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docxology/README.md

Daniel Ari Friedman, PhD

Computational Biologist · Active Inference · Cognitive Security · Artist

Active Inference · Bayesian Modeling · Computational Biology · Cognitive Security*

Active Inference InstituteGoogle ScholarORCID

LinkedInYouTubeTelegramEmailCOGSECWebsiteResearchGateCurio Cards

Quick links:📚 Publications · 📄 Works · 🔬 Research · 🧭 Domains · 💻 Software · 📁 Papers · 📊 Reports & Counts · ✅ Reproducibility · 🔎 Search · 🧾 Cite & Verify · 🧭 Discovery · 🗃️ Catalog · 📝 Updates · 🖼️ Art · 🪙 NFT · 🧘 Meditations · 🎥 Media · 📺 Videos · 👤 Profile · 🤝 Collaborators · ℹ️ About · 🔗 All Links · 📄 Resume/CV · 🔊 Read Aloud (press T)


🔬 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. Full biography →

  • 🐜 Entomologist — PhD (Stanford, 2014–2019, advisor: Deborah Gordon) on behavioral, physiological, and transcriptomic bases of collective behavior in harvester ants; NSF Postdoctoral Research Fellow (PRFB award 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 (501(c)(3) non-profit; governance pages at activeinference.institute); co-author with Karl Friston; 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
  • 🎨 Early NFT Artist — Abstract pen drawings; Curio Cards 24/25/26 (recognized in NFT archaeology as early Ethereum art NFTs, minted May 9, 2017; Christie's auction Oct 2021); William Blake & Buckminster Fuller scholarship; Art portfolio · Local Gallery
  • 📺 Educator — 500+ Active Inference livestreams, 200+ personal streams, AII Textbook Group (10 cohorts through 2026; Parr, Pezzulo & Friston, 2022 · Namjoshi, 2026), College of the Redwoods (BIOL-1 at Pelican Bay, BIOL-8 Human Biology; Spring 2026), Udemy courses, conference workshops
  • 🌐 Community Builder — Co-founder of Complexity Weekend (2019-2024); co-organized Stanford Complexity Group

Current generated totals: see 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 and propagated into the resume and claim exports.


📁 Repository Map

Current catalog totals are generated in reports/current_counts.md. Canonical source tables are pages/BIBLIOGRAPHY.md, pages/SOFTWARE.md, papers/README.md, and data/github-repositories.json.

ResourceWhat's Inside
📚 pages/BIBLIOGRAPHY.mdUnified sortable table of all works in the bibliography — DOI links, domain tags, and per-paper docs
📄 works/Generated per-work landing pages — one canonical HTML page per bibliography row with citation, DOI, primary source, and documentation link
🔎 search.html / opensearch.xmlHuman and browser search — searchable index over works, software, people, organizations, claims, and key pages
📝 updates.html / CHANGELOG.mdHuman-readable update history — recent public-index and generated-site changes
🧭 domains.html / pages/DOMAINS.mdDomain landing-page hub — Entomology, Active Inference, Cognitive Security, Art & Synergetics, Computational, Presentations & Media, AII Ecosystem, Biomedicine (each cluster has its own domain-*.html)
💻 pages/SOFTWARE.mdCurated owned repos + Active Inference Institute contributions — AI frameworks, geometry engines, entomology tools, and developer infrastructure; see the primary repository inventory and fork archive for public GitHub coverage
📁 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/Documentation Hub — Centralized directories for videos, courses, pathways, and repository integrations
🔗 pages/LINKS.mdComprehensive directory of all web presences — academic profiles, social media, art, NFTs, podcasts, courses, organizations
📖 pages/WIKIPEDIA.mdWikipedia presence — Wikidata/Wikipedia entries and identity-graph links
🧭 pages/DISCOVERY.mdAgentic discovery map — canonical IDs, public APIs, source queries, and verification notes
🧾 cite-verify.html / evidence.htmlCitation and evidence layer — preferred citation, public identifiers, source-of-truth rules, and claim ledger (CITE_VERIFY · EVIDENCE)
📄 resume/ / data/resume.jsonStructured resume/CV exports — source-backed JSON, plaintext variants, and generated PDF built from canonical works, software, metrics, and resume-specific records
pages/VERIFICATION_LOG.mdIndependent 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)
👤 pages/PROFILE.mdDetailed biography — education, research areas, organizations, teaching, awards, art, and key metrics
🤝 pages/COLLABORATORS.mdResearch network — key collaborators (Friston, Gordon, Albarracin, Fields, etc.) with joint publications and institutional map
🎥 pages/MEDIA.mdTalks, podcasts & press — conference presentations, podcast appearances, video series, courses, interviews, and press coverage
📚 pages/RESOURCES.md / pages/VIDEOS.mdResources & video index source — curated resource compendium and the videos/courses catalogue
🖼️ art.html / nft.html / meditations.htmlArt & creative portfolio — gallery, NFT collectibles (Curio Cards), and meditations pages (art/ holds local gallery assets)
🤖 llms.txt / CITATION.cff / codemeta.json / search-index.json / feed.xmlMachine-readable discovery metadata — agent map, citation metadata, CodeMeta, search index, and RSS feed
🗃️ catalog.html / data/catalog.json / GENERATED.mdStructured data and rebuild map — Schema.org DataCatalog plus generated-artifact manifest and commands
📦 exports.html / bibliography.bib / bibliography.csl.json / bibliography.ris / data/Exports for citation managers and agents — HTML export hub, BibTeX, CSL JSON, RIS, works/artworks/software/people/organization/claims/reconciliation JSON
reports/ / CHANGELOG.md / docs/Maintenance evidence & documentation — source snapshots, reconciliation/accessibility/visual-QA reports, changelog, and the documentation index (architecture, operations, canonical URL policy, design, security, releases)
📊 reports.html / research.html / reproducibility.htmlReports, research & reproducibility hub — generated report index, research overview, and the reproducibility ledger (Markdown)
🧑‍🚀 AGENT_START.md / humans.txt / .well-known/security.txtOperational entrypoints — agent task recipes, human credits/contact, and responsible disclosure metadata
agent-verify.html / about.htmlAgent verification & about — agent-ready verification recipes and a short bio page
🛠️ code/Repository Source Codeorchestrators/, src/, and tests/ directories containing executable pipelines and core functions
📖 docs/Central Documentation — Repository-wide operational documentation

