# Daniel Ari Friedman, PhD **Computational Biologist · Active Inference · Cognitive Security · Artist** Active Inference · Bayesian Modeling · Computational Biology · Cognitive Security* *Available for consulting, tutoring, and research collaboration* [![Active Inference Institute](https://img.shields.io/badge/Active_Inference_Institute-President-6C3483?style=for-the-badge)](https://activeinference.org/) [![Google Scholar](https://img.shields.io/badge/Google_Scholar-current_snapshot-4285F4?style=for-the-badge&logo=google-scholar&logoColor=white)](https://scholar.google.com/citations?user=DXjPFtYAAAAJ&hl=en) [![ORCID](https://img.shields.io/badge/ORCID-0000--0001--6232--9096-A6CE39?style=for-the-badge&logo=orcid&logoColor=white)](https://orcid.org/0000-0001-6232-9096) [![LinkedIn](https://img.shields.io/badge/LinkedIn-%230077B5.svg?logo=linkedin&logoColor=white)](https://linkedin.com/in/danielarifriedman) [![YouTube](https://img.shields.io/badge/YouTube-%23FF0000.svg?logo=YouTube&logoColor=white)](https://youtube.com/@danielarifriedman) [![Telegram](https://img.shields.io/badge/Telegram-2CA5E0?logo=telegram&logoColor=white)](https://t.me/docxology) [![Email](https://img.shields.io/badge/Email-D14836?logo=gmail&logoColor=white)](mailto:Daniel@ActiveInference.Institute) [![COGSEC](https://img.shields.io/badge/COGSEC.org-Cognitive_Security-2E86C1?style=flat&logo=shield&logoColor=white)](https://cogsec.org) [![Website](https://img.shields.io/badge/Website-danielarifriedman.com-000?logo=globe&logoColor=white)](https://danielarifriedman.com/) [![ResearchGate](https://img.shields.io/badge/ResearchGate-00CCBB?logo=researchgate&logoColor=white)](https://www.researchgate.net/profile/Daniel-Friedman-2) [![Curio Cards](https://img.shields.io/badge/Curio_Cards-NFT_Pioneer-FF6B6B?style=flat)](https://curio.cards/artist/danielfriedman/)
**Quick links:** [📚 Publications](publications.html) · [📄 Works](works/) · [📄 Resume/CV](resume/resume.pdf) · [🔎 Search](search.html) · [🧭 Domains](domains.html) · [💻 Software](software.html) · [📁 Papers](papers/) · [🔗 All Links](pages/LINKS.md) · [🧾 Cite & Verify](cite-verify.html) · [🧭 Discovery](discovery.html) · [🗃️ Data Catalog](catalog.html) · [📝 Updates](updates.html) · [👤 Full Profile](pages/PROFILE.md) · [🤝 Collaborators](collaborators.html) · [🎥 Media & Talks](media.html) · [🎯 Consulting](#available-for-consulting-tutoring) --- ## 🔬 About — Computational Biologist & Active Inference Researcher I study **ants**, **Active Inference**, and **cognitive security** — and build open-source tools at the intersection of Bayesian modeling, computational biology, and information ecosystem design. I am available for **AI research consulting**, **tutoring**, and **collaboration** on projects involving Active Inference, machine learning, and computational science. [Full biography →](pages/PROFILE.md) - 🐜 **Entomologist** — PhD (Stanford, 2014–2019, advisor: [Deborah Gordon](pages/COLLABORATORS.md#deborah-gordon-stanford-university)) on behavioral, physiological, and transcriptomic bases of collective behavior in harvester ants; NSF Postdoctoral Research Fellow (PRFB [award DBI-2010290](https://grantome.com/grant/NSF/DBI-2010290)) at UC Davis, 2020–2023 (NSF budget period 2020–2022, extended to 2023) - 🧠 **Active Inference Researcher** — President and co-founder of the **[Active Inference Institute](https://activeinference.org/)** (501(c)(3) non-profit; governance pages at [activeinference.institute](https://www.activeinference.institute/)); co-author with [Karl Friston](pages/COLLABORATORS.md#karl-friston-ucl-london); builder of **CEREBRUM**, **GNN**, **InferAnts**, and **goference** frameworks - 🛡️ **Cognitive Security Researcher** — bibliography-indexed work on narrative ecosystems, digital rhetoric, and multiagent security at **[COGSEC.org](https://cogsec.org)** - 🎨 **Early NFT Artist** — Abstract pen drawings; [Curio Cards](https://curio.cards/artist/danielfriedman/) 24/25/26 (recognized in NFT archaeology as early Ethereum art NFTs, minted May 9, 2017; [Christie's auction Oct 2021](https://www.christies.com/en/lot/lot-6337619)); William Blake & Buckminster Fuller scholarship; [Art portfolio](https://danielarifriedman.com/art.html) · [Local Gallery](art/README.md) - 📺 **Educator** — 500+ Active Inference livestreams, 200+ personal streams, [AII Textbook Group](https://activeinference.org/) (10 cohorts through 2026; [Parr, Pezzulo & Friston, 2022](https://direct.mit.edu/books/oa-monograph/5299/Active-InferenceThe-Free-Energy-Principle-in-Mind) · [Namjoshi, 2026](https://mitpress.mit.edu/9780262050951/fundamentals-of-active-inference/)), College of the Redwoods ([BIOL-1](https://github.com/docxology/biol-1) at Pelican Bay, [BIOL-8](https://github.com/docxology/biol-8) Human Biology; Spring 2026), [Udemy courses](https://www.udemy.com/course/communication-for-remote-teams/), conference workshops, and private tutoring - 🌐 **Community Builder** — Co-founder of [Complexity Weekend](https://www.complexityadventures.com/) (since 2019); co-organized Stanford Complexity Group --- ## 🎯 Available for Consulting & Tutoring | Service | Areas of Expertise | Get in Touch | |---------|-------------------|--------------| | 🔬 **Research Consulting** | Active Inference · Bayesian modeling · Computational biology · Cognitive security · Multi-agent systems | [📧 Email](mailto:Daniel@ActiveInference.Institute) | | 🎓 **Tutoring & Mentorship** | Active Inference fundamentals · Python/Rust AI frameworks · Scientific writing · Graduate-level Bayesian methods | [📧 Email](mailto:Daniel@ActiveInference.Institute) | | 💬 **Speaking & Workshops** | Conference keynotes · Team workshops on AI/ML · Course development · Institutional training | [📧 Email](mailto:Daniel@ActiveInference.Institute) | | 🤝 **Research Collaboration** | Joint publications · Framework co-development · Grant partnerships · Open-source contributions | [📧 Email](mailto:Daniel@ActiveInference.Institute) | > **Current generated totals**: see [`reports/current_counts.md`](reports/current_counts.md) for bibliography, paper-folder, software, GitHub inventory, public-source snapshot, and paired-publication counts with generation metadata and rebuild commands. Scholar metrics are sourced from [`data/scholar-snapshot.json`](data/scholar-snapshot.json) and propagated into the resume and claim exports. --- ## 📁 Repository Map > **Current catalog totals** are generated in [`reports/current_counts.md`](reports/current_counts.md). Canonical source tables are [`pages/BIBLIOGRAPHY.md`](pages/BIBLIOGRAPHY.md), [`pages/SOFTWARE.md`](pages/SOFTWARE.md), [`papers/README.md`](papers/README.md), and [`data/github-repositories.json`](data/github-repositories.json). | Resource | What's Inside | |----------|---------------| | 📚 [**pages/BIBLIOGRAPHY.md**](pages/BIBLIOGRAPHY.md) | Unified sortable table of **all works** in the bibliography — DOI links, domain tags, and per-paper docs | | 📄 [**works/**](works/) | **Generated per-work landing pages** — one canonical HTML page per bibliography row with citation, DOI, primary source, and documentation link | | 🔎 [**search.html**](search.html) / [**opensearch.xml**](opensearch.xml) | **Human and browser search** — searchable index over