---
title: "BIBLIOGRAPHY - Daniel Ari Friedman"
description: "Daniel Ari Friedman's BIBLIOGRAPHY - AI, Active Inference, and Cognitive Security."
keywords: "Daniel Ari Friedman, active inference, BIBLIOGRAPHY"
---
<div align="center">

# 📚 Complete Bibliography — Daniel Ari Friedman, PhD

> **Navigation**: [🏠 Home](../README.md) | [📚 Bibliography](BIBLIOGRAPHY.md) | [💻 Software](SOFTWARE.md) | [🔗 Links](LINKS.md) | [🧭 Discovery](DISCOVERY.md) | [👤 Profile](PROFILE.md) | [🤝 Collaborators](COLLABORATORS.md) | [🎥 Media](MEDIA.md) | [📺 Videos](VIDEOS.md) | [📦 Resources](RESOURCES.md) | [📖 Wikipedia](WIKIPEDIA.md)


**Peer-Reviewed Publications in Active Inference, Entomology, Cognitive Security, Bayesian Modeling & Computational Neuroscience**

**115 works** spanning peer-reviewed papers, books, presentations, courses, and policy comments (2015–2026)

[![Google Scholar](https://img.shields.io/badge/Google_Scholar-812_citations-4285F4?style=flat&logo=google-scholar&logoColor=white)](https://scholar.google.com/citations?user=DXjPFtYAAAAJ&hl=en)
[![ORCID](https://img.shields.io/badge/ORCID-0000--0001--6232--9096-A6CE39?style=flat&logo=orcid&logoColor=white)](https://orcid.org/0000-0001-6232-9096)
[![ResearchGate](https://img.shields.io/badge/ResearchGate-00CCBB?style=flat&logo=researchgate&logoColor=white)](https://www.researchgate.net/profile/Daniel-Friedman-2)
[![LinkedIn](https://img.shields.io/badge/LinkedIn-%230077B5.svg?logo=linkedin&logoColor=white)](https://linkedin.com/in/danielarifriedman)
[![GitHub Profile](https://img.shields.io/badge/GitHub-docxology-181717?logo=github)](https://github.com/docxology)

*Stanford PhD · Active Inference Institute President · Available for [research consulting & tutoring](README.md#-available-for-consulting--tutoring) · [All links](LINKS.md) · [Full profile](PROFILE.md)*

</div>

---

### Domain Legend

🐜 Entomology · 🧠 Active Inference · 🛡️ Cognitive Security · 🎨 Art & Synergetics · 💻 Computational · 🌍 AII Ecosystem · 🎥 Presentations & Media · 🧬 Genetics & Biomedical

**97** Papers · **8** Presentations · **3** Books · **3** Courses · **2** Playbooks · **2** Series

> **115** works in the table below **·** **108** indexed paper folders in [papers/](../papers/) **·** the **Docs** column links to a folder where one exists; some rows (e.g. YouTube series) have no per-paper folder in this table.

