---
title: "DOMAINS - Daniel Ari Friedman"
description: "Research domain map linking works, software, collaborators, and learning paths."
keywords: "Daniel Ari Friedman, research domains, Active Inference, entomology, cognitive security"
---
<div align="center">

# Research Domains

> **Navigation**: [🏠 Home](../README.md) | [📚 Bibliography](BIBLIOGRAPHY.md) | [💻 Software](SOFTWARE.md) | [🧭 Discovery](DISCOVERY.md) | [🧾 Evidence](EVIDENCE.md)

[Website domain index](../domains.html)

</div>

---

## 🐜 [Entomology & Collective Behavior](../domain-entomology.html)

Ant colony behavior, physiology, transcriptomics, and computational models of collective cognition.

- Works: 23
- Selected repositories: 7
- Collaborator context: Deborah Gordon, Karl Friston, Chris Fields

**Learning path**

- Read the foundational pillar guide on Computational Entomology for simulation models and neurogenomic algorithms.
- Explore Insect Cognition &amp; Collective Intelligence for distributed cognition and stigmergic coordination.
- See the ant drawings as art in the Collective Behavior &amp; Ants collection — one page per drawing.
- Investigate behavioral neurochemistry in Measurement of Natural Variation in Neurotransmitter Content.
- Study molecular and transcriptomic foundations in Gene Expression Variation in Harvester Ant Foragers.
- Examine distributed active inference modeling in Active Inferants: An Active Inference Framework for Ant Colony Behavior.
- Explore modern software implementations via MetaInformAnt and ActiveInferAnts.
- Inspect global bibliometric archives via the FORMINDEX interface to FORMIS.

**Selected works**

- 2026 — [Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology](https://doi.org/10.5281/zenodo.19574117)
- 2026 — [Illegal States, Mostly Unrepresentable](https://doi.org/10.5281/zenodo.21298885)
- 2025 — [Computational Complexity and Energetics of the Ant Stack](https://doi.org/10.5281/zenodo.17238736)
- 2025 — [The Ant Stack](https://doi.org/10.5281/zenodo.16782756)
- 2025 — [Towards a Science of Consciousness and Social Complexity... For Ants](https://www.editorafi.org/ebook/c128-colonias-formigas-conscientes)
- 2024 — [Chemical and transcriptomic diversity do not correlate with ascending levels of social complexity in the insect order Blattodea](https://doi.org/10.1002/ece3.70063)

**Selected repositories**

- [MetaInformAnt](https://github.com/docxology/MetaInformAnt) — Meta-framework integrating computational entomology, Active Inference, and information theory for modeling ant colony cognition and beyond
- [ActiveInferAnts](https://github.com/docxology/ActiveInferAnts) — Active Inference for ants — multi-language implementations (Python) for modeling ant-colony cognition as Bayesian agents minimizing free energy
- [Active_InferAnts](https://github.com/ActiveInferenceInstitute/Active_InferAnts) — Active Inference models for/of ants across 32+ programming languages — multi-language reference implementation of stigmergic Active Inference
- [ant_stack](https://github.com/docxology/ant_stack) — The Ant Stack — layered computational model of collective ant-colony intelligence
- [ant-pheromone](https://github.com/docxology/ant-pheromone) — Computational simulation of ant pheromone trail dynamics and stigmergic communication
- [ento_linguistics](https://github.com/docxology/ento_linguistics) — Ento-Linguistics corpus pipeline — term extraction, terminology networks, semantic entropy, CACE scoring ·  · Zenodo
- [FORMINDEX](https://github.com/docxology/FORMINDEX) — Analysis and tooling around FORMIS, the world's largest ant-literature database; bibliometric mining and structured index generation

## 🧠 [Active Inference & Free Energy Principle](../domain-active-inference.html)

Free Energy Principle, generative models, belief sharing, formalization, and educational infrastructure.