works, software, people, organizations, claims, and key pages | | 📝 [**updates.html**](updates.html) / [**CHANGELOG.md**](CHANGELOG.md) | **Human-readable update history** — recent public-index and generated-site changes | | 🧭 [**domains.html**](domains.html) / [**pages/DOMAINS.md**](pages/DOMAINS.md) | Domain landing pages for Entomology, Active Inference, Cognitive Security, Art & Synergetics, and Computational work | | 💻 [**pages/SOFTWARE.md**](pages/SOFTWARE.md) | Curated owned repos + Active Inference Institute contributions — AI frameworks, geometry engines, entomology tools, and developer infrastructure; see the [full generated repository inventory](repositories.html) for public GitHub coverage | | 📁 [**papers/**](papers/) | Per-paper folders — each with README.md, AGENTS.md, and Claude Code-compatible SKILL.md where a bibliography row has in-tree documentation | | 📄 [**pages/**](pages/) | **Documentation Hub** — Centralized directories for videos, courses, pathways, and repository integrations | | 🔗 [**pages/LINKS.md**](pages/LINKS.md) | **Comprehensive directory** of all web presences — academic profiles, social media, art, NFTs, podcasts, courses, organizations | | 🧭 [**pages/DISCOVERY.md**](pages/DISCOVERY.md) | **Agentic discovery map** — canonical IDs, public APIs, source queries, and verification notes | | 🧾 [**cite-verify.html**](cite-verify.html) / [**evidence.html**](evidence.html) | **Citation and evidence layer** — preferred citation, public identifiers, source-of-truth rules, and claim ledger ([Markdown](pages/CITE_VERIFY.md)) | | 📄 [**resume/**](resume/) / [**data/resume.json**](data/resume.json) | **Structured resume/CV exports** — source-backed JSON, plaintext variants, and generated PDF built from canonical works, software, metrics, and resume-specific records | | ✅ [**pages/VERIFICATION_LOG.md**](pages/VERIFICATION_LOG.md) | **Independent verification log** — dated primary-source corroboration of load-bearing claims (Scholar metrics, EIN, NSF award, DOIs, identity graph) against sources not controlled by the subject ([JSON](data/verification-log.json)) | | 👤 [**pages/PROFILE.md**](pages/PROFILE.md) | **Detailed biography** — education, research areas, organizations, teaching, awards, art, and key metrics | | 🤝 [**pages/COLLABORATORS.md**](pages/COLLABORATORS.md) | **Research network** — key collaborators (Friston, Gordon, Albarracin, Fields, etc.) with joint publications and institutional map | | 🎥 [**pages/MEDIA.md**](pages/MEDIA.md) | **Talks, podcasts & press** — conference presentations, podcast appearances, video series, courses, interviews, and press coverage | | 🤖 [**llms.txt**](llms.txt) / [**CITATION.cff**](CITATION.cff) / [**codemeta.json**](codemeta.json) / [**search-index.json**](search-index.json) / [**feed.xml**](feed.xml) | **Machine-readable discovery metadata** — agent map, citation metadata, CodeMeta, search index, and RSS feed | | 🗃️ [**catalog.html**](catalog.html) / [**data/catalog.json**](data/catalog.json) / [**GENERATED.md**](GENERATED.md) | **Structured data and rebuild map** — Schema.org DataCatalog plus generated-artifact manifest and commands | | 📦 [**bibliography.bib**](bibliography.bib) / [**bibliography.csl.json**](bibliography.csl.json) / [**bibliography.ris**](bibliography.ris) / [**data/**](data/) | **Exports for citation managers and agents** — BibTeX, CSL JSON, RIS, works/artworks/software/people/organization/claims/reconciliation JSON | | ✅ [**reports/**](reports/) / [**CHANGELOG.md**](CHANGELOG.md) / [**docs/**](docs/README.md) | **Maintenance evidence & documentation** — source snapshots, reconciliation/accessibility/visual-QA