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docxology/README.md

Daniel Ari Friedman, PhD

Computational Biologist Β· Active Inference Β· Cognitive Security Β· Artist

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

Available for consulting, tutoring, and research collaboration

Active Inference Institute Google Scholar ORCID

LinkedIn YouTube Telegram Email COGSEC Website ResearchGate Curio Cards

Quick links: πŸ“š Publications Β· πŸ“„ Works Β· πŸ“„ Resume/CV Β· πŸ”Ž Search Β· 🧭 Domains Β· πŸ’» Software Β· πŸ“ Papers Β· πŸ”— All Links Β· 🧾 Cite & Verify Β· 🧭 Discovery Β· πŸ—ƒοΈ Data Catalog Β· πŸ“ Updates Β· πŸ‘€ Full Profile Β· 🀝 Collaborators Β· πŸŽ₯ Media & Talks Β· 🎯 Consulting


πŸ”¬ About β€” Computational Biologist & Active Inference Researcher

I study ants, Active Inference, and cognitive security β€” 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 β†’

  • 🐜 Entomologist β€” 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 β€” 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
  • πŸ›‘οΈ Cognitive Security Researcher β€” bibliography-indexed work on narrative ecosystems, digital rhetoric, and multiagent security at COGSEC.org
  • 🎨 Early NFT Artist β€” 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 Β· Local Gallery
  • πŸ“Ί Educator β€” 500+ Active Inference livestreams, 200+ personal streams, AII Textbook Group (10 cohorts through 2026; Parr, Pezzulo & Friston, 2022 Β· Namjoshi, 2026), College of the Redwoods (BIOL-1 at Pelican Bay, BIOL-8 Human Biology; Spring 2026), Udemy courses, conference workshops, and private tutoring
  • 🌐 Community Builder β€” Co-founder of Complexity Weekend (since 2019); co-organized Stanford Complexity Group

🎯 Available for Consulting & Tutoring

Service Areas of Expertise Get in Touch
πŸ”¬ Research Consulting Active Inference Β· Bayesian modeling Β· Computational biology Β· Cognitive security Β· Multi-agent systems πŸ“§ Email
πŸŽ“ Tutoring & Mentorship Active Inference fundamentals Β· Python/Rust AI frameworks Β· Scientific writing Β· Graduate-level Bayesian methods πŸ“§ Email
πŸ’¬ Speaking & Workshops Conference keynotes Β· Team workshops on AI/ML Β· Course development Β· Institutional training πŸ“§ Email
🀝 Research Collaboration Joint publications Β· Framework co-development Β· Grant partnerships Β· Open-source contributions πŸ“§ Email

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.


πŸ“ 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.

Resource What's Inside
πŸ“š pages/BIBLIOGRAPHY.md Unified sortable table of all works in the bibliography β€” DOI links, domain tags, and per-paper docs
πŸ“„ works/ Generated per-work landing pages β€” one canonical HTML page per bibliography row with citation, DOI, primary source, and documentation link
πŸ”Ž search.html / opensearch.xml Human and browser search β€” searchable index over works, software, people, organizations, claims, and key pages
πŸ“ updates.html / CHANGELOG.md Human-readable update history β€” recent public-index and generated-site changes
🧭 domains.html / pages/DOMAINS.md Domain landing pages for Entomology, Active Inference, Cognitive Security, Art & Synergetics, and Computational work
πŸ’» pages/SOFTWARE.md Curated owned repos + Active Inference Institute contributions β€” AI frameworks, geometry engines, entomology tools, and developer infrastructure; see the full generated repository inventory for public GitHub coverage
πŸ“ papers/ Per-paper folders β€” each with README.md, AGENTS.md, and Claude Code-compatible SKILL.md where a bibliography row has in-tree documentation
πŸ“„ pages/ Documentation Hub β€” Centralized directories for videos, courses, pathways, and repository integrations
πŸ”— pages/LINKS.md Comprehensive directory of all web presences β€” academic profiles, social media, art, NFTs, podcasts, courses, organizations
🧭 pages/DISCOVERY.md Agentic discovery map β€” canonical IDs, public APIs, source queries, and verification notes
🧾 cite-verify.html / evidence.html Citation and evidence layer β€” preferred citation, public identifiers, source-of-truth rules, and claim ledger (Markdown)
πŸ“„ resume/ / data/resume.json Structured resume/CV exports β€” source-backed JSON, plaintext variants, and generated PDF built from canonical works, software, metrics, and resume-specific records
βœ… pages/VERIFICATION_LOG.md Independent verification log β€” dated primary-source corroboration of load-bearing claims (Scholar metrics, EIN, NSF award, DOIs, identity graph) against sources not controlled by the subject (JSON)
πŸ‘€ pages/PROFILE.md Detailed biography β€” education, research areas, organizations, teaching, awards, art, and key metrics
🀝 pages/COLLABORATORS.md Research network β€” key collaborators (Friston, Gordon, Albarracin, Fields, etc.) with joint publications and institutional map
πŸŽ₯ pages/MEDIA.md Talks, podcasts & press β€” conference presentations, podcast appearances, video series, courses, interviews, and press coverage
πŸ€– llms.txt / CITATION.cff / codemeta.json / search-index.json / feed.xml Machine-readable discovery metadata β€” agent map, citation metadata, CodeMeta, search index, and RSS feed
πŸ—ƒοΈ catalog.html / data/catalog.json / GENERATED.md Structured data and rebuild map β€” Schema.org DataCatalog plus generated-artifact manifest and commands
πŸ“¦ bibliography.bib / bibliography.csl.json / bibliography.ris / data/ Exports for citation managers and agents β€” BibTeX, CSL JSON, RIS, works/artworks/software/people/organization/claims/reconciliation JSON
βœ… reports/ / CHANGELOG.md / docs/REDIRECTS.md Maintenance evidence β€” source snapshots, reconciliation reports, accessibility reports, visual QA screenshots, changelog, and canonical URL policy
πŸ§‘β€πŸš€ AGENT_START.md / humans.txt / .well-known/security.txt Operational entrypoints β€” agent task recipes, human credits/contact, and responsible disclosure metadata
πŸ› οΈ code/ Repository Source Code β€” orchestrators/, src/, and tests/ directories containing executable pipelines and core functions
πŸ“– docs/ Central Documentation β€” Repository-wide operational documentation