- Works: 46
- Selected repositories: 11
- Collaborator context: Karl Friston, Thomas Parr, Maxwell J. D. Ramstead, Conor Heins, Tim Verbelen

**Learning path**

- Read the comprehensive Active Inference &amp; Free Energy Principle Tutorial.
- Explore neurosymbolic integrations in Neurosymbolic AI &amp; Active Inference.
- See the theory rendered as drawing in the Active Inference art collection — one page per drawing.
- Trace multi-agent coordination theory in Shared Protentions in Multi-Agent Active Inference.
- Examine distributed belief updates in Federated Inference and Belief Sharing.
- Study formal mathematical notation systems in Generalized Notation Notation (GNN).
- Explore theorem proving in Lean 4 via Towards Lean 4 Formalization of Active Inference and the fep_lean repository.
- Engage with multi-agent orchestration and case-based reasoning in CEREBRUM and active_torchference.

**Selected works**

- 2026 — [A Living Meta-Analysis Architecture for Active Inference: Assertion Extraction, Nanopublications, and Hypothesis Scoring](https://doi.org/10.5281/zenodo.19461933)
- 2026 — [Dynamic Attentional Agents in Focused Attention Meditation: Hierarchical Computational Modeling of Expert-Novice Differences](https://doi.org/10.1007/978-3-032-16955-6_11)
- 2026 — [Cognitive Diagrams: Reviewing Categorical Accounts of Linguistic Case](https://doi.org/10.5281/zenodo.19695259)
- 2026 — [Towards Lean 4 Formalization of the Free Energy Principle: AI-Driven Theorem Sketching and Verification for Active Inference and Bayesian Mechanics](https://doi.org/10.5281/zenodo.19699233)
- 2026 — [GeneralizedNotationNotation (GNN)](https://doi.org/10.5281/zenodo.7803313)
- 2026 — [On-Policy Distillation as Active Inference in Finite Variational Models](https://doi.org/10.5281/zenodo.20747834)

**Selected repositories**

- [active_inference](https://github.com/docxology/active_inference) — Active Inference for, with, and by Generative AI — Python implementations of free-energy-minimizing agents integrated with modern AI tooling
- [active_torchference](https://github.com/docxology/active_torchference) — PyTorch-based Active Inference implementations — GPU-accelerated variational inference and free energy minimization
- [goference](https://github.com/docxology/goference) — Active Goference — production-ready Go framework for Active Inference autonomous agents; genuine variational inference, free energy minimization, POMDP policy planning via gonum
- [AgenticMesh](https://github.com/docxology/AgenticMesh) — Active Inference & Agentic Mesh — modular Python infrastructure for building agentic systems using free-energy-minimizing Active Inference principles
- [ActiveInferAnts](https://github.com/docxology/ActiveInferAnts) — Active Inference for ants — multi-language implementations (Python) for modeling ant-colony cognition as Bayesian agents minimizing free energy
- [Active_InferAnts](https://github.com/ActiveInferenceInstitute/Active_InferAnts) — Active Inference models for/of ants across 32+ programming languages — multi-language reference implementation of stigmergic Active Inference
- [Generalized_Notation_Notation](https://github.com/ActiveInferenceInstitute/Generalized_Notation_Notation) — GNN — formal notation standard for specifying Active Inference generative models; JSON/YAML schema, validators, and transpilers to Python, Julia, and MATLAB · Zenodo software
- [fep_formal](https://github.com/ActiveInferenceInstitute/fep_formal) — Formal mathematics catalog for FEP and Active Inference — Lean 4 / Mathlib4 compilation, qualified semantic review, drafting tools, and manuscript pipeline ·  · Zenodo artifact v1.1.0 · Citation DOI · Zenodo software archive

## 🛡️ [Cognitive Security](../domain-cognitive-security.html)

Narrative ecosystems, information commons, digital rhetoric, and multiagent security.