reports, changelog, and the documentation index (architecture, operations, [canonical URL policy](docs/seo/canonical-policy.md), design, security, releases) | | 🧑‍🚀 [**AGENT_START.md**](AGENT_START.md) / [**humans.txt**](humans.txt) / [**.well-known/security.txt**](.well-known/security.txt) | **Operational entrypoints** — agent task recipes, human credits/contact, and responsible disclosure metadata | | 🛠️ [**code/**](code/) | **Repository Source Code** — `orchestrators/`, `src/`, and `tests/` directories containing executable pipelines and core functions | | 📖 [**docs/**](docs/) | **Central Documentation** — Repository-wide operational documentation | ### By Domain | Domain | Publications | Highlights | Software | |--------|:-----------:|------------|----------| | 🐜 Entomology | [works](pages/BIBLIOGRAPHY.md#entomology) | [EntoLinguistics](papers/2026_EntoLinguistics/) · [ActiveInferants](papers/2021_ActiveInferants/) · [AntStack](papers/2025_AntStack/) · [PhD](papers/2019_PhDDissertation/) | [ento_linguistics](https://github.com/docxology/ento_linguistics) · [MetaInformAnt](https://github.com/docxology/MetaInformAnt) · [ant_stack](https://github.com/docxology/ant_stack) | | 🧠 Active Inference | [works](pages/BIBLIOGRAPHY.md#active-inference) | [FEPLean](papers/2026_FEPLean/) · [CognitiveCaseDiagrams](papers/2026_CognitiveCaseDiagrams/) · [CEREBRUM](papers/2025_CEREBRUM/) | [fep_lean](https://github.com/ActiveInferenceInstitute/fep_lean) · [cognitive_case_diagrams](https://github.com/docxology/cognitive_case_diagrams) · [goference](https://github.com/docxology/goference) | | 🛡️ Cognitive Security | [works](pages/BIBLIOGRAPHY.md#cognitive-security) | [CognitiveIntegrity](papers/2026_CognitiveIntegrity/) · [InformationCommons](papers/2022_InformationCommons/) · [P3IF](papers/2023_P3IF/) | [p3if](https://github.com/docxology/p3if) · [opentir](https://github.com/docxology/opentir) | | 🎨 Art & Synergetics | [works](pages/BIBLIOGRAPHY.md#art-synergetics) | [BlakeJiang](papers/2026_BlakeJiang/) · [DoorsOfPerception](papers/2026_DoorsOfPerception/) · [BlakeFuller](papers/2023_BlakeFuller/) · [QuadMath](papers/2025_QuadMath/) | [QuadCraft](https://github.com/docxology/QuadCraft) · [symergetics](https://github.com/docxology/symergetics) · [ivm-xyz](https://github.com/docxology/ivm-xyz) | | 💻 Computational | [works](pages/BIBLIOGRAPHY.md#computational) | [DeterministicTestbedSelf](papers/2026_DeterministicTestbedSelf/) · [RecoveringLLMPersona](papers/2026_RecoveringLLMPersona/) · [Triplicate](papers/2026_Triplicate/) · [TemplateTextbook](papers/2026_TemplateTextbook/) · [BiologyTextbook](papers/2026_BiologyTextbook/) | [template](https://github.com/docxology/template) · [template_autoscientists](https://github.com/docxology/template_autoscientists) · [ntqr_llm](https://github.com/docxology/ntqr_llm) | | 🧬 Genetics & Biomedical | [works](pages/BIBLIOGRAPHY.md#genetics-biomedical) | [HoneyBeeEvolution](papers/2015_HoneyBeeEvolution/) · [NuclearStructure](papers/2016_NuclearStructure/) · [DennettExplained](papers/2019_DennettExplained/) | [FORMINDEX](https://github.com/docxology/FORMINDEX) | --- ## 📚 Selected Publications & Works ### 🐜 Entomology & Social Insect Biology > Entomology domain works include peer-reviewed and Zenodo records on ant genetics, behavior, collective intelligence, and scientific language. Current domain totals live in [`reports/current_counts.md`](reports/current_counts.md); [Full list in Bibliography →](pages/BIBLIOGRAPHY.md#entomology)
Key publications (click to expand) | Year | Title | Venue | DOI | |------|-------|-------|-----| | 2026 | Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology | *Zenodo* | [10.5281/zenodo.19574117](https://doi.org/10.5281/zenodo.19574117) | | 2025 | The Ant Stack | *Zenodo* | [10.5281/zenodo.16782756](https://doi.org/10.5281/zenodo.16782756) | | 2021 | Active Inferants: An Active Inference Framework for Ant Colony Behavior | *Frontiers in Behavioral Neuroscience* | [10.3389/fnbeh.2021.647732](https://doi.org/10.3389/fnbeh.2021.647732) | | 2020 | Gene expression variation in the brains of harvester ant foragers is associated with collective behavior | *Communications Biology* | [10.1038/s42003-020-0813-8](https://doi.org/10.1038/s42003-020-0813-8) | | 2019 | The ant colony as a test for scientific theories of consciousness | *Synthese* | [10.1007/s11229-019-02130-y](https://doi.org/10.1007/s11229-019-02130-y) | | 2018 | The Role of Dopamine in Collective Regulation of Foraging in Harvester Ants | *iScience* | [10.1016/j.isci.2018.09.001](https://doi.org/10.1016/j.isci.2018.09.001) | | 2016 | Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior | *Annual Review of Neuroscience* | [10.1146/annurev-neuro-070815-013927](https://doi.org/10.1146/annurev-neuro-070815-013927) | > 📁 **Paper folders**: [EntoLinguistics](papers/2026_EntoLinguistics/) · [AntStack](papers/2025_AntStack/) · [ActiveInferants](papers/2021_ActiveInferants/) · [PhDDissertation](papers/2019_PhDDissertation/) · [DopamineForaging](papers/2018_DopamineForaging/) · [AntGenetics](papers/2016_AntGenetics/)
--- ### 🧠 Active Inference & Free Energy Principle > Theoretical, computational, and applied Active Inference works. Current domain totals live in [`reports/current_counts.md`](reports/current_counts.md); [Full list in Bibliography →](pages/BIBLIOGRAPHY.md#active-inference)
Key publications (click to expand) | Year | Title | Venue | DOI | |------|-------|-------|-----| | 2025 | CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling | *Zenodo* | [10.5281/zenodo.15170907](https://doi.org/10.5281/zenodo.15170907) | | 2025 | Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought Dynamics | *Entropy* | [10.3390/e27050459](https://doi.org/10.3390/e27050459) | | 2024 | Federated inference and belief sharing | *Neuroscience & Biobehavioral Reviews* | [10.1016/j.neubiorev.2023.105500](https://doi.org/10.1016/j.neubiorev.2023.105500) | | 2023 | A variational synthesis of evolutionary and developmental dynamics | *Entropy* | [10.3390/e25070964](https://doi.org/10.3390/e25070964) | | 2023 | Generalized Notation Notation for Active Inference Models | *Zenodo* | [10.5281/zenodo.7803327](https://doi.org/10.5281/zenodo.7803327) | | 2018 | Of woodlice and men (with Karl Friston) | *ALIUS Bulletin* | [10.34700/h460-nz89](https://doi.org/10.34700/h460-nz89) | > 📁 **Paper folders**: [CEREBRUM](papers/2025_CEREBRUM/) · [GNN](papers/2023_GNN/) · [FederatedInference](papers/2024_FederatedInference/) · [Thoughtseeds](papers/2025_Thoughtseeds/) · [EvoJump](papers/2025_EvoJump/)
--- ### 🛡️ Cognitive Security & Information Ecosystems > Narrative security, memes, trust, and policy works. Current domain and type totals live in [`reports/current_counts.md`](reports/current_counts.md); [Full list in Bibliography →](pages/BIBLIOGRAPHY.md#cognitive-security)
