://github.com/ActiveInferenceInstitute/Knowledge-Engineering", "summary": "Knowledge engineering tools and workflows — ontology alignment, concept mapping, and structured knowledge-base construction for Active Inference", "domain": "active-inference-institute", "tags": [ "software", "Jupyter", "ActiveInferenceInstitute" ], "content": "Knowledge-Engineering Knowledge engineering tools and workflows — ontology alignment, concept mapping, and structured knowledge-base construction for Active Inference Jupyter ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:ActInf_RxInfer", "type": "software", "title": "ActInf_RxInfer", "url": "https://github.com/ActiveInferenceInstitute/ActInf_RxInfer", "summary": "Active Inference with RxInfer.jl — Julia-based reactive message passing for efficient Bayesian inference in Active Inference models", "domain": "active-inference-institute", "tags": [ "software", "", "ActiveInferenceInstitute" ], "content": "ActInf_RxInfer Active Inference with RxInfer.jl — Julia-based reactive message passing for efficient Bayesian inference in Active Inference models ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:pymcp", "type": "software", "title": "pymcp", "url": "https://github.com/ActiveInferenceInstitute/pymcp", "summary": "PyMCP — Model Context Protocol bridge for PyMDP, enabling Active Inference agents to interoperate with MCP-compatible AI tooling", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "pymcp PyMCP — Model Context Protocol bridge for PyMDP, enabling Active Inference agents to interoperate with MCP-compatible AI tooling Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:GEN24", "type": "software", "title": "GEN24", "url": "https://github.com/ActiveInferenceInstitute/GEN24", "summary": "GEN-24 working project — collaborative generative systems research from the 2024 active inference cohort", "domain": "active-inference-institute", "tags": [ "software", "Jupyter", "ActiveInferenceInstitute" ], "content": "GEN24 GEN-24 working project — collaborative generative systems research from the 2024 active inference cohort Jupyter ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:NoOrg", "type": "software", "title": "NoOrg", "url": "https://github.com/ActiveInferenceInstitute/NoOrg", "summary": "NoOrg is a Real Org — experimental organizational infrastructure and governance frameworks for decentralized scientific institutions", "domain": "active-inference-institute", "tags": [ "software", "HTML", "ActiveInferenceInstitute" ], "content": "NoOrg NoOrg is a Real Org — experimental organizational infrastructure and governance frameworks for decentralized scientific institutions HTML ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:ultralink", "type": "software", "title": "ultralink", "url": "https://github.com/ActiveInferenceInstitute/ultralink", "summary": "UltraLink — framework for linking, rendering, and transforming richly cross-referenced documents across multiple output formats", "domain": "active-inference-institute", "tags": [ "software", "", "ActiveInferenceInstitute" ], "content": "ultralink UltraLink — framework for linking, rendering, and transforming richly cross-referenced documents across multiple output formats ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:ActiveInferenceImplementations", "type": "software", "title": "ActiveInferenceImplementations", "url": "https://github.com/ActiveInferenceInstitute/ActiveInferenceImplementations", "summary": "Learning and exploring probabilistic inference — beginner-accessible Jupyter notebooks for Active Inference from first principles", "domain": "active-inference-institute", "tags": [ "software", "Jupyter", "ActiveInferenceInstitute" ], "content": "ActiveInferenceImplementations Learning and exploring probabilistic inference — beginner-accessible Jupyter notebooks for Active Inference from first principles Jupyter ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:ATLAS", "type": "software", "title": "ATLAS", "url": "https://github.com/ActiveInferenceInstitute/ATLAS", "summary": "Question-Oriented Pattern Languages for Knowledge Management — structured templates for navigating complex scientific knowledge spaces", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "ATLAS Question-Oriented Pattern Languages for Knowledge Management — structured templates for navigating complex scientific knowledge spaces Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Bots", "type": "software", "title": "Bots", "url": "https://github.com/ActiveInferenceInstitute/Bots", "summary": "Institute bot infrastructure — automation, notification, and community management bots for the Active Inference Institute's platforms", "domain": "active-inference-institute", "tags": [ "software", "", "ActiveInferenceInstitute" ], "content": "Bots Institute bot infrastructure — automation, notification, and community management bots for the Active Inference Institute's platforms ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:Garden-of-Iris", "type": "software", "title": "Garden-of-Iris", "url": "https://github.com/ActiveInferenceInstitute/Garden-of-Iris", "summary": "Interactive visualization garden — generative art and data-visualization experiments exploring Active Inference dynamics", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "Garden-of-Iris Interactive visualization garden — generative art and data-visualization experiments exploring Active Inference dynamics Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:gen25", "type": "software", "title": "gen25", "url": "https://github.com/ActiveInferenceInstitute/gen25", "summary": "GEN-25 working project — generative systems and collaborative research from the 2025 active inference cohort", "domain": "active-inference-institute", "tags": [ "software", "", "ActiveInferenceInstitute" ], "content": "gen25 GEN-25 working project — generative systems and collaborative research from the 2025 active inference cohort ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:gnn", "type": "software", "title": "gnn", "url": "https://github.com/ActiveInferenceInstitute/gnn", "summary": "Generalized Notation Notation v2 — next-generation GNN specification with extended model classes and improved toolchain", "domain": "active-inference-institute", "tags": [ "software", "", "ActiveInferenceInstitute" ], "content": "gnn Generalized Notation Notation v2 — next-generation GNN specification with extended model classes and improved toolchain ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:ISSS", "type": "software", "title": "ISSS", "url": "https://github.com/ActiveInferenceInstitute/ISSS", "summary": "International Society for the Systems Sciences collaboration — joint research and educational materials bridging Active Inference and systems science", "domain": "active-inference-institute", "tags": [ "software", "Python", "ActiveInferenceInstitute" ], "content": "ISSS International Society for the Systems Sciences collaboration — joint research and educational materials bridging Active Inference and systems science Python ActiveInferenceInstitute" }, { "id": "software:ActiveInferenceInstitute:topp", "type": "software", "title": "topp", "url": "https://github.com/ActiveInferenceInstitute/topp", "summary": "The Open Problems Project — curated registry of open scientific problems in Active Inference and the free energy principle", "domain": "active-inference-institute", "tags": [ "software", "TeX", "ActiveInferenceInstitute" ], "content": "topp The Open Problems Project — curated registry of open scientific problems in Active Inference and the free energy principle TeX ActiveInferenceInstitute" }, { "id": "github-repo:ActiveInferenceInstitute/A2A", "type": "github_repository", "title": "ActiveInferenceInstitute/A2A", "url": "https://github.com/ActiveInferenceInstitute/A2A", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/A2A ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/act_inf_metaanalysis", "type": "github_repository", "title": "ActiveInferenceInstitute/act_inf_metaanalysis", "url": "https://github.com/ActiveInferenceInstitute/act_inf_metaanalysis", "summary": "A computational meta-analysis of the Active Inference literature. An automated LLM pipeline extracts assertions from 849 papers across theory, tools, and domains, structuring them as nanopublications. By mapping these into a citation-weighted knowledge graph, this project provides a reproducible, living review of hypothesis-level consensus.", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "TeX", "ActiveInferenceInstitute", "recent" ], "content": "ActiveInferenceInstitute/act_inf_metaanalysis A computational meta-analysis of the Active Inference literature. An automated LLM pipeline extracts assertions from 849 papers across theory, tools, and domains, structuring them as nanopublications. By mapping these into a citation-weighted knowledge graph, this project provides a reproducible, living review of hypothesis-level consensus. TeX ActiveInferenceInstitute recent" }, { "id": "github-repo:ActiveInferenceInstitute/ActInf_RxInfer", "type": "github_repository", "title": "ActiveInferenceInstitute/ActInf_RxInfer", "url": "https://github.com/ActiveInferenceInstitute/ActInf_RxInfer", "summary": "Active Inference and RxInfer.jl", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/ActInf_RxInfer Active Inference and RxInfer.jl ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/action-oriented", "type": "github_repository", "title": "ActiveInferenceInstitute/action-oriented", "url": "https://github.com/ActiveInferenceInstitute/action-oriented", "summary": "Repository for \"Learning action-oriented models through active inference\"", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/action-oriented Repository for \"Learning action-oriented models through active inference\" ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/Active_Inference_Ontology", "type": "github_repository", "title": "ActiveInferenceInstitute/Active_Inference_Ontology", "url": "https://github.com/ActiveInferenceInstitute/Active_Inference_Ontology", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/Active_Inference_Ontology ActiveInferenceInstitute active active-inference inference ontology curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/ActiveBlockference", "type": "github_repository", "title": "ActiveInferenceInstitute/ActiveBlockference", "url": "https://github.com/ActiveInferenceInstitute/ActiveBlockference", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Jupyter Notebook", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/ActiveBlockference Jupyter Notebook ActiveInferenceInstitute active active-inference cadcad inference simulation curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/ActiveInferAnts", "type": "github_repository", "title": "ActiveInferenceInstitute/ActiveInferAnts", "url": "https://github.com/ActiveInferenceInstitute/ActiveInferAnts", "summary": "Active Inference models of/for Ants", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/ActiveInferAnts Active Inference models of/for Ants Python ActiveInferenceInstitute curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/ActiveInferenceCategoryTheory", "type": "github_repository", "title": "ActiveInferenceInstitute/ActiveInferenceCategoryTheory", "url": "https://github.com/ActiveInferenceInstitute/ActiveInferenceCategoryTheory", "summary": "Active Inference & Category Theory", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/ActiveInferenceCategoryTheory Active Inference & Category Theory ActiveInferenceInstitute active active-inference category category-theory inference curated" }, { "id": "github-repo:ActiveInferenceInstitute/ActiveInferenceImplementations", "type": "github_repository", "title": "ActiveInferenceInstitute/ActiveInferenceImplementations", "url": "https://github.com/ActiveInferenceInstitute/ActiveInferenceImplementations", "summary": "For learning and exploring Probabilistic Inference", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Jupyter Notebook", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/ActiveInferenceImplementations For learning and exploring Probabilistic Inference Jupyter Notebook ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/ActiveInferenceJournal", "type": "github_repository", "title": "ActiveInferenceInstitute/ActiveInferenceJournal", "url": "https://github.com/ActiveInferenceInstitute/ActiveInferenceJournal", "summary": "Content of the Active Inference Journal", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "HTML", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/ActiveInferenceJournal Content of the Active Inference Journal HTML ActiveInferenceInstitute curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/AEOS", "type": "github_repository", "title": "ActiveInferenceInstitute/AEOS", "url": "https://github.com/ActiveInferenceInstitute/AEOS", "summary": "Active Entity Ontology for Science ", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/AEOS Active Entity Ontology for Science ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/aii-org", "type": "github_repository", "title": "ActiveInferenceInstitute/aii-org", "url": "https://github.com/ActiveInferenceInstitute/aii-org", "summary": "Active Inference Institute organizational website. ", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "HTML", "ActiveInferenceInstitute", "recent" ], "content": "ActiveInferenceInstitute/aii-org Active Inference Institute organizational website. HTML ActiveInferenceInstitute recent" }, { "id": "github-repo:ActiveInferenceInstitute/ants", "type": "github_repository", "title": "ActiveInferenceInstitute/ants", "url": "https://github.com/ActiveInferenceInstitute/ants", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/ants ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/ATLAS", "type": "github_repository", "title": "ActiveInferenceInstitute/ATLAS", "url": "https://github.com/ActiveInferenceInstitute/ATLAS", "summary": "ATLAS ", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/ATLAS ATLAS ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/Biofirm", "type": "github_repository", "title": "ActiveInferenceInstitute/Biofirm", "url": "https://github.com/ActiveInferenceInstitute/Biofirm", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/Biofirm Python ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/Bots", "type": "github_repository", "title": "ActiveInferenceInstitute/Bots", "url": "https://github.com/ActiveInferenceInstitute/Bots", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/Bots ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/CEREBRUM", "type": "github_repository", "title": "ActiveInferenceInstitute/CEREBRUM", "url": "https://github.com/ActiveInferenceInstitute/CEREBRUM", "summary": "CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/CEREBRUM CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling Python ActiveInferenceInstitute curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/cognitive", "type": "github_repository", "title": "ActiveInferenceInstitute/cognitive", "url": "https://github.com/ActiveInferenceInstitute/cognitive", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/cognitive Python ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/courses", "type": "github_repository", "title": "ActiveInferenceInstitute/courses", "url": "https://github.com/ActiveInferenceInstitute/courses", "summary": "Courses for learning Active Inference", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "HTML", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/courses Courses for learning Active Inference HTML ActiveInferenceInstitute curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/DeepActiveInference", "type": "github_repository", "title": "ActiveInferenceInstitute/DeepActiveInference", "url": "https://github.com/ActiveInferenceInstitute/DeepActiveInference", "summary": "Code for the paper Deep Active Inference as Variational Policy Gradients.", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/DeepActiveInference Code for the paper Deep Active Inference as Variational Policy Gradients. ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/entropix", "type": "github_repository", "title": "ActiveInferenceInstitute/entropix", "url": "https://github.com/ActiveInferenceInstitute/entropix", "summary": "Entropy Based Sampling and Parallel CoT Decoding ", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/entropix Entropy Based Sampling and Parallel CoT Decoding ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/fabric", "type": "github_repository", "title": "ActiveInferenceInstitute/fabric", "url": "https://github.com/ActiveInferenceInstitute/fabric", "summary": "fabric is an open-source framework for augmenting humans using AI. It provides a modular framework for solving specific problems using a crowdsourced set of AI prompts that can be used anywhere.", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Go", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/fabric fabric is an open-source framework for augmenting humans using AI. It provides a modular framework for solving specific problems using a crowdsourced set of AI prompts that can be used anywhere. Go ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/FEP_Active_Inference_Papers", "type": "github_repository", "title": "ActiveInferenceInstitute/FEP_Active_Inference_Papers", "url": "https://github.com/ActiveInferenceInstitute/FEP_Active_Inference_Papers", "summary": "A repository for major/influential FEP and active inference papers.", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/FEP_Active_Inference_Papers A repository for major/influential FEP and active inference papers. ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/fep_lean", "type": "github_repository", "title": "ActiveInferenceInstitute/fep_lean", "url": "https://github.com/ActiveInferenceInstitute/fep_lean", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/fep_lean Python ActiveInferenceInstitute curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/FEPS", "type": "github_repository", "title": "ActiveInferenceInstitute/FEPS", "url": "https://github.com/ActiveInferenceInstitute/FEPS", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/FEPS ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/Flowise", "type": "github_repository", "title": "ActiveInferenceInstitute/Flowise", "url": "https://github.com/ActiveInferenceInstitute/Flowise", "summary": "Drag & drop UI to build your customized LLM flow", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/Flowise Drag & drop UI to build your customized LLM flow ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/fundamentals", "type": "github_repository", "title": "ActiveInferenceInstitute/fundamentals", "url": "https://github.com/ActiveInferenceInstitute/fundamentals", "summary": "Unofficial repo for materials and code related to \"Fundamentals of Active Inference\" (Namjoshi 2026). ", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "recent" ], "content": "ActiveInferenceInstitute/fundamentals Unofficial repo for materials and code related to \"Fundamentals of Active Inference\" (Namjoshi 2026). Python ActiveInferenceInstitute recent" }, { "id": "github-repo:ActiveInferenceInstitute/Garden-of-Iris", "type": "github_repository", "title": "ActiveInferenceInstitute/Garden-of-Iris", "url": "https://github.com/ActiveInferenceInstitute/Garden-of-Iris", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/Garden-of-Iris ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/GEN24", "type": "github_repository", "title": "ActiveInferenceInstitute/GEN24", "url": "https://github.com/ActiveInferenceInstitute/GEN24", "summary": "Working/Exploring branch for GEN-24 project https://coda.io/d/Active-Blockference_dIvNESFmyj6/GEN-24_su2DYdSx#_luRI0xVN", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Jupyter Notebook", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/GEN24 Working/Exploring branch for GEN-24 project https://coda.io/d/Active-Blockference_dIvNESFmyj6/GEN-24_su2DYdSx#_luRI0xVN Jupyter Notebook ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/gen25", "type": "github_repository", "title": "ActiveInferenceInstitute/gen25", "url": "https://github.com/ActiveInferenceInstitute/gen25", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/gen25 ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/GeneralizedNotationNotation", "type": "github_repository", "title": "ActiveInferenceInstitute/GeneralizedNotationNotation", "url": "https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Pkl", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/GeneralizedNotationNotation Pkl ActiveInferenceInstitute active active-inference active-inference-notation inference curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/generative_agents", "type": "github_repository", "title": "ActiveInferenceInstitute/generative_agents", "url": "https://github.com/ActiveInferenceInstitute/generative_agents", "summary": "Generative Agents: Interactive Simulacra of Human Behavior", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/generative_agents Generative Agents: Interactive Simulacra of Human Behavior ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/Genesis", "type": "github_repository", "title": "ActiveInferenceInstitute/Genesis", "url": "https://github.com/ActiveInferenceInstitute/Genesis", "summary": "A generative world for general-purpose robotics & embodied AI learning.", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/Genesis A generative world for general-purpose robotics & embodied AI learning. ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/GEO-INFER", "type": "github_repository", "title": "ActiveInferenceInstitute/GEO-INFER", "url": "https://github.com/ActiveInferenceInstitute/GEO-INFER", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "HTML", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/GEO-INFER HTML ActiveInferenceInstitute curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/gnn", "type": "github_repository", "title": "ActiveInferenceInstitute/gnn", "url": "https://github.com/ActiveInferenceInstitute/gnn", "summary": "generalized notation notation", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/gnn generalized notation notation ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/institute_website", "type": "github_repository", "title": "ActiveInferenceInstitute/institute_website", "url": "https://github.com/ActiveInferenceInstitute/institute_website", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "HTML", "ActiveInferenceInstitute", "recent" ], "content": "ActiveInferenceInstitute/institute_website HTML ActiveInferenceInstitute recent" }, { "id": "github-repo:ActiveInferenceInstitute/ISSS", "type": "github_repository", "title": "ActiveInferenceInstitute/ISSS", "url": "https://github.com/ActiveInferenceInstitute/ISSS", "summary": "ISSS", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/ISSS ISSS Python ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/jock-lang", "type": "github_repository", "title": "ActiveInferenceInstitute/jock-lang", "url": "https://github.com/ActiveInferenceInstitute/jock-lang", "summary": "A simple scripting language that compiles to Nock.", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork", "recent" ], "content": "ActiveInferenceInstitute/jock-lang A simple scripting language that compiles to Nock. ActiveInferenceInstitute fork recent" }, { "id": "github-repo:ActiveInferenceInstitute/Journal-Utilities", "type": "github_repository", "title": "ActiveInferenceInstitute/Journal-Utilities", "url": "https://github.com/ActiveInferenceInstitute/Journal-Utilities", "summary": "Utilities and Documentation for creating contents for the Active Inference Journal", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "HTML", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/Journal-Utilities Utilities and Documentation for creating contents for the Active Inference Journal HTML ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/Knowledge-Engineering", "type": "github_repository", "title": "ActiveInferenceInstitute/Knowledge-Engineering", "url": "https://github.com/ActiveInferenceInstitute/Knowledge-Engineering", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Jupyter Notebook", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/Knowledge-Engineering Jupyter Notebook ActiveInferenceInstitute curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/metta", "type": "github_repository", "title": "ActiveInferenceInstitute/metta", "url": "https://github.com/ActiveInferenceInstitute/metta", "summary": "A reinforcement learning codebase focusing on the emergence of cooperation and alignment in multi-agent AI systems.", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/metta A reinforcement learning codebase focusing on the emergence of cooperation and alignment in multi-agent AI systems. ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/NoOrg", "type": "github_repository", "title": "ActiveInferenceInstitute/NoOrg", "url": "https://github.com/ActiveInferenceInstitute/NoOrg", "summary": "NoOrg is a Real Org", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "HTML", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/NoOrg NoOrg is a Real Org HTML ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/Parr_et_al_2022_ActInf_Textbook", "type": "github_repository", "title": "ActiveInferenceInstitute/Parr_et_al_2022_ActInf_Textbook", "url": "https://github.com/ActiveInferenceInstitute/Parr_et_al_2022_ActInf_Textbook", "summary": "Active Inference Textbook Group", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Julia", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/Parr_et_al_2022_ActInf_Textbook Active Inference Textbook Group Julia ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/policy_entanglement", "type": "github_repository", "title": "ActiveInferenceInstitute/policy_entanglement", "url": "https://github.com/ActiveInferenceInstitute/policy_entanglement", "summary": "Policy Entanglement in Active Inference v1.0.0", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "recent" ], "content": "ActiveInferenceInstitute/policy_entanglement Policy Entanglement in Active Inference v1.0.0 Python ActiveInferenceInstitute recent" }, { "id": "github-repo:ActiveInferenceInstitute/pymcp", "type": "github_repository", "title": "ActiveInferenceInstitute/pymcp", "url": "https://github.com/ActiveInferenceInstitute/pymcp", "summary": "PyMCP -- MCP for PyMDP", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/pymcp PyMCP -- MCP for PyMDP Python ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/pymdp", "type": "github_repository", "title": "ActiveInferenceInstitute/pymdp", "url": "https://github.com/ActiveInferenceInstitute/pymdp", "summary": "A Python implementation of active inference for Markov Decision Processes", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/pymdp A Python implementation of active inference for Markov Decision Processes Python ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/Research-Discovery-Engine", "type": "github_repository", "title": "ActiveInferenceInstitute/Research-Discovery-Engine", "url": "https://github.com/ActiveInferenceInstitute/Research-Discovery-Engine", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "HTML", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/Research-Discovery-Engine HTML ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/rl-inference", "type": "github_repository", "title": "ActiveInferenceInstitute/rl-inference", "url": "https://github.com/ActiveInferenceInstitute/rl-inference", "summary": "Reinforcement Learning through Active Inference", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "fork" ], "content": "ActiveInferenceInstitute/rl-inference Reinforcement Learning through Active Inference ActiveInferenceInstitute fork" }, { "id": "github-repo:ActiveInferenceInstitute/Start", "type": "github_repository", "title": "ActiveInferenceInstitute/Start", "url": "https://github.com/ActiveInferenceInstitute/Start", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/Start Python ActiveInferenceInstitute curated" }, { "id": "github-repo:ActiveInferenceInstitute/Symposium", "type": "github_repository", "title": "ActiveInferenceInstitute/Symposium", "url": "https://github.com/ActiveInferenceInstitute/Symposium", "summary": "ActiveInferenceInstitute repository", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "Python", "ActiveInferenceInstitute", "curated", "recent" ], "content": "ActiveInferenceInstitute/Symposium Python ActiveInferenceInstitute curated recent" }, { "id": "github-repo:ActiveInferenceInstitute/topp", "type": "github_repository", "title": "ActiveInferenceInstitute/topp", "url": "https://github.com/ActiveInferenceInstitute/topp", "summary": "The Open Problems Project", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated", "fork" ], "content": "ActiveInferenceInstitute/topp The Open Problems Project ActiveInferenceInstitute curated fork" }, { "id": "github-repo:ActiveInferenceInstitute/ultralink", "type": "github_repository", "title": "ActiveInferenceInstitute/ultralink", "url": "https://github.com/ActiveInferenceInstitute/ultralink", "summary": "Framework for Linking, Rendering, and More", "domain": "ActiveInferenceInstitute", "tags": [ "github", "repository", "", "ActiveInferenceInstitute", "curated" ], "content": "ActiveInferenceInstitute/ultralink Framework for Linking, Rendering, and More ActiveInferenceInstitute curated" }, { "id": "github-repo:docxology/10-Bins-template", "type": "github_repository", "title": "docxology/10-Bins-template", "url": "https://github.com/docxology/10-Bins-template", "summary": "How to organize your personal files and directories ", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/10-Bins-template How to organize your personal files and directories docxology fork" }, { "id": "github-repo:docxology/actinf_varsynth", "type": "github_repository", "title": "docxology/actinf_varsynth", "url": "https://github.com/docxology/actinf_varsynth", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/actinf_varsynth docxology fork" }, { "id": "github-repo:docxology/active-inference-pocket-lab", "type": "github_repository", "title": "docxology/active-inference-pocket-lab", "url": "https://github.com/docxology/active-inference-pocket-lab", "summary": "Active Inference Pocket Lab — portable simulation and learning environment for Active Inference experiments", "domain": "docxology", "tags": [ "github", "repository", "JavaScript", "docxology", "recent" ], "content": "docxology/active-inference-pocket-lab Active Inference Pocket Lab — portable simulation and learning environment for Active Inference experiments JavaScript docxology active-inference bayesian-modeling education pocket-lab python research simulation recent" }, { "id": "github-repo:docxology/active-inference-sim-lab", "type": "github_repository", "title": "docxology/active-inference-sim-lab", "url": "https://github.com/docxology/active-inference-sim-lab", "summary": "Lightweight toolkit for building active inference agents based on the Free Energy Principle. Includes C++ core for performance, Python bindings for ease of use, and integration with popular RL environments. Achieves human-level Atari performance with 10x less data than PPO.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/active-inference-sim-lab Lightweight toolkit for building active inference agents based on the Free Energy Principle. Includes C++ core for performance, Python bindings for ease of use, and integration with popular RL environments. Achieves human-level Atari performance with 10x less data than PPO. Python docxology fork" }, { "id": "github-repo:docxology/active_inference", "type": "github_repository", "title": "docxology/active_inference", "url": "https://github.com/docxology/active_inference", "summary": "Active Inference for, with, by, Generative AI. ", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/active_inference Active Inference for, with, by, Generative AI. Python docxology curated" }, { "id": "github-repo:docxology/Active_Inference_for_Fun", "type": "github_repository", "title": "docxology/Active_Inference_for_Fun", "url": "https://github.com/docxology/Active_Inference_for_Fun", "summary": "Tiny, transparent experiments in Active Inference using pymdp", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork", "recent" ], "content": "docxology/Active_Inference_for_Fun Tiny, transparent experiments in Active Inference using pymdp Python docxology active-inference bayesian-modeling education free-energy-principle neuroscience pymdp python tutorial fork recent" }, { "id": "github-repo:docxology/active_torchference", "type": "github_repository", "title": "docxology/active_torchference", "url": "https://github.com/docxology/active_torchference", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/active_torchference Python docxology curated" }, { "id": "github-repo:docxology/ActiveACO", "type": "github_repository", "title": "docxology/ActiveACO", "url": "https://github.com/docxology/ActiveACO", "summary": "Augmenting Ant Colony Optimization with Active Inference", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/ActiveACO Augmenting Ant Colony Optimization with Active Inference Python docxology fork" }, { "id": "github-repo:docxology/ActiveInferAnts", "type": "github_repository", "title": "docxology/ActiveInferAnts", "url": "https://github.com/docxology/ActiveInferAnts", "summary": "Active InferAnts", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/ActiveInferAnts Active InferAnts Python docxology curated recent" }, { "id": "github-repo:docxology/ActiveInferAnts_Fork", "type": "github_repository", "title": "docxology/ActiveInferAnts_Fork", "url": "https://github.com/docxology/ActiveInferAnts_Fork", "summary": "Active Inference models of/for Ants", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/ActiveInferAnts_Fork Active Inference models of/for Ants Python docxology fork" }, { "id": "github-repo:docxology/ActiveInference.jl", "type": "github_repository", "title": "docxology/ActiveInference.jl", "url": "https://github.com/docxology/ActiveInference.jl", "summary": "A Julia Package for Active Inference", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/ActiveInference.jl A Julia Package for Active Inference docxology fork" }, { "id": "github-repo:docxology/ad4m", "type": "github_repository", "title": "docxology/ad4m", "url": "https://github.com/docxology/ad4m", "summary": "Agent-centric social network and interoperability dApp framework", "domain": "docxology", "tags": [ "github", "repository", "JavaScript", "docxology", "fork" ], "content": "docxology/ad4m Agent-centric social network and interoperability dApp framework JavaScript docxology fork" }, { "id": "github-repo:docxology/AFFiNE", "type": "github_repository", "title": "docxology/AFFiNE", "url": "https://github.com/docxology/AFFiNE", "summary": "There can be more than Notion and Miro. AFFiNE(pronounced [ə‘fain]) is a next-gen knowledge base that brings planning, sorting and creating all together. Privacy first, open-source, customizable and ready to use. ", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/AFFiNE There can be more than Notion and Miro. AFFiNE(pronounced [ə‘fain]) is a next-gen knowledge base that brings planning, sorting and creating all together. Privacy first, open-source, customizable and ready to use. docxology fork" }, { "id": "github-repo:docxology/agentic-cursorrules", "type": "github_repository", "title": "docxology/agentic-cursorrules", "url": "https://github.com/docxology/agentic-cursorrules", "summary": "A practical approach to managing multiple AI agents in Cursor through strict file-tree partitioning and domain boundaries.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/agentic-cursorrules A practical approach to managing multiple AI agents in Cursor through strict file-tree partitioning and domain boundaries. docxology fork" }, { "id": "github-repo:docxology/agentic_coding_flywheel_setup", "type": "github_repository", "title": "docxology/agentic_coding_flywheel_setup", "url": "https://github.com/docxology/agentic_coding_flywheel_setup", "summary": "Bootstraps a fresh Ubuntu VPS into a complete multi-agent AI development environment in 30 minutes: coding agents, session management, safety tools, and coordination infrastructure", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/agentic_coding_flywheel_setup Bootstraps a fresh Ubuntu VPS into a complete multi-agent AI development environment in 30 minutes: coding agents, session management, safety tools, and coordination infrastructure docxology fork" }, { "id": "github-repo:docxology/AgenticMesh", "type": "github_repository", "title": "docxology/AgenticMesh", "url": "https://github.com/docxology/AgenticMesh", "summary": "Active Inference & Agentic Mesh", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/AgenticMesh Active Inference & Agentic Mesh Python docxology curated" }, { "id": "github-repo:docxology/AgentLaboratory", "type": "github_repository", "title": "docxology/AgentLaboratory", "url": "https://github.com/docxology/AgentLaboratory", "summary": "Agent Laboratory is an end-to-end autonomous research workflow meant to assist you as the human researcher toward implementing your research ideas", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/AgentLaboratory Agent Laboratory is an end-to-end autonomous research workflow meant to assist you as the human researcher toward implementing your research ideas Python docxology fork" }, { "id": "github-repo:docxology/AGI_fork", "type": "github_repository", "title": "docxology/AGI_fork", "url": "https://github.com/docxology/AGI_fork", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/AGI_fork docxology fork" }, { "id": "github-repo:docxology/AI-ConductorBlindSpot", "type": "github_repository", "title": "docxology/AI-ConductorBlindSpot", "url": "https://github.com/docxology/AI-ConductorBlindSpot", "summary": "Computational artifacts for The Conductor Blind Spot of the Quadratic Curvature Class on Ring-Structured Categorical Heads, exact-arithmetic certificate verification", "domain": "docxology", "tags": [ "github", "repository", "TeX", "docxology", "fork", "recent" ], "content": "docxology/AI-ConductorBlindSpot Computational artifacts for The Conductor Blind Spot of the Quadratic Curvature Class on Ring-Structured Categorical Heads, exact-arithmetic certificate verification TeX docxology fork recent" }, { "id": "github-repo:docxology/aif-fep-db", "type": "github_repository", "title": "docxology/aif-fep-db", "url": "https://github.com/docxology/aif-fep-db", "summary": "A database of publications related to active inference and the free energy principle", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/aif-fep-db A database of publications related to active inference and the free energy principle Python docxology fork" }, { "id": "github-repo:docxology/AIF_for_CC", "type": "github_repository", "title": "docxology/AIF_for_CC", "url": "https://github.com/docxology/AIF_for_CC", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/AIF_for_CC docxology fork" }, { "id": "github-repo:docxology/aif_iwai2025_thoughtseeds", "type": "github_repository", "title": "docxology/aif_iwai2025_thoughtseeds", "url": "https://github.com/docxology/aif_iwai2025_thoughtseeds", "summary": "Towards a fuller Act Inf implementation of Thoughtseeds Framework. Initial ideas only!", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/aif_iwai2025_thoughtseeds Towards a fuller Act Inf implementation of Thoughtseeds Framework. Initial ideas only! Python docxology fork" }, { "id": "github-repo:docxology/Algorithms", "type": "github_repository", "title": "docxology/Algorithms", "url": "https://github.com/docxology/Algorithms", "summary": "A collection of algorithms and data structures", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Algorithms A collection of algorithms and data structures docxology fork" }, { "id": "github-repo:docxology/amalgkit", "type": "github_repository", "title": "docxology/amalgkit", "url": "https://github.com/docxology/amalgkit", "summary": "RNA-seq data amalgamation for a large-scale evolutionary transcriptomics", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/amalgkit RNA-seq data amalgamation for a large-scale evolutionary transcriptomics Python docxology fork" }, { "id": "github-repo:docxology/amplify", "type": "github_repository", "title": "docxology/amplify", "url": "https://github.com/docxology/amplify", "summary": "Open Source Fellow Sandbox", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/amplify Open Source Fellow Sandbox docxology fork" }, { "id": "github-repo:docxology/ant-pheromone", "type": "github_repository", "title": "docxology/ant-pheromone", "url": "https://github.com/docxology/ant-pheromone", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/ant-pheromone Python docxology curated" }, { "id": "github-repo:docxology/ant_social_complexity", "type": "github_repository", "title": "docxology/ant_social_complexity", "url": "https://github.com/docxology/ant_social_complexity", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Shell", "docxology", "fork", "recent" ], "content": "docxology/ant_social_complexity Shell docxology fork recent" }, { "id": "github-repo:docxology/ant_stack", "type": "github_repository", "title": "docxology/ant_stack", "url": "https://github.com/docxology/ant_stack", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/ant_stack Python docxology curated recent" }, { "id": "github-repo:docxology/ants", "type": "github_repository", "title": "docxology/ants", "url": "https://github.com/docxology/ants", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/ants Python docxology fork" }, { "id": "github-repo:docxology/aqua-js-cli", "type": "github_repository", "title": "docxology/aqua-js-cli", "url": "https://github.com/docxology/aqua-js-cli", "summary": "JS Client for external verifier", "domain": "docxology", "tags": [ "github", "repository", "JavaScript", "docxology", "fork" ], "content": "docxology/aqua-js-cli JS Client for external verifier JavaScript docxology fork" }, { "id": "github-repo:docxology/Aragon_Conviction_Voting", "type": "github_repository", "title": "docxology/Aragon_Conviction_Voting", "url": "https://github.com/docxology/Aragon_Conviction_Voting", "summary": "Notebook Link: https://github.com/BlockScience/Aragon_Conviction_Voting/blob/master/models/v3/Aragon_Conviction_Voting_Model.ipynb", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Aragon_Conviction_Voting Notebook Link: https://github.com/BlockScience/Aragon_Conviction_Voting/blob/master/models/v3/Aragon_Conviction_Voting_Model.ipynb docxology fork" }, { "id": "github-repo:docxology/ATLAS", "type": "github_repository", "title": "docxology/ATLAS", "url": "https://github.com/docxology/ATLAS", "summary": "ATLAS ", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/ATLAS ATLAS Python docxology fork" }, { "id": "github-repo:docxology/Auto-GPT", "type": "github_repository", "title": "docxology/Auto-GPT", "url": "https://github.com/docxology/Auto-GPT", "summary": "An experimental open-source attempt to make GPT-4 fully autonomous.