---

| # | Year | Domain | Type | Title | Venue | DOI/Link | Docs |
|--:|:----:|:------:|:----:|-------|-------|----------|:----:|
| 1 | 2026 | 💻 | Paper | A template/ approach to Reproducible Generative Research: Architecture and Ergonomics from Configuration through Publication | *Zenodo* | [10.5281/zenodo.19139090](https://doi.org/10.5281/zenodo.19139090) | [📁](../papers/2026_ReproducibleResearch/) |
| 2 | 2026 | 🎥 | Series | Active Inference Journal — 500+ videos on Active Inference with transcripts | *YouTube* | [video.activeinference.institute](https://video.activeinference.institute/) | — |
| 3 | 2026 | 🎨 | Paper | Before Pragmatism Had a Name: Blake's "America A Prophecy" Anticipates American Anticipatory Epistemology | *Zenodo* | [10.5281/zenodo.18807970](https://doi.org/10.5281/zenodo.18807970) | [📁](../papers/2026_BeforePragmatism/) |
| 4 | 2026 | 🎨 | Paper | The Golden Compass and the Lunar Flux: William Blake, Bimetallic Meta-stability, and the Architecture of Value | *Zenodo* | [10.5281/zenodo.19335196](https://doi.org/10.5281/zenodo.19335196) | [📁](../papers/2026_Bimetalism/) |
| 5 | 2026 | 🛡️ | Paper | Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory) | *Zenodo* | [10.5281/zenodo.18364119](https://doi.org/10.5281/zenodo.18364119) | [📁](../papers/2026_CognitiveIntegrity/) |
| 6 | 2026 | 🎥 | Series | Personal YouTube — 200+ livestreams: drawings, Synergetics, paper discussions | *YouTube* | [youtube.com/@danielarifriedman](https://www.youtube.com/@danielarifriedman/playlists) | — |
| 7 | 2026 | 🎨 | Paper | The Doors of Perception are the Threshold of Prediction: Active Inference and William Blake's Theory of Seeing | *Zenodo* | [10.5281/zenodo.18600041](https://doi.org/10.5281/zenodo.18600041) | [📁](../papers/2026_DoorsOfPerception/) |
| 8 | 2025 | 🎥 | Presentation | 5th Applied Active Inference Symposium — Abstract Book | *Presentation* | [10.5281/zenodo.17555266](https://doi.org/10.5281/zenodo.17555266) | [📁](../papers/2025_5thSymposium/) |
| 9 | 2025 | 💻 | Paper | Adaptive Basic Income (AuBI): Integrating AI, Decentralized Infrastructure, and Active Inference | *Zenodo* | [10.5281/zenodo.17228945](https://doi.org/10.5281/zenodo.17228945) | [📁](../papers/2025_AuBI/) |
| 10 | 2025 | 🧠 | Paper | CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling | *Zenodo* | [10.5281/zenodo.15170907](https://doi.org/10.5281/zenodo.15170907) | [📁](../papers/2025_CEREBRUM/) |
| 11 | 2025 | 🐜 | Paper | Computational Complexity and Energetics of the Ant Stack | *Zenodo* | [10.5281/zenodo.17238736](https://doi.org/10.5281/zenodo.17238736) | [📁](../papers/2025_AntStackComplexity/) |
| 12 | 2025 | 🧠 | Paper | EvoJump: Stochastic Modeling of Evolutionary Ontogenetic Trajectories | *Zenodo* | [10.5281/zenodo.17229924](https://doi.org/10.5281/zenodo.17229924) | [📁](../papers/2025_EvoJump/) |
| 13 | 2025 | 🧠 | Paper | Increasing the Accessibility and Applicability of Active Inference | *Zenodo* | [10.5281/zenodo.15061667](https://doi.org/10.5281/zenodo.15061667) | [📁](../papers/2025_AccessibilityActiveInference/) |
| 14 | 2025 | 💻 | Paper | MDKV: A Multitrack Markdown Container for Structured, Portable Documents | *Zenodo* | [10.5281/zenodo.16790554](https://doi.org/10.5281/zenodo.16790554) | [📁](../papers/2025_MDKV/) |
| 15 | 2025 | 💻 | Paper | Markdown Decision Process: A Framework for Probabilistic Document Analysis | *Zenodo* | [10.5281/zenodo.17244386](https://doi.org/10.5281/zenodo.17244386) | [📁](../papers/2025_MarkdownDecisionProcess/) |
| 16 | 2025 | 🎨 | Paper | On Cognitive Art & Science: Toward Wholeness From Both Sides | *Zenodo* | [10.5281/zenodo.16740439](https://doi.org/10.5281/zenodo.16740439) | [📁](../papers/2025_CognitiveArtScience/) |
| 17 | 2025 | 🎨 | Paper | On Time | *Zenodo* | [10.5281/zenodo.15168381](https://doi.org/10.5281/zenodo.15168381) | [📁](../papers/2025_OnTime/) |
| 18 | 2025 | 🎨 | Paper | QuadMath: An Analytical Review of 4D and Quadray Coordinates | *Zenodo* | [10.5281/zenodo.16887800](https://doi.org/10.5281/zenodo.16887800) | [📁](../papers/2025_QuadMath/) |
| 19 | 2025 | 💻 | Paper | ResNei: Solution Design Document | *Zenodo* | [10.5281/zenodo.15389682](https://doi.org/10.5281/zenodo.15389682) | [📁](../papers/2025_ResNei/) |
| 20 | 2025 | 🎨 | Paper | Symergetics: Symbolic Synergetics for Rational Arithmetic | *Zenodo* | [10.5281/zenodo.17114389](https://doi.org/10.5281/zenodo.17114389) | [📁](../papers/2025_Symergetics/) |
| 21 | 2025 | 🎨 | Paper | Synthesis of Agent and Niche | *Zenodo* | [10.5281/zenodo.17235137](https://doi.org/10.5281/zenodo.17235137) | [📁](../papers/2025_AgentAndNiche/) |
| 22 | 2025 | 🎥 | Presentation | Systems Processes, Active Inference, and Beyond | *Presentation* | [10.5281/zenodo.17138223](https://doi.org/10.5281/zenodo.17138223) | [📁](../papers/2025_SystemsProcesses/) |