Key publications (click to expand) #### 📕 Books | Year | Title | Publisher | |------|-------|----------| | 2022 | Structuring the Information Commons: Open Standards and Cognitive Security | COGSEC.org | | 2021 | Narrative Information Ecosystems: Conflict and Trust on the Endless Frontier | COGSEC.org | | 2020 | The Great Preset: Remote Teams and Operational Art | COGSEC.org | #### 📄 Selected Papers | Year | Title | Venue | DOI | |------|-------|-------|-----| | 2026 | Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory) | *Zenodo* | [10.5281/zenodo.18364118](https://doi.org/10.5281/zenodo.18364118) | | 2024 | Bridging gaps in image meme research: A multidisciplinary paradigm | *JASIST* | [10.1002/asi.24900](https://doi.org/10.1002/asi.24900) | | 2024 | FarmWorks: Decentralized AI Agents for Personalized Solutions | *Zenodo* | [10.5281/zenodo.13754585](https://doi.org/10.5281/zenodo.13754585) | | 2023 | Cognitive Sovereignty & Active Inference in the State of Exception | *Zenodo* | [10.5281/zenodo.10038231](https://doi.org/10.5281/zenodo.10038231) | > 📁 **Paper folders**: [CognitiveIntegrity](papers/2026_CognitiveIntegrity/) · [InformationCommons](papers/2022_InformationCommons/) · [NarrativeEcosystems](papers/2021_NarrativeEcosystems/) · [FarmWorks](papers/2024_FarmWorks/)
--- ### 🎨 Art, Philosophy & Synergetics > Works on William Blake, Buckminster Fuller, visual art, and interdisciplinary philosophy. Current domain totals live in [`reports/current_counts.md`](reports/current_counts.md); [Full list in Bibliography →](pages/BIBLIOGRAPHY.md#art-synergetics)
Key publications (click to expand) | Year | Title | Venue | DOI | |------|-------|-------|-----| | 2026 | The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single Vision | *Zenodo* | [10.5281/zenodo.20144983](https://doi.org/10.5281/zenodo.20144983) | | 2026 | The Doors of Perception are the Threshold of Prediction: Active Inference and Blake's Theory of Seeing | *Zenodo* | [10.5281/zenodo.18600040](https://doi.org/10.5281/zenodo.18600040) | | 2026 | Before Pragmatism Had a Name: Blake's "America A Prophecy" | *Zenodo* | [10.5281/zenodo.18807970](https://doi.org/10.5281/zenodo.18807970) | | 2025 | Synthesis of Agent and Niche | *Zenodo* | [10.5281/zenodo.17235137](https://doi.org/10.5281/zenodo.17235137) | | 2025 | QuadMath: An Analytical Review of 4D and Quadray Coordinates | *Zenodo* | [10.5281/zenodo.16887799](https://doi.org/10.5281/zenodo.16887799) | | 2023 | William Blake & Buckminster Fuller: Lives in Juxtaposition | *Zenodo* | [10.5281/zenodo.7514367](https://doi.org/10.5281/zenodo.7514367) | > 📁 **Paper folders**: [BlakeJiang](papers/2026_BlakeJiang/) · [DoorsOfPerception](papers/2026_DoorsOfPerception/) · [BeforePragmatism](papers/2026_BeforePragmatism/) · [BlakeFuller](papers/2023_BlakeFuller/) · [QuadMath](papers/2025_QuadMath/) · [Symergetics](papers/2025_Symergetics/)
--- ### 💻 Computational Frameworks & Software > Computational works and software catalogs. Current bibliography, curated-software, and GitHub-inventory totals live in [`reports/current_counts.md`](reports/current_counts.md); [Works in Bibliography →](pages/BIBLIOGRAPHY.md#computational) · [Curated repos →](pages/SOFTWARE.md) · [Full inventory →](repositories.html)
Key publications & repositories (click to expand) #### 📄 Papers | Year | Title | Venue | DOI | |------|-------|-------|-----| | 2025 | The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge Landscapes | *ArXiv* | [10.48550/arXiv.2505.17500](https://doi.org/10.48550/arXiv.2505.17500) | | 2025 | MDKV: A Multitrack Markdown Container for Structured, Portable Documents | *Zenodo* | [10.5281/zenodo.16790554](https://doi.org/10.5281/zenodo.16790554) | | 2025 | Markdown Decision Process: A Framework for Probabilistic Document Analysis | *Zenodo* | [10.5281/zenodo.17244386](https://doi.org/10.5281/zenodo.17244386) | | 2026 | A Deterministic Testbed for Self-Organizing Agent-Team Coordination | *Zenodo* | [10.5281/zenodo.20533669](https://doi.org/10.5281/zenodo.20533669) | | 