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Auto-GPT An experimental open-source attempt to make GPT-4 fully autonomous. docxology fork" }, { "id": "github-repo:docxology/AutoMaticAssistant", "type": "github_repository", "title": "docxology/AutoMaticAssistant", "url": "https://github.com/docxology/AutoMaticAssistant", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/AutoMaticAssistant docxology fork" }, { "id": "github-repo:docxology/Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference", "type": "github_repository", "title": "docxology/Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference", "url": "https://github.com/docxology/Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "curated" ], "content": "docxology/Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference docxology curated" }, { "id": "github-repo:docxology/autumn", "type": "github_repository", "title": "docxology/autumn", "url": "https://github.com/docxology/autumn", "summary": "Autumn is an open-source pricing & billing platform", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/autumn Autumn is an open-source pricing & billing platform docxology fork" }, { "id": "github-repo:docxology/awesome", "type": "github_repository", "title": "docxology/awesome", "url": "https://github.com/docxology/awesome", "summary": "😎 Awesome lists about all kinds of interesting topics", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/awesome 😎 Awesome lists about all kinds of interesting topics docxology fork" }, { "id": "github-repo:docxology/awesome-python", "type": "github_repository", "title": "docxology/awesome-python", "url": "https://github.com/docxology/awesome-python", "summary": "A curated list of awesome Python frameworks, libraries, software and resources", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/awesome-python A curated list of awesome Python frameworks, libraries, software and resources docxology fork" }, { "id": "github-repo:docxology/awesome-qubes-os", "type": "github_repository", "title": "docxology/awesome-qubes-os", "url": "https://github.com/docxology/awesome-qubes-os", "summary": "A curated list of awesome qubes os links", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/awesome-qubes-os A curated list of awesome qubes os links docxology fork" }, { "id": "github-repo:docxology/awesome-selfhosted", "type": "github_repository", "title": "docxology/awesome-selfhosted", "url": "https://github.com/docxology/awesome-selfhosted", "summary": "A list of Free Software network services and web applications which can be hosted on your own servers", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/awesome-selfhosted A list of Free Software network services and web applications which can be hosted on your own servers docxology fork" }, { "id": "github-repo:docxology/axiom", "type": "github_repository", "title": "docxology/axiom", "url": "https://github.com/docxology/axiom", "summary": "Implementation and evaluation of the AXIOM architecture from the preprint \"AXIOM: Learning to Play Games in Minutes with Expanding Object Centric Models\"", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/axiom Implementation and evaluation of the AXIOM architecture from the preprint \"AXIOM: Learning to Play Games in Minutes with Expanding Object Centric Models\" Python docxology fork" }, { "id": "github-repo:docxology/babyagi3", "type": "github_repository", "title": "docxology/babyagi3", "url": "https://github.com/docxology/babyagi3", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/babyagi3 docxology agents ai artificial-intelligence autonomous-agents llm python task-planning fork recent" }, { "id": "github-repo:docxology/bdh", "type": "github_repository", "title": "docxology/bdh", "url": "https://github.com/docxology/bdh", "summary": "Baby Dragon Hatchling (BDH) – Architecture and Code", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/bdh Baby Dragon Hatchling (BDH) – Architecture and Code docxology fork" }, { "id": "github-repo:docxology/BeeStack", "type": "github_repository", "title": "docxology/BeeStack", "url": "https://github.com/docxology/BeeStack", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "recent" ], "content": "docxology/BeeStack Python docxology recent" }, { "id": "github-repo:docxology/biol-1", "type": "github_repository", "title": "docxology/biol-1", "url": "https://github.com/docxology/biol-1", "summary": "BIOL-1: General Biology Course Materials - College of the Redwoods", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "curated", "recent" ], "content": "docxology/biol-1 BIOL-1: General Biology Course Materials - College of the Redwoods HTML docxology curated recent" }, { "id": "github-repo:docxology/biol-8", "type": "github_repository", "title": "docxology/biol-8", "url": "https://github.com/docxology/biol-8", "summary": "BIOL-8: Human Anatomy & Physiology Course Materials - College of the Redwoods", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "curated", "recent" ], "content": "docxology/biol-8 BIOL-8: Human Anatomy & Physiology Course Materials - College of the Redwoods HTML docxology curated recent" }, { "id": "github-repo:docxology/biology_textbook", "type": "github_repository", "title": "docxology/biology_textbook", "url": "https://github.com/docxology/biology_textbook", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/biology_textbook Python docxology curated recent" }, { "id": "github-repo:docxology/blackarch", "type": "github_repository", "title": "docxology/blackarch", "url": "https://github.com/docxology/blackarch", "summary": "An ArchLinux based distribution for penetration testers and security researchers.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/blackarch An ArchLinux based distribution for penetration testers and security researchers. docxology fork" }, { "id": "github-repo:docxology/blackbox_node", "type": "github_repository", "title": "docxology/blackbox_node", "url": "https://github.com/docxology/blackbox_node", "summary": "Off-grid mesh node with local AI TAK integration and Bitcoin Cashu payments built on Meshtastic", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/blackbox_node Off-grid mesh node with local AI TAK integration and Bitcoin Cashu payments built on Meshtastic docxology fork recent" }, { "id": "github-repo:docxology/blake_jiang", "type": "github_repository", "title": "docxology/blake_jiang", "url": "https://github.com/docxology/blake_jiang", "summary": "William Blake, Professor Jiang, and the Architecture of Intelligence — rapid AI-augmented scholarly response to Game Theory #24: The AI Apocalypse (12 May 2026). Triangulates Jiang's diagnosis with Blake's perceptual diagnostics and Friston's Active Inference.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/blake_jiang William Blake, Professor Jiang, and the Architecture of Intelligence — rapid AI-augmented scholarly response to Game Theory #24: The AI Apocalypse (12 May 2026). Triangulates Jiang's diagnosis with Blake's perceptual diagnostics and Friston's Active Inference. Python docxology active-inference ai-alignment cognitive-science cognitive-security four-zoas free-energy-principle jiang-xueqin markov-blanket newtons-sleep rapid-publication scholarly-communication william-blake curated recent" }, { "id": "github-repo:docxology/bnlearn", "type": "github_repository", "title": "docxology/bnlearn", "url": "https://github.com/docxology/bnlearn", "summary": "Python package for Causal Discovery by learning the graphical structure of Bayesian networks. Structure Learning, Parameter Learning, Inferences, Sampling methods.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/bnlearn Python package for Causal Discovery by learning the graphical structure of Bayesian networks. Structure Learning, Parameter Learning, Inferences, Sampling methods. docxology fork recent" }, { "id": "github-repo:docxology/bookwyrm", "type": "github_repository", "title": "docxology/bookwyrm", "url": "https://github.com/docxology/bookwyrm", "summary": "ingest, index, and encode information into one long file 🐉", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/bookwyrm ingest, index, and encode information into one long file 🐉 docxology fork" }, { "id": "github-repo:docxology/buzz", "type": "github_repository", "title": "docxology/buzz", "url": "https://github.com/docxology/buzz", "summary": "Buzz transcribes and translates audio offline on your personal computer. Powered by OpenAI's Whisper.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/buzz Buzz transcribes and translates audio offline on your personal computer. Powered by OpenAI's Whisper. docxology fork" }, { "id": "github-repo:docxology/cadCAD", "type": "github_repository", "title": "docxology/cadCAD", "url": "https://github.com/docxology/cadCAD", "summary": "Design, simulate, validate, and operate within complex systems", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/cadCAD Design, simulate, validate, and operate within complex systems Python docxology fork" }, { "id": "github-repo:docxology/cadcad-ri", "type": "github_repository", "title": "docxology/cadcad-ri", "url": "https://github.com/docxology/cadcad-ri", "summary": "The Reference Implementation", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/cadcad-ri The Reference Implementation docxology fork" }, { "id": "github-repo:docxology/cascadia", "type": "github_repository", "title": "docxology/cascadia", "url": "https://github.com/docxology/cascadia", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/cascadia Python docxology curated" }, { "id": "github-repo:docxology/CatColab", "type": "github_repository", "title": "docxology/CatColab", "url": "https://github.com/docxology/CatColab", "summary": "A collaborative environment for formal, interoperable, conceptual modeling", "domain": "docxology", "tags": [ "github", "repository", "Rust", "docxology", "fork" ], "content": "docxology/CatColab A collaborative environment for formal, interoperable, conceptual modeling Rust docxology fork" }, { "id": "github-repo:docxology/Classes", "type": "github_repository", "title": "docxology/Classes", "url": "https://github.com/docxology/Classes", "summary": "This repository contains codes and materials of each meeting.", "domain": "docxology", "tags": [ "github", "repository", "Jupyter Notebook", "docxology", "fork" ], "content": "docxology/Classes This repository contains codes and materials of each meeting. Jupyter Notebook docxology fork" }, { "id": "github-repo:docxology/claude-squad", "type": "github_repository", "title": "docxology/claude-squad", "url": "https://github.com/docxology/claude-squad", "summary": "Manage multiple AI agents like Claude Code and Aider. 10x your productivity", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/claude-squad Manage multiple AI agents like Claude Code and Aider. 10x your productivity docxology fork" }, { "id": "github-repo:docxology/claude-task-master", "type": "github_repository", "title": "docxology/claude-task-master", "url": "https://github.com/docxology/claude-task-master", "summary": "An AI-powered task-management system you can drop into Cursor, Lovable, Windsurf, Roo, and others.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/claude-task-master An AI-powered task-management system you can drop into Cursor, Lovable, Windsurf, Roo, and others. docxology fork" }, { "id": "github-repo:docxology/client", "type": "github_repository", "title": "docxology/client", "url": "https://github.com/docxology/client", "summary": "Keybase Go Library, Client, Service, OS X, iOS, Android, Electron", "domain": "docxology", "tags": [ "github", "repository", "Go", "docxology", "fork" ], "content": "docxology/client Keybase Go Library, Client, Service, OS X, iOS, Android, Electron Go docxology fork" }, { "id": "github-repo:docxology/codomyrmex", "type": "github_repository", "title": "docxology/codomyrmex", "url": "https://github.com/docxology/codomyrmex", "summary": "🐜 AI-native modular coding workspace — 127 modules, 424 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/codomyrmex 🐜 AI-native modular coding workspace — 127 modules, 424 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration Python docxology agents ai ai-agents claude developer-tools llm mcp model-context-protocol modular multi-agent orchestration personal-ai python security testing zero-mock curated recent" }, { "id": "github-repo:docxology/cogames", "type": "github_repository", "title": "docxology/cogames", "url": "https://github.com/docxology/cogames", "summary": " CoGames is a collection of multi-agent cooperative and competitive environments designed for reinforcement learning research.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/cogames CoGames is a collection of multi-agent cooperative and competitive environments designed for reinforcement learning research. Python docxology fork" }, { "id": "github-repo:docxology/cognitive", "type": "github_repository", "title": "docxology/cognitive", "url": "https://github.com/docxology/cognitive", "summary": "Cognitive science research workspace — Active Inference, Bayesian modeling, ant behavior, and computational neuroscience", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/cognitive Cognitive science research workspace — Active Inference, Bayesian modeling, ant behavior, and computational neuroscience Python docxology active-inference ant-behavior bayesian-modeling cognitive-science computational-biology neuroscience research curated recent" }, { "id": "github-repo:docxology/cognitive-engine", "type": "github_repository", "title": "docxology/cognitive-engine", "url": "https://github.com/docxology/cognitive-engine", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/cognitive-engine Python docxology curated" }, { "id": "github-repo:docxology/cognitive_case_diagrams", "type": "github_repository", "title": "docxology/cognitive_case_diagrams", "url": "https://github.com/docxology/cognitive_case_diagrams", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "TeX", "docxology", "curated", "recent" ], "content": "docxology/cognitive_case_diagrams TeX docxology curated recent" }, { "id": "github-repo:docxology/cohereants", "type": "github_repository", "title": "docxology/cohereants", "url": "https://github.com/docxology/cohereants", "summary": "When do bugs see (infra)red? Computational research on insect IR sensing and olfaction modeling — engineering bounds and protocol design.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/cohereants When do bugs see (infra)red? Computational research on insect IR sensing and olfaction modeling — engineering bounds and protocol design. Python docxology curated recent" }, { "id": "github-repo:docxology/constructor-theory-simulator", "type": "github_repository", "title": "docxology/constructor-theory-simulator", "url": "https://github.com/docxology/constructor-theory-simulator", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/constructor-theory-simulator docxology fork" }, { "id": "github-repo:docxology/course", "type": "github_repository", "title": "docxology/course", "url": "https://github.com/docxology/course", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/course Python docxology curated" }, { "id": "github-repo:docxology/COVID19_USA", "type": "github_repository", "title": "docxology/COVID19_USA", "url": "https://github.com/docxology/COVID19_USA", "summary": "Data analysis on the COVID19 data about the US: Logistic fit", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/COVID19_USA Data analysis on the COVID19 data about the US: Logistic fit docxology fork" }, { "id": "github-repo:docxology/crescent-city", "type": "github_repository", "title": "docxology/crescent-city", "url": "https://github.com/docxology/crescent-city", "summary": "Complete pipeline for the Crescent City, CA municipal code.", "domain": "docxology", "tags": [ "github", "repository", "TypeScript", "docxology", "curated", "recent" ], "content": "docxology/crescent-city Complete pipeline for the Crescent City, CA municipal code. TypeScript docxology california civic-tech community crescent-city government municipal-code open-source curated recent" }, { "id": "github-repo:docxology/crescent_city", "type": "github_repository", "title": "docxology/crescent_city", "url": "https://github.com/docxology/crescent_city", "summary": "A comprehensive, reproducible scholarly history of Crescent City, California — Tolowa Dee-ni' habitation through the Cascadia-margin present. 46 chapters, 24 reproducible figures, Pandoc+XeLaTeX pipeline. DOI 10.5281/zenodo.20286171", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "recent" ], "content": "docxology/crescent_city A comprehensive, reproducible scholarly history of Crescent City, California — Tolowa Dee-ni' habitation through the Cascadia-margin present. 46 chapters, 24 reproducible figures, Pandoc+XeLaTeX pipeline. DOI 10.5281/zenodo.20286171 Python docxology recent" }, { "id": "github-repo:docxology/Crypto-OpSec-SelfGuard-RoadMap", "type": "github_repository", "title": "docxology/Crypto-OpSec-SelfGuard-RoadMap", "url": "https://github.com/docxology/Crypto-OpSec-SelfGuard-RoadMap", "summary": "Here we collect and discuss the best DeFi, Blockchain and crypto-related OpSec researches and data terminals - contributions are welcome.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Crypto-OpSec-SelfGuard-RoadMap Here we collect and discuss the best DeFi, Blockchain and crypto-related OpSec researches and data terminals - contributions are welcome. docxology fork" }, { "id": "github-repo:docxology/curriculum", "type": "github_repository", "title": "docxology/curriculum", "url": "https://github.com/docxology/curriculum", "summary": "Course materials and curriculum for biology, ecology, and Active Inference education", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "curated", "recent" ], "content": "docxology/curriculum Course materials and curriculum for biology, ecology, and Active Inference education HTML docxology active-inference biology course-materials curriculum ecology education open-education teaching curated recent" }, { "id": "github-repo:docxology/cursor-boost", "type": "github_repository", "title": "docxology/cursor-boost", "url": "https://github.com/docxology/cursor-boost", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/cursor-boost docxology fork" }, { "id": "github-repo:docxology/dagaz", "type": "github_repository", "title": "docxology/dagaz", "url": "https://github.com/docxology/dagaz", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/dagaz docxology fork recent" }, { "id": "github-repo:docxology/DagBall", "type": "github_repository", "title": "docxology/DagBall", "url": "https://github.com/docxology/DagBall", "summary": "A game where you slide a 2d surface (the screen) through a space of possible 300-dimensional voxels (up to 1000) defined by small pieces of code and artistic use of the high dimensional editing tools. Balls roll around pushing on the 300 dimensional heightmap, moving the screen in 300d.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/DagBall A game where you slide a 2d surface (the screen) through a space of possible 300-dimensional voxels (up to 1000) defined by small pieces of code and artistic use of the high dimensional editing tools. Balls roll around pushing on the 300 dimensional heightmap, moving the screen in 300d. docxology fork" }, { "id": "github-repo:docxology/dangerzone", "type": "github_repository", "title": "docxology/dangerzone", "url": "https://github.com/docxology/dangerzone", "summary": "Take potentially dangerous PDFs, office documents, or images and convert them to safe PDFs", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/dangerzone Take potentially dangerous PDFs, office documents, or images and convert them to safe PDFs Python docxology fork" }, { "id": "github-repo:docxology/developer", "type": "github_repository", "title": "docxology/developer", "url": "https://github.com/docxology/developer", "summary": "with 100k context windows on the way, it's now feasible for every dev to have their own smol developer", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/developer with 100k context windows on the way, it's now feasible for every dev to have their own smol developer Python docxology fork" }, { "id": "github-repo:docxology/Devon", "type": "github_repository", "title": "docxology/Devon", "url": "https://github.com/docxology/Devon", "summary": "Devon: An open-source pair programmer", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Devon Devon: An open-source pair programmer docxology fork" }, { "id": "github-repo:docxology/dialecticalclaims", "type": "github_repository", "title": "docxology/dialecticalclaims", "url": "https://github.com/docxology/dialecticalclaims", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "TypeScript", "docxology", "fork" ], "content": "docxology/dialecticalclaims TypeScript docxology fork" }, { "id": "github-repo:docxology/dickens-arxiv24", "type": "github_repository", "title": "docxology/dickens-arxiv24", "url": "https://github.com/docxology/dickens-arxiv24", "summary": "Experiments for Experiments for \"A Mathematical Framework, a Taxonomy of Modeling Paradigms, and a Suite of Learning Techniques for Neural-Symbolic Systems\".", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/dickens-arxiv24 Experiments for Experiments for \"A Mathematical Framework, a Taxonomy of Modeling Paradigms, and a Suite of Learning Techniques for Neural-Symbolic Systems\". Python docxology fork" }, { "id": "github-repo:docxology/docs", "type": "github_repository", "title": "docxology/docs", "url": "https://github.com/docxology/docs", "summary": "A collaborative note taking, wiki and documentation platform that scales. Built with Django and React. Opensource alternative to Notion or Outline.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/docs A collaborative note taking, wiki and documentation platform that scales. Built with Django and React. Opensource alternative to Notion or Outline. docxology fork" }, { "id": "github-repo:docxology/docxology", "type": "github_repository", "title": "docxology/docxology", "url": "https://github.com/docxology/docxology", "summary": "Daniel Ari Friedman, PhD public research and software index: updated with works, papers, art, media, and software repositories.", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "recent" ], "content": "docxology/docxology Daniel Ari Friedman, PhD public research and software index: updated with works, papers, art, media, and software repositories. HTML docxology active-inference ai-consulting ai-researcher ai-tutoring bayesian-modeling cognitive-security computational-biology entomology free-energy-principle machine-learning python research-portfolio rust stanford recent" }, { "id": "github-repo:docxology/dotscope", "type": "github_repository", "title": "docxology/dotscope", "url": "https://github.com/docxology/dotscope", "summary": "The Physics Engine for AI Coding Agents.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/dotscope The Physics Engine for AI Coding Agents. docxology fork recent" }, { "id": "github-repo:docxology/EFEasVFE", "type": "github_repository", "title": "docxology/EFEasVFE", "url": "https://github.com/docxology/EFEasVFE", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Julia", "docxology", "fork" ], "content": "docxology/EFEasVFE Julia docxology fork" }, { "id": "github-repo:docxology/eliza", "type": "github_repository", "title": "docxology/eliza", "url": "https://github.com/docxology/eliza", "summary": "Autonomous agents for everyone", "domain": "docxology", "tags": [ "github", "repository", "TypeScript", "docxology", "fork" ], "content": "docxology/eliza Autonomous agents for everyone TypeScript docxology fork" }, { "id": "github-repo:docxology/embodied-computation-group.github.io", "type": "github_repository", "title": "docxology/embodied-computation-group.github.io", "url": "https://github.com/docxology/embodied-computation-group.github.io", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/embodied-computation-group.github.io docxology fork" }, { "id": "github-repo:docxology/enact", "type": "github_repository", "title": "docxology/enact", "url": "https://github.com/docxology/enact", "summary": "A framework for generative software.