| 23 | 2025 | 🧠 | Paper | Temporal Depth in a Coherent Self and in Depersonalization | *Frontiers in Psychology* | [10.3389/fpsyg.2025.1585315](https://doi.org/10.3389/fpsyg.2025.1585315) | [📁](../papers/2025_TemporalDepth/) |
| 24 | 2025 | 🌍 | Paper | The Active Inference Institute & Active Inference Ecosystem (v3, 2025 snapshot) | *Zenodo* | [10.5281/zenodo.14108991](https://doi.org/10.5281/zenodo.14108991) | [📁](../papers/2025_AII_v3/) |
| 25 | 2025 | 🐜 | Paper | The Ant Stack | *Zenodo* | [10.5281/zenodo.16782756](https://doi.org/10.5281/zenodo.16782756) | [📁](../papers/2025_AntStack/) |
| 26 | 2025 | 💻 | Paper | The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge Landscapes | *ArXiv* | [10.48550/arXiv.2505.17500](https://doi.org/10.48550/arXiv.2505.17500) | [📁](../papers/2025_DiscoveryEngine/) |
| 27 | 2025 | 🧠 | Paper | Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought Dynamics in Meditative States | *Entropy* | [10.3390/e27050459](https://doi.org/10.3390/e27050459) | [📁](../papers/2025_Thoughtseeds/) |
| 28 | 2025 | 🐜 | Paper | Towards a Science of Consciousness and Social Complexity... For Ants | *Book Chapter* | [978-65-5272-128-0](https://www.editorafi.org/ebook/c128-colonias-formigas-conscientes) | [📁](../papers/2025_ConsciousnessAnts/) |
| 29 | 2024 | 🌍 | Paper | Aligning Active Inference Ontology to SUMO | *Zenodo* | [10.5281/zenodo.11459322](https://doi.org/10.5281/zenodo.11459322) | [📁](../papers/2024_OntologySUMO/) |
| 30 | 2024 | 🎥 | Presentation | BioFirm Development at Applied Active Inference Symposium 2024 | *Presentation* | [10.5281/zenodo.14861595](https://doi.org/10.5281/zenodo.14861595) | [📁](../papers/2024_BioFirm/) |
| 31 | 2024 | 🛡️ | Paper | Bridging gaps in image meme research: A multidisciplinary paradigm | *JASIST* | [10.1002/asi.24900](https://doi.org/10.1002/asi.24900) | [📁](../papers/2024_ImageMemeResearch/) |
| 32 | 2024 | 🐜 | Paper | Chemical and transcriptomic diversity do not correlate with ascending levels of social complexity in Blattodea | *Ecology & Evolution* | [10.1002/ece3.70063](https://doi.org/10.1002/ece3.70063) | [📁](../papers/2024_BlattodeaDiversity/) |
| 33 | 2024 | 🛡️ | Paper | Comments on National Digital Twins R&D Strategic Plan | *Zenodo* | [10.5281/zenodo.13273681](https://doi.org/10.5281/zenodo.13273681) | [📁](../papers/2024_DigitalTwins/) |
| 34 | 2024 | 🧠 | Paper | Enhancing Population-based Search with Active Inference | *ArXiv* | [10.48550/arXiv.2408.09548](https://doi.org/10.48550/arXiv.2408.09548) | [📁](../papers/2024_PopulationSearch/) |
| 35 | 2024 | 🛡️ | Paper | FarmWorks: Decentralized AI Agents for Personalized Solutions | *Zenodo* | [10.5281/zenodo.13754585](https://doi.org/10.5281/zenodo.13754585) | [📁](../papers/2024_FarmWorks/) |
| 36 | 2024 | 🧠 | Paper | Federated inference and belief sharing | *Neuroscience & Biobehavioral Reviews* | [10.1016/j.neubiorev.2023.105500](https://doi.org/10.1016/j.neubiorev.2023.105500) | [📁](../papers/2024_FederatedInference/) |
| 37 | 2024 | 🎨 | Paper | Four-fold Fields of Quantum Dreams | *Zenodo* | [10.5281/zenodo.10798145](https://doi.org/10.5281/zenodo.10798145) | [📁](../papers/2024_QuantumDreams/) |
| 38 | 2024 | 🎥 | Presentation | MathArt Stream #8: William Blake and Active Inference | *Presentation* | [10.5281/zenodo.13711301](https://doi.org/10.5281/zenodo.13711301) | [📁](../papers/2024_MathArtBlake/) |
| 39 | 2024 | 🎥 | Presentation | Sensemaking Federation: Exploring the Frontiers of Digital Innovation | *Presentation* | [10.5281/zenodo.14574046](https://doi.org/10.5281/zenodo.14574046) | [📁](../papers/2024_SensemakingFederation/) |
| 40 | 2024 | 🧠 | Paper | Shared Protentions in Multi-Agent Active Inference | *Entropy* | [10.3390/e26040303](https://doi.org/10.3390/e26040303) | [📁](../papers/2024_SharedProtentions/) |
| 41 | 2024 | 🌍 | Paper | The Active Inference Institute & Active Inference Ecosystem (v2, 2024 snapshot) | *Zenodo* | [10.5281/zenodo.14108991](https://doi.org/10.5281/zenodo.14108991) | [📁](../papers/2024_AII_v2/) |
| 42 | 2024 | 🎨 | Paper | Way Finding in the Infinite Imaginarium | *Zenodo* | [10.5281/zenodo.10601082](https://doi.org/10.5281/zenodo.10601082) | [📁](../papers/2024_InfiniteImaginarium/) |
| 43 | 2024 | 🧬 | Paper | Why Paleolithic Rockstars were both enigmatic and sporadic | *Physics of Life Reviews* | [10.1016/j.plrev.2024.04.010](https://doi.org/10.1016/j.plrev.2024.04.010) | [📁](../papers/2024_PaleolithicRockstars/) |
| 44 | 2024 | 🎨 | Paper | Writing on Curio Cards for the "On NFT" book | *Taschen* | 978-3-8365-9970-2 | [📁](../papers/2024_CurioCards/) |
| 45 | 2023 | 🧠 | Paper | A guided tour through the spaces of particular "minds" | *Physics of Life Reviews* | [10.1016/j.plrev.2023.11.001](https://doi.org/10.1016/j.plrev.2023.11.001) | [📁](../papers/2023_GuidedTourMinds/) |
| 46 | 2023 | 🐜 | Paper | A single-pheromone model accounts for empirical patterns of ant colony foraging | *Cognitive Systems Research* | [10.1016/j.cogsys.2023.02.005](https://doi.org/10.1016/j.cogsys.2023.02.005) | [📁](../papers/2023_SinglePheromone/) |