2026 | Recovering LLM-Persona Accuracies from Unlabeled Votes | *Zenodo* | [10.5281/zenodo.20498699](https://doi.org/10.5281/zenodo.20498699) | | 2026 | The Triplicate: A Data-Driven Large-Format Newspaper Layout Engine | *Zenodo* | [10.5281/zenodo.20533675](https://doi.org/10.5281/zenodo.20533675) | | 2026 | The Template Textbook | *Zenodo* | [10.5281/zenodo.20533125](https://doi.org/10.5281/zenodo.20533125) | | 2026 | COGANT: Deterministic Codebase-to-GNN Translation | *Zenodo* | [10.5281/zenodo.20705350](https://doi.org/10.5281/zenodo.20705350) | | 2026 | AGEINT: Agentic Intelligence | *Zenodo* | [10.5281/zenodo.20732275](https://doi.org/10.5281/zenodo.20732275) | #### 🔧 Highlighted Repositories | Repository | Description | |-----------|-------------| | [codomyrmex](https://github.com/docxology/codomyrmex) | 🐜 AI-native modular coding workspace — 100+ modules, 500+ MCP tools | | [template](https://github.com/docxology/template) | Multi-project research template with 10-stage build pipeline | | [template_autoscientists](https://github.com/docxology/template_autoscientists) | Deterministic multi-agent scientific-discovery coordination harness | | [template_newspaper](https://github.com/docxology/template_newspaper) | Data-driven large-format newspaper layout engine | | [ntqr_llm](https://github.com/docxology/ntqr_llm) | Algebraic NTQR evaluation for LLM-persona accuracy recovery | | [steganographer](https://github.com/docxology/steganographer) | High-performance Rust cryptographic watermarking | | [QuadCraft](https://github.com/docxology/QuadCraft) | MineCraft with Tetrahedra (Quadray coordinates) | | [MetaInformAnt](https://github.com/docxology/MetaInformAnt) | Integration for Ants and Beyond | | [p3if](https://github.com/docxology/p3if) | Properties, Processes, and Perspectives Inter-Framework | > **Full curated software list**: [pages/SOFTWARE.md →](pages/SOFTWARE.md). For all public GitHub repositories including forks and uncataloged projects, see [repositories.html →](repositories.html). Current totals live in [`reports/current_counts.md`](reports/current_counts.md).
--- ### 🌍 Active Inference Institute & Ecosystem > Institute snapshots, ecosystem maps, and organizational design works. Current domain totals live in [`reports/current_counts.md`](reports/current_counts.md); [Full list in Bibliography →](pages/BIBLIOGRAPHY.md#aii-ecosystem)
Institute ecosystem publications (click to expand) | Year | Title | Venue | DOI | |------|-------|-------|-----| | 2025 | The Active Inference Institute & Active Inference Ecosystem (v3) | *Zenodo* | [10.5281/zenodo.17982447](https://doi.org/10.5281/zenodo.17982447) | | 2024 | The Active Inference Institute & Active Inference Ecosystem (v2) | *Zenodo* | [10.5281/zenodo.14108992](https://doi.org/10.5281/zenodo.14108992) | | 2024 | Aligning Active Inference Ontology to SUMO | *Zenodo* | [10.5281/zenodo.11459322](https://doi.org/10.5281/zenodo.11459322) | | 2023 | The Active Inference Institute and Active Inference Ecosystem (v1) | *Zenodo* | [10.5281/zenodo.8266280](https://doi.org/10.5281/zenodo.8266280) | > 📁 **Paper folders**: [AII_v3](papers/2025_AII_v3/) · [AII_v2](papers/2024_AII_v2/) · [AII_v1](papers/2023_AII_v1/)
--- ### 🎥 Presentations, Courses & Media > Livestreams, conference talks, courses, and collaborative media — [Full list in Bibliography →](pages/BIBLIOGRAPHY.md#presentations-media)