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/enact A framework for generative software. Python docxology fork" }, { "id": "github-repo:docxology/enactive_inference_model", "type": "github_repository", "title": "docxology/enactive_inference_model", "url": "https://github.com/docxology/enactive_inference_model", "summary": "Three‑level hierarchical enactive inference model of mental action (focused‑attention meditation with expert–novice profiles) with reproducible simulations and figures.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "fork", "recent" ], "content": "docxology/enactive_inference_model Three‑level hierarchical enactive inference model of mental action (focused‑attention meditation with expert–novice profiles) with reproducible simulations and figures. Python docxology active-inference bayesian-modeling cognitive-science enactivism meditation neuroscience python simulation curated fork recent" }, { "id": "github-repo:docxology/ento_linguistics", "type": "github_repository", "title": "docxology/ento_linguistics", "url": "https://github.com/docxology/ento_linguistics", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/ento_linguistics Python docxology curated recent" }, { "id": "github-repo:docxology/eshkol", "type": "github_repository", "title": "docxology/eshkol", "url": "https://github.com/docxology/eshkol", "summary": "High-Performance LISP-like language for Scientific Computing and AI written in C", "domain": "docxology", "tags": [ "github", "repository", "C", "docxology", "fork" ], "content": "docxology/eshkol High-Performance LISP-like language for Scientific Computing and AI written in C C docxology fork" }, { "id": "github-repo:docxology/eventeum", "type": "github_repository", "title": "docxology/eventeum", "url": "https://github.com/docxology/eventeum", "summary": "A resilient Ethereum event listener that bridges your smart contract events and backend microservices", "domain": "docxology", "tags": [ "github", "repository", "Java", "docxology", "fork" ], "content": "docxology/eventeum A resilient Ethereum event listener that bridges your smart contract events and backend microservices Java docxology fork" }, { "id": "github-repo:docxology/EvoJump", "type": "github_repository", "title": "docxology/EvoJump", "url": "https://github.com/docxology/EvoJump", "summary": "A Comprehensive Framework for Evolutionary Ontogenetic Analysis", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/EvoJump A Comprehensive Framework for Evolutionary Ontogenetic Analysis Python docxology curated" }, { "id": "github-repo:docxology/fabric", "type": "github_repository", "title": "docxology/fabric", "url": "https://github.com/docxology/fabric", "summary": "fabric is an open-source framework for augmenting humans using AI. It provides a modular framework for solving specific problems using a crowdsourced set of AI prompts that can be used anywhere.", "domain": "docxology", "tags": [ "github", "repository", "JavaScript", "docxology", "fork" ], "content": "docxology/fabric fabric is an open-source framework for augmenting humans using AI. It provides a modular framework for solving specific problems using a crowdsourced set of AI prompts that can be used anywhere. JavaScript docxology fork" }, { "id": "github-repo:docxology/FacilitatorsCatechism", "type": "github_repository", "title": "docxology/FacilitatorsCatechism", "url": "https://github.com/docxology/FacilitatorsCatechism", "summary": "The Facilitator's Catechism is an operations order for use by small teams.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/FacilitatorsCatechism The Facilitator's Catechism is an operations order for use by small teams. docxology fork" }, { "id": "github-repo:docxology/fact-graph", "type": "github_repository", "title": "docxology/fact-graph", "url": "https://github.com/docxology/fact-graph", "summary": "Fact Graph ", "domain": "docxology", "tags": [ "github", "repository", "Scala", "docxology", "fork" ], "content": "docxology/fact-graph Fact Graph Scala docxology fork" }, { "id": "github-repo:docxology/farmOS", "type": "github_repository", "title": "docxology/farmOS", "url": "https://github.com/docxology/farmOS", "summary": "farmOS: A web-based farm record keeping application.", "domain": "docxology", "tags": [ "github", "repository", "PHP", "docxology", "fork" ], "content": "docxology/farmOS farmOS: A web-based farm record keeping application. PHP docxology fork" }, { "id": "github-repo:docxology/FEP_RL_VAE", "type": "github_repository", "title": "docxology/FEP_RL_VAE", "url": "https://github.com/docxology/FEP_RL_VAE", "summary": "A variational autoencoder using reinforcement learning and the free energy principle to show the power of my general_FEP_RL package.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork", "recent" ], "content": "docxology/FEP_RL_VAE A variational autoencoder using reinforcement learning and the free energy principle to show the power of my general_FEP_RL package. Python docxology active-inference bayesian deep-learning free-energy-principle machine-learning python reinforcement-learning variational-autoencoder fork recent" }, { "id": "github-repo:docxology/firecrawl", "type": "github_repository", "title": "docxology/firecrawl", "url": "https://github.com/docxology/firecrawl", "summary": "🔥 Turn entire websites into LLM-ready markdown or structured data. Scrape, crawl and extract with a single API.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/firecrawl 🔥 Turn entire websites into LLM-ready markdown or structured data. Scrape, crawl and extract with a single API. docxology fork" }, { "id": "github-repo:docxology/firm", "type": "github_repository", "title": "docxology/firm", "url": "https://github.com/docxology/firm", "summary": "A text-based work management system for technologists.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/firm A text-based work management system for technologists. docxology fork" }, { "id": "github-repo:docxology/flash-clifford", "type": "github_repository", "title": "docxology/flash-clifford", "url": "https://github.com/docxology/flash-clifford", "summary": "⚡ Triton implementation of Clifford algebra neural networks.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/flash-clifford ⚡ Triton implementation of Clifford algebra neural networks. Python docxology fork" }, { "id": "github-repo:docxology/flick", "type": "github_repository", "title": "docxology/flick", "url": "https://github.com/docxology/flick", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/flick Python docxology curated" }, { "id": "github-repo:docxology/flybody", "type": "github_repository", "title": "docxology/flybody", "url": "https://github.com/docxology/flybody", "summary": "MuJoCo fruit fly body model and locomotion RL tasks", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork", "recent" ], "content": "docxology/flybody MuJoCo fruit fly body model and locomotion RL tasks Python docxology computational-biology drosophila fly-brain locomotion mujoco neuroscience reinforcement-learning simulation fork recent" }, { "id": "github-repo:docxology/foam", "type": "github_repository", "title": "docxology/foam", "url": "https://github.com/docxology/foam", "summary": "A personal knowledge management and sharing system for VSCode", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/foam A personal knowledge management and sharing system for VSCode Python docxology fork" }, { "id": "github-repo:docxology/formal-conjectures", "type": "github_repository", "title": "docxology/formal-conjectures", "url": "https://github.com/docxology/formal-conjectures", "summary": "A collection of formalized statements of conjectures in Lean.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/formal-conjectures A collection of formalized statements of conjectures in Lean. docxology fork" }, { "id": "github-repo:docxology/FORMINDEX", "type": "github_repository", "title": "docxology/FORMINDEX", "url": "https://github.com/docxology/FORMINDEX", "summary": "FORMIS analysis", "domain": "docxology", "tags": [ "github", "repository", "Rich Text Format", "docxology", "curated" ], "content": "docxology/FORMINDEX FORMIS analysis Rich Text Format docxology curated" }, { "id": "github-repo:docxology/foundation", "type": "github_repository", "title": "docxology/foundation", "url": "https://github.com/docxology/foundation", "summary": "The Foundation repository contains the initial guidance documents, recommendations, and resources needed to build a psychosecurity-first operation.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/foundation The Foundation repository contains the initial guidance documents, recommendations, and resources needed to build a psychosecurity-first operation. docxology fork" }, { "id": "github-repo:docxology/FPF", "type": "github_repository", "title": "docxology/FPF", "url": "https://github.com/docxology/FPF", "summary": "First Principle Framework", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork", "recent" ], "content": "docxology/FPF First Principle Framework Python docxology fork recent" }, { "id": "github-repo:docxology/fractiverse-ontology", "type": "github_repository", "title": "docxology/fractiverse-ontology", "url": "https://github.com/docxology/fractiverse-ontology", "summary": "A unified ontological framework", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/fractiverse-ontology A unified ontological framework docxology fork" }, { "id": "github-repo:docxology/fuller-obsidian", "type": "github_repository", "title": "docxology/fuller-obsidian", "url": "https://github.com/docxology/fuller-obsidian", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "curated" ], "content": "docxology/fuller-obsidian docxology curated" }, { "id": "github-repo:docxology/Fusion", "type": "github_repository", "title": "docxology/Fusion", "url": "https://github.com/docxology/Fusion", "summary": "Multi node agent orchestrator - build faster and better", "domain": "docxology", "tags": [ "github", "repository", "TypeScript", "docxology", "fork", "recent" ], "content": "docxology/Fusion Multi node agent orchestrator - build faster and better TypeScript docxology fork recent" }, { "id": "github-repo:docxology/G.A.T.E-Research", "type": "github_repository", "title": "docxology/G.A.T.E-Research", "url": "https://github.com/docxology/G.A.T.E-Research", "summary": "a research study dedicated about the G.A.T.E program and its occult connections", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/G.A.T.E-Research a research study dedicated about the G.A.T.E program and its occult connections docxology fork" }, { "id": "github-repo:docxology/gaia-hub", "type": "github_repository", "title": "docxology/gaia-hub", "url": "https://github.com/docxology/gaia-hub", "summary": "Digital Gaia's Global Sustainability Information and Collaboration Hub", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/gaia-hub Digital Gaia's Global Sustainability Information and Collaboration Hub docxology fork" }, { "id": "github-repo:docxology/galileo-s-perfect-harmonics", "type": "github_repository", "title": "docxology/galileo-s-perfect-harmonics", "url": "https://github.com/docxology/galileo-s-perfect-harmonics", "summary": "in this project we propose a solution for Galileos harmonics problem, with code and neural networks.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/galileo-s-perfect-harmonics in this project we propose a solution for Galileos harmonics problem, with code and neural networks. docxology fork" }, { "id": "github-repo:docxology/gastown", "type": "github_repository", "title": "docxology/gastown", "url": "https://github.com/docxology/gastown", "summary": "Gas Town - multi-agent workspace manager", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/gastown Gas Town - multi-agent workspace manager docxology fork recent" }, { "id": "github-repo:docxology/gfacs", "type": "github_repository", "title": "docxology/gfacs", "url": "https://github.com/docxology/gfacs", "summary": "Official repository for GFACS", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/gfacs Official repository for GFACS Python docxology fork" }, { "id": "github-repo:docxology/gitdiagram", "type": "github_repository", "title": "docxology/gitdiagram", "url": "https://github.com/docxology/gitdiagram", "summary": "Replace 'hub' with 'diagram' in any GitHub url to instantly visualize the codebase as an interactive diagram", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/gitdiagram Replace 'hub' with 'diagram' in any GitHub url to instantly visualize the codebase as an interactive diagram docxology fork" }, { "id": "github-repo:docxology/GitNexus", "type": "github_repository", "title": "docxology/GitNexus", "url": "https://github.com/docxology/GitNexus", "summary": "GitNexus: The Zero-Server Code Intelligence Engine - GitNexus is a client-side knowledge graph creator that runs entirely in your browser. Drop in a GitHub repo or ZIP file, and get an interactive knowledge graph wit a built in Graph RAG Agent. Perfect for code exploration", "domain": "docxology", "tags": [ "github", "repository", "TypeScript", "docxology", "fork", "recent" ], "content": "docxology/GitNexus GitNexus: The Zero-Server Code Intelligence Engine - GitNexus is a client-side knowledge graph creator that runs entirely in your browser. Drop in a GitHub repo or ZIP file, and get an interactive knowledge graph wit a built in Graph RAG Agent. Perfect for code exploration TypeScript docxology browser code-analysis code-exploration developer-tools graph-rag javascript knowledge-graph rag fork recent" }, { "id": "github-repo:docxology/GLOSSOPETRAE", "type": "github_repository", "title": "docxology/GLOSSOPETRAE", "url": "https://github.com/docxology/GLOSSOPETRAE", "summary": "LINGUISTIC ENGINE FOR AI", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/GLOSSOPETRAE LINGUISTIC ENGINE FOR AI docxology ai etymology language-model linguistics natural-language-processing nlp python fork recent" }, { "id": "github-repo:docxology/gno", "type": "github_repository", "title": "docxology/gno", "url": "https://github.com/docxology/gno", "summary": "Gno: An interpreted, stack-based Go virtual machine to build succinct and composable apps + gno.land: a blockchain for timeless code and fair open-source.", "domain": "docxology", "tags": [ "github", "repository", "Go", "docxology", "fork" ], "content": "docxology/gno Gno: An interpreted, stack-based Go virtual machine to build succinct and composable apps + gno.land: a blockchain for timeless code and fair open-source. Go docxology fork" }, { "id": "github-repo:docxology/go-foks", "type": "github_repository", "title": "docxology/go-foks", "url": "https://github.com/docxology/go-foks", "summary": "Go implementation of FOKS -- client and server", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/go-foks Go implementation of FOKS -- client and server docxology fork" }, { "id": "github-repo:docxology/godel_ivm", "type": "github_repository", "title": "docxology/godel_ivm", "url": "https://github.com/docxology/godel_ivm", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/godel_ivm Python docxology curated" }, { "id": "github-repo:docxology/Goedel-Prover-V2", "type": "github_repository", "title": "docxology/Goedel-Prover-V2", "url": "https://github.com/docxology/Goedel-Prover-V2", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Goedel-Prover-V2 docxology fork" }, { "id": "github-repo:docxology/goference", "type": "github_repository", "title": "docxology/goference", "url": "https://github.com/docxology/goference", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Go", "docxology", "curated" ], "content": "docxology/goference Go docxology curated" }, { "id": "github-repo:docxology/goNEAT", "type": "github_repository", "title": "docxology/goNEAT", "url": "https://github.com/docxology/goNEAT", "summary": "The GOLang implementation of NeuroEvolution of Augmented Topologies (NEAT) method to grow and teach Artificial Neural Networks without back propagation", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/goNEAT The GOLang implementation of NeuroEvolution of Augmented Topologies (NEAT) method to grow and teach Artificial Neural Networks without back propagation docxology fork" }, { "id": "github-repo:docxology/gpt-author", "type": "github_repository", "title": "docxology/gpt-author", "url": "https://github.com/docxology/gpt-author", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/gpt-author docxology fork" }, { "id": "github-repo:docxology/gpt-engineer", "type": "github_repository", "title": "docxology/gpt-engineer", "url": "https://github.com/docxology/gpt-engineer", "summary": "Specify what you want it to build, the AI asks for clarification, and then builds it.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/gpt-engineer Specify what you want it to build, the AI asks for clarification, and then builds it. docxology fork" }, { "id": "github-repo:docxology/gpt-prompt-engineer", "type": "github_repository", "title": "docxology/gpt-prompt-engineer", "url": "https://github.com/docxology/gpt-prompt-engineer", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/gpt-prompt-engineer docxology fork" }, { "id": "github-repo:docxology/gpt-researcher", "type": "github_repository", "title": "docxology/gpt-researcher", "url": "https://github.com/docxology/gpt-researcher", "summary": "GPT based autonomous agent that does online comprehensive research on any given topic", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/gpt-researcher GPT based autonomous agent that does online comprehensive research on any given topic docxology fork" }, { "id": "github-repo:docxology/gpt4all", "type": "github_repository", "title": "docxology/gpt4all", "url": "https://github.com/docxology/gpt4all", "summary": "gpt4all: an ecosystem of open-source chatbots trained on a massive collections of clean assistant data including code, stories and dialogue", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/gpt4all gpt4all: an ecosystem of open-source chatbots trained on a massive collections of clean assistant data including code, stories and dialogue docxology fork" }, { "id": "github-repo:docxology/GPTeam", "type": "github_repository", "title": "docxology/GPTeam", "url": "https://github.com/docxology/GPTeam", "summary": "GPTeam uses GPT-4 to create multiple agents who collaborate to achieve predefined goals.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/GPTeam GPTeam uses GPT-4 to create multiple agents who collaborate to achieve predefined goals. Python docxology fork" }, { "id": "github-repo:docxology/GradientFreeVI", "type": "github_repository", "title": "docxology/GradientFreeVI", "url": "https://github.com/docxology/GradientFreeVI", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/GradientFreeVI docxology fork" }, { "id": "github-repo:docxology/grateful_data", "type": "github_repository", "title": "docxology/grateful_data", "url": "https://github.com/docxology/grateful_data", "summary": "The Music Never Stopped — a citation-bound Grateful Dead data compendium (shows, songs, performances, venues, personnel, recordings, reception) with a category-theoretic interpretation.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/grateful_data The Music Never Stopped — a citation-bound Grateful Dead data compendium (shows, songs, performances, venues, personnel, recordings, reception) with a category-theoretic interpretation. Python docxology curated recent" }, { "id": "github-repo:docxology/GrowthModel", "type": "github_repository", "title": "docxology/GrowthModel", "url": "https://github.com/docxology/GrowthModel", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology" ], "content": "docxology/GrowthModel docxology" }, { "id": "github-repo:docxology/GUIdev", "type": "github_repository", "title": "docxology/GUIdev", "url": "https://github.com/docxology/GUIdev", "summary": "\"Development of GUI for image analysis\"", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/GUIdev \"Development of GUI for image analysis\" docxology fork" }, { "id": "github-repo:docxology/GuildNet", "type": "github_repository", "title": "docxology/GuildNet", "url": "https://github.com/docxology/GuildNet", "summary": "Sovereign Compute, Automation and Agents for All", "domain": "docxology", "tags": [ "github", "repository", "Go", "docxology", "fork" ], "content": "docxology/GuildNet Sovereign Compute, Automation and Agents for All Go docxology fork" }, { "id": "github-repo:docxology/h4cker", "type": "github_repository", "title": "docxology/h4cker", "url": "https://github.com/docxology/h4cker", "summary": "This repository is primarily maintained by Omar Santos and includes thousands of resources related to ethical hacking / penetration testing, digital forensics and incident response (DFIR), vulnerability research, exploit development, reverse engineering, and more.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/h4cker This repository is primarily maintained by Omar Santos and includes thousands of resources related to ethical hacking / penetration testing, digital forensics and incident response (DFIR), vulnerability research, exploit development, reverse engineering, and more. docxology fork" }, { "id": "github-repo:docxology/haiku.rag", "type": "github_repository", "title": "docxology/haiku.rag", "url": "https://github.com/docxology/haiku.rag", "summary": "Retrieval Augmented Generation based on SQLite", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/haiku.rag Retrieval Augmented Generation based on SQLite docxology fork" }, { "id": "github-repo:docxology/hermes-agent-self-evolution", "type": "github_repository", "title": "docxology/hermes-agent-self-evolution", "url": "https://github.com/docxology/hermes-agent-self-evolution", "summary": "⚒ Evolutionary self-improvement for Hermes Agent — optimize skills, prompts, and code using DSPy + GEPA", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork", "recent" ], "content": "docxology/hermes-agent-self-evolution ⚒ Evolutionary self-improvement for Hermes Agent — optimize skills, prompts, and code using DSPy + GEPA Python docxology agents ai dspy evolution llm optimization prompt-engineering python self-improvement fork recent" }, { "id": "github-repo:docxology/HGM", "type": "github_repository", "title": "docxology/HGM", "url": "https://github.com/docxology/HGM", "summary": "🧬 The Huxley-Gödel Machine", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/HGM 🧬 The Huxley-Gödel Machine docxology fork" }, { "id": "github-repo:docxology/hhs-opendata", "type": "github_repository", "title": "docxology/hhs-opendata", "url": "https://github.com/docxology/hhs-opendata", "summary": "Analysis of HHS data ", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/hhs-opendata Analysis of HHS data Python docxology curated" }, { "id": "github-repo:docxology/hongos", "type": "github_repository", "title": "docxology/hongos", "url": "https://github.com/docxology/hongos", "summary": "Autonomous AI Video Generation Tool", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/hongos Autonomous AI Video Generation Tool Python docxology fork" }, { "id": "github-repo:docxology/HSMM_covariates", "type": "github_repository", "title": "docxology/HSMM_covariates", "url": "https://github.com/docxology/HSMM_covariates", "summary": "Code to estimate an Hidden semi-Markov model where the dwell-time distribution may depend on time-varying covariates", "domain": "docxology", "tags": [ "github", "repository", "R", "docxology", "fork" ], "content": "docxology/HSMM_covariates Code to estimate an Hidden semi-Markov model where the dwell-time distribution may depend on time-varying covariates R docxology fork" }, { "id": "github-repo:docxology/iddqd", "type": "github_repository", "title": "docxology/iddqd", "url": "https://github.com/docxology/iddqd", "summary": "3301 - Unmodified files, transcription and other assets.