| 47 | 2023 | 🐜 | Paper | A snapshot and pipeline for tissue-specific gene expression meta-analysis in honey bees | *Zenodo* | [10.5281/zenodo.10400744](https://doi.org/10.5281/zenodo.10400744) | [📁](../papers/2023_HoneyBeeGeneExpression/) |
| 48 | 2023 | 🧠 | Paper | A variational synthesis of evolutionary and developmental dynamics | *Entropy* | [10.3390/e25070964](https://doi.org/10.3390/e25070964) | [📁](../papers/2023_VariationalSynthesis/) |
| 49 | 2023 | 🛡️ | Paper | ATLAS: A Question Oriented Approach to Pattern Languages in Knowledge Management | *Zenodo* | [10.5281/zenodo.10296601](https://doi.org/10.5281/zenodo.10296601) | [📁](../papers/2023_ATLAS/) |
| 50 | 2023 | 🧠 | Paper | An Account of Active Inference Modeling | *Zenodo* | [10.5281/zenodo.8415313](https://doi.org/10.5281/zenodo.8415313) | [📁](../papers/2023_AccountActiveInference/) |
| 51 | 2023 | 🛡️ | Paper | Cognitive Sovereignty & Active Inference in the State of Exception | *Zenodo* | [10.5281/zenodo.10038232](https://doi.org/10.5281/zenodo.10038232) | [📁](../papers/2023_CognitiveSovereignty/) |
| 52 | 2023 | 🛡️ | Paper | Comments on AI Accountability Policy to NTIA | *NTIA* | [10.5281/zenodo.8025957](https://doi.org/10.5281/zenodo.8025957) | [📁](../papers/2023_AIAccountability/) |
| 53 | 2023 | 🧠 | Paper | Distributed Science — The Scientific Process as Multi-Scale Active Inference | *OSF* | [10.31219/osf.io/dnw5k](https://doi.org/10.31219/osf.io/dnw5k) | [📁](../papers/2023_DistributedScience/) |
| 54 | 2023 | 💻 | Paper | Enhanced NSF Postdoctoral Reporting via Synthetic Intelligence Language Processing | *Zenodo* | [10.5281/zenodo.10160656](https://doi.org/10.5281/zenodo.10160656) | [📁](../papers/2023_NSFReporting/) |
| 55 | 2023 | 🐜 | Paper | Experimental Entomology in the Age of Video | *JoVE* | [10.3791/65002](https://doi.org/10.3791/65002) | [📁](../papers/2023_VideoEntomology/) |
| 56 | 2023 | 🧠 | Paper | Generalized Notation Notation for Active Inference Models | *Zenodo* | [10.5281/zenodo.7803328](https://doi.org/10.5281/zenodo.7803328) | [📁](../papers/2023_GNN/) |
| 57 | 2023 | 🧠 | Paper | Generative Research Teams: Active Inference Compositions for Research and Meta-Science | *Zenodo* | [10.5281/zenodo.8164667](https://doi.org/10.5281/zenodo.8164667) | [📁](../papers/2023_GenerativeResearchTeams/) |
| 58 | 2023 | 🎥 | Presentation | Of Ants & Aging | *Presentation* | [10.5281/zenodo.7855582](https://doi.org/10.5281/zenodo.7855582) | [📁](../papers/2023_AntsAging/) |
| 59 | 2023 | 🛡️ | Paper | Open Access science needs Open Science Sensemaking (OSSm) | *MetaArXiv* | [10.31222/osf.io/9nb3u](https://doi.org/10.31222/osf.io/9nb3u) | [📁](../papers/2023_OpenScienceSensemaking/) |
| 60 | 2023 | 🎥 | Presentation | Postdoc review (2020–2023) | *Presentation* | [10.5281/zenodo.8377988](https://doi.org/10.5281/zenodo.8377988) | [📁](../papers/2023_PostdocReview/) |
| 61 | 2023 | 🌍 | Paper | The Active Inference Institute and Active Inference Ecosystem (v1) | *Zenodo* | [10.5281/zenodo.8266281](https://doi.org/10.5281/zenodo.8266281) | [📁](../papers/2023_AII_v1/) |
| 62 | 2023 | 🛡️ | Paper | The P3IF: Properties, Processes, and Perspectives Inter-Framework | *Zenodo* | [10.5281/zenodo.10034512](https://doi.org/10.5281/zenodo.10034512) | [📁](../papers/2023_P3IF/) |
| 63 | 2023 | 🧬 | Paper | To comment or not to comment | *Physics of Life Reviews* | [10.1016/j.plrev.2023.06.002](https://doi.org/10.1016/j.plrev.2023.06.002) | [📁](../papers/2023_ToComment/) |
| 64 | 2023 | 🎥 | Course | Transcript of Chris Fields, "Physics as Information Processing" course | *Zenodo* | [10.5281/zenodo.10447642](https://doi.org/10.5281/zenodo.10447642) | — |
| 65 | 2023 | 🎨 | Paper | William Blake & Buckminster Fuller: Lives in Juxtaposition | *Zenodo* | [10.5281/zenodo.7514368](https://doi.org/10.5281/zenodo.7514368) | [📁](../papers/2023_BlakeFuller/) |
| 66 | 2022 | 🧠 | Paper | An Active Inference Ontology for Decentralized Science | *Zenodo* | [10.5281/zenodo.6320574](https://doi.org/10.5281/zenodo.6320574) | [📁](../papers/2022_ActiveInferenceOntology/) |
| 67 | 2022 | 🌍 | Paper | Catechism for Towards Active Diffusion | *Zenodo* | [10.5281/zenodo.7443848](https://doi.org/10.5281/zenodo.7443848) | [📁](../papers/2022_ActiveDiffusion/) |
| 68 | 2022 | 🛡️ | Paper | From Users to (Sense)Makers: Stigmergic Social Annotation | *Hypertext '22* | [10.48550/arXiv.2205.06345](https://doi.org/10.48550/arXiv.2205.06345) | [📁](../papers/2022_StigmergicAnnotation/) |
| 69 | 2022 | 🧬 | Paper | On free will or the lack thereof (interview with Robert Sapolsky) | *ALIUS Bulletin* | [10.5281/zenodo.7394901](https://doi.org/10.5281/zenodo.7394901) | [📁](../papers/2022_FreeWillSapolsky/) |
| 70 | 2022 | 🎨 | Paper | Predictive Processing Interpretation of the Mirror Test | *Zenodo* | [10.5281/zenodo.7377256](https://doi.org/10.5281/zenodo.7377256) | [📁](../papers/2022_MirrorTest/) |
