📋 Document Metadata
Type: Navigation Hub | Audience: All Users | Complexity: Beginner
Status: Production-Ready
Cross-References: Setup Guide | Contributing | AGENTS.md (doc tree index) | Doc audit (uv run python doc/development/docs_audit.py --strict)
Welcome to the documentation for Generalized Notation Notation (GNN), a standardized text-based language for expressing Active Inference generative models.
⚠️ Important: For setup and installation instructions, please refer to the GNN Project Setup Guide.
🎯 Learning Path: Beginner → Intermediate → Advanced (Estimated Time: 2-8 hours total)
New to GNN? Follow the Beginner Path in our Learning Paths Guide:
- What is GNN? - Overview and motivation
- Cross-refs: GNN Overview, Academic Paper
- Quickstart Tutorial - Comprehensive getting started guide
- Cross-refs: Basic Examples, Template System
- Your First GNN Model - Simple example walkthrough
- Cross-refs: Basic Template, Syntax Reference
- Basic Syntax Guide - Essential notation rules
- Cross-refs: File Structure, Implementation Guide
- Tools Setup - Get GNN tools running
- Cross-refs: Pipeline Guide, API Documentation
📚 Complete Learning Paths: See Learning Paths Guide for structured beginner → intermediate → advanced progression
🧭 Navigation by User Type | 🔗 Related: Comprehensive cross-reference system
📖 Learning Path: Concepts → Syntax → Examples → Practice (Full Beginner Path)
- GNN Overview - High-level concepts and ecosystem
- See Also: About GNN, Academic Paper
- Next Steps: Quickstart Tutorial
- About GNN - Motivation, goals, and "triple play" approach
- See Also: GNN Overview, Ontology System
- Next Steps: Basic Examples
- Basic Examples - Step-by-step model development
- See Also: Template System, Quickstart Tutorial
- Next Steps: Syntax Reference
🛠️ Learning Path: Syntax → Structure → Implementation → Tools (Full Intermediate Path)
- GNN Syntax Reference - Complete notation specification
- See Also: File Structure, Examples
- Related Tools: Type Checker, Templates
- File Structure Guide - How to organize GNN files
- See Also: Syntax Reference, Implementation Guide
- Related Tools: Pipeline Documentation
- Implementation Guide - Best practices for creating models
- See Also: Advanced Patterns, Framework Integration
- Related Tools: Testing Guide, API Documentation
- Tools and Resources - Available software and utilities
- See Also: Pipeline Guide, API Documentation
- Related: Configuration Guide, Deployment Guide
⚙️ Learning Path: APIs → Architecture → Integration → Development
- Integration Guides - Framework-specific documentation
- Featured: PyMDP, RxInfer, DisCoPy
- See Also: API Documentation, Development Guide
- Advanced Topics - Complex modeling patterns
- Featured: Advanced Patterns, Multi-agent
- See Also: Cognitive Phenomena, LLM Integration
- Tool Development - Creating GNN-compatible tools
- See Also: API Documentation, Pipeline Architecture
- Related: MCP Integration, Testing Framework
🔬 Learning Path: Theory → Specification → Applications → Research
- Academic Paper - Formal specification and theory
- See Also: About GNN, Ontology System
- Related Research: Advanced Patterns, Multi-agent
- Multiagent Systems - Multi-agent modeling approaches
- See Also: Multi-agent Template, Advanced Patterns
- Framework Integration: RxInfer Examples
- LLM Integration - AI-assisted modeling
- See Also: DSPy Integration, AutoGenLib
- Related Tools: MCP Protocol, Pipeline Step 11
- PoE-World Integration - Compositional world modeling research
- See Also: PoE-World GNN Integration, Program Synthesis
- Research Applications: Hierarchical Template, Advanced Patterns
🔗 Cross-Platform Compatibility | 📊 Coverage: Complete framework integration guides
| Framework | Documentation | Description | Template Compatibility | Examples |
|---|---|---|---|---|
| PyMDP | gnn_pymdp.md | Python