By Domain

Domain Publications Highlights Software
🐜 Entomology works EntoLinguistics · ActiveInferants · AntStack · PhD ento_linguistics · MetaInformAnt · ant_stack
🧠 Active Inference works FEPLean · CognitiveCaseDiagrams · CEREBRUM fep_lean · cognitive_case_diagrams · goference
πŸ›‘οΈ Cognitive Security works CognitiveIntegrity Β· InformationCommons Β· P3IF p3if Β· opentir
🎨 Art & Synergetics works BlakeJiang · DoorsOfPerception · BlakeFuller · QuadMath QuadCraft · symergetics · ivm-xyz
πŸ’» Computational works DeterministicTestbedSelf Β· RecoveringLLMPersona Β· Triplicate Β· TemplateTextbook Β· BiologyTextbook template Β· template_autoscientists Β· ntqr_llm
🧬 Genetics & Biomedical works HoneyBeeEvolution · NuclearStructure · DennettExplained FORMINDEX

πŸ“š 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 β†’

Key publications (click to expand)
Year Title Venue DOI
2026 Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology Zenodo 10.5281/zenodo.19574118
2025 The Ant Stack Zenodo 10.5281/zenodo.16782756
2021 Active Inferants: An Active Inference Framework for Ant Colony Behavior Frontiers in Behavioral Neuroscience 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
2019 The ant colony as a test for scientific theories of consciousness Synthese 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
2016 Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior Annual Review of Neuroscience 10.1146/annurev-neuro-070815-013927

πŸ“ Paper folders: EntoLinguistics Β· AntStack Β· ActiveInferants Β· PhDDissertation Β· DopamineForaging Β· 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 β†’

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
2025 Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought Dynamics Entropy 10.3390/e27050459
2024 Federated inference and belief sharing Neuroscience & Biobehavioral Reviews 10.1016/j.neubiorev.2023.105500
2023 A variational synthesis of evolutionary and developmental dynamics Entropy 10.3390/e25070964
2023 Generalized Notation Notation for Active Inference Models Zenodo 10.5281/zenodo.7803328
2018 Of woodlice and men (with Karl Friston) ALIUS Bulletin 10.34700/h460-nz89

πŸ“ Paper folders: CEREBRUM Β· GNN Β· FederatedInference Β· Thoughtseeds Β· EvoJump


πŸ›‘οΈ 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 β†’

Key publications (click to expand)

πŸ“• 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

πŸ“„ Selected Papers

Year Title Venue DOI
2026 Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory) Zenodo 10.5281/zenodo.18364119
2024 Bridging gaps in image meme research: A multidisciplinary paradigm JASIST 10.1002/asi.24900
2024 FarmWorks: Decentralized AI Agents for Personalized Solutions Zenodo 10.5281/zenodo.13754585
2023 Cognitive Sovereignty & Active Inference in the State of Exception Zenodo 10.5281/zenodo.10038232

πŸ“ Paper folders: CognitiveIntegrity Β· InformationCommons Β· NarrativeEcosystems Β· 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 β†’

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.20144984
2026 The Doors of Perception are the Threshold of Prediction: Active Inference and Blake's Theory of Seeing Zenodo 10.5281/zenodo.18600041
2026 Before Pragmatism Had a Name: Blake's "America A Prophecy" Zenodo 10.5281/zenodo.18807970
2025 Synthesis of Agent and Niche Zenodo 10.5281/zenodo.17235137
2025 QuadMath: An Analytical Review of 4D and Quadray Coordinates Zenodo 10.5281/zenodo.16887800
2023 William Blake & Buckminster Fuller: Lives in Juxtaposition Zenodo 10.5281/zenodo.7514368

πŸ“ Paper folders: BlakeJiang Β· DoorsOfPerception Β· BeforePragmatism Β· BlakeFuller Β· QuadMath Β· Symergetics