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/iddqd 3301 - Unmodified files, transcription and other assets. docxology fork" }, { "id": "github-repo:docxology/identity", "type": "github_repository", "title": "docxology/identity", "url": "https://github.com/docxology/identity", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology" ], "content": "docxology/identity docxology" }, { "id": "github-repo:docxology/IF", "type": "github_repository", "title": "docxology/IF", "url": "https://github.com/docxology/IF", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/IF docxology fork" }, { "id": "github-repo:docxology/iheartla", "type": "github_repository", "title": "docxology/iheartla", "url": "https://github.com/docxology/iheartla", "summary": "compilable markdown for linear algebra", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/iheartla compilable markdown for linear algebra docxology fork" }, { "id": "github-repo:docxology/infra-calc", "type": "github_repository", "title": "docxology/infra-calc", "url": "https://github.com/docxology/infra-calc", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "JavaScript", "docxology", "curated" ], "content": "docxology/infra-calc JavaScript docxology curated" }, { "id": "github-repo:docxology/InsightSpike-AI", "type": "github_repository", "title": "docxology/InsightSpike-AI", "url": "https://github.com/docxology/InsightSpike-AI", "summary": "Brain-Inspired Multi-Agent Architecture for “Spike of Insight” (ΔEPC × ΔIG)", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/InsightSpike-AI Brain-Inspired Multi-Agent Architecture for “Spike of Insight” (ΔEPC × ΔIG) Python docxology fork" }, { "id": "github-repo:docxology/institute_website", "type": "github_repository", "title": "docxology/institute_website", "url": "https://github.com/docxology/institute_website", "summary": "Public GitHub Pages website for Active Inference Institute information", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "recent" ], "content": "docxology/institute_website Public GitHub Pages website for Active Inference Institute information HTML docxology recent" }, { "id": "github-repo:docxology/InterBrain", "type": "github_repository", "title": "docxology/InterBrain", "url": "https://github.com/docxology/InterBrain", "summary": "MVP for ProjectLiminality's vision for a collective intelligence protocol", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/InterBrain MVP for ProjectLiminality's vision for a collective intelligence protocol docxology fork" }, { "id": "github-repo:docxology/intermediatePython", "type": "github_repository", "title": "docxology/intermediatePython", "url": "https://github.com/docxology/intermediatePython", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/intermediatePython docxology fork" }, { "id": "github-repo:docxology/IntroductionToAlgebraicEvaluation", "type": "github_repository", "title": "docxology/IntroductionToAlgebraicEvaluation", "url": "https://github.com/docxology/IntroductionToAlgebraicEvaluation", "summary": "A collection of essays and code on algebraic methods to evaluate noisy judges on unlabeled test data.", "domain": "docxology", "tags": [ "github", "repository", "Jupyter Notebook", "docxology", "fork" ], "content": "docxology/IntroductionToAlgebraicEvaluation A collection of essays and code on algebraic methods to evaluate noisy judges on unlabeled test data. Jupyter Notebook docxology fork" }, { "id": "github-repo:docxology/itrace", "type": "github_repository", "title": "docxology/itrace", "url": "https://github.com/docxology/itrace", "summary": "Verification-first webcam eye-movement analysis (gaze, saccades, pupillometry) — MIT-licensed Python core, algorithmically verified. Zenodo DOI 10.5281/zenodo.20614908", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/itrace Verification-first webcam eye-movement analysis (gaze, saccades, pupillometry) — MIT-licensed Python core, algorithmically verified. Zenodo DOI 10.5281/zenodo.20614908 Python docxology curated recent" }, { "id": "github-repo:docxology/ivm-xyz", "type": "github_repository", "title": "docxology/ivm-xyz", "url": "https://github.com/docxology/ivm-xyz", "summary": "package for working with 3D and 4D geometries. ", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/ivm-xyz package for working with 3D and 4D geometries. Python docxology curated recent" }, { "id": "github-repo:docxology/Jessie", "type": "github_repository", "title": "docxology/Jessie", "url": "https://github.com/docxology/Jessie", "summary": "Tiny subset of JavaScript for ocap-safe universal mobile code", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Jessie Tiny subset of JavaScript for ocap-safe universal mobile code docxology fork" }, { "id": "github-repo:docxology/Journal-Utilities", "type": "github_repository", "title": "docxology/Journal-Utilities", "url": "https://github.com/docxology/Journal-Utilities", "summary": "Utilities and Documentation for creating contents for the Active Inference Journal", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Journal-Utilities Utilities and Documentation for creating contents for the Active Inference Journal docxology fork" }, { "id": "github-repo:docxology/kafka", "type": "github_repository", "title": "docxology/kafka", "url": "https://github.com/docxology/kafka", "summary": "Mirror of Apache Kafka", "domain": "docxology", "tags": [ "github", "repository", "Java", "docxology", "fork" ], "content": "docxology/kafka Mirror of Apache Kafka Java docxology fork" }, { "id": "github-repo:docxology/karma_system", "type": "github_repository", "title": "docxology/karma_system", "url": "https://github.com/docxology/karma_system", "summary": "Umbrella repo for the sym-cog-robotics project of the Active Inference Institute", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/karma_system Umbrella repo for the sym-cog-robotics project of the Active Inference Institute docxology fork" }, { "id": "github-repo:docxology/kepano-obsidian", "type": "github_repository", "title": "docxology/kepano-obsidian", "url": "https://github.com/docxology/kepano-obsidian", "summary": "My personal Obsidian vault template. A bottom-up approach to note-taking and organizing things I am interested in.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/kepano-obsidian My personal Obsidian vault template. A bottom-up approach to note-taking and organizing things I am interested in. docxology fork" }, { "id": "github-repo:docxology/ki_us", "type": "github_repository", "title": "docxology/ki_us", "url": "https://github.com/docxology/ki_us", "summary": "Optimizing the United States of America", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/ki_us Optimizing the United States of America Python docxology fork" }, { "id": "github-repo:docxology/kilocode", "type": "github_repository", "title": "docxology/kilocode", "url": "https://github.com/docxology/kilocode", "summary": "Open Source AI coding assistant for planning, building, and fixing code. We're a superset of Roo, Cline, and our own features. Follow us: kilocode.ai/social", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/kilocode Open Source AI coding assistant for planning, building, and fixing code. We're a superset of Roo, Cline, and our own features. Follow us: kilocode.ai/social docxology fork" }, { "id": "github-repo:docxology/KnowledgeBase", "type": "github_repository", "title": "docxology/KnowledgeBase", "url": "https://github.com/docxology/KnowledgeBase", "summary": "never forget anything again! combine AI and intelligent tooling for a local knowledge base to track catalogue, annotate, and plan for you!", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/KnowledgeBase never forget anything again! combine AI and intelligent tooling for a local knowledge base to track catalogue, annotate, and plan for you! docxology fork" }, { "id": "github-repo:docxology/KnowSelf", "type": "github_repository", "title": "docxology/KnowSelf", "url": "https://github.com/docxology/KnowSelf", "summary": "Agentic Knowledgeable Self-awareness", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/KnowSelf Agentic Knowledgeable Self-awareness docxology fork" }, { "id": "github-repo:docxology/LAIF", "type": "github_repository", "title": "docxology/LAIF", "url": "https://github.com/docxology/LAIF", "summary": "Experiments with deriving epistemics aware message passing algos", "domain": "docxology", "tags": [ "github", "repository", "Julia", "docxology", "fork" ], "content": "docxology/LAIF Experiments with deriving epistemics aware message passing algos Julia docxology fork" }, { "id": "github-repo:docxology/langtons-ant", "type": "github_repository", "title": "docxology/langtons-ant", "url": "https://github.com/docxology/langtons-ant", "summary": "Langton's Ant Simulator with options", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/langtons-ant Langton's Ant Simulator with options docxology fork" }, { "id": "github-repo:docxology/LatentSeek", "type": "github_repository", "title": "docxology/LatentSeek", "url": "https://github.com/docxology/LatentSeek", "summary": "Official Repository of LatentSeek", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/LatentSeek Official Repository of LatentSeek docxology fork" }, { "id": "github-repo:docxology/lean_niche", "type": "github_repository", "title": "docxology/lean_niche", "url": "https://github.com/docxology/lean_niche", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/lean_niche Python docxology curated" }, { "id": "github-repo:docxology/links", "type": "github_repository", "title": "docxology/links", "url": "https://github.com/docxology/links", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "recent" ], "content": "docxology/links HTML docxology recent" }, { "id": "github-repo:docxology/literature", "type": "github_repository", "title": "docxology/literature", "url": "https://github.com/docxology/literature", "summary": "Curated research literature collection — papers, references, and reading lists in Active Inference, ecology, and computational biology", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/literature Curated research literature collection — papers, references, and reading lists in Active Inference, ecology, and computational biology Python docxology academic active-inference bibliography ecology literature-review papers reading-list research curated recent" }, { "id": "github-repo:docxology/Ludii", "type": "github_repository", "title": "docxology/Ludii", "url": "https://github.com/docxology/Ludii", "summary": "The Ludii general game system, developed as part of the ERC-funded Digital Ludeme Project.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Ludii The Ludii general game system, developed as part of the ERC-funded Digital Ludeme Project. docxology fork" }, { "id": "github-repo:docxology/m4w", "type": "github_repository", "title": "docxology/m4w", "url": "https://github.com/docxology/m4w", "summary": "math4wisdom", "domain": "docxology", "tags": [ "github", "repository", "Jupyter Notebook", "docxology", "fork" ], "content": "docxology/m4w math4wisdom Jupyter Notebook docxology fork" }, { "id": "github-repo:docxology/maestro", "type": "github_repository", "title": "docxology/maestro", "url": "https://github.com/docxology/maestro", "summary": "A framework for Claude Opus to intelligently orchestrate subagents.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/maestro A framework for Claude Opus to intelligently orchestrate subagents. Python docxology fork" }, { "id": "github-repo:docxology/manim", "type": "github_repository", "title": "docxology/manim", "url": "https://github.com/docxology/manim", "summary": "A community-maintained Python framework for creating mathematical animations. ", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/manim A community-maintained Python framework for creating mathematical animations. docxology fork" }, { "id": "github-repo:docxology/markdown_decision_process", "type": "github_repository", "title": "docxology/markdown_decision_process", "url": "https://github.com/docxology/markdown_decision_process", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/markdown_decision_process Python docxology curated" }, { "id": "github-repo:docxology/Markov_Blanket_Detection", "type": "github_repository", "title": "docxology/Markov_Blanket_Detection", "url": "https://github.com/docxology/Markov_Blanket_Detection", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/Markov_Blanket_Detection Python docxology curated" }, { "id": "github-repo:docxology/mcp-coq-lsp", "type": "github_repository", "title": "docxology/mcp-coq-lsp", "url": "https://github.com/docxology/mcp-coq-lsp", "summary": "MCP server for Coq LSP", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/mcp-coq-lsp MCP server for Coq LSP docxology fork recent" }, { "id": "github-repo:docxology/mcp_agent_mail", "type": "github_repository", "title": "docxology/mcp_agent_mail", "url": "https://github.com/docxology/mcp_agent_mail", "summary": "Like gmail for your coding agents. Lets various different agents communicate and coordinate with each other.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/mcp_agent_mail Like gmail for your coding agents. Lets various different agents communicate and coordinate with each other. docxology agents automation claude email mcp model-context-protocol multi-agent-systems python fork recent" }, { "id": "github-repo:docxology/mdkv", "type": "github_repository", "title": "docxology/mdkv", "url": "https://github.com/docxology/mdkv", "summary": "MKV-like format and methods for Markdown", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/mdkv MKV-like format and methods for Markdown Python docxology curated" }, { "id": "github-repo:docxology/MemOS", "type": "github_repository", "title": "docxology/MemOS", "url": "https://github.com/docxology/MemOS", "summary": "MemOS (Preview) | Intelligence Begins with Memory", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/MemOS MemOS (Preview) | Intelligence Begins with Memory Python docxology fork" }, { "id": "github-repo:docxology/memvid", "type": "github_repository", "title": "docxology/memvid", "url": "https://github.com/docxology/memvid", "summary": "Video-based AI memory library. Store millions of text chunks in MP4 files with lightning-fast semantic search. No database needed.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/memvid Video-based AI memory library. Store millions of text chunks in MP4 files with lightning-fast semantic search. No database needed. docxology fork" }, { "id": "github-repo:docxology/MetaInformAnt", "type": "github_repository", "title": "docxology/MetaInformAnt", "url": "https://github.com/docxology/MetaInformAnt", "summary": "Integration for Ants and Beyond", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/MetaInformAnt Integration for Ants and Beyond Python docxology active-inference ant-behavior ants computational-biology ecology entomology hymenoptera multi-agent-systems python curated recent" }, { "id": "github-repo:docxology/metta", "type": "github_repository", "title": "docxology/metta", "url": "https://github.com/docxology/metta", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/metta Python docxology fork" }, { "id": "github-repo:docxology/metta-1", "type": "github_repository", "title": "docxology/metta-1", "url": "https://github.com/docxology/metta-1", "summary": "A reinforcement learning codebase focusing on the emergence of cooperation and alignment in multi-agent AI systems.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/metta-1 A reinforcement learning codebase focusing on the emergence of cooperation and alignment in multi-agent AI systems. Python docxology fork" }, { "id": "github-repo:docxology/mindgraph", "type": "github_repository", "title": "docxology/mindgraph", "url": "https://github.com/docxology/mindgraph", "summary": "proof of concept prototype for generating and querying against a large knowledge graph with ai", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/mindgraph proof of concept prototype for generating and querying against a large knowledge graph with ai Python docxology fork" }, { "id": "github-repo:docxology/mission-control", "type": "github_repository", "title": "docxology/mission-control", "url": "https://github.com/docxology/mission-control", "summary": "The open-source dashboard for AI agent orchestration. Manage agent fleets, track tasks, monitor costs, and orchestrate workflows — with direct CLI integration, GitHub sync, and real-time monitoring.", "domain": "docxology", "tags": [ "github", "repository", "TypeScript", "docxology", "fork", "recent" ], "content": "docxology/mission-control The open-source dashboard for AI agent orchestration. Manage agent fleets, track tasks, monitor costs, and orchestrate workflows — with direct CLI integration, GitHub sync, and real-time monitoring. TypeScript docxology fork recent" }, { "id": "github-repo:docxology/movrax", "type": "github_repository", "title": "docxology/movrax", "url": "https://github.com/docxology/movrax", "summary": "Military-Grade Persistent Memory Operating System", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/movrax Military-Grade Persistent Memory Operating System docxology fork" }, { "id": "github-repo:docxology/Mr.-Ranedeer-AI-Tutor", "type": "github_repository", "title": "docxology/Mr.-Ranedeer-AI-Tutor", "url": "https://github.com/docxology/Mr.-Ranedeer-AI-Tutor", "summary": "A GPT-4 AI Tutor Prompt for customizable personalized learning experiences.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Mr.-Ranedeer-AI-Tutor A GPT-4 AI Tutor Prompt for customizable personalized learning experiences. docxology fork" }, { "id": "github-repo:docxology/multi-time", "type": "github_repository", "title": "docxology/multi-time", "url": "https://github.com/docxology/multi-time", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "recent" ], "content": "docxology/multi-time Python docxology recent" }, { "id": "github-repo:docxology/navi", "type": "github_repository", "title": "docxology/navi", "url": "https://github.com/docxology/navi", "summary": "An interactive cheatsheet tool for the command-line", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/navi An interactive cheatsheet tool for the command-line docxology fork" }, { "id": "github-repo:docxology/nCov2019", "type": "github_repository", "title": "docxology/nCov2019", "url": "https://github.com/docxology/nCov2019", "summary": "query stats of infected coronavirus cases", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/nCov2019 query stats of infected coronavirus cases docxology fork" }, { "id": "github-repo:docxology/ngc-learn", "type": "github_repository", "title": "docxology/ngc-learn", "url": "https://github.com/docxology/ngc-learn", "summary": "NGC-Learn: Neurobiological Systems Simulation and NeuroAI Design in Python", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/ngc-learn NGC-Learn: Neurobiological Systems Simulation and NeuroAI Design in Python Python docxology fork" }, { "id": "github-repo:docxology/nockchain", "type": "github_repository", "title": "docxology/nockchain", "url": "https://github.com/docxology/nockchain", "summary": "Nockchain protocol monorepo", "domain": "docxology", "tags": [ "github", "repository", "Rust", "docxology", "fork" ], "content": "docxology/nockchain Nockchain protocol monorepo Rust docxology fork" }, { "id": "github-repo:docxology/non-typical-OSINT-guide", "type": "github_repository", "title": "docxology/non-typical-OSINT-guide", "url": "https://github.com/docxology/non-typical-OSINT-guide", "summary": "The most unusual OSINT guide you've ever seen. The repository is intended for bored professionals only. PRs are welcome! ", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/non-typical-OSINT-guide The most unusual OSINT guide you've ever seen. The repository is intended for bored professionals only. PRs are welcome! docxology fork" }, { "id": "github-repo:docxology/ntqr_llm", "type": "github_repository", "title": "docxology/ntqr_llm", "url": "https://github.com/docxology/ntqr_llm", "summary": "Algebraic NTQR evaluation study of LLM-persona ensembles on unlabeled votes", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/ntqr_llm Algebraic NTQR evaluation study of LLM-persona ensembles on unlabeled votes Python docxology curated recent" }, { "id": "github-repo:docxology/nvmath-python", "type": "github_repository", "title": "docxology/nvmath-python", "url": "https://github.com/docxology/nvmath-python", "summary": "NVIDIA Math Libraries for the Python Ecosystem", "domain": "docxology", "tags": [ "github", "repository", "Cython", "docxology", "fork" ], "content": "docxology/nvmath-python NVIDIA Math Libraries for the Python Ecosystem Cython docxology fork" }, { "id": "github-repo:docxology/observer-patch-holography", "type": "github_repository", "title": "docxology/observer-patch-holography", "url": "https://github.com/docxology/observer-patch-holography", "summary": "OPH is an active research program aiming to construct a fundamental theory of physics from observer consistency.