| 71 | 2022 | 🛡️ | Book | Structuring the Information Commons: Open Standards and Cognitive Security | *COGSEC.org* | 978-1-7364269-3-7 | [📁](../papers/2022_InformationCommons/) |
| 72 | 2022 | 🛡️ | Paper | Systems Modeling and Cognitive Audits for Hypercert Ecosystems | *Zenodo* | [10.5281/zenodo.7626769](https://doi.org/10.5281/zenodo.7626769) | [📁](../papers/2022_HypercertEcosystems/) |
| 73 | 2022 | 🧠 | Paper | The Free Energy Principle & Active Inference: a Systematic Literature Analysis | *Zenodo* | [10.5281/zenodo.7449368](https://doi.org/10.5281/zenodo.7449368) | [📁](../papers/2022_SystematicLiteratureAnalysis/) |
| 74 | 2022 | 🛡️ | Paper | TrustFinder: Recommendations for Community-Based Trust Systems | *Zenodo* | [10.5281/zenodo.7093837](https://doi.org/10.5281/zenodo.7093837) | [📁](../papers/2022_TrustFinder/) |
| 75 | 2021 | 🐜 | Paper | Active Inferants: An Active Inference Framework for Ant Colony Behavior | *Frontiers in Behavioral Neuroscience* | [10.3389/fnbeh.2021.647732](https://doi.org/10.3389/fnbeh.2021.647732) | [📁](../papers/2021_ActiveInferants/) |
| 76 | 2021 | 🧠 | Paper | Active Inference in Modeling Conflict | *Zenodo* | [10.5281/zenodo.5759807](https://doi.org/10.5281/zenodo.5759807) | [📁](../papers/2021_ModelingConflict/) |
| 77 | 2021 | 🛡️ | Paper | Digital Rhetorical Ecosystem Analysis: Sensemaking of Digital Memetic Discourse | *Zenodo* | [10.5281/zenodo.5573947](https://doi.org/10.5281/zenodo.5573947) | [📁](../papers/2021_DigitalRhetorical/) |
| 78 | 2021 | 🎥 | Playbook | Innovator's Digital Playbook | *Web* | [innovatorsdigitalplaybook.com](https://innovatorsdigitalplaybook.com/) | — |
| 79 | 2021 | 🛡️ | Book | Narrative Information Ecosystems: Conflict and Trust on the Endless Frontier | *COGSEC.org* | 978-1-7364269-2-0 | [📁](../papers/2021_NarrativeEcosystems/) |
| 80 | 2021 | 🛡️ | Paper | Narrative Information Management | *Zenodo* | [10.5281/zenodo.5573287](https://doi.org/10.5281/zenodo.5573287) | [📁](../papers/2021_NarrativeInformationMgmt/) |
| 81 | 2021 | 🎥 | Playbook | The Facilitator's Catechism Playbook | *Zenodo* | [10.5281/zenodo.4579414](https://doi.org/10.5281/zenodo.4579414) | — |
| 82 | 2020 | 🧠 | Paper | Active Inference & Behavior Engineering for Teams | *Zenodo* | [10.5281/zenodo.4021163](https://doi.org/10.5281/zenodo.4021163) | [📁](../papers/2020_BehaviorEngineering/) |
| 83 | 2020 | 🎥 | Course | Communication for Remote Teams | *Udemy* | [Udemy](https://www.udemy.com/course/communication-for-remote-teams/) | — |
| 84 | 2020 | 🐜 | Paper | Distributed physiology and the molecular basis of social life in eusocial insects | *Hormones & Behavior* | [10.1016/j.yhbeh.2020.104757](https://doi.org/10.1016/j.yhbeh.2020.104757) | [📁](../papers/2020_DistributedPhysiology/) |
| 85 | 2020 | 🛡️ | Paper | Emergent Teams for Complex Threats | *Zenodo* | [10.5281/zenodo.3986085](https://doi.org/10.5281/zenodo.3986085) | [📁](../papers/2020_EmergentTeams/) |
| 86 | 2020 | 🐜 | Paper | Gene expression variation in the brains of harvester ant foragers is associated with collective behavior | *Communications Biology* | [10.1038/s42003-020-0813-8](https://doi.org/10.1038/s42003-020-0813-8) | [📁](../papers/2020_GeneExpressionForagers/) |
| 87 | 2020 | 🎥 | Course | How to use Keybase for remote teams | *Udemy* | [Udemy](https://www.udemy.com/course/keybase-for-remote-teams/) | — |
| 88 | 2020 | 🐜 | Paper | Measurement of natural variation of neurotransmitter tissue content in red harvester ant brains | *Analytical & Bioanalytical Chemistry* | [10.1007/s00216-019-02355-3](https://doi.org/10.1007/s00216-019-02355-3) | [📁](../papers/2020_NeurotransmitterVariation/) |
| 89 | 2020 | 🛡️ | Book | The Great Preset: Remote Teams and Operational Art | *COGSEC.org* | 978-1-7364269-0-6 | [📁](../papers/2020_GreatPreset/) |
| 90 | 2020 | 🛡️ | Paper | The Innovator's Catechism | *Zenodo* | [10.5281/zenodo.4383230](https://doi.org/10.5281/zenodo.4383230) | [📁](../papers/2020_InnovatorsCatechism/) |
| 91 | 2020 | 🧬 | Paper | The neuroscience of decision making (interview with Timothy Hanks) | *ALIUS Bulletin* | [10.34700/8pg4-0h12](https://doi.org/10.34700/8pg4-0h12) | [📁](../papers/2020_NeuroscienceDecision/) |
| 92 | 2019 | 🧬 | Paper | Dennett Explained (interview with Daniel Dennett) | *ALIUS Bulletin* | [10.34700/7gkw-zh08](https://doi.org/10.34700/7gkw-zh08) | [📁](../papers/2019_DennettExplained/) |
| 93 | 2019 | 🐜 | Paper | PhD: Behavioral, Physiological, and Transcriptomic Variation Among Colonies of *Pogonomyrmex barbatus* | *Stanford University* | [purl.stanford.edu](http://purl.stanford.edu/pb813wm1484) | [📁](../papers/2019_PhDDissertation/) |
| 94 | 2019 | 🐜 | Paper | The ant colony as a test for scientific theories of consciousness | *Synthese* | [10.1007/s11229-019-02130-y](https://doi.org/10.1007/s11229-019-02130-y) | [📁](../papers/2019_AntConsciousness/) |