- Works: 38
- Selected repositories: 4
- Collaborator context: RJ Cordes, Carlos Gershenson, Micah Musser

**Learning path**

- Read the comprehensive explainer guide What Is Cognitive Security? Theory, Threat Models, and Defense.
- Survey the foundational COGSEC publications: Information Resonance &amp; Narrative Information Ecosystems, Narrative Information Management (NIM-21), and Emergent Teams for Complex Threats.
- Examine multiagent epistemic defense in Cognitive Integrity Framework: Formal Foundations (Part 1: Theory).
- Analyze information commons and open standards in Structuring the Information Commons: Open Standards and Cognitive Security.
- Study multi-perspective property framing in The P3IF: Properties, Processes, and Perspectives Inter-Framework.
- Implement multi-agent cognitive security tools using p3if and the ATLAS framework.
- Examine ecosystem dependency profiles and intelligence mapping via opentir.

**Selected works**

- 2026 — [Cognitive Integrity Framework: Formal Foundations (Part 1 of 3: Theoretical Foundations)](https://doi.org/10.5281/zenodo.18364118)
- 2026 — [Crescent City in Living Waves: Space, Time, People, and Minds on the Southern Cascadian Coast](https://doi.org/10.5281/zenodo.20286170)
- 2026 — [California Public Records: A Technical and Legal Reference for the Post-AB 473 Era](https://doi.org/10.5281/zenodo.20789899)
- 2026 — [CogSecSkills: Multiharness Agentic Skills for Cognitive Security](https://doi.org/10.5281/zenodo.21513316)
- 2026 — [Active FractalRabbit: A Synthetic Benchmark for Belief Filtering Under Sparse Waypoint Observations](https://doi.org/10.5281/zenodo.21330636)
- 2026 — [Personal Red Lines for Development](https://doi.org/10.5281/zenodo.21754239)

**Selected repositories**

- [p3if](https://github.com/docxology/p3if) — Properties, Processes, and Perspectives Inter-Framework (P3IF) — multiplexing interdisciplinary requirements frameworks to manage information risk and foster cognitive security
- [opentir](https://github.com/docxology/opentir) — Comprehensive toolkit analyzing 250+ Palantir open-source repositories (6.2M+ lines of code) — automated discovery, multi-language analysis, dependency mapping, statistical profiling, and professional visualizations
- [cognitive-engine](https://github.com/docxology/cognitive-engine) — Hybrid neuro-symbolic AI combining fractal symbolic representations with probabilistic neural models for enhanced reasoning; includes Unipixel fractal building blocks and PEFF ethical reasoning
- [ATLAS](https://github.com/ActiveInferenceInstitute/ATLAS) — Question-Oriented Pattern Languages for Knowledge Management — structured templates for navigating complex scientific knowledge spaces

## 🎨 [Art & Synergetics](../domain-art-synergetics.html)

William Blake, Buckminster Fuller, visual art, Curio Cards, quadray coordinates, and synergetics.

- Works: 16
- Selected repositories: 6
- Collaborator context: Buckminster Fuller source tradition, William Blake source tradition, Curio Cards artists

**Learning path**

- Browse the curated visual archive on the Visual Art Gallery (940+ catalogued pen-and-ink drawings).
- Browse the themed drawing collections: Sacred Geometry &amp; Kabbalistic Triangles and Americana &amp; Seals, each with one page per artwork.
- Explore early blockchain history with Curio Cards (Cards 24, 25, 26 — Complexity, Passion, Education; 2017).
- Study prophetic economics and metaphysics in The Golden Compass and the Lunar Flux: William Blake and the Architecture of Value.
- Examine anticipatory epistemology in Before Pragmatism Had a Name: Blake's America A Prophecy.
- Investigate tetrahedral geometry and coordinate systems in QuadMath: An Analytical Review of 4D and Quadray Coordinates.
- Interact with 3D synergetics environments through QuadCraft and ivm-xyz.
- Explore digital knowledge graphs of synergetics with fuller-obsidian.

