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"Data Catalog Structured DataCatalog for public JSON exports. catalog structured data" }, { "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": 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"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_2026-05-13.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:accessibility", "type": "report", "title": "Static Accessibility Report", "url": "/reports/accessibility_static_2026-05-13.json", "summary": "Static accessibility and metadata audit output.", "tags": [ "accessibility", "reports" ], 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"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_2026-05-13.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/2026-05-13/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_2026-05-13.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.14108991", "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.14108991 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.14108991", "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.14108991 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": "This study investigates the role of coding sequence changes in the evolution of postdevelopmental novelty in honey bees, challenging the traditional evo-devo paradigm. Through RNA-Seq experiments, we demonstrate that pos", "year": 2023, "domain": "Entomology", "tags": [ "Paper", "Entomology", "bibliography", "honey bees", "Apis mellifera", "gene expression", "RNA-Seq", "novel traits", "taxonomically restricted genes", "coding sequence evolution" ], "content": "A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees Zenodo 10.5281/zenodo.10400744 Friedman2023SnapshotPipelineTissueSpecific047 Entomology 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. Through RNA-Seq experiments, we demonstrate that positively selected tissue-specific genes, particularly taxonomically restricted genes (TRGs), are crucial for novel physiological functions in adult honey bees. honey bees Apis mellifera gene expression RNA-Seq novel traits taxonomically restricted genes coding sequence evolution Identified the significance of coding sequence changes in the evolution of adult phenotypic novelty in honey bees. Demonstrated that positively selected tissue-specific genes underlie novel physiological functions. Highlighted the role of taxonomically restricted genes (TRGs) in conferring specialized cellular functions. Challenged the evo-devo paradigm by showing that low network connectedness in genes facilitates rapid coding sequence changes. Conducted ten RNA-Seq experiments across various tissues in honey bees. Analyzed gene expression patterns to identify highly expressed taxonomically restricted genes (HE-TRGs). Examined differential gene expression between nurses and foragers to identify genes involved in social functions. Utilized statistical tests to assess the significance of TRG expression in novel versus conserved tissues." }, { "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": "TrustFinder is a sociotechnical system designed to enhance situational awareness in the information environment by enabling users to collaboratively manage and evaluate claims and sources. It aims to structure the inform", "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 TrustFinder is a sociotechnical system designed to enhance situational awareness in the information environment by enabling users to collaboratively manage and evaluate claims and sources. It aims to structure the information landscape to facilitate the discovery of trusted information and streamline the assessment of claims. Active Inference Institute open science research organization Free Energy Principle community building Development of a collaborative platform for managing the information supply chain. Implementation of user-driven trust scoring for evaluating sources and claims. Integration of web and document annotation tools to enhance content interaction. Establishment of a framework for argument representation and crowdsourcing design principles. Creation of 'Workspaces' for users to collaborate and share information. Utilization of annotation affordances for marking up and enriching content. Application of trust scores to assess the quality and intent of authors and claims. Design of interconnected informational structures such as Claims, Questions, and Claim Instances." }, { "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": "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 mo", "year": 2023, "domain": "Genetics & Biomedical", "tags": [ "Paper", "Genetics & Biomedical", "bibliography", "rhetorical analysis", "image memes", "digital discourse", "narrative ecosystems", "DRE3 model", "public sphere" ], "content": "To comment or not to comment Physics of Life Reviews 10.1016/j.plrev.2023.06.002 Friedman2023CommentOrNotComment063 Genetics & Biomedical 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 more comprehensive approach to studying image memes, which are often overlooked in favor of text-based formats. rhetorical analysis image memes digital discourse narrative ecosystems DRE3 model public sphere Proposes a combined rhetorical and ecological framework for analyzing digital discourse. Introduces the Digital Rhetorical Ecosystem three-tiered model (DRE3) for understanding meme impact on public narratives. Emphasizes the narrative power of image memes through parsimony and polysemy. Explores implications for computational analysis systems in digital discourse. Utilizes a rhetorical approach to analyze message form and audience engagement. Applies ecological concepts to trace narratives across digital platforms. Develops a three-tiered model (DRE3) to categorize and index digital artifacts. Focuses on the interaction between memes and audience identity construction." }, { "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:Friedman2026LiteratureReviewArchitectureActive110", "type": "work", "title": "A Literature Review Architecture for Active Inference: Scalable Assertion Extraction, Nanopublications, and Citation-Weighted Hypothesis Scoring", "url": "/works/Friedman2026LiteratureReviewArchitectureActive110.html", "external_url": "https://doi.org/10.5281/zenodo.19461934", "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 Literature Review Architecture for Active Inference: Scalable Assertion Extraction, Nanopublications, and Citation-Weighted Hypothesis Scoring Active Inference Journal 10.5281/zenodo.19461934 Friedman2026LiteratureReviewArchitectureActive110 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": "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:template", "type": "software", "title": "template", "url": "https://github.com/docxology/template", "summary": "Multi-project research template with 10-stage CI/CD pipeline, Ruff linting, multi-Python-version testing, issue/PR templates, and security scanning", "domain": "docxology", "tags": [ "software", "Python", "docxology" ], "content": "template Multi-project research template with 10-stage CI/CD pipeline, Ruff linting, multi-Python-version testing, issue/PR templates, and security scanning Python 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 — 127 modules, 424 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 — 127 modules, 424 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: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: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", "Python", "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 Python 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", "", "docxology" ], "content": "Autonomous-Drone-Navigation-in-AirSim-With-Active-Inference Active Inference-driven autonomous drone navigation in Microsoft AirSim simulation environment 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: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: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: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", "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 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" 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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://www.wikidata.org/wiki/Q139600792 https://github.com/ActiveInferenceInstitute 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 115 works.", "url": "/evidence.html", "summary": "curated-local · confidence: high", "tags": [ "claim", "curated-local", "high" ], "content": "The curated bibliography contains 115 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 108 per-paper documentation folders.", "url": "/evidence.html", "summary": "curated-local · confidence: high", "tags": [ "claim", "curated-local", "high" ], "content": "The repository contains 108 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 286 public repositories.", "url": "/evidence.html", "summary": "public-api · confidence: high", "tags": [ "claim", "public-api", "high" ], "content": "The docxology GitHub profile has 286 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 Active Inference Institute GitHub organization has 50 public repositories.", "url": "/evidence.html", "summary": "public-api · confidence: high", "tags": [ "claim", "public-api", "high" ], "content": "The Active Inference Institute GitHub organization has 50 public repositories. Local software catalog tracks 32 AII repositories with docxology contributions. GitHub REST API organization profile response." }, { "id": "claim:orcid-canonical-identifier", "type": "claim", "title": "ORCID 0000-0001-6232-9096 is the canonical researcher identifier.", "url": "/evidence.html", "summary": "public-identifier · confidence: high", "tags": [ "claim", "public-identifier", "high" ], "content": "ORCID 0000-0001-6232-9096 is the canonical researcher identifier. ORCID public work groups may lag new deposits and may group versions differently. ORCID profile and public works endpoint." }, { "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.", "url": "/evidence.html", "summary": "public-profile · confidence: medium", "tags": [ "claim", "public-profile", "medium" ], "content": "Curio Cards 24, 25, and 26 are early Ethereum art NFTs minted on May 9, 2017. Use conservative phrasing; broader first/earliest claims vary by source and definition. Curio Cards artist profile, Christie's lot page, and local paper notes." } ] }