Computational Biologist Β· Active Inference Β· Cognitive Security Β· Artist
Active Inference Β· Bayesian Modeling Β· Computational Biology Β· Cognitive Security*
Quick links: π Publications Β· π Works Β· π¬ Research Β· π§ Domains Β· π» Software Β· π Papers Β· π Reports & Counts Β· β
Reproducibility Β· π Search Β· π§Ύ Cite & Verify Β· π§ Discovery Β· ποΈ Catalog Β· π Updates Β· πΌοΈ Art Β· πͺ NFT Β· π§ Meditations Β· π₯ Media Β· πΊ Videos Β· π€ Profile Β· π€ Collaborators Β· βΉοΈ About Β· π All Links Β· π Resume/CV Β· π― Consulting Β· π Read Aloud (press T)
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
- π Entomologist β PhD (Stanford, 2014β2019, 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, 2020β2023 (NSF budget period 2020β2022, extended to 2023)
- π§ 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
- π‘οΈ Cognitive Security Researcher β bibliography-indexed work on narrative ecosystems, digital rhetoric, and multiagent security at COGSEC.org
- π¨ 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
- πΊ 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
- π Community Builder β Co-founder of Complexity Weekend (since 2019); co-organized Stanford Complexity Group
| Service | Areas of Expertise | Get in Touch |
|---|---|---|
| π¬ Research Consulting | Active Inference Β· Bayesian modeling Β· Computational biology Β· Cognitive security Β· Multi-agent systems | π§ Email |
| π Tutoring & Mentorship | Active Inference fundamentals Β· Python/Rust AI frameworks Β· Scientific writing Β· Graduate-level Bayesian methods | π§ Email |
| π¬ Speaking & Workshops | Conference keynotes Β· Team workshops on AI/ML Β· Course development Β· Institutional training | π§ Email |
| π€ Research Collaboration | Joint publications Β· Framework co-development Β· Grant partnerships Β· Open-source contributions | π§ Email |
Current generated totals: see
reports/current_counts.mdfor bibliography, paper-folder, software, GitHub inventory, public-source snapshot, and paired-publication counts with generation metadata and rebuild commands. Scholar metrics are sourced fromdata/scholar-snapshot.jsonand propagated into the resume and claim exports.
Current catalog totals are generated in
reports/current_counts.md. Canonical source tables arepages/BIBLIOGRAPHY.md,pages/SOFTWARE.md,papers/README.md, anddata/github-repositories.json.
| Resource | What's Inside |
|---|---|
| π pages/BIBLIOGRAPHY.md | Unified sortable table of all works in the bibliography β DOI links, domain tags, and per-paper docs |
| π works/ | Generated per-work landing pages β one canonical HTML page per bibliography row with citation, DOI, primary source, and documentation link |
| π search.html / opensearch.xml | Human and browser search β searchable index over works, software, people, organizations, claims, and key pages |
| π updates.html / CHANGELOG.md | Human-readable update history β recent public-index and generated-site changes |
| π§ domains.html / pages/DOMAINS.md | Domain landing-page hub β Entomology, Active Inference, Cognitive Security, Art & Synergetics, Computational, Presentations & Media, AII Ecosystem, Biomedicine (each cluster has its own domain-*.html) |
| π» pages/SOFTWARE.md | Curated owned repos + Active Inference Institute contributions β AI frameworks, geometry engines, entomology tools, and developer infrastructure; see the primary repository inventory and fork archive for public GitHub coverage |
| π 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 |
| π pages/ | Documentation Hub β Centralized directories for videos, courses, pathways, and repository integrations |
| π pages/LINKS.md | Comprehensive directory of all web presences β academic profiles, social media, art, NFTs, podcasts, courses, organizations |
| π pages/WIKIPEDIA.md | Wikipedia presence β Wikidata/Wikipedia entries and identity-graph links |
| π§ pages/DISCOVERY.md | Agentic discovery map β canonical IDs, public APIs, source queries, and verification notes |
| π§Ύ cite-verify.html / evidence.html | Citation and evidence layer β preferred citation, public identifiers, source-of-truth rules, and claim ledger (CITE_VERIFY Β· EVIDENCE) |
| π 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 |
| β 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) |
| π€ pages/PROFILE.md | Detailed biography β education, research areas, organizations, teaching, awards, art, and key metrics |
| π€ pages/COLLABORATORS.md | Research network β key collaborators (Friston, Gordon, Albarracin, Fields, etc.) with joint publications and institutional map |
| π₯ pages/MEDIA.md | Talks, podcasts & press β conference presentations, podcast appearances, video series, courses, interviews, and press coverage |
| π pages/RESOURCES.md / pages/VIDEOS.md | Resources & video index source β curated resource compendium and the videos/courses catalogue |
| πΌοΈ art.html / nft.html / meditations.html | Art & creative portfolio β gallery, NFT collectibles (Curio Cards), and meditations pages (art/ holds local gallery assets) |
| π€ 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 |
| ποΈ catalog.html / data/catalog.json / GENERATED.md | Structured data and rebuild map β Schema.org DataCatalog plus generated-artifact manifest and commands |
| π¦ exports.html / bibliography.bib / bibliography.csl.json / bibliography.ris / data/ | Exports for citation managers and agents β HTML export hub, BibTeX, CSL JSON, RIS, works/artworks/software/people/organization/claims/reconciliation JSON |
| β reports/ / CHANGELOG.md / docs/ | Maintenance evidence & documentation β source snapshots, reconciliation/accessibility/visual-QA reports, changelog, and the documentation index (architecture, operations, canonical URL policy, design, security, releases) |