By Domain

DomainPublicationsHighlightsSoftware
🐜 EntomologyworksEntoLinguistics · ActiveInferants · AntStack · PhDento_linguistics · MetaInformAnt · ant_stack
🧠 Active InferenceworksFEPLean · CognitiveCaseDiagrams · CEREBRUMfep_lean · cognitive_case_diagrams · goference
🛡️ Cognitive SecurityworksCognitiveIntegrity · InformationCommons · P3IFp3if · opentir
🎨 Art & SynergeticsworksBlakeJiang · DoorsOfPerception · BlakeFuller · QuadMathQuadCraft · symergetics · ivm-xyz
💻 ComputationalworksDeterministicTestbedSelf · RecoveringLLMPersona · THALIA · WitnessRegister · Triplicate · TemplateTextbook · BiologyTextbooktemplate · template_autoscientists · ntqr_llm · thalia
🧬 Genetics & BiomedicalworksHoneyBeeEvolution · NuclearStructure · DennettExplainedFORMINDEX

📚 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; Full list in Bibliography →

Key publications (click to expand)
YearTitleVenueDOI
2026Ento-Linguistics: Language, Ambiguity, and Scientific Communication in EntomologyZenodo10.5281/zenodo.19574117
2025The Ant StackZenodo10.5281/zenodo.16782756
2021Active Inferants: An Active Inference Framework for Ant Colony BehaviorFrontiers in Behavioral Neuroscience10.3389/fnbeh.2021.647732
2020Gene expression variation in the brains of harvester ant foragers is associated with collective behaviorCommunications Biology10.1038/s42003-020-0813-8
2019The ant colony as a test for scientific theories of consciousnessSynthese10.1007/s11229-019-02130-y
2018The Role of Dopamine in Collective Regulation of Foraging in Harvester AntsiScience10.1016/j.isci.2018.09.001
2016Ant Genetics: Reproductive Physiology, Worker Morphology, and BehaviorAnnual Review of Neuroscience10.1146/annurev-neuro-070815-013927

📁 Paper folders: EntoLinguistics · AntStack · ActiveInferants · PhDDissertation · DopamineForaging · AntGenetics


🧠 Active Inference & Free Energy Principle

Theoretical, computational, and applied Active Inference works. Current domain totals live in reports/current_counts.md; Full list in Bibliography →