**Selected works**

- 2026 — [Before Pragmatism Had a Name: Blake's "America A Prophecy" Anticipates American Anticipatory Epistemology](https://doi.org/10.5281/zenodo.18807970)
- 2026 — [The Golden Compass and the Lunar Flux: William Blake, Bimetallic Meta-stability, and the Architecture of Value](https://doi.org/10.5281/zenodo.19335195)
- 2026 — [The Doors of Perception are the Threshold of Prediction: Active Inference and William Blake's Theory of Seeing](https://doi.org/10.5281/zenodo.18600040)
- 2026 — [The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single Vision](https://doi.org/10.5281/zenodo.20144983)
- 2026 — [Fourfold Vision: William Blake, Buckminster Fuller, and the Geometry of Omnirational Seeing](https://doi.org/10.5281/zenodo.21388456)
- 2025 — [On Cognitive Art & Science: Toward Wholeness From Both Sides](https://doi.org/10.5281/zenodo.16740438)

**Selected repositories**

- [QuadCraft](https://github.com/docxology/QuadCraft) — Minecraft variant built on tetrahedral geometry — voxels replaced by Quadray-coordinate tetrahedra, exploring Buckminster Fuller's synergetics in an interactive 3D world
- [QuadMath](https://github.com/docxology/QuadMath) — Mathematical exposition of Quadray coordinate systems (4-vector tetrahedral coordinates); LaTeX documentation and computation library
- [ivm-xyz](https://github.com/docxology/ivm-xyz) — Python library for 3D and 4D Quadray/IVM (Isotropic Vector Matrix) geometry — coordinate conversion, volume calculations, and polyhedral operations
- [godel_ivm](https://github.com/docxology/godel_ivm) — Gödel numbering meets the IVM (Isotropic Vector Matrix) — formal encoding of geometric objects as prime products
- [symergetics](https://github.com/docxology/symergetics) — Symbolic Synergetics — computer algebra and formal symbolic systems for Buckminster Fuller's synergetics mathematics
- [fuller-obsidian](https://github.com/docxology/fuller-obsidian) — Obsidian vault dedicated to R. Buckminster Fuller's ideas — synergetics, geodesics, and design science

## 💻 [Computational Methods & Open Science](../domain-computational.html)

Research templates, markdown containers, discovery engines, reproducible workflows, and software infrastructure.

- Works: 63
- Selected repositories: 9
- Collaborator context: Active Inference Institute contributors, Open-source repository contributors

**Learning path**

- Explore the principles of verifiable open research in AI Provenance &amp; Verification Architecture.
- Review the infrastructure-as-code research methodology in A template/ approach to Reproducible Generative Research.
- Study structured document semantics in Markdown Decision Process Framework.
- Inspect verified software execution records in the Reproducibility Ledger.
- Explore modular AI-agent development environments with codomyrmex and template.
- Query canonical knowledge graph endpoints via the Discovery Map and Data Catalog.

**Selected works**

- 2026 — [A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication](https://doi.org/10.5281/zenodo.16903351)
- 2026 — [Introduction to Biology: A Generative Approach](https://doi.org/10.5281/zenodo.20286477)
- 2026 — [Policy Entanglement in Active Inference](https://doi.org/10.5281/zenodo.20418904)
- 2026 — [Bounded AutoResearch for a Tiny Reproducible Machine-Learning Task](https://doi.org/10.5281/zenodo.20417016)
- 2026 — [Convergence Analysis of Gradient Descent Optimization](https://doi.org/10.5281/zenodo.20417136)
- 2026 — [Editorial Quality at Scale: A Reproducible Prose-Review Pipeline](https://doi.org/10.5281/zenodo.20417104)

**Selected repositories**

- [template](https://github.com/docxology/template) — Production-grade scaffold for reproducible computational research — 10-stage DAG pipelines, ≥90% test coverage, cryptographic provenance, multi-project workspace, and agent-ready documentation · Zenodo software v3.3.0 · Zenodo
- [mdkv](https://github.com/docxology/mdkv) — MKV-like key-value format and methods for Markdown — structured metadata embedding in plain-text documents
- [markdown_decision_process](https://github.com/docxology/markdown_decision_process) — Framework for Probabilistic Document Analysis — Markov Decision Process over Markdown artifacts for structured document reasoning
- [steganographer](https://github.com/docxology/steganographer) — High-performance Rust tool for embedding BLAKE3+Ed25519 cryptographic signatures and visible watermarks into live video/audio via LSB steganography; four Rust crates, 484 tests, GStreamer integration
- [timeline_generator](https://github.com/docxology/timeline_generator) — Networked Life Encoding — interactive D3 knowledge graph of human intellectual history; 24 relationship types, Perplexity AI enrichment; seeded around R. Buckminster Fuller's network
- [codomyrmex](https://github.com/docxology/codomyrmex) — AI-native modular coding workspace — 100+ modules, 500+ MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration ·  · Citation DOI
- [biology_textbook](https://github.com/docxology/biology_textbook) — Open generative biology textbook — Markdown source, tested Python modules, programmatic figures; archived at Zenodo artifact · Citation DOI
- [biol-1](https://github.com/docxology/biol-1) — BIOL-1: General Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content