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/observer-patch-holography OPH is an active research program aiming to construct a fundamental theory of physics from observer consistency. docxology fork recent" }, { "id": "github-repo:docxology/obsidian-construction-from-text", "type": "github_repository", "title": "docxology/obsidian-construction-from-text", "url": "https://github.com/docxology/obsidian-construction-from-text", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/obsidian-construction-from-text Python docxology curated" }, { "id": "github-repo:docxology/obsidian-scientific-research-vault", "type": "github_repository", "title": "docxology/obsidian-scientific-research-vault", "url": "https://github.com/docxology/obsidian-scientific-research-vault", "summary": "An already-configured Obsidian vault for scientific research", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/obsidian-scientific-research-vault An already-configured Obsidian vault for scientific research docxology fork" }, { "id": "github-repo:docxology/oh-my-opencode", "type": "github_repository", "title": "docxology/oh-my-opencode", "url": "https://github.com/docxology/oh-my-opencode", "summary": "#1 OpenCode Plugin- Battery included. ASYNC SUBAGENTS (YES LIKE CLAUDE CODE) · Curated agents with proper models · Crafted tools like LSP/AST included · Curated MCPs · Claude Code Compatible Layer — Steroids for your OpenCode. The Best LLM Agent Experience is Here.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/oh-my-opencode #1 OpenCode Plugin- Battery included. ASYNC SUBAGENTS (YES LIKE CLAUDE CODE) · Curated agents with proper models · Crafted tools like LSP/AST included · Curated MCPs · Claude Code Compatible Layer — Steroids for your OpenCode. The Best LLM Agent Experience is Here. docxology fork" }, { "id": "github-repo:docxology/omlx", "type": "github_repository", "title": "docxology/omlx", "url": "https://github.com/docxology/omlx", "summary": "LLM inference server with continuous batching & SSD caching for Apple Silicon — managed from the macOS menu bar", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/omlx LLM inference server with continuous batching & SSD caching for Apple Silicon — managed from the macOS menu bar docxology fork recent" }, { "id": "github-repo:docxology/onefilellm", "type": "github_repository", "title": "docxology/onefilellm", "url": "https://github.com/docxology/onefilellm", "summary": "Specify a github or local repo, github pull request, arXiv or Sci-Hub paper, Youtube transcript or documentation URL on the web and scrape into a text file and clipboard for easier LLM ingestion", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/onefilellm Specify a github or local repo, github pull request, arXiv or Sci-Hub paper, Youtube transcript or documentation URL on the web and scrape into a text file and clipboard for easier LLM ingestion docxology fork" }, { "id": "github-repo:docxology/OnlyKey-App", "type": "github_repository", "title": "docxology/OnlyKey-App", "url": "https://github.com/docxology/OnlyKey-App", "summary": "The OnlyKey App is used for the initial setup and configuration of OnlyKey. Supported on Windows, macOS, Linux, and Chromebook (with Chrome App).", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/OnlyKey-App The OnlyKey App is used for the initial setup and configuration of OnlyKey. Supported on Windows, macOS, Linux, and Chromebook (with Chrome App). docxology fork" }, { "id": "github-repo:docxology/OnlyKey-Firmware", "type": "github_repository", "title": "docxology/OnlyKey-Firmware", "url": "https://github.com/docxology/OnlyKey-Firmware", "summary": "The OnlyKey Firmware runs on the OnlyKey itself and provides the core functionality of OnlyKey.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/OnlyKey-Firmware The OnlyKey Firmware runs on the OnlyKey itself and provides the core functionality of OnlyKey. docxology fork" }, { "id": "github-repo:docxology/Open-Higgsfield-AI", "type": "github_repository", "title": "docxology/Open-Higgsfield-AI", "url": "https://github.com/docxology/Open-Higgsfield-AI", "summary": "Open-source alternative to Higgsfield AI — Free AI image generation & cinema studio with 20+ models (Flux, SDXL, Midjourney, Ideogram). Self-hosted, customizable, MIT licensed.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/Open-Higgsfield-AI Open-source alternative to Higgsfield AI — Free AI image generation & cinema studio with 20+ models (Flux, SDXL, Midjourney, Ideogram). Self-hosted, customizable, MIT licensed. docxology fork recent" }, { "id": "github-repo:docxology/open-source-mentorship", "type": "github_repository", "title": "docxology/open-source-mentorship", "url": "https://github.com/docxology/open-source-mentorship", "summary": "Inspiring the next generation of open source contributors and maintainers", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/open-source-mentorship Inspiring the next generation of open source contributors and maintainers docxology fork" }, { "id": "github-repo:docxology/OpenData", "type": "github_repository", "title": "docxology/OpenData", "url": "https://github.com/docxology/OpenData", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/OpenData docxology fork" }, { "id": "github-repo:docxology/OpenDevin", "type": "github_repository", "title": "docxology/OpenDevin", "url": "https://github.com/docxology/OpenDevin", "summary": "🐚 OpenDevin: Code Less, Make More", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/OpenDevin 🐚 OpenDevin: Code Less, Make More docxology fork" }, { "id": "github-repo:docxology/openevolve", "type": "github_repository", "title": "docxology/openevolve", "url": "https://github.com/docxology/openevolve", "summary": "Open-source implementation of AlphaEvolve", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/openevolve Open-source implementation of AlphaEvolve docxology fork" }, { "id": "github-repo:docxology/OpenGauss", "type": "github_repository", "title": "docxology/OpenGauss", "url": "https://github.com/docxology/OpenGauss", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork", "recent" ], "content": "docxology/OpenGauss Python docxology fork recent" }, { "id": "github-repo:docxology/OpenManus", "type": "github_repository", "title": "docxology/OpenManus", "url": "https://github.com/docxology/OpenManus", "summary": "No fortress, purely open ground. OpenManus is Coming.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/OpenManus No fortress, purely open ground. OpenManus is Coming. Python docxology fork" }, { "id": "github-repo:docxology/OpenPlanter", "type": "github_repository", "title": "docxology/OpenPlanter", "url": "https://github.com/docxology/OpenPlanter", "summary": "Open-source smart planting system — IoT sensors, automated irrigation, and sustainable agriculture tools", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/OpenPlanter Open-source smart planting system — IoT sensors, automated irrigation, and sustainable agriculture tools docxology agriculture arduino iot open-source plants sensors smart-farming sustainability fork recent" }, { "id": "github-repo:docxology/opentir", "type": "github_repository", "title": "docxology/opentir", "url": "https://github.com/docxology/opentir", "summary": "OpenTIR — Open-source tool for multi-repo analysis, code visualization, and software research intelligence", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/opentir OpenTIR — Open-source tool for multi-repo analysis, code visualization, and software research intelligence Python docxology code-analysis multi-repo open-source python research-tools software-analysis visualization curated recent" }, { "id": "github-repo:docxology/osc-geo-h3grid-srv", "type": "github_repository", "title": "docxology/osc-geo-h3grid-srv", "url": "https://github.com/docxology/osc-geo-h3grid-srv", "summary": "Geospatial Data Mesh: Index Service", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/osc-geo-h3grid-srv Geospatial Data Mesh: Index Service Python docxology fork" }, { "id": "github-repo:docxology/osc-geo-h3loader-cli", "type": "github_repository", "title": "docxology/osc-geo-h3loader-cli", "url": "https://github.com/docxology/osc-geo-h3loader-cli", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/osc-geo-h3loader-cli Python docxology fork" }, { "id": "github-repo:docxology/OSINT-Framework", "type": "github_repository", "title": "docxology/OSINT-Framework", "url": "https://github.com/docxology/OSINT-Framework", "summary": "OSINT Framework", "domain": "docxology", "tags": [ "github", "repository", "JavaScript", "docxology", "fork" ], "content": "docxology/OSINT-Framework OSINT Framework JavaScript docxology fork" }, { "id": "github-repo:docxology/osint_stuff_tool_collection", "type": "github_repository", "title": "docxology/osint_stuff_tool_collection", "url": "https://github.com/docxology/osint_stuff_tool_collection", "summary": "A collection of several hundred online tools for OSINT", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "fork" ], "content": "docxology/osint_stuff_tool_collection A collection of several hundred online tools for OSINT HTML docxology fork" }, { "id": "github-repo:docxology/p3if", "type": "github_repository", "title": "docxology/p3if", "url": "https://github.com/docxology/p3if", "summary": "The Properties, Processes, and Perspectives Inter-Framework (P3IF): Multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/p3if The Properties, Processes, and Perspectives Inter-Framework (P3IF): Multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security Python docxology curated" }, { "id": "github-repo:docxology/PageIndex", "type": "github_repository", "title": "docxology/PageIndex", "url": "https://github.com/docxology/PageIndex", "summary": "📄🧠 PageIndex: Document Index for Reasoning-based RAG", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/PageIndex 📄🧠 PageIndex: Document Index for Reasoning-based RAG docxology fork" }, { "id": "github-repo:docxology/pandoc", "type": "github_repository", "title": "docxology/pandoc", "url": "https://github.com/docxology/pandoc", "summary": "Universal markup converter", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/pandoc Universal markup converter docxology fork" }, { "id": "github-repo:docxology/paws-on-mcp", "type": "github_repository", "title": "docxology/paws-on-mcp", "url": "https://github.com/docxology/paws-on-mcp", "summary": "A comprehensive Model Context Protocol (MCP) server implementing the latest specification.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/paws-on-mcp A comprehensive Model Context Protocol (MCP) server implementing the latest specification. Python docxology fork" }, { "id": "github-repo:docxology/peepo", "type": "github_repository", "title": "docxology/peepo", "url": "https://github.com/docxology/peepo", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/peepo docxology fork" }, { "id": "github-repo:docxology/perplexityai", "type": "github_repository", "title": "docxology/perplexityai", "url": "https://github.com/docxology/perplexityai", "summary": "A python api to use perplexity.ai", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/perplexityai A python api to use perplexity.ai docxology fork" }, { "id": "github-repo:docxology/personal-security-checklist", "type": "github_repository", "title": "docxology/personal-security-checklist", "url": "https://github.com/docxology/personal-security-checklist", "summary": "🔒 A curated checklist of 300+ tips for protecting digital security and privacy in 2022", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/personal-security-checklist 🔒 A curated checklist of 300+ tips for protecting digital security and privacy in 2022 docxology fork" }, { "id": "github-repo:docxology/Personal_AI_Infrastructure", "type": "github_repository", "title": "docxology/Personal_AI_Infrastructure", "url": "https://github.com/docxology/Personal_AI_Infrastructure", "summary": "Personal AI Infrastructure for upgrading humans.", "domain": "docxology", "tags": [ "github", "repository", "TypeScript", "docxology", "fork", "recent" ], "content": "docxology/Personal_AI_Infrastructure Personal AI Infrastructure for upgrading humans. TypeScript docxology ai-tools automation infrastructure personal-ai productivity python self-improvement fork recent" }, { "id": "github-repo:docxology/pkl", "type": "github_repository", "title": "docxology/pkl", "url": "https://github.com/docxology/pkl", "summary": "A configuration as code language with rich validation and tooling.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/pkl A configuration as code language with rich validation and tooling. docxology fork" }, { "id": "github-repo:docxology/plandex", "type": "github_repository", "title": "docxology/plandex", "url": "https://github.com/docxology/plandex", "summary": "An AI coding engine for complex tasks", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/plandex An AI coding engine for complex tasks docxology fork" }, { "id": "github-repo:docxology/polis", "type": "github_repository", "title": "docxology/polis", "url": "https://github.com/docxology/polis", "summary": ":milky_way: Open Source AI for large scale open ended feedback", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/polis :milky_way: Open Source AI for large scale open ended feedback docxology fork" }, { "id": "github-repo:docxology/PRefLexOR", "type": "github_repository", "title": "docxology/PRefLexOR", "url": "https://github.com/docxology/PRefLexOR", "summary": "Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/PRefLexOR Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning docxology fork" }, { "id": "github-repo:docxology/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers", "type": "github_repository", "title": "docxology/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers", "url": "https://github.com/docxology/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers", "summary": "aka \"Bayesian Methods for Hackers\": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;) ", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers aka \"Bayesian Methods for Hackers\": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;) docxology fork" }, { "id": "github-repo:docxology/pyDMBD", "type": "github_repository", "title": "docxology/pyDMBD", "url": "https://github.com/docxology/pyDMBD", "summary": "Dynamic Markov Blanket Discovery", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/pyDMBD Dynamic Markov Blanket Discovery Python docxology fork" }, { "id": "github-repo:docxology/pydymax", "type": "github_repository", "title": "docxology/pydymax", "url": "https://github.com/docxology/pydymax", "summary": "Python Dymaxion Projection Module", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/pydymax Python Dymaxion Projection Module Python docxology fork" }, { "id": "github-repo:docxology/pymdp", "type": "github_repository", "title": "docxology/pymdp", "url": "https://github.com/docxology/pymdp", "summary": "A Python implementation of active inference for Markov Decision Processes", "domain": "docxology", "tags": [ "github", "repository", "Jupyter Notebook", "docxology", "fork", "recent" ], "content": "docxology/pymdp A Python implementation of active inference for Markov Decision Processes Jupyter Notebook docxology fork recent" }, { "id": "github-repo:docxology/pyreason", "type": "github_repository", "title": "docxology/pyreason", "url": "https://github.com/docxology/pyreason", "summary": "An explainable inference software supporting annotated, real valued, graph based and temporal logic ", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/pyreason An explainable inference software supporting annotated, real valued, graph based and temporal logic docxology fork" }, { "id": "github-repo:docxology/python-cheatsheet", "type": "github_repository", "title": "docxology/python-cheatsheet", "url": "https://github.com/docxology/python-cheatsheet", "summary": "Comprehensive Python Cheatsheet", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/python-cheatsheet Comprehensive Python Cheatsheet docxology fork" }, { "id": "github-repo:docxology/qr_live_protocol", "type": "github_repository", "title": "docxology/qr_live_protocol", "url": "https://github.com/docxology/qr_live_protocol", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/qr_live_protocol Python docxology curated" }, { "id": "github-repo:docxology/qrdate", "type": "github_repository", "title": "docxology/qrdate", "url": "https://github.com/docxology/qrdate", "summary": "Signed timestamps inside QR codes for verifying dates in realtime reporting", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/qrdate Signed timestamps inside QR codes for verifying dates in realtime reporting docxology fork" }, { "id": "github-repo:docxology/QuadCraft", "type": "github_repository", "title": "docxology/QuadCraft", "url": "https://github.com/docxology/QuadCraft", "summary": "MineCraft with Tetrahedra (Quadray coordinates)", "domain": "docxology", "tags": [ "github", "repository", "JavaScript", "docxology", "curated", "recent" ], "content": "docxology/QuadCraft MineCraft with Tetrahedra (Quadray coordinates) JavaScript docxology 3d game geometry javascript minecraft open-source quadray-coordinates tetrahedra voxel curated recent" }, { "id": "github-repo:docxology/QuadMath", "type": "github_repository", "title": "docxology/QuadMath", "url": "https://github.com/docxology/QuadMath", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "TeX", "docxology", "curated" ], "content": "docxology/QuadMath TeX docxology curated" }, { "id": "github-repo:docxology/quantum-logical-framework", "type": "github_repository", "title": "docxology/quantum-logical-framework", "url": "https://github.com/docxology/quantum-logical-framework", "summary": "quantum genesis constructive possibilist quantum logical synthesis", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork", "recent" ], "content": "docxology/quantum-logical-framework quantum genesis constructive possibilist quantum logical synthesis Python docxology fork recent" }, { "id": "github-repo:docxology/quantum_geometric_tensor", "type": "github_repository", "title": "docxology/quantum_geometric_tensor", "url": "https://github.com/docxology/quantum_geometric_tensor", "summary": "High performance hybrid classical-quantum computing learning framework written in C", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/quantum_geometric_tensor High performance hybrid classical-quantum computing learning framework written in C docxology fork" }, { "id": "github-repo:docxology/ragapp", "type": "github_repository", "title": "docxology/ragapp", "url": "https://github.com/docxology/ragapp", "summary": "The easiest way to use Agentic RAG in any enterprise", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/ragapp The easiest way to use Agentic RAG in any enterprise docxology fork" }, { "id": "github-repo:docxology/RamiGPT", "type": "github_repository", "title": "docxology/RamiGPT", "url": "https://github.com/docxology/RamiGPT", "summary": "Autonomous Privilege Escalation using OpenAI", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/RamiGPT Autonomous Privilege Escalation using OpenAI docxology fork" }, { "id": "github-repo:docxology/rchain", "type": "github_repository", "title": "docxology/rchain", "url": "https://github.com/docxology/rchain", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Scala", "docxology", "fork" ], "content": "docxology/rchain Scala docxology fork" }, { "id": "github-repo:docxology/README", "type": "github_repository", "title": "docxology/README", "url": "https://github.com/docxology/README", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology" ], "content": "docxology/README docxology" }, { "id": "github-repo:docxology/red", "type": "github_repository", "title": "docxology/red", "url": "https://github.com/docxology/red", "summary": "Red is a next-generation programming language strongly inspired by Rebol, but with a broader field of usage thanks to its native-code compiler, from system programming to high-level scripting and cross-platform reactive GUI, while providing modern support for concurrency, all in a zero-install, zero-config, single ~1MB file! ", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/red Red is a next-generation programming language strongly inspired by Rebol, but with a broader field of usage thanks to its native-code compiler, from system programming to high-level scripting and cross-platform reactive GUI, while providing modern support for concurrency, all in a zero-install, zero-config, single ~1MB file! docxology fork" }, { "id": "github-repo:docxology/romeremastered", "type": "github_repository", "title": "docxology/romeremastered", "url": "https://github.com/docxology/romeremastered", "summary": "Total War: ROME REMASTERED modding documentation ", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/romeremastered Total War: ROME REMASTERED modding documentation docxology fork" }, { "id": "github-repo:docxology/rules_py", "type": "github_repository", "title": "docxology/rules_py", "url": "https://github.com/docxology/rules_py", "summary": "More compatible Bazel rules for running Python tools and building Python projects", "domain": "docxology", "tags": [ "github", "repository", "Starlark", "docxology", "fork" ], "content": "docxology/rules_py More compatible Bazel rules for running Python tools and building Python projects Starlark docxology fork" }, { "id": "github-repo:docxology/RxInfer.jl", "type": "github_repository", "title": "docxology/RxInfer.jl", "url": "https://github.com/docxology/RxInfer.jl", "summary": "Julia package for automated Bayesian inference on a factor graph with reactive message passing", "domain": "docxology", "tags": [ "github", "repository", "Jupyter Notebook", "docxology", "fork" ], "content": "docxology/RxInfer.jl Julia package for automated Bayesian inference on a factor graph with reactive message passing Jupyter Notebook docxology fork" }, { "id": "github-repo:docxology/RxInferExamples.jl", "type": "github_repository", "title": "docxology/RxInferExamples.jl", "url": "https://github.com/docxology/RxInferExamples.jl", "summary": "This repository contains examples for RxInfer.jl", "domain": "docxology", "tags": [ "github", "repository", "Julia", "docxology", "fork" ], "content": "docxology/RxInferExamples.jl This repository contains examples for RxInfer.jl Julia docxology fork" }, { "id": "github-repo:docxology/RxInferServer", "type": "github_repository", "title": "docxology/RxInferServer", "url": "https://github.com/docxology/RxInferServer", "summary": "RESTful HTTP endpoints to RxInfer", "domain": "docxology", "tags": [ "github", "repository", "Julia", "docxology", "fork" ], "content": "docxology/RxInferServer RESTful HTTP endpoints to RxInfer Julia docxology fork" }, { "id": "github-repo:docxology/salmon", "type": "github_repository", "title": "docxology/salmon", "url": "https://github.com/docxology/salmon", "summary": "🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/salmon 🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment docxology fork" }, { "id": "github-repo:docxology/School_of_Tomorrow", "type": "github_repository", "title": "docxology/School_of_Tomorrow", "url": "https://github.com/docxology/School_of_Tomorrow", "summary": "Putting a curriculum into practice. Inspired in part by The House of Tomorrow.