Key publications (click to expand)
YearTitleVenueDOI
2025CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified ModelingZenodo10.5281/zenodo.15170907
2026Active Inference Power Suite: Conditional Statistical Power under Controlled Generative SettingsZenodo10.5281/zenodo.21695160
2025Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought DynamicsEntropy10.3390/e27050459
2024Federated inference and belief sharingNeuroscience & Biobehavioral Reviews10.1016/j.neubiorev.2023.105500
2023A variational synthesis of evolutionary and developmental dynamicsEntropy10.3390/e25070964
2023Generalized Notation Notation for Active Inference ModelsZenodo10.5281/zenodo.7803327
2018Of woodlice and men (with Karl Friston)ALIUS Bulletin10.34700/h460-nz89

📁 Paper folders: CEREBRUM · GNN · FederatedInference · Thoughtseeds · EvoJump


🛡️ Cognitive Security & Information Ecosystems

Narrative security, memes, trust, and policy works. Current domain and type totals live in reports/current_counts.md; Full list in Bibliography →

Key publications (click to expand)

📕 Books

YearTitlePublisher
2022Structuring the Information Commons: Open Standards and Cognitive SecurityCOGSEC.org
2021Narrative Information Ecosystems: Conflict and Trust on the Endless FrontierCOGSEC.org
2020The Great Preset: Remote Teams and Operational ArtCOGSEC.org

📄 Selected Papers

YearTitleVenueDOI
2026Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory)Zenodo10.5281/zenodo.18364118
2026Personal Red Lines for DevelopmentZenodo10.5281/zenodo.21754239
2026Black Line: Strong Work in PublicZenodo10.5281/zenodo.21754235
2024Bridging gaps in image meme research: A multidisciplinary paradigmJASIST10.1002/asi.24900
2024FarmWorks: Decentralized AI Agents for Personalized SolutionsZenodo10.5281/zenodo.13754585
2023Cognitive Sovereignty & Active Inference in the State of ExceptionZenodo10.5281/zenodo.10038231

📁 Paper folders: CognitiveIntegrity · InformationCommons · NarrativeEcosystems · FarmWorks


🎨 Art, Philosophy & Synergetics

Works on William Blake, Buckminster Fuller, visual art, and interdisciplinary philosophy. Current domain totals live in reports/current_counts.md; Full list in Bibliography →

Key publications (click to expand)
YearTitleVenueDOI
2026The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single VisionZenodo10.5281/zenodo.20144983
2026The Doors of Perception are the Threshold of Prediction: Active Inference and Blake's Theory of SeeingZenodo10.5281/zenodo.18600040
2026Before Pragmatism Had a Name: Blake's "America A Prophecy"Zenodo10.5281/zenodo.18807970
2025Synthesis of Agent and NicheZenodo10.5281/zenodo.17235137
2025QuadMath: An Analytical Review of 4D and Quadray CoordinatesZenodo10.5281/zenodo.16887799
2023William Blake & Buckminster Fuller: Lives in JuxtapositionZenodo10.5281/zenodo.7514367

📁 Paper folders: BlakeJiang · DoorsOfPerception · BeforePragmatism · BlakeFuller · QuadMath · Symergetics


💻 Computational Frameworks & Software

Computational works and software catalogs. Current bibliography, curated-software, and GitHub-inventory totals live in reports/current_counts.md; Works in Bibliography → · Curated repos → · Primary inventory →

Key publications & repositories (click to expand)

📄 Papers

YearTitleVenueDOI
2025The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge LandscapesArXiv10.48550/arXiv.2505.17500
2025MDKV: A Multitrack Markdown Container for Structured, Portable DocumentsZenodo10.5281/zenodo.16790554
2025Markdown Decision Process: A Framework for Probabilistic Document AnalysisZenodo10.5281/zenodo.17244386
2026A Deterministic Testbed for Self-Organizing Agent-Team CoordinationZenodo10.5281/zenodo.20533669
2026Recovering LLM-Persona Accuracies from Unlabeled VotesZenodo10.5281/zenodo.20498699
2026The Triplicate: A Data-Driven Large-Format Newspaper Layout EngineZenodo10.5281/zenodo.20533675
2026The Template TextbookZenodo10.5281/zenodo.20533125
2026COGANT: Deterministic Codebase-to-GNN TranslationZenodo10.5281/zenodo.20705350
2026AGEINT: Agentic IntelligenceZenodo10.5281/zenodo.20732275
2026THALIA: Typed Harness with Analytical Lexical-Integrated ArchitectureZenodo10.5281/zenodo.21763244
2026Codomyrmex: An Artificial Ecology for Agentic Software DevelopmentZenodo10.5281/zenodo.21750800

🔬 Research-Practice Line Set

The DAF "line set" — six small evaluative instruments for research practice and evidence discipline (2026). A typed ledger for absence (White Line), a directional long-horizon record (Golden Line), an evidence-gated personal No (Personal Red Lines), a concise-inspectable practice instrument (Black Line), a co-registration register (Witness Register), and a thin reader over the set (Line Set).