## 🧬 [Genetics & Biomedicine](../domain-biomedicine.html)

Honey bee evolution, gene expression variation, nuclear structure, population genetics, and biomedical mechanisms.

- Works: 13
- Selected repositories: 5
- Collaborator context: Deborah Gordon, UC Davis Genetics, Stanford Biology

**Learning path**

- Explore empirical behavioral genomics in Gene Expression Variation in Harvester Ant Forager Brains.
- Study tissue-specific transcriptomic pipelines in Pipeline for Tissue-Specific Gene Expression Meta-Analysis in Honey Bees.
- Read evolutionary and developmental synthesis in A Variational Synthesis of Evolutionary and Developmental Dynamics.
- Investigate cellular biophysics and mechanobiology in Cells, Mechanobiology, and Osteopathy.
- Review undergraduate open curriculum materials in biology_textbook, biol-1, and biol-8.
- Query public biomedical indexing records directly via the PubMed Author Query and Europe PMC.

**Selected works**

- 2025 — [BevCyc - posit on primitive drivers of creatures](https://doi.org/10.5281/zenodo.14737075)
- 2025 — [Con-cat-enate: pilot overview](https://doi.org/10.5281/zenodo.14737042)
- 2024 — [Why Paleolithic Rockstars were both enigmatic and sporadic](https://doi.org/10.1016/j.plrev.2024.04.010)
- 2023 — [To comment or not to comment, that is the question!](https://doi.org/10.1016/j.plrev.2023.06.002)
- 2022 — [On free will or the lack thereof (interview with Robert Sapolsky)](https://doi.org/10.5281/zenodo.7394900)
- 2020 — [The neuroscience of decision making (interview with Timothy Hanks)](https://doi.org/10.34700/8pg4-0h12)

**Selected repositories**

- [MetaInformAnt](https://github.com/docxology/MetaInformAnt) — Meta-framework integrating computational entomology, Active Inference, and information theory for modeling ant colony cognition and beyond
- [EvoJump](https://github.com/docxology/EvoJump) — Comprehensive Framework for Evolutionary Ontogenetic Analysis — modeling developmental trajectories and evolutionary dynamics · Zenodo
- [biology_textbook](https://github.com/docxology/biology_textbook) — Open generative biology textbook — Markdown source, tested Python modules, programmatic figures; archived at Zenodo artifact · Citation DOI
- [biol-8](https://github.com/docxology/biol-8) — BIOL-8: Human Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content
- [biol-1](https://github.com/docxology/biol-1) — BIOL-1: General Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content

## 🌍 [AII Ecosystem](../domain-aii-ecosystem.html)

Active Inference Institute programs, infrastructure, textbook cohorts, and organizational ecosystem work.

- Works: 7
- Selected repositories: 5
- Collaborator context: Active Inference Institute educators and contributors, Institute program participants

**Learning path**

- Discover the organizational mission, governance, and programs on the Active Inference Institute Official Portal.
- Survey ecosystem development and open research milestones in The Active Inference Institute &amp; Active Inference Ecosystem (v3, 2025 snapshot).
- Explore ontology standardization efforts in Aligning Active Inference Ontology to SUMO.
- Participate in community education through the Textbook Group Cohorts and Institute Video Archives.
- Engage with formal mathematical specifications on the fep_lean repository.
- Review verified non-profit records via the ProPublica Nonprofit Explorer (EIN 88-2985125).

