---
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: 21
- Selected repositories: 7
- Collaborator context: Deborah Gordon, Karl Friston, Chris Fields

**Learning path**

- Start with the Stanford dissertation for biological context.
- Read Active Inferants for the Active Inference bridge.
- Use Ant Stack and Ento-Linguistics for recent computational extensions.

**Selected works**

- 2026 — [Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology](https://doi.org/10.5281/zenodo.19574118)
- 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 Blattodea](https://doi.org/10.1002/ece3.70063)
- 2023 — [A single-pheromone model accounts for empirical patterns of ant colony foraging](https://doi.org/10.1016/j.cogsys.2023.02.005)

**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/ActiveInferenceInstitute/ActiveInferAnts) — Active Inference models for/of ants across 32+ programming languages — multi-language reference implementation of stigmergic Active Inference
- [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
- [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
- [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: 28
- Selected repositories: 11
- Collaborator context: Karl Friston, Thomas Parr, Maxwell J. D. Ramstead, Conor Heins, Tim Verbelen

**Learning path**

- Start with the literature review and ontology papers.
- Move to GNN, CEREBRUM, and Cognitive Case Diagrams for notation and modeling.
- Use FEP_Lean for formalization-oriented work.

**Selected works**

- 2026 — [A Literature Review Architecture for Active Inference: Scalable Assertion Extraction, Nanopublications, and Citation-Weighted Hypothesis Scoring](https://doi.org/10.5281/zenodo.19461934)
- 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 — [Compositional Approaches to Linguistic Case for Cognitive Modeling](https://doi.org/10.5281/zenodo.19695260)
- 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.19699234)
- 2025 — [CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling](https://doi.org/10.5281/zenodo.15170907)
- 2025 — [EvoJump: Stochastic Modeling of Evolutionary Ontogenetic Trajectories](https://doi.org/10.5281/zenodo.17229924)

**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/ActiveInferenceInstitute/ActiveInferAnts) — Active Inference models for/of ants across 32+ programming languages — multi-language reference implementation of stigmergic Active Inference
- [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
- [GeneralizedNotationNotation](https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation) — GNN — formal notation standard for specifying Active Inference generative models; JSON/YAML schema, validators, and transpilers to Python, Julia, and MATLAB · Zenodo software
- [FEP_Lean](https://github.com/ActiveInferenceInstitute/FEP_Lean) — Lean 4 / Mathlib4 formalization of FEP-related mathematics — 50-topic sorry-free catalog, Hermes/OpenGauss LLM drafting, zero-mock verification, manuscript pipeline

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

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

- Works: 20
- Selected repositories: 4
- Collaborator context: RJ Cordes, Carlos Gershenson, Micah Musser

**Learning path**

- Start with the three COGSEC books for the program arc.
- Read P3IF, Narrative Information Management, and Cognitive Integrity for the formal thread.
- Use opentir and p3if as software companions.

**Selected works**

- 2026 — [Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory)](https://doi.org/10.5281/zenodo.18364119)
- 2024 — [Bridging gaps in image meme research: A multidisciplinary paradigm](https://doi.org/10.1002/asi.24900)
- 2024 — [Comments on National Digital Twins R&D Strategic Plan](https://doi.org/10.5281/zenodo.13273681)
- 2024 — [FarmWorks: Decentralized AI Agents for Personalized Solutions](https://doi.org/10.5281/zenodo.13754585)
- 2023 — [ATLAS: A Question Oriented Approach to Pattern Languages in Knowledge Management](https://doi.org/10.5281/zenodo.10296601)
- 2023 — [Cognitive Sovereignty & Active Inference in the State of Exception](https://doi.org/10.5281/zenodo.10038232)

**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: 15
- Selected repositories: 6
- Collaborator context: Buckminster Fuller source tradition, William Blake source tradition, Curio Cards artists

**Learning path**

- Start with Blake & Fuller for the historical bridge.
- Read QuadMath and Symergetics for the formal geometry thread.
- Use the art gallery and Curio Cards materials for visual context.

**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.19335196)
- 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.18600041)
- 2026 — [The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single Vision](https://doi.org/10.5281/zenodo.20144984)
- 2025 — [On Cognitive Art & Science: Toward Wholeness From Both Sides](https://doi.org/10.5281/zenodo.16740439)
- 2025 — [On Time](https://doi.org/10.5281/zenodo.15168381)

**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: 7
- Selected repositories: 6
- Collaborator context: Active Inference Institute contributors, Open-source repository contributors

**Learning path**

- Start with the reproducible generative research template.
- Use MDKV and Markdown Decision Process for structured document work.
- Use the Discovery Engine and software catalog for agentic research navigation.

**Selected works**

- 2026 — [A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication](https://doi.org/10.5281/zenodo.19139090)
- 2025 — [Adaptive Basic Income (AuBI): Integrating AI, Decentralized Infrastructure, and Active Inference](https://doi.org/10.5281/zenodo.17228945)
- 2025 — [MDKV: A Multitrack Markdown Container for Structured, Portable Documents](https://doi.org/10.5281/zenodo.16790554)
- 2025 — [Markdown Decision Process: A Framework for Probabilistic Document Analysis](https://doi.org/10.5281/zenodo.17244386)
- 2025 — [ResNei: Solution Design Document](https://doi.org/10.5281/zenodo.15389682)
- 2025 — [The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge Landscapes](https://doi.org/10.48550/arXiv.2505.17500)

**Selected repositories**

- [template](https://github.com/docxology/template) — Multi-project research template with 10-stage CI/CD pipeline, Ruff linting, multi-Python-version testing, issue/PR templates, and security scanning
- [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, 132 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 — 127 modules, 424 MCP tools, 21K+ zero-mock tests, multi-agent orchestration (Claude/Gemini/GPT), PAI integration