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/School_of_Tomorrow Putting a curriculum into practice. Inspired in part by The House of Tomorrow. Python docxology fork" }, { "id": "github-repo:docxology/SciSciGPT", "type": "github_repository", "title": "docxology/SciSciGPT", "url": "https://github.com/docxology/SciSciGPT", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/SciSciGPT docxology ai bibliometrics gpt nlp python research science-of-science scientometrics fork recent" }, { "id": "github-repo:docxology/service", "type": "github_repository", "title": "docxology/service", "url": "https://github.com/docxology/service", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/service Python docxology curated" }, { "id": "github-repo:docxology/sirji", "type": "github_repository", "title": "docxology/sirji", "url": "https://github.com/docxology/sirji", "summary": "Inspired by Devin, Sirji is an open-source AI software development agent.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/sirji Inspired by Devin, Sirji is an open-source AI software development agent. docxology fork" }, { "id": "github-repo:docxology/sivers", "type": "github_repository", "title": "docxology/sivers", "url": "https://github.com/docxology/sivers", "summary": "my database and the web apps that use it", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/sivers my database and the web apps that use it docxology fork" }, { "id": "github-repo:docxology/smartville", "type": "github_repository", "title": "docxology/smartville", "url": "https://github.com/docxology/smartville", "summary": "A batteries-included testbed for deep learning based intrusion detection and mitigation.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/smartville A batteries-included testbed for deep learning based intrusion detection and mitigation. Python docxology fork" }, { "id": "github-repo:docxology/smolagents", "type": "github_repository", "title": "docxology/smolagents", "url": "https://github.com/docxology/smolagents", "summary": "🤗 smolagents: a barebones library for agents. Agents write python code to call tools and orchestrate other agents.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/smolagents 🤗 smolagents: a barebones library for agents. Agents write python code to call tools and orchestrate other agents. docxology fork" }, { "id": "github-repo:docxology/snake", "type": "github_repository", "title": "docxology/snake", "url": "https://github.com/docxology/snake", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/snake Python docxology curated" }, { "id": "github-repo:docxology/SpikingBrain-7B", "type": "github_repository", "title": "docxology/SpikingBrain-7B", "url": "https://github.com/docxology/SpikingBrain-7B", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/SpikingBrain-7B docxology fork" }, { "id": "github-repo:docxology/spin_based_neural_network", "type": "github_repository", "title": "docxology/spin_based_neural_network", "url": "https://github.com/docxology/spin_based_neural_network", "summary": "Spin-Based Neural Computation Framework for simulating quantum mechanical systems written in C", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/spin_based_neural_network Spin-Based Neural Computation Framework for simulating quantum mechanical systems written in C docxology fork" }, { "id": "github-repo:docxology/SPL-FRAMEWORK", "type": "github_repository", "title": "docxology/SPL-FRAMEWORK", "url": "https://github.com/docxology/SPL-FRAMEWORK", "summary": "SUBSUMPTION PATTERN LEARNING (SPL) MULTI-AGENT FRAMEWORK: Hierarchical foundation model agent architecture that reduces costs by 10-50x through intelligent suppression of expensive foundation model calls. Grounded in R. Arkin's behavior-based robotics and R. Brooks' subsumption architecture, SPL brings 40+ years of proven autonomous systems design", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/SPL-FRAMEWORK SUBSUMPTION PATTERN LEARNING (SPL) MULTI-AGENT FRAMEWORK: Hierarchical foundation model agent architecture that reduces costs by 10-50x through intelligent suppression of expensive foundation model calls. Grounded in R. Arkin's behavior-based robotics and R. Brooks' subsumption architecture, SPL brings 40+ years of proven autonomous systems design docxology fork" }, { "id": "github-repo:docxology/spm", "type": "github_repository", "title": "docxology/spm", "url": "https://github.com/docxology/spm", "summary": "SPM (Statistical Parametric Mapping) - Development Version", "domain": "docxology", "tags": [ "github", "repository", "MATLAB", "docxology", "fork" ], "content": "docxology/spm SPM (Statistical Parametric Mapping) - Development Version MATLAB docxology fork" }, { "id": "github-repo:docxology/SPM.jl", "type": "github_repository", "title": "docxology/SPM.jl", "url": "https://github.com/docxology/SPM.jl", "summary": "SPM in Julia", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/SPM.jl SPM in Julia docxology fork" }, { "id": "github-repo:docxology/steganographer", "type": "github_repository", "title": "docxology/steganographer", "url": "https://github.com/docxology/steganographer", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Rust", "docxology", "curated", "recent" ], "content": "docxology/steganographer Rust docxology cryptography media-verification open-source python security steganography watermarking curated recent" }, { "id": "github-repo:docxology/sunspot", "type": "github_repository", "title": "docxology/sunspot", "url": "https://github.com/docxology/sunspot", "summary": "Correlating Github activity with Solar activity", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "recent" ], "content": "docxology/sunspot Correlating Github activity with Solar activity Python docxology recent" }, { "id": "github-repo:docxology/surf", "type": "github_repository", "title": "docxology/surf", "url": "https://github.com/docxology/surf", "summary": "Personal AI Notebooks. Organize files & webpages and generate notes from them. Open source, local & open data, open model choice (incl. local).", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/surf Personal AI Notebooks. Organize files & webpages and generate notes from them. Open source, local & open data, open model choice (incl. local). docxology fork" }, { "id": "github-repo:docxology/SWE-agent", "type": "github_repository", "title": "docxology/SWE-agent", "url": "https://github.com/docxology/SWE-agent", "summary": "SWE-agent: Agent Computer Interfaces Enable Software Engineering Language Models", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/SWE-agent SWE-agent: Agent Computer Interfaces Enable Software Engineering Language Models Python docxology fork" }, { "id": "github-repo:docxology/symergetics", "type": "github_repository", "title": "docxology/symergetics", "url": "https://github.com/docxology/symergetics", "summary": "Symbolic Synergetic for Math & Beyond ", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/symergetics Symbolic Synergetic for Math & Beyond Python docxology curated" }, { "id": "github-repo:docxology/sympy-mcp", "type": "github_repository", "title": "docxology/sympy-mcp", "url": "https://github.com/docxology/sympy-mcp", "summary": "A MCP server for symbolic manipulation of mathematical expressions", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/sympy-mcp A MCP server for symbolic manipulation of mathematical expressions docxology fork" }, { "id": "github-repo:docxology/Syntheverse", "type": "github_repository", "title": "docxology/Syntheverse", "url": "https://github.com/docxology/Syntheverse", "summary": "This repository houses all code and documentation for the Syntheverse Hydrogen-Holographic Fractal Crypto AI Game and Ecosystem, including the Proof-of-Contribution (PoC) protocol and SYNTH tokenomics. Explore, contribute, validate discoveries, and help build a distributed, immutable, living scientific, technological, AI, and alignment economy.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Syntheverse This repository houses all code and documentation for the Syntheverse Hydrogen-Holographic Fractal Crypto AI Game and Ecosystem, including the Proof-of-Contribution (PoC) protocol and SYNTH tokenomics. Explore, contribute, validate discoveries, and help build a distributed, immutable, living scientific, technological, AI, and alignment economy. docxology fork" }, { "id": "github-repo:docxology/systematics-v0.5", "type": "github_repository", "title": "docxology/systematics-v0.5", "url": "https://github.com/docxology/systematics-v0.5", "summary": "Systematics v0.5 - Refactored version", "domain": "docxology", "tags": [ "github", "repository", "Rust", "docxology", "fork" ], "content": "docxology/systematics-v0.5 Systematics v0.5 - Refactored version Rust docxology fork" }, { "id": "github-repo:docxology/TCSDecomp", "type": "github_repository", "title": "docxology/TCSDecomp", "url": "https://github.com/docxology/TCSDecomp", "summary": "Trend Cycle Seasonal Decomposition Using the Kalman Filter", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/TCSDecomp Trend Cycle Seasonal Decomposition Using the Kalman Filter docxology fork" }, { "id": "github-repo:docxology/template", "type": "github_repository", "title": "docxology/template", "url": "https://github.com/docxology/template", "summary": "Production-grade scaffold for reproducible computational research — 10-stage DAG pipelines, ≥90% test coverage, cryptographic provenance (SHA-256 + steganographic PDF watermarking), multi-project workspace, AI-agent-ready with AGENTS.md / SKILL.md throughout.", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/template Production-grade scaffold for reproducible computational research — 10-stage DAG pipelines, ≥90% test coverage, cryptographic provenance (SHA-256 + steganographic PDF watermarking), multi-project workspace, AI-agent-ready with AGENTS.md / SKILL.md throughout. Python docxology agents-md ai-agents claude-code computational-research cursor latex multi-project ollama pandoc provenance pytest python reproducible-research research-template scientific-computing steganography uv zenodo curated recent" }, { "id": "github-repo:docxology/template-release-smoke", "type": "github_repository", "title": "docxology/template-release-smoke", "url": "https://github.com/docxology/template-release-smoke", "summary": "Integration smoke test for template release orchestrator (do not cite)", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "recent" ], "content": "docxology/template-release-smoke Integration smoke test for template release orchestrator (do not cite) docxology recent" }, { "id": "github-repo:docxology/template_active_inference", "type": "github_repository", "title": "docxology/template_active_inference", "url": "https://github.com/docxology/template_active_inference", "summary": "Active inference multi-track exemplar releases", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "recent" ], "content": "docxology/template_active_inference Active inference multi-track exemplar releases docxology recent" }, { "id": "github-repo:docxology/template_autoresearch_project", "type": "github_repository", "title": "docxology/template_autoresearch_project", "url": "https://github.com/docxology/template_autoresearch_project", "summary": "Template autoresearch project exemplar releases", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "recent" ], "content": "docxology/template_autoresearch_project Template autoresearch project exemplar releases docxology recent" }, { "id": "github-repo:docxology/template_autoscientists", "type": "github_repository", "title": "docxology/template_autoscientists", "url": "https://github.com/docxology/template_autoscientists", "summary": "AutoScientists: a deterministic multi-agent scientific-discovery coordination harness — public exemplar of the docxology/template reproducible-research paradigm (≥90% test coverage, no mocks, double-published GitHub + Zenodo 10.5281/zenodo.20533669).", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/template_autoscientists AutoScientists: a deterministic multi-agent scientific-discovery coordination harness — public exemplar of the docxology/template reproducible-research paradigm (≥90% test coverage, no mocks, double-published GitHub + Zenodo 10.5281/zenodo.20533669). Python docxology curated recent" }, { "id": "github-repo:docxology/template_bioinformatics_project", "type": "github_repository", "title": "docxology/template_bioinformatics_project", "url": "https://github.com/docxology/template_bioinformatics_project", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "recent" ], "content": "docxology/template_bioinformatics_project Python docxology recent" }, { "id": "github-repo:docxology/template_code_project", "type": "github_repository", "title": "docxology/template_code_project", "url": "https://github.com/docxology/template_code_project", "summary": "Template code project exemplar releases", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "recent" ], "content": "docxology/template_code_project Template code project exemplar releases docxology recent" }, { "id": "github-repo:docxology/template_newspaper", "type": "github_repository", "title": "docxology/template_newspaper", "url": "https://github.com/docxology/template_newspaper", "summary": "The Triplicate: a data-driven large-format newspaper layout engine — public exemplar of the docxology/template reproducible-research paradigm (≥90% test coverage, no mocks, double-published GitHub + Zenodo 10.5281/zenodo.20533675).", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated", "recent" ], "content": "docxology/template_newspaper The Triplicate: a data-driven large-format newspaper layout engine — public exemplar of the docxology/template reproducible-research paradigm (≥90% test coverage, no mocks, double-published GitHub + Zenodo 10.5281/zenodo.20533675). Python docxology curated recent" }, { "id": "github-repo:docxology/template_prose_project", "type": "github_repository", "title": "docxology/template_prose_project", "url": "https://github.com/docxology/template_prose_project", "summary": "Template prose project exemplar releases", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "recent" ], "content": "docxology/template_prose_project Template prose project exemplar releases docxology recent" }, { "id": "github-repo:docxology/template_template", "type": "github_repository", "title": "docxology/template_template", "url": "https://github.com/docxology/template_template", "summary": "Template meta-research exemplar: self-documenting reproducible research repo", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "recent" ], "content": "docxology/template_template Template meta-research exemplar: self-documenting reproducible research repo docxology recent" }, { "id": "github-repo:docxology/template_textbook", "type": "github_repository", "title": "docxology/template_textbook", "url": "https://github.com/docxology/template_textbook", "summary": "The Template Textbook — a modular, fillable scaffold for book-length technical works (data-driven manuscript, tested computational backbone, deterministic figures + Mermaid diagrams, multi-format render).", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "curated", "recent" ], "content": "docxology/template_textbook The Template Textbook — a modular, fillable scaffold for book-length technical works (data-driven manuscript, tested computational backbone, deterministic figures + Mermaid diagrams, multi-format render). HTML docxology curated recent" }, { "id": "github-repo:docxology/test_public", "type": "github_repository", "title": "docxology/test_public", "url": "https://github.com/docxology/test_public", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology" ], "content": "docxology/test_public docxology" }, { "id": "github-repo:docxology/thrml", "type": "github_repository", "title": "docxology/thrml", "url": "https://github.com/docxology/thrml", "summary": "Thermodynamic Hypergraphical Model Library", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/thrml Thermodynamic Hypergraphical Model Library Python docxology fork" }, { "id": "github-repo:docxology/timeline_generator", "type": "github_repository", "title": "docxology/timeline_generator", "url": "https://github.com/docxology/timeline_generator", "summary": "Timeline Generator — Knowledge Graph Explorer for historical figures, networks, and OSINT research", "domain": "docxology", "tags": [ "github", "repository", "TypeScript", "docxology", "curated", "recent" ], "content": "docxology/timeline_generator Timeline Generator — Knowledge Graph Explorer for historical figures, networks, and OSINT research TypeScript docxology data-visualization history knowledge-graph open-source osint timeline typescript visualization curated recent" }, { "id": "github-repo:docxology/tolaria", "type": "github_repository", "title": "docxology/tolaria", "url": "https://github.com/docxology/tolaria", "summary": "Desktop app to manage markdown knowledge bases", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/tolaria Desktop app to manage markdown knowledge bases docxology fork recent" }, { "id": "github-repo:docxology/TradingAgents", "type": "github_repository", "title": "docxology/TradingAgents", "url": "https://github.com/docxology/TradingAgents", "summary": "TradingAgents: Multi-Agents LLM Financial Trading Framework", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/TradingAgents TradingAgents: Multi-Agents LLM Financial Trading Framework docxology fork recent" }, { "id": "github-repo:docxology/transformer", "type": "github_repository", "title": "docxology/transformer", "url": "https://github.com/docxology/transformer", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "curated" ], "content": "docxology/transformer Python docxology curated" }, { "id": "github-repo:docxology/triton", "type": "github_repository", "title": "docxology/triton", "url": "https://github.com/docxology/triton", "summary": "Development repository for the Triton language and compiler", "domain": "docxology", "tags": [ "github", "repository", "Python", "docxology", "fork" ], "content": "docxology/triton Development repository for the Triton language and compiler Python docxology fork" }, { "id": "github-repo:docxology/uhubctl", "type": "github_repository", "title": "docxology/uhubctl", "url": "https://github.com/docxology/uhubctl", "summary": "uhubctl - USB hub per-port power control", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/uhubctl uhubctl - USB hub per-port power control docxology fork" }, { "id": "github-repo:docxology/ultralink-docx", "type": "github_repository", "title": "docxology/ultralink-docx", "url": "https://github.com/docxology/ultralink-docx", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "HTML", "docxology", "curated" ], "content": "docxology/ultralink-docx HTML docxology curated" }, { "id": "github-repo:docxology/urtext", "type": "github_repository", "title": "docxology/urtext", "url": "https://github.com/docxology/urtext", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/urtext docxology fork" }, { "id": "github-repo:docxology/urtext_sublime", "type": "github_repository", "title": "docxology/urtext_sublime", "url": "https://github.com/docxology/urtext_sublime", "summary": "Urtext is a headless plaintext framework for writing and information management. For desktop use (PC/Mac/Linux) Urtext is implemented in Sublime Text.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/urtext_sublime Urtext is a headless plaintext framework for writing and information management. For desktop use (PC/Mac/Linux) Urtext is implemented in Sublime Text. docxology fork" }, { "id": "github-repo:docxology/VariationalLaplace", "type": "github_repository", "title": "docxology/VariationalLaplace", "url": "https://github.com/docxology/VariationalLaplace", "summary": "docxology repository", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/VariationalLaplace docxology fork" }, { "id": "github-repo:docxology/vec2text", "type": "github_repository", "title": "docxology/vec2text", "url": "https://github.com/docxology/vec2text", "summary": "utilities for decoding deep representations (like sentence embeddings) back to text", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/vec2text utilities for decoding deep representations (like sentence embeddings) back to text docxology fork" }, { "id": "github-repo:docxology/vibeship-spawner-skills", "type": "github_repository", "title": "docxology/vibeship-spawner-skills", "url": "https://github.com/docxology/vibeship-spawner-skills", "summary": "a skill directory for world-class specialized agents, in your terminal / IDE. more sophisticated than skills with just md files. and they're free.", "domain": "docxology", "tags": [ "github", "repository", "JavaScript", "docxology", "fork", "recent" ], "content": "docxology/vibeship-spawner-skills a skill directory for world-class specialized agents, in your terminal / IDE. more sophisticated than skills with just md files. and they're free. JavaScript docxology fork recent" }, { "id": "github-repo:docxology/web3privacy", "type": "github_repository", "title": "docxology/web3privacy", "url": "https://github.com/docxology/web3privacy", "summary": "Web3privacy now is a research project aimed at building a culture of privacy industry in web3: the most extensive database of privacy-enhancing solutions, the framework for PEDApps ideation, use-cases database & many more. Feel free to collaborate.