Presentations, courses, and media (click to expand) #### 📺 Ongoing Series | Platform | Description | Link | |----------|-------------|------| | Active Inference Journal | 500+ videos on Active Inference with transcripts | [video.activeinference.institute](https://video.activeinference.institute/) | | Personal YouTube | 200+ livestreams including drawings, Synergetics, paper discussions | [youtube.com/@danielarifriedman](https://www.youtube.com/@danielarifriedman/playlists) | #### Selected Presentations | Year | Title | Venue | |------|-------|-------| | 2025 | Systems Processes, Active Inference, and Beyond | [Zenodo](https://doi.org/10.5281/zenodo.17138223) | | 2025 | 5th Applied Active Inference Symposium — Abstract Book | [Zenodo](https://doi.org/10.5281/zenodo.17555266) | | 2024 | BioFirm Development at Applied Active Inference Symposium 2024 | [Zenodo](https://doi.org/10.5281/zenodo.14861595) | | 2023 | Of Ants & Aging | [Zenodo](https://doi.org/10.5281/zenodo.7855581) |
--- ### 🧬 Genetics & Biomedical Research > Genetics, radiation biology, and biomedical research works. Current domain totals live in [`reports/current_counts.md`](reports/current_counts.md); [Full list in Bibliography →](pages/BIBLIOGRAPHY.md#genetics-biomedical)
Earlier work in genetics, radiation biology, and biomedical research (click to expand) | Year | Title | Venue | DOI | |------|-------|-------|-----| | 2024 | Why Paleolithic Rockstars were both enigmatic and sporadic | *Physics of Life Reviews* | [10.1016/j.plrev.2024.04.010](https://doi.org/10.1016/j.plrev.2024.04.010) | | 2022 | On free will or the lack thereof (interview with Robert Sapolsky) | *ALIUS Bulletin* | [10.5281/zenodo.7394900](https://doi.org/10.5281/zenodo.7394900) | | 2019 | Dennett Explained (interview with Daniel Dennett) | *ALIUS Bulletin* | [10.34700/7gkw-zh08](https://doi.org/10.34700/7gkw-zh08) | | 2015 | Large Scale Coding Sequence Change Underlies the Evolution of Post-developmental Novelty in Honey Bees | *Molecular Biology & Evolution* | [10.1093/molbev/msu292](https://doi.org/10.1093/molbev/msu292) |
--- ## 🗺️ Research Themes & Expertise Areas ``` Active Inference ──── Entomology ──── Cognitive Security │ │ │ Bayesian Ant Colonies Information Modeling Social Insects Ecosystems │ │ │ Computational ──── Biology ──────── Digital Rhetoric │ │ │ CEREBRUM, GNN Genetics COGSEC, P3IF │ │ │ Synergetics ────── Ecology ─────── Decentralized (Fuller, Blake) (Consciousness) Science (DeSci) ``` **Keywords**: Active Inference, free energy principle, Bayesian brain, computational neuroscience, ant colony optimization, collective intelligence, myrmecology, cognitive security, information warfare, narrative ecosystems, Buckminster Fuller, synergetics, William Blake, AI consulting, machine learning tutoring, research collaboration, Python, Rust, multi-agent systems, variational inference --- ## 📊 GitHub Stats
![](https://github-readme-stats.vercel.app/api?username=docxology&theme=dark&hide_border=true&include_all_commits=true&count_private=true) ![](https://nirzak-streak-stats.vercel.app/?user=docxology&theme=dark&hide_border=true) ![](https://github-readme-stats.vercel.app/api/top-langs/?username=docxology&theme=dark&hide_border=true&include_all_commits=true&count_private=true&layout=compact)
## 🏆 GitHub Trophies
![](https://github-profile-trophy.vercel.app/?username=docxology&theme=dark&no-frame=true&no-bg=true&margin-w=4)
### 🔝 Top Contributed Repo ![](https://github-contributor-stats.vercel.app/api?username=docxology&limit=5&theme=dark&combine_all_yearly_contributions=true) ---
[![](https://visitcount.itsvg.in/api?id=docxology&icon=0&color=4)](https://visitcount.itsvg.in) ### 💰 Support My Work [![PayPal](https://img.shields.io/badge/PayPal-00457C?style=for-the-badge&logo=paypal&logoColor=white)](https://paypal.me/DanielAriFriedman)