YearTitleVenueDOI
2026The Witness Register: Co-Registration Without AggregationZenodo10.5281/zenodo.21754245
2026The Line Set: Holding Instruments ApartZenodo10.5281/zenodo.21754243
2026White Line: A Typed Ledger for the Edge of the ClaimZenodo10.5281/zenodo.21754241
2026Golden Line: Toward What MattersZenodo10.5281/zenodo.21754237

🔧 Highlighted Repositories

RepositoryDescription
codomyrmex🐜 AI-native modular coding workspace — 100+ modules, 500+ MCP tools
templateMulti-project research template with 10-stage build pipeline
template_autoscientistsDeterministic multi-agent scientific-discovery coordination harness
template_newspaperData-driven large-format newspaper layout engine
ntqr_llmAlgebraic NTQR evaluation for LLM-persona accuracy recovery
steganographerHigh-performance Rust cryptographic watermarking
QuadCraftMineCraft with Tetrahedra (Quadray coordinates)
MetaInformAntIntegration for Ants and Beyond
thaliaTyped agentic harness for reproducible long-context memory experiments
p3ifProperties, Processes, and Perspectives Inter-Framework

Full curated software list: pages/SOFTWARE.md →. For public GitHub coverage, use the primary repository inventory →; forks are separated into the fork archive →. Current totals live in 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; Full list in Bibliography →

Institute ecosystem publications (click to expand)
YearTitleVenueDOI
2025The Active Inference Institute & Active Inference Ecosystem (v3)Zenodo10.5281/zenodo.17982447
2024The Active Inference Institute & Active Inference Ecosystem (v2)Zenodo10.5281/zenodo.14108992
2024Aligning Active Inference Ontology to SUMOZenodo10.5281/zenodo.11459322
2023The Active Inference Institute and Active Inference Ecosystem (v1)Zenodo10.5281/zenodo.8266280

📁 Paper folders: AII_v3 · AII_v2 · AII_v1


🎥 Presentations, Courses & Media

Livestreams, conference talks, courses, and collaborative media — Full list in Bibliography →

Presentations, courses, and media (click to expand)

📺 Ongoing Series

PlatformDescriptionLink
Active Inference Journal500+ videos on Active Inference with transcriptsvideo.activeinference.institute
Personal YouTube200+ livestreams including drawings, Synergetics, paper discussionsyoutube.com/@danielarifriedman

Selected Presentations

YearTitleVenue
2025Systems Processes, Active Inference, and BeyondZenodo
20255th Applied Active Inference Symposium — Abstract BookZenodo
2024BioFirm Development at Applied Active Inference Symposium 2024Zenodo
2023Of Ants & AgingZenodo

🧬 Genetics & Biomedical Research

Genetics, radiation biology, and biomedical research works. Current domain totals live in reports/current_counts.md; Full list in Bibliography →

Earlier work in genetics, radiation biology, and biomedical research (click to expand)
YearTitleVenueDOI
2024Why Paleolithic Rockstars were both enigmatic and sporadicPhysics of Life Reviews10.1016/j.plrev.2024.04.010
2022On free will or the lack thereof (interview with Robert Sapolsky)ALIUS Bulletin10.5281/zenodo.7394900
2019Dennett Explained (interview with Daniel Dennett)ALIUS Bulletin10.34700/7gkw-zh08
2015Large Scale Coding Sequence Change Underlies the Evolution of Post-developmental Novelty in Honey BeesMolecular Biology & Evolution10.1093/molbev/msu292

🗺️ Research Themes & Expertise Areas

flowchart TD
AI[Active Inference] --- ENT[Entomology] --- CS[Cognitive Security]
AI --> BM[Bayesian Modeling]
ENT --> ANT[Ant Colonies / Social Insects]
CS --> IE[Information Ecosystems]
BM --> COMP[Computational]
ANT --> BIO[Biology]
IE --> DR[Digital Rhetoric]
COMP --- BIO --- DR
COMP --> CEREB[CEREBRUM, GNN]
BIO --> GEN[Genetics]
DR --> CP[COGSEC, P3IF]
CEREB --> SYN[Synergetics<br/>Fuller, Blake]
GEN --> ECO[Ecology<br/>Consciousness]
CP --> DESC[Decentralized Science<br/>DeSci]
SYN --- ECO --- DESC
Loading

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, research collaboration, Python, Rust, multi-agent systems, variational inference


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🏆 GitHub Trophies

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