**Selected works**

- 2026 — [Coordinating the Field: The Case for Ecosystem-Level Technology Roadmapping and Community Working Groups in Active Inference](https://doi.org/10.5281/zenodo.23066903)
- 2025 — [The Active Inference Institute & Active Inference Ecosystem (v3, 2025 snapshot)](https://doi.org/10.5281/zenodo.17982447)
- 2024 — [Aligning Active Inference Ontology to SUMO](https://doi.org/10.5281/zenodo.11459322)
- 2024 — [The Active Inference Institute & Active Inference Ecosystem (v2, 2024 snapshot)](https://doi.org/10.5281/zenodo.14108992)
- 2023 — [The Active Inference Institute and Active Inference Ecosystem (v1)](https://doi.org/10.5281/zenodo.8266280)
- 2022 — [Catechism for Towards Active Diffusion](https://doi.org/10.5281/zenodo.7443847)

**Selected repositories**

- [active_inference](https://github.com/docxology/active_inference) — Active Inference for, with, and by Generative AI — Python implementations of free-energy-minimizing agents integrated with modern AI tooling
- [fep_formal](https://github.com/ActiveInferenceInstitute/fep_formal) — Formal mathematics catalog for FEP and Active Inference — Lean 4 / Mathlib4 compilation, qualified semantic review, drafting tools, and manuscript pipeline ·  · Zenodo artifact v1.1.0 · Citation DOI · Zenodo software archive
- [cognitive](https://github.com/ActiveInferenceInstitute/cognitive) — Cognitive modeling and simulation tools — multi-agent Active Inference environments, benchmarks, and visualization
- [cognitive](https://github.com/docxology/cognitive) — Cognitive Ecosystem Modeling Framework — Active Inference agents with Obsidian-compatible knowledge management, bidirectional graph validation, belief updating, and network visualization
- [AgenticMesh](https://github.com/docxology/AgenticMesh) — Active Inference & Agentic Mesh — modular Python infrastructure for building agentic systems using free-energy-minimizing Active Inference principles

## 🎥 [Presentations & Media](../domain-presentations-media.html)

Talks, courses, presentations, and media artifacts connected to the research and teaching program.

- Works: 14
- Selected repositories: 3
- Collaborator context: Active Inference Institute educators, Course and media collaborators

**Learning path**

- Browse 500+ indexed lectures, symposia, and live streams on the Video Index &amp; Interactive Timeline.
- Explore media appearances, podcasts, and interview features on the Media Appearances Hub.
- Study active-inference live streams in Active Inference Journal — 500+ Videos with Transcripts.
- Access generative biology curriculum and lecture materials in Introduction to Biology: A Generative Approach.
- Review transcript processing software pipelines in the Journal-Utilities Software Release (Zenodo 18686966).
- Explore public video channels on Active Inference YouTube and Personal YouTube Channel.

**Selected works**

- 2026 — [Active Inference Journal — 500+ videos on Active Inference with transcripts](https://video.activeinference.institute/)
- 2026 — [Personal YouTube — 200+ livestreams: drawings, Synergetics, paper discussions](https://www.youtube.com/@danielarifriedman/playlists)
- 2025 — [5th Applied Active Inference Symposium — Abstract Book](https://doi.org/10.5281/zenodo.17555266)
- 2025 — [Systems Processes, Active Inference, and Beyond](https://doi.org/10.5281/zenodo.17138223)
- 2024 — [MathArt Stream #8: William Blake and Active Inference](https://doi.org/10.5281/zenodo.13711301)
- 2024 — [Sensemaking Federation: Exploring the Frontiers of Digital Innovation](https://doi.org/10.5281/zenodo.14574046)

**Selected repositories**

- [biology_textbook](https://github.com/docxology/biology_textbook) — Open generative biology textbook — Markdown source, tested Python modules, programmatic figures; archived at Zenodo artifact · Citation DOI
- [biol-1](https://github.com/docxology/biol-1) — BIOL-1: General Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content
- [biol-8](https://github.com/docxology/biol-8) — BIOL-8: Human Biology course materials — College of the Redwoods; lectures, labs, and interactive HTML content