| 95 | 2019 | 🐜 | Paper | The physiology of forager hydration and variation among harvester ant colonies | *Scientific Reports* | [10.1038/s41598-019-41586-3](https://doi.org/10.1038/s41598-019-41586-3) | [📁](../papers/2019_ForagerHydration/) |
| 96 | 2018 | 🐜 | Paper | Foraging behavior and locomotion of the invasive Argentine ant from winter aggregations | *PLoS One* | [10.1371/journal.pone.0202117](https://doi.org/10.1371/journal.pone.0202117) | [📁](../papers/2018_ArgentineAnt/) |
| 97 | 2018 | 🎥 | Presentation | MVEE: A Framework for Evolutionary Studies | *Presentation* | [10.5281/zenodo.13999298](https://doi.org/10.5281/zenodo.13999298) | [📁](../papers/2018_MVEE/) |
| 98 | 2018 | 🧠 | Paper | Of woodlice and men: A Bayesian account of cognition, life and consciousness (with Karl Friston) | *ALIUS Bulletin* | [10.34700/h460-nz89](https://doi.org/10.34700/h460-nz89) | [📁](../papers/2018_WoodliceAndMen/) |
| 99 | 2018 | 🎨 | Paper | Partner Pen Play in Parallel (PPPiP): A New Paradigm for Relationship Improvement | *Arts* | [10.3390/arts7030039](https://doi.org/10.3390/arts7030039) | [📁](../papers/2018_PPPiP/) |
| 100 | 2018 | 🐜 | Paper | The Role of Dopamine in Collective Regulation of Foraging in Harvester Ants | *iScience* | [10.1016/j.isci.2018.09.001](https://doi.org/10.1016/j.isci.2018.09.001) | [📁](../papers/2018_DopamineForaging/) |
| 101 | 2017 | 🐜 | Paper | The MutAnts are here | *Cell* | [10.1016/j.cell.2017.07.046](https://doi.org/10.1016/j.cell.2017.07.046) | [📁](../papers/2017_MutAnts/) |
| 102 | 2017 | 🐜 | Paper | Two lineages that need each other | *Molecular Ecology* | [10.1111/mec.13964](https://doi.org/10.1111/mec.13964) | [📁](../papers/2017_TwoLineages/) |
| 103 | 2016 | 🐜 | Paper | Ant Genetics: Reproductive Physiology, Worker Morphology, and Behavior | *Annual Review of Neuroscience* | [10.1146/annurev-neuro-070815-013927](https://doi.org/10.1146/annurev-neuro-070815-013927) | [📁](../papers/2016_AntGenetics/) |
| 104 | 2016 | 🐜 | Paper | Context-dependent expression of the foraging gene in field colonies of ants | *Proceedings of the Royal Society B* | [10.1098/rspb.2016.0841](https://doi.org/10.1098/rspb.2016.0841) | [📁](../papers/2016_ForagingGene/) |
| 105 | 2016 | 🧬 | Paper | Influence of Nuclear Structure on formation of radiation-induced lethal lesions | *Int. J. Radiation Biology* | [10.3109/09553002.2016.1144941](https://doi.org/10.3109/09553002.2016.1144941) | [📁](../papers/2016_NuclearStructure/) |
| 106 | 2015 | 🧬 | Paper | Commentary: Portuguese crypto-Jews: the genetic heritage of a complex history | *Frontiers in Genetics* | [10.3389/fgene.2015.00261](https://doi.org/10.3389/fgene.2015.00261) | [📁](../papers/2015_CryptoJews/) |
| 107 | 2015 | 🧬 | Paper | Could Ehrlichial Infection Cause Some Changes Associated with Leukemia? | *Medical Hypotheses* | [10.1016/j.mehy.2015.09.015](https://doi.org/10.1016/j.mehy.2015.09.015) | [📁](../papers/2015_EhrlichialInfection/) |
| 108 | 2015 | 🧬 | Paper | Large Scale Coding Sequence Change Underlies the Evolution of Post-developmental Novelty in Honey Bees | *Molecular Biology & Evolution* | [10.1093/molbev/msu292](https://doi.org/10.1093/molbev/msu292) | [📁](../papers/2015_HoneyBeeEvolution/) |
| 109 | 2026 | 🐜 | Paper | Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology | *Zenodo* | [10.5281/zenodo.19574118](https://doi.org/10.5281/zenodo.19574118) | [📁](../papers/2026_EntoLinguistics/) |
| 110 | 2026 | 🧠 | Paper | A Literature Review Architecture for Active Inference: Scalable Assertion Extraction, Nanopublications, and Citation-Weighted Hypothesis Scoring | *Active Inference Journal* | [10.5281/zenodo.19461934](https://doi.org/10.5281/zenodo.19461934) | [📁](../papers/2026_ActInfMetaAnalysis/) |
| 111 | 2026 | 🧠 | Paper | Dynamic Attentional Agents in Focused Attention Meditation: Hierarchical Computational Modeling of Expert-Novice Differences | *CSCIS vol 2857, Springer* | [10.1007/978-3-032-16955-6_11](https://doi.org/10.1007/978-3-032-16955-6_11) | [📁](../papers/2026_FocusedAttentionMeditation/) |
| 112 | 2026 | 🧠 | Paper | Compositional Approaches to Linguistic Case for Cognitive Modeling | *Active Inference Journal* | [10.5281/zenodo.19695260](https://doi.org/10.5281/zenodo.19695260) | [📁](../papers/2026_CognitiveCaseDiagrams/) |
| 113 | 2026 | 🧠 | Paper | Towards Lean 4 Formalization of the Free Energy Principle: AI-Driven Theorem Sketching and Verification for Active Inference and Bayesian Mechanics | *Active Inference Journal* | [10.5281/zenodo.19699234](https://doi.org/10.5281/zenodo.19699234) | [📁](../papers/2026_FEPLean/) |
| 114 | 2020 | 🛡️ | Paper | The Facilitator's Catechism | *Zenodo* | [10.5281/zenodo.4203765](https://doi.org/10.5281/zenodo.4203765) | [📁](../papers/2020_FacilitatorsCatechism/) |
| 115 | 2026 | 🎨 | Paper | The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single Vision | *Zenodo* | [10.5281/zenodo.20144984](https://doi.org/10.5281/zenodo.20144984) | [📁](../papers/2026_BlakeJiang/) |

---

## Domain Index

### 🐜 Entomology

> 21 works (2016–2026)

- **2026** — Ento-Linguistics: Language, Ambiguity, and Scientific Communication in Entomology · [📁](../papers/2026_EntoLinguistics/)
- **2025** — Computational Complexity and Energetics of the Ant Stack · [📁](../papers/2025_AntStackComplexity/)
- **2025** — The Ant Stack · [📁](../papers/2025_AntStack/)
- **2025** — Towards a Science of Consciousness and Social Complexity... For Ants · [📁](../papers/2025_ConsciousnessAnts/)
- **2024** — Chemical and transcriptomic diversity do not correlate with ascending levels of social complexity in Blattodea · [📁](../papers/2024_BlattodeaDiversity/)
- **2023** — A single-pheromone model accounts for empirical patterns of ant colony foraging · [📁](../papers/2023_SinglePheromone/)
- *...and 14 more in the table above*

### 🧠 Active Inference

> 23 works (2018–2026)

- **2026** — Towards Lean 4 Formalization of the Free Energy Principle: AI-Driven Theorem Sketching and Verification for Active Inference and Bayesian Mechanics · [📁](../papers/2026_FEPLean/)
- **2026** — Compositional Approaches to Linguistic Case for Cognitive Modeling · [📁](../papers/2026_CognitiveCaseDiagrams/)
- **2026** — A Literature Review Architecture for Active Inference: Scalable Assertion Extraction, Nanopublications, and Citation-Weighted Hypothesis Scoring · [📁](../papers/2026_ActInfMetaAnalysis/)
- **2026** — Dynamic Attentional Agents in Focused Attention Meditation: Hierarchical Computational Modeling of Expert-Novice Differences · [📁](../papers/2026_FocusedAttentionMeditation/)
- **2025** — CEREBRUM: Case-Enabled Reasoning Engine with Bayesian Representations for Unified Modeling · [📁](../papers/2025_CEREBRUM/)
- **2025** — EvoJump: Stochastic Modeling of Evolutionary Ontogenetic Trajectories · [📁](../papers/2025_EvoJump/)
- **2025** — Increasing the Accessibility and Applicability of Active Inference · [📁](../papers/2025_AccessibilityActiveInference/)
- **2025** — Temporal Depth in a Coherent Self and in Depersonalization · [📁](../papers/2025_TemporalDepth/)
- **2025** — Thoughtseeds: A Hierarchical and Agentic Framework for Investigating Thought Dynamics in Meditative States · [📁](../papers/2025_Thoughtseeds/)
- *...and 14 more in the table above*

### 🛡️ Cognitive Security

> 20 works (2020–2026)

- **2026** — Cognitive Integrity Framework: Formal Foundations for Multiagent Security (Part 1: Theory) · [📁](../papers/2026_CognitiveIntegrity/)
- **2020** — The Facilitator's Catechism · [📁](../papers/2020_FacilitatorsCatechism/)
- **2024** — Bridging gaps in image meme research: A multidisciplinary paradigm · [📁](../papers/2024_ImageMemeResearch/)
- **2024** — Comments on National Digital Twins R&D Strategic Plan · [📁](../papers/2024_DigitalTwins/)
- **2024** — FarmWorks: Decentralized AI Agents for Personalized Solutions · [📁](../papers/2024_FarmWorks/)
- **2023** — ATLAS: A Question Oriented Approach to Pattern Languages in Knowledge Management · [📁](../papers/2023_ATLAS/)
- *...and 14 more in the table above*

### 🎨 Art & Synergetics

> 15 works (2018–2026)

- **2026** — The Architecture of False Gods: William Blake, Professor Jiang, and the Active Inference Corrective to Single Vision · [📁](../papers/2026_BlakeJiang/)
- **2026** — Before Pragmatism Had a Name: Blake's "America A Prophecy" Anticipates American Anticipatory Epistemology · [📁](../papers/2026_BeforePragmatism/)
- **2026** — The Doors of Perception are the Threshold of Prediction: Active Inference and William Blake's Theory of Seeing · [📁](../papers/2026_DoorsOfPerception/)
- **2025** — On Cognitive Art & Science: Toward Wholeness From Both Sides · [📁](../papers/2025_CognitiveArtScience/)
- **2025** — On Time · [📁](../papers/2025_OnTime/)
- **2025** — QuadMath: An Analytical Review of 4D and Quadray Coordinates · [📁](../papers/2025_QuadMath/)
- *...and 9 more in the table above*

### 💻 Computational

> 7 works (2023–2026)

- **2025** — Adaptive Basic Income (AuBI): Integrating AI, Decentralized Infrastructure, and Active Inference · [📁](../papers/2025_AuBI/)
- **2025** — MDKV: A Multitrack Markdown Container for Structured, Portable Documents · [📁](../papers/2025_MDKV/)
- **2025** — Markdown Decision Process: A Framework for Probabilistic Document Analysis · [📁](../papers/2025_MarkdownDecisionProcess/)
- **2025** — ResNei: Solution Design Document · [📁](../papers/2025_ResNei/)
- **2025** — The Discovery Engine: AI-Driven Synthesis and Navigation of Scientific Knowledge Landscapes · [📁](../papers/2025_DiscoveryEngine/)
- *...and 2 more in the table above*

### 🌍 AII Ecosystem

> 5 works (2022–2025)

- **2025** — The Active Inference Institute & Active Inference Ecosystem (v3, 2025 snapshot) · [📁](../papers/2025_AII_v3/)
- **2024** — Aligning Active Inference Ontology to SUMO · [📁](../papers/2024_OntologySUMO/)
- **2024** — The Active Inference Institute & Active Inference Ecosystem (v2, 2024 snapshot) · [📁](../papers/2024_AII_v2/)
- **2023** — The Active Inference Institute and Active Inference Ecosystem (v1) · [📁](../papers/2023_AII_v1/)
- **2022** — Catechism for Towards Active Diffusion · [📁](../papers/2022_ActiveDiffusion/)

### 🎥 Presentations & Media

> 15 works (2018–2026)

- **2026** — Active Inference Journal — 500+ videos on Active Inference with transcripts
- **2026** — Personal YouTube — 200+ livestreams: drawings, Synergetics, paper discussions
- **2025** — 5th Applied Active Inference Symposium — Abstract Book · [📁](../papers/2025_5thSymposium/)
- **2025** — Systems Processes, Active Inference, and Beyond · [📁](../papers/2025_SystemsProcesses/)
- **2024** — BioFirm Development at Applied Active Inference Symposium 2024 · [📁](../papers/2024_BioFirm/)
- *...and 10 more in the table above*

### 🧬 Genetics & Biomedical

> 9 works (2015–2024)

- **2024** — Why Paleolithic Rockstars were both enigmatic and sporadic · [📁](../papers/2024_PaleolithicRockstars/)
- **2023** — To comment or not to comment · [📁](../papers/2023_ToComment/)
- **2022** — On free will or the lack thereof (interview with Robert Sapolsky) · [📁](../papers/2022_FreeWillSapolsky/)
- **2020** — The neuroscience of decision making (interview with Timothy Hanks) · [📁](../papers/2020_NeuroscienceDecision/)
- **2019** — Dennett Explained (interview with Daniel Dennett) · [📁](../papers/2019_DennettExplained/)
- *...and 4 more in the table above*

---

<div align="center">

*Compiled from [docxology/docxology](https://github.com/docxology/docxology) — See also [SOFTWARE.md](SOFTWARE.md) for open-source repositories*

</div>


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*Maintained by Daniel Ari Friedman | [← Back to Home](../README.md)*

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