| π reports.html / research.html / reproducibility.html | Reports, research & reproducibility hub β generated report index, research overview, and the reproducibility ledger (Markdown) |
| π§βπ AGENT_START.md / humans.txt / .well-known/security.txt | Operational entrypoints β agent task recipes, human credits/contact, and responsible disclosure metadata |
| β agent-verify.html / about.html | Agent verification & about β agent-ready verification recipes and a short bio page |
| π οΈ code/ | Repository Source Code β orchestrators/, src/, and tests/ directories containing executable pipelines and core functions |
| π docs/ | Central Documentation β Repository-wide operational documentation |
| Domain | Publications | Highlights | Software |
|---|---|---|---|
| π Entomology | works | EntoLinguistics Β· ActiveInferants Β· AntStack Β· PhD | ento_linguistics Β· MetaInformAnt Β· ant_stack |
| π§ Active Inference | works | FEPLean Β· CognitiveCaseDiagrams Β· CEREBRUM | fep_lean Β· cognitive_case_diagrams Β· goference |
| π‘οΈ Cognitive Security | works | CognitiveIntegrity Β· InformationCommons Β· P3IF | p3if Β· opentir |
| π¨ Art & Synergetics | works | BlakeJiang Β· DoorsOfPerception Β· BlakeFuller Β· QuadMath | QuadCraft Β· symergetics Β· ivm-xyz |
| π» Computational | works | DeterministicTestbedSelf Β· RecoveringLLMPersona Β· THALIA Β· WitnessRegister Β· Triplicate Β· TemplateTextbook Β· BiologyTextbook | template Β· template_autoscientists Β· ntqr_llm Β· thalia |
| 𧬠Genetics & Biomedical | works | HoneyBeeEvolution · NuclearStructure · DennettExplained | FORMINDEX |
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.19574117 |
| 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 |
π Paper folders: EntoLinguistics Β· AntStack Β· ActiveInferants Β· PhDDissertation Β· DopamineForaging Β· AntGenetics
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 |
| 2026 | Active Inference Power Suite: Conditional Statistical Power under Controlled Generative Settings | Zenodo | 10.5281/zenodo.21695160 |
| 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.7803327 |
| 2018 | Of woodlice and men (with Karl Friston) | ALIUS Bulletin | 10.34700/h460-nz89 |
π Paper folders: CEREBRUM Β· GNN Β· FederatedInference Β· Thoughtseeds Β· EvoJump
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)
| 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 |
| Year | Title | Venue | DOI |
|---|---|---|---|
| 2026 | Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory) | Zenodo | 10.5281/zenodo.18364118 |
| 2026 | Personal Red Lines for Development | Zenodo | 10.5281/zenodo.21754239 |
| 2026 | Black Line: Strong Work in Public | Zenodo | 10.5281/zenodo.21754235 |
| 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.10038231 |
π Paper folders: CognitiveIntegrity Β· InformationCommons Β· NarrativeEcosystems Β· FarmWorks
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.20144983 |
| 2026 | The Doors of Perception are the Threshold of Prediction: Active Inference and Blake's Theory of Seeing | Zenodo | 10.5281/zenodo.18600040 |
| 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.16887799 |
| 2023 | William Blake & Buckminster Fuller: Lives in Juxtaposition | Zenodo | 10.5281/zenodo.7514367 |
π Paper folders: BlakeJiang Β· DoorsOfPerception Β· BeforePragmatism Β· BlakeFuller Β· QuadMath Β· Symergetics
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· Primary inventory β
Key publications & repositories (click to expand)
| 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.20533669 |
| 2026 | Recovering LLM-Persona Accuracies from Unlabeled Votes | Zenodo | 10.5281/zenodo.20498699 |
| 2026 | The Triplicate: A Data-Driven Large-Format Newspaper Layout Engine | Zenodo | 10.5281/zenodo.20533675 |
| 2026 | The Template Textbook | Zenodo | 10.5281/zenodo.20533125 |
| 2026 | COGANT: Deterministic Codebase-to-GNN Translation | Zenodo | 10.5281/zenodo.20705350 |
| 2026 | AGEINT: Agentic Intelligence | Zenodo | 10.5281/zenodo.20732275 |
| 2026 | THALIA: Typed Harness with Analytical Lexical-Integrated Architecture | Zenodo | 10.5281/zenodo.21763244 |
| 2026 | Codomyrmex: An Artificial Ecology for Agentic Software Development | Zenodo | 10.5281/zenodo.21750800 |
The DAF "line set" β 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).
| Year | Title | Venue | DOI |
|---|---|---|---|
| 2026 | The Witness Register: Co-Registration Without Aggregation | Zenodo | 10.5281/zenodo.21754245 |
| 2026 | The Line Set: Holding Instruments Apart | Zenodo | 10.5281/zenodo.21754243 |
| 2026 | White Line: A Typed Ledger for the Edge of the Claim | Zenodo | 10.5281/zenodo.21754241 |
| 2026 | Golden Line: Toward What Matters | Zenodo | 10.5281/zenodo.21754237 |
| Repository | Description |
|---|---|
| codomyrmex | π AI-native modular coding workspace β 100+ modules, 500+ 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 |
| thalia | Typed agentic harness for reproducible long-context memory experiments |
| p3if | Properties, Processes, and Perspectives Inter-Framework |
Full curated software list: pages/SOFTWARE.md β. For public GitHub coverage, use the primary repository inventory β; forks are separated into the fork archive β. Current totals live in
reports/current_counts.md.
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.8266280 |
Livestreams, conference talks, courses, and collaborative media β Full list in Bibliography β
Presentations, courses, and media (click to expand)
| 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 |
| 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, 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.7394900 |
| 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 |
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
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