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/web3privacy Web3privacy now is a research project aimed at building a culture of privacy industry in web3: the most extensive database of privacy-enhancing solutions, the framework for PEDApps ideation, use-cases database & many more. Feel free to collaborate. docxology fork" }, { "id": "github-repo:docxology/wildebeest", "type": "github_repository", "title": "docxology/wildebeest", "url": "https://github.com/docxology/wildebeest", "summary": "RTL logic synthesis", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/wildebeest RTL logic synthesis docxology fork" }, { "id": "github-repo:docxology/WorldGrow", "type": "github_repository", "title": "docxology/WorldGrow", "url": "https://github.com/docxology/WorldGrow", "summary": "WorldGrow: Generating Infinite 3D World", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/WorldGrow WorldGrow: Generating Infinite 3D World docxology fork" }, { "id": "github-repo:docxology/worldmonitor", "type": "github_repository", "title": "docxology/worldmonitor", "url": "https://github.com/docxology/worldmonitor", "summary": "Real-time global intelligence dashboard — AI-powered news aggregation, geopolitical monitoring, and infrastructure tracking in a unified situational awareness interface", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/worldmonitor Real-time global intelligence dashboard — AI-powered news aggregation, geopolitical monitoring, and infrastructure tracking in a unified situational awareness interface docxology dashboard data-visualization geopolitics monitoring news-aggregation osint python situational-awareness fork recent" }, { "id": "github-repo:docxology/xai-gpt-agent-toolkit", "type": "github_repository", "title": "docxology/xai-gpt-agent-toolkit", "url": "https://github.com/docxology/xai-gpt-agent-toolkit", "summary": "Xircuits toolkit for creating and experimenting with BabyAGI/AutoGPT-style agents", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/xai-gpt-agent-toolkit Xircuits toolkit for creating and experimenting with BabyAGI/AutoGPT-style agents docxology fork" }, { "id": "github-repo:docxology/xyops", "type": "github_repository", "title": "docxology/xyops", "url": "https://github.com/docxology/xyops", "summary": "A complete workflow automation and server monitoring system.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork", "recent" ], "content": "docxology/xyops A complete workflow automation and server monitoring system. docxology fork recent" }, { "id": "github-repo:docxology/yt-transcriber", "type": "github_repository", "title": "docxology/yt-transcriber", "url": "https://github.com/docxology/yt-transcriber", "summary": "TUI app- Give it a YouTube URL and you get a transcription with possible speaker identification and optional summary or translation, all thanks to open-source AI tooling and my lack of enough free time to watch content-sparse YouTube videos", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/yt-transcriber TUI app- Give it a YouTube URL and you get a transcription with possible speaker identification and optional summary or translation, all thanks to open-source AI tooling and my lack of enough free time to watch content-sparse YouTube videos docxology fork" }, { "id": "github-repo:docxology/Zenroom", "type": "github_repository", "title": "docxology/Zenroom", "url": "https://github.com/docxology/Zenroom", "summary": "Embedded no-code VM executing human-like language to manipulate data and process cryptographic operations.", "domain": "docxology", "tags": [ "github", "repository", "", "docxology", "fork" ], "content": "docxology/Zenroom Embedded no-code VM executing human-like language to manipulate data and process cryptographic operations. docxology fork" }, { "id": "person:Daniel Ari Friedman", "type": "person", "title": "Daniel Ari Friedman", "url": "https://danielarifriedman.com/", "summary": "Computational biologist; cognitive scientist; President and Treasurer of the Active Inference Institute", "tags": [ "person", "collaborator" ], "content": "Daniel Ari Friedman Computational biologist; cognitive scientist; President and Treasurer of the Active Inference Institute https://orcid.org/0000-0001-6232-9096 https://www.wikidata.org/wiki/Q138781444 https://danielarifriedman.com/ https://github.com/docxology" }, { "id": "person:Karl Friston", "type": "person", "title": "Karl Friston", "url": "pages/COLLABORATORS.md#karl-friston--ucl-london", "summary": "Active Inference and Free Energy Principle collaborator", "tags": [ "person", "collaborator" ], "content": "Karl Friston Active Inference and Free Energy Principle collaborator pages/COLLABORATORS.md#karl-friston--ucl-london" }, { "id": "person:Deborah Gordon", "type": "person", "title": "Deborah Gordon", "url": "pages/COLLABORATORS.md#deborah-gordon--stanford-university", "summary": "Stanford PhD advisor and ant collective behavior collaborator", "tags": [ "person", "collaborator" ], "content": "Deborah Gordon Stanford PhD advisor and ant collective behavior collaborator pages/COLLABORATORS.md#deborah-gordon--stanford-university" }, { "id": "person:Thomas Parr", "type": "person", "title": "Thomas Parr", "url": "pages/COLLABORATORS.md#thomas-parr--ucl-london", "summary": "Active Inference collaborator and textbook co-author", "tags": [ "person", "collaborator" ], "content": "Thomas Parr Active Inference collaborator and textbook co-author pages/COLLABORATORS.md#thomas-parr--ucl-london" }, { "id": "person:MJ Ramstead", "type": "person", "title": "MJ Ramstead", "url": "pages/COLLABORATORS.md#maxwell-j-d-ramstead--mila--mcgill", "summary": "Active Inference and cognitive science collaborator", "tags": [ "person", "collaborator" ], "content": "MJ Ramstead Active Inference and cognitive science collaborator pages/COLLABORATORS.md#maxwell-j-d-ramstead--mila--mcgill" }, { "id": "organization:Active Inference Institute", "type": "organization", "title": "Active Inference Institute", "url": "https://www.activeinference.institute/", "summary": "Research and education nonprofit focused on Active Inference and the Free Energy Principle", "tags": [ "organization" ], "content": "Active Inference Institute https://www.activeinference.institute/ https://activeinference.org/ https://www.wikidata.org/wiki/Q139600792 https://github.com/ActiveInferenceInstitute user The ActiveInferenceInstitute GitHub account is a User account, not an Organization; requests to /orgs/ActiveInferenceInstitute return 404. Use /users/ActiveInferenceInstitute. 88-2985125 501(c)(3) public charity; IRS ruling March 2024 https://projects.propublica.org/nonprofits/organizations/882985125 Research and education nonprofit focused on Active Inference and the Free Energy Principle" }, { "id": "organization:COGSEC.org", "type": "organization", "title": "COGSEC.org", "url": "https://cogsec.org", "summary": "Cognitive security publication and research context", "tags": [ "organization" ], "content": "COGSEC.org https://cogsec.org Cognitive security publication and research context" }, { "id": "organization:Stanford University", "type": "organization", "title": "Stanford University", "url": "https://www.stanford.edu/", "summary": "PhD institution", "tags": [ "organization" ], "content": "Stanford University https://www.stanford.edu/ PhD institution" }, { "id": "organization:College of the Redwoods", "type": "organization", "title": "College of the Redwoods", "url": "https://www.redwoods.edu/", "summary": "Teaching affiliation", "tags": [ "organization" ], "content": "College of the Redwoods https://www.redwoods.edu/ Teaching affiliation" }, { "id": "claim:curated-work-count", "type": "claim", "title": "The curated bibliography contains 165 works.", "url": "/evidence.html", "summary": "curated-local · confidence: high", "tags": [ "claim", "curated-local", "high" ], "content": "The curated bibliography contains 165 works. Curated count includes papers, books, presentations, courses, playbooks, and series. Generated from the 8-column bibliography table and cross-checked against publications.html." }, { "id": "claim:paper-folder-count", "type": "claim", "title": "The repository contains 148 per-paper documentation folders.", "url": "/evidence.html", "summary": "curated-local · confidence: high", "tags": [ "claim", "curated-local", "high" ], "content": "The repository contains 148 per-paper documentation folders. Not every bibliography row has a paper folder; media/course rows may not. Folder inventory and paper metadata count." }, { "id": "claim:docxology-github-public-repos", "type": "claim", "title": "The docxology GitHub profile has 307 public repositories.", "url": "/evidence.html", "summary": "public-api · confidence: high", "tags": [ "claim", "public-api", "high" ], "content": "The docxology GitHub profile has 307 public repositories. GitHub profile count includes forks and repositories not catalogued in SOFTWARE.md. GitHub REST API user profile response." }, { "id": "claim:aii-github-public-repos", "type": "claim", "title": "The ActiveInferenceInstitute GitHub account (a User account, not an Organization) has 52 public repositories.", "url": "/evidence.html", "summary": "public-api · confidence: high", "tags": [ "claim", "public-api", "high" ], "content": "The ActiveInferenceInstitute GitHub account (a User account, not an Organization) has 52 public repositories. Use /users/ActiveInferenceInstitute, not /orgs/. Local software catalog tracks 32 AII repositories with docxology contributions. GitHub REST API user profile response (type: User). The /orgs/ActiveInferenceInstitute endpoint returns 404 because the account is a User, not an Organization." }, { "id": "claim:orcid-canonical-identifier", "type": "claim", "title": "ORCID 0000-0001-6232-9096 is the canonical researcher identifier. The canonical Google Scholar profile is DXjPFtYAAAAJ; a secondary Scholar profile (Y2bMf3MAAAAJ) is linked from ORCID and should be consolidated/disambiguated.", "url": "/evidence.html", "summary": "public-identifier · confidence: high", "tags": [ "claim", "public-identifier", "high" ], "content": "ORCID 0000-0001-6232-9096 is the canonical researcher identifier. The canonical Google Scholar profile is DXjPFtYAAAAJ; a secondary Scholar profile (Y2bMf3MAAAAJ) is linked from ORCID and should be consolidated/disambiguated. Use DXjPFtYAAAAJ as the single canonical Scholar profile for metrics. ORCID public work groups may lag new deposits and may group versions differently. ORCID profile and public works endpoint. ORCID also exposes a secondary Google Scholar ID (Y2bMf3MAAAAJ) distinct from the canonical DXjPFtYAAAAJ used for all public metrics." }, { "id": "claim:curio-cards-early-ethereum-art", "type": "claim", "title": "Curio Cards 24, 25, and 26 are early Ethereum art NFTs minted on May 9, 2017; a complete Curio Cards set later sold at Christie's 'Post-War to Present' (New York, Oct 1, 2021) for 393 ETH (~$1.2M), seven artists.", "url": "/evidence.html", "summary": "public-profile · confidence: high", "tags": [ "claim", "public-profile", "high" ], "content": "Curio Cards 24, 25, and 26 are early Ethereum art NFTs minted on May 9, 2017; a complete Curio Cards set later sold at Christie's 'Post-War to Present' (New York, Oct 1, 2021) for 393 ETH (~$1.2M), seven artists. Present the sale facts as independently verified; present the specific Christie's lot number as a first-party (Christie's) reference only, not independently corroborated. Avoid unqualified 'first/earliest NFT' superlatives. Artist attribution and mint date confirmed via Curio Cards official docs and Wikipedia; the Christie's sale (date, 393 ETH/~$1.2M, seven artists) is independently corroborated. The specific Christie's lot URL (6337619) resolves and its first-party page matches the exact Curio set, but the lot number itself is not corroborated by any source independent of Christie's." }, { "id": "claim:google-scholar-citations", "type": "claim", "title": "Google Scholar metrics are recorded as a dated snapshot: 777 citations, h-index 15, i10-index 17 (as of 2026-06-09).", "url": "/evidence.html", "summary": "dated-snapshot · confidence: high", "tags": [ "claim", "dated-snapshot", "high" ], "content": "Google Scholar metrics are recorded as a dated snapshot: 777 citations, h-index 15, i10-index 17 (as of 2026-06-09). Single source of truth: data/scholar-snapshot.json. Update only from a direct (non-cached) Scholar fetch, recording the new value, as_of date, and method there; regenerate surfaces via code/orchestrators/sync_scholar_metrics.py. Never publish a citation number above the most recent direct-fetch value. Direct logged-in browser-session fetch of the canonical profile on 2026-06-09 (non-cached, non-anonymous): All-time 777 citations, h-index 15, i10-index 17 (Since-2021: 544 / 14 / 15)." }, { "id": "claim:stanford-phd", "type": "claim", "title": "Daniel Ari Friedman earned a PhD at Stanford University with dissertation record pb813wm1484.", "url": "/evidence.html", "summary": "public-institutional-record · confidence: high", "tags": [ "claim", "public-institutional-record", "high" ], "content": "Daniel Ari Friedman earned a PhD at Stanford University with dissertation record pb813wm1484. Use the Stanford PURL as the public institutional source. Stanford PURL dissertation record and local paper folder." }, { "id": "claim:nsf-postdoc-affiliation", "type": "claim", "title": "Daniel Ari Friedman held an NSF Postdoctoral Research Fellowship in Biology (award DBI-2010290) co-trained at UC Davis; NSF budget period 2020-2022 with a no-cost extension to 2023.", "url": "/evidence.html", "summary": "public-grant-record · confidence: high", "tags": [ "claim", "public-grant-record", "high" ], "content": "Daniel Ari Friedman held an NSF Postdoctoral Research Fellowship in Biology (award DBI-2010290) co-trained at UC Davis; NSF budget period 2020-2022 with a no-cost extension to 2023. Cite the NSF award ID (DBI-2010290) as the authoritative public record. The funding record shows 2020-2022; present 2023 as a no-cost-extension affiliation, not a funded period. NSF award DBI-2010290 confirmed via Grantome (NSF PRFB, FY2020, $138,000, Davis CA). The 2020-2022 budget period is on the NSF record; the extension to 2023 aligns with the ORCID UC Davis employment span but is not itself on the funding record." }, { "id": "claim:aii-officer-roles", "type": "claim", "title": "Active Inference Institute officers: Daniel Friedman is President and Treasurer; Alexandra Mikhailova is Vice-President and Secretary (2025-ongoing). V. Bleu Knight was Secretary 2022-2024 and is a current member of the Board of Directors. The Institute is a 501(c)(3) public charity, EIN 88-2985125, IRS ruling March 2024.", "url": "/evidence.html", "summary": "public-profile · confidence: high", "tags": [ "claim", "public-profile", "high" ], "content": "Active Inference Institute officers: Daniel Friedman is President and Treasurer; Alexandra Mikhailova is Vice-President and Secretary (2025-ongoing). V. Bleu Knight was Secretary 2022-2024 and is a current member of the Board of Directors. The Institute is a 501(c)(3) public charity, EIN 88-2985125, IRS ruling March 2024. Officer roles are time-sensitive. Do not conflate Mikhailova (current VP+Secretary) with Knight (former Secretary 2022-2024, current Board member). AII officers page; 501(c)(3) status and EIN independently confirmed via ProPublica Nonprofit Explorer (IRS data, ruling March 2024)." }, { "id": "claim:aii-board-count", "type": "claim", "title": "The Active Inference Institute board page lists 10 current directors.", "url": "/evidence.html", "summary": "public-profile · confidence: high", "tags": [ "claim", "public-profile", "high" ], "content": "The Active Inference Institute board page lists 10 current directors. Board membership is time-sensitive; retain access dates in narrative pages. AII board page and local governance notes." }, { "id": "claim:aii-scientific-advisory-board-count", "type": "claim", "title": "The Active Inference Institute site lists a 33-member Scientific Advisory Board cohort for 2026.", "url": "/evidence.html", "summary": "public-profile · confidence: medium", "tags": [ "claim", "public-profile", "medium" ], "content": "The Active Inference Institute site lists a 33-member Scientific Advisory Board cohort for 2026. State the cohort as 'listed for 2026' (33 members). Do not assert a specific announcement month unless the source page states one. AII SAB page lists the 2026 cohort (33 members). The member count is corroborated; no specific announcement date (e.g. a January 2026 announcement) is independently verified." }, { "id": "claim:aii-textbook-cohorts", "type": "claim", "title": "AII Textbook Group copy references 10 cohorts through 2026.", "url": "/evidence.html", "summary": "curated-program-copy · confidence: medium", "tags": [ "claim", "curated-program-copy", "medium" ], "content": "AII Textbook Group copy references 10 cohorts through 2026. Program pages may use different public summary counts; keep local copy aligned with preferred site wording. Curated site copy and AII program page." }, { "id": "claim:college-of-the-redwoods-teaching", "type": "claim", "title": "Homepage teaching copy lists BIOL-1 at Pelican Bay and BIOL-8 Human Biology for Spring 2026.", "url": "/evidence.html", "summary": "curated-profile · confidence: medium", "tags": [ "claim", "curated-profile", "medium" ], "content": "Homepage teaching copy lists BIOL-1 at Pelican Bay and BIOL-8 Human Biology for Spring 2026. Term-specific teaching claims should be updated after each semester. Curated homepage and profile synchronization." }, { "id": "claim:cogsec-role", "type": "claim", "title": "COGSEC.org is the cognitive security publication and research context linked from the profile.", "url": "/evidence.html", "summary": "public-site · confidence: medium", "tags": [ "claim", "public-site", "medium" ], "content": "COGSEC.org is the cognitive security publication and research context linked from the profile. Prefer COGSEC pages for COGSEC-specific publication claims. Public site link and curated profile copy." }, { "id": "resume:structured-cv", "type": "resume", "title": "Daniel Ari Friedman Resume / CV", "url": "/resume/resume.pdf", "summary": "Structured CV export: 165 works, 89 software rows, education, experience, service, media, and art-use records.", "tags": [ "resume", "cv", "profile", "plaintext", "pdf" ], "content": "Daniel Ari Friedman Computational biologist, Active Inference researcher, cognitive security researcher, educator, and artist Multidisciplinary researcher and open-source builder working across social insect biology, Active Inference, cognitive security, computational frameworks, education, and art. danielarifriedman@gmail.com daniel@activeinference.institute Del Norte Triplicate Active Inference Institute Complexity Adventures COGSEC Stanford Complexity Group Stealth Startup Stealth Startup Remotor fm.analytics Cryptoptera Johnson Lab / Linksvayer Lab Gordon Lab Kopp Lab Pedicab People Movers Stanford University UC Davis University of California, Davis Stanford University University of California, Davis Crystal Springs Uplands School S3E10 The FEP: A Tool for Understanding and Modelling Complex Systems (DIA 1/SESSAO 1) Lancamento do Livro: As Colonias de Formigas Sao Conscientes? From Ants to Active Inference with Daniel Ari Friedman Building Smarter AI: Active Inference and Nested Models Interaction. In Search of Daniel Friedman's Deepest Value Active Inference and The Free Energy Principle with Daniel Friedman Episode 6: Daniel Friedman - Active Inference Institute - What is Active Inference? Artist of Curio Cards 24-26 Shares Incredible Journey through Art and Science What Ant Behavior Reveals About Complexity Science with Daniel Friedman What is Active Inference?...with Daniel Friedman Great discussion with Daniel, OG Curio Card artist, cards 24, 25, 26 Daniel Friedman Interview - Adventures in NFTs #3 Banging the Drum with Daniel Friedman KB7 Fireside: Scaling Principled Games KBCast Episode 7: Kernel Block 5 Week 6 and special guest Daniel Ari Friedman Daniel Friedman Interview - Adventures in NFTs #3 Interview with Monica Kang about Complexity Weekend, with co-founder Shaun Swanson and organizer JP Gonzales Blurb in Science magazine inventing the word disinforge Complexity Weekend featured on InnovatorsBox blog, with quotes from Friedman and others Blurb in Science magazine about rethinking time use for scientists Blurb in Science magazine about what ants can teach human city planners Blurb in Science magazine about time travel Public lecture: Red Vic lecture series, San Francisco. History and philosophy of Art and Biology. Public lecture: Red Vic lecture series, San Francisco. History and philosophy of self-organization, stigmergy, and eusocial insects. Quoted in Dopamine Nation by Dr. Anna Lembke, p. 75: The world is sensory rich and causal poor. No Signal 006: Daniel Ari Friedman and Jakub Smekal || Active Inference Daniel Friedman: Drawing Decentralized Beauty From Biology Written interview with RosyBVM Radio Interview, KPOO 89.5 FM in San Francisco Vice-President for Communication and Systems Education on the International Society for the Systems Sciences Board. Co-editor, Field and Laboratory Methods for Modern Entomology. Member (MCybS), Cybernetics Society. Information Professional Association. Active Inference Institute co-founder. Davis Complexity Group. Complexity Adventures co-founder. ALIUS Research Group contributor, editor, and co-organizer. Wonderfest Science Envoy; science outreach and community training. Entomological Society of America. NeuroChoice group, Stanford Neurosciences Institute. Graduate student member of Arts Committee for Stanford Biology department. Stanford Complexity Group. Science Teaching Through Art (STAR) outreach program; poster presentations and conversations about ants at local middle and high schools. Santa Fe Institute Complex Systems Summer School, one-month residential program. Five summers of ant fieldwork during PhD under Prof. Deborah Gordon at Southwestern Research Station, Arizona. Summer field ecology class with Stanford Prof. Rodolfo Dirzo at Las Tuxtlas tropical research station, Mexico. Summer workshop on Evolutionary and Quantitative Genetics at NIMBioS, University of Tennessee, Knoxville. Drosophila work with Dr. Michael Lang in Arizona. Invited peer reviewer for 1-10 articles per year across different journals. International Union for the Study of Social Insects. Stanford Center for Evolutionary and Human Genomics outreach programs, including teaching genetics in local middle schools and hosting high school students at Stanford. Stanford Bio Core Explorations hands-on lecture/workshop for undergraduates: Art and Biology. Science mentoring at Woodland High School. Drums and percussion for UC Davis production of RENT. Volunteer in emergency room at hospital in Sacramento, four hours per week for six months. Chess Club at UC Davis President (2012-2014), organizing free outdoor chess at the farmer's market twice weekly for two years." } ] }