AI Researcher · Consultant · Educator · Artist
Active Inference · Bayesian Modeling · Computational Biology · Cognitive Security*
Available for consulting, tutoring, and research collaboration
Quick links: 📚 Publications · 💻 Software · 📁 Papers · 🎯 Consulting & Tutoring · 🐜 Entomology · 🧠 Active Inference · 🛡️ Cognitive Security · 🎨 Art & Synergetics
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.
- 🐜 Entomologist — PhD (Stanford University, 2014-2019 with Prof. Deborah Gordon) on the behavioral, physiological, and transcriptomic bases of collective behavior in harvester ants
- 🧠 Active Inference Researcher — Researcher, educator, and organizer at the Active Inference Institute working on federated inference, variational evolutionary dynamics, and multi-agent generative models; builder of computational AI frameworks (CEREBRUM, GNN, InferAnts)
- 🛡️ Cognitive Security Expert — Author of books and papers on narrative information ecosystems, digital rhetorical analysis, and formal multiagent security frameworks at COGSEC.org
- 🎨 Artist & Philosopher — Ink, metal, and collaborative art; explorations of William Blake, Buckminster Fuller, and Synergetics
- 📺 Educator & Tutor — 500+ Active Inference livestreams, 200+ personal channel streams, university courses, conference workshops, open-source curricula, and private tutoring
| Service | Areas of Expertise | Get in Touch |
|---|---|---|
| 🔬 Research Consulting | Active Inference · Bayesian modeling · Computational biology · Cognitive security · Multi-agent systems | |
| 🎓 Tutoring & Mentorship | Active Inference fundamentals · Python/Rust AI frameworks · Scientific writing · Graduate-level Bayesian methods | |
| 💬 Speaking & Workshops | Conference keynotes · Team workshops on AI/ML · Course development · Institutional training | |
| 🤝 Research Collaboration | Joint publications · Framework co-development · Grant partnerships · Open-source contributions |
106 publications · 77 open-source repositories · 700+ livestreams · Stanford PhD · Co-authored with Karl Friston, Deborah Gordon, and 50+ collaborators
Full catalog: 106 works spanning peer-reviewed papers, books, presentations, courses, and policy comments (2015–2026) · 46 owned repos · 31 AII contributions
| Resource | What's Inside |
|---|---|
| 📚 BIBLIOGRAPHY.md | Unified sortable table of all 106 publications — every paper, book, and presentation with DOI links, domain tags, and deep-links to paper folders |
| 💻 SOFTWARE.md | 46 owned repos + 31 Active Inference Institute contributions — AI frameworks, geometry engines, entomology tools, and developer infrastructure |
| 📁 papers/ | 99 per-paper folders (2015–2026) — each with README.md, AGENTS.md, and Claude Code-compatible SKILL.md |
| Domain | Publications | Highlights | Software |
|---|---|---|---|
| 🐜 Entomology | 20 papers | ActiveInferants · AntStack · PhD | MetaInformAnt · ant_stack · ActiveInferAnts |
| 🧠 Active Inference | 19 papers | CEREBRUM · FederatedInference · GNN | codomyrmex · cognitive-engine · goference |
| 🛡️ Cognitive Security | 19 papers | CognitiveIntegrity · InformationCommons · P3IF | p3if · opentir |
| 🎨 Art & Synergetics | 13 papers | DoorsOfPerception · BlakeFuller · QuadMath | QuadCraft · symergetics · ivm-xyz |
| 💻 Computational | 6 papers | DiscoveryEngine · MDKV · MarkdownDecisionProcess | template · steganographer |
| 🧬 Genetics & Biomedical | 9 papers | HoneyBeeEvolution · NuclearStructure · DennettExplained | FORMINDEX |
20 peer-reviewed papers on ant genetics, behavior, and collective intelligence — Full list in Bibliography →
Key publications (click to expand)
| Year | Title | Venue | DOI |
|---|---|---|---|
| 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 |
📁 Paper folders: AntStack · ActiveInferants · PhDDissertation · DopamineForaging · AntGenetics
19 works on theoretical, computational, and applied Active Inference — Full list in Bibliography →
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 |
📁 Paper folders: CEREBRUM · GNN · FederatedInference · Thoughtseeds · EvoJump
3 books + 16 papers on narrative security, memes, trust, and policy — Full list in Bibliography →
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.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 |
📁 Paper folders: CognitiveIntegrity · InformationCommons · NarrativeEcosystems · FarmWorks
13 works on William Blake, Buckminster Fuller, visual art, and interdisciplinary philosophy — Full list in Bibliography →
Key publications (click to expand)
| Year | Title | Venue | DOI |
|---|---|---|---|
| 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 |
📁 Paper folders: DoorsOfPerception · BeforePragmatism · BlakeFuller · QuadMath · Symergetics
6 papers + 46 repositories — Papers in Bibliography → · All repos →
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 |
| Repository | Description |
|---|---|
| codomyrmex | 🐜 AI-native modular coding workspace — 127 modules, 424 MCP tools |
| template | Multi-project research template with 10-stage build pipeline |
| 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 list of 46 personal repos + 31 Active Inference Institute contributions: SOFTWARE.md →
5 works on institute snapshots, ecosystem maps, and organizational design — Full list in Bibliography →
Institute ecosystem publications (click to expand)
| Year | Title | Venue | DOI |
|---|---|---|---|
| 2025 | The Active Inference Institute & Active Inference Ecosystem (v3) | Zenodo | 10.5281/zenodo.14108991 |
| 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 |
Livestreams, conference talks, courses, and collaborative media — Full list in Bibliography →
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 — Abstract Book | Zenodo |
| 2024 | BioFirm Development at Applied Active Inference Symposium 2024 | Zenodo |
| 2023 | Of Ants & Aging | Zenodo |
9 works on genetics, radiation biology, and biomedical research — Full list in Bibliography →
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 |
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