πŸ’» 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 β†’ Β· Curated repos β†’ Β· Full inventory β†’

Key publications & repositories (click to expand)

πŸ“„ Papers

Year Title Venue DOI
2025 The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge Landscapes ArXiv 10.48550/arXiv.2505.17500
2025 MDKV: A Multitrack Markdown Container for Structured, Portable Documents Zenodo 10.5281/zenodo.16790554
2025 Markdown Decision Process: A Framework for Probabilistic Document Analysis Zenodo 10.5281/zenodo.17244386
2026 A Deterministic Testbed for Self-Organizing Agent-Team Coordination Zenodo 10.5281/zenodo.20533670
2026 Recovering LLM-Persona Accuracies from Unlabeled Votes Zenodo 10.5281/zenodo.20498700
2026 The Triplicate: A Data-Driven Large-Format Newspaper Layout Engine Zenodo 10.5281/zenodo.20533676
2026 The Template Textbook Zenodo 10.5281/zenodo.20533126

πŸ”§ Highlighted Repositories

Repository Description
codomyrmex 🐜 AI-native modular coding workspace β€” 128 modules, 600 MCP tools
template Multi-project research template with 10-stage build pipeline
template_autoscientists Deterministic multi-agent scientific-discovery coordination harness
template_newspaper Data-driven large-format newspaper layout engine
ntqr_llm Algebraic NTQR evaluation for LLM-persona accuracy recovery
steganographer High-performance Rust cryptographic watermarking
QuadCraft MineCraft with Tetrahedra (Quadray coordinates)
MetaInformAnt Integration for Ants and Beyond
p3if Properties, Processes, and Perspectives Inter-Framework

Full curated software list: pages/SOFTWARE.md β†’. For all public GitHub repositories including forks and uncataloged projects, see repositories.html β†’. 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 β†’

Institute ecosystem publications (click to expand)
Year Title Venue DOI
2025 The Active Inference Institute & Active Inference Ecosystem (v3) Zenodo 10.5281/zenodo.17982447
2024 The Active Inference Institute & Active Inference Ecosystem (v2) Zenodo 10.5281/zenodo.14108992
2024 Aligning Active Inference Ontology to SUMO Zenodo 10.5281/zenodo.11459322
2023 The Active Inference Institute and Active Inference Ecosystem (v1) Zenodo 10.5281/zenodo.8266281

πŸ“ Paper folders: AII_v3 Β· AII_v2 Β· AII_v1


πŸŽ₯ Presentations, Courses & Media

Livestreams, conference talks, courses, and collaborative media β€” Full list in Bibliography β†’

Presentations, courses, and media (click to expand)

πŸ“Ί Ongoing Series

Platform Description Link
Active Inference Journal 500+ videos on Active Inference with transcripts video.activeinference.institute
Personal YouTube 200+ livestreams including drawings, Synergetics, paper discussions youtube.com/@danielarifriedman

Selected Presentations

Year Title Venue
2025 Systems Processes, Active Inference, and Beyond Zenodo
2025 5th Applied Active Inference Symposium β€” Abstract Book Zenodo
2024 BioFirm Development at Applied Active Inference Symposium 2024 Zenodo
2023 Of Ants & Aging Zenodo

🧬 Genetics & Biomedical Research

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

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
2022 On free will or the lack thereof (interview with Robert Sapolsky) ALIUS Bulletin 10.5281/zenodo.7394901
2019 Dennett Explained (interview with Daniel Dennett) ALIUS Bulletin 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

πŸ—ΊοΈ Research Themes & Expertise Areas

Active Inference ──── Entomology ──── Cognitive Security
       β”‚                   β”‚                  β”‚
   Bayesian            Ant Colonies       Information
   Modeling            Social Insects     Ecosystems
       β”‚                   β”‚                  β”‚
   Computational ──── Biology ──────── Digital Rhetoric
       β”‚                   β”‚                  β”‚
   CEREBRUM, GNN      Genetics          COGSEC, P3IF
       β”‚                   β”‚                  β”‚
   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


πŸ“Š GitHub Stats

πŸ† GitHub Trophies

πŸ” Top Contributed Repo


πŸ’° Support My Work

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  1. codomyrmex codomyrmex Public

    🐜 AI-native modular coding workspace β€” 127 modules, 424 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration

    Python 6 1

  2. MetaInformAnt MetaInformAnt Public

    Integration for Ants and Beyond

    Python 6 1

  3. QuadCraft QuadCraft Public

    MineCraft with Tetrahedra (Quadray coordinates)

    JavaScript 9

  4. template template Public template

    Production-grade scaffold for reproducible computational research β€” 10-stage DAG pipelines, β‰₯90% test coverage, cryptographic provenance (SHA-256 + steganographic PDF watermarking), multi-project w…

    Python 17 1

  5. ActiveInferenceInstitute/GeneralizedNotationNotation ActiveInferenceInstitute/GeneralizedNotationNotation Public

    Pkl 24 3

  6. ActiveInferenceInstitute/GEO-INFER ActiveInferenceInstitute/GEO-INFER Public

    HTML 11 2