Research

JaxLife open-ended agentic simulator for emergent behavior, tool use,

ACSet-native reinforcement learning environment for contributor network dynamics.

Hesse-inspired interdisciplinary synthesis game with Badiou triangle

Bengio's GFlowNets: Generative Flow Networks that sample proportionally to reward. Diversity over maximization for causal discovery and molecule design.

Galois connections for lawful conversions and bi-Heyting topos logic. Lift adjoint pairs as behaviors with floor/ceiling/round/truncate. Derives ∧∨⇒¬∼ from adjoints.

Propagator-based parallel structure for exploiting knowledge differentials

Pattern expansion and schema evolution for DuckLake databases

DuckDB file discovery agent with verified absolute paths

Deep multi-source research combining academic MCPs (arxiv, semantic-scholar, paper-search, deepwiki), Exa semantic search, and local ~/.topos knowledge base. Use for comprehensive research requiring multiple sources. NEVER fall back to web_search - ask user for help instead.

Gay MCP skill at invocation 6

Assists in writing high-quality content by conducting research, adding

clj-kondo linter with Gay.jl 3-color integration for GF(3) conservation

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.

Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug dev...

Bengio's causal inference for AI: Interventional reasoning, counterfactuals, and System 2 deep learning. World models with causal structure.

cats.for" (Categories for AI)

This skill integrates **Boxxy sandbox boundary testing** with the complete Trail of Bits firmware extraction methodology. Use this for extracting and analyzing firmware in heavily obfuscated, containerized, or restricted environments.

Safe proof ↔ theorem navigation with non-backtracking constraint.

Assets skill

Artificial Life atlas covering open-ended evolution, chemical reaction networks, morphogenesis, self-replication, and programmable chemistry. Use when picking a simulation framework, wiring ALife models into the skill graph, or onboarding contributors to the ALife cluster.

ACSets (Attributed C-Sets): Algebraic databases with Specter-style bidirectional

ACSets (Attributed C-Sets): Algebraic databases with Specter-style bidirectional navigation. Category-theoretic formalism for relational databases.

Search academic papers across arXiv, PubMed, Semantic Scholar, bioRxiv, medRxiv, Google Scholar, and more. Get BibTeX citations, download PDFs, analyze citation networks. Use for literature reviews, finding papers, and academic research.

Hypothesis-Test Loops via REPL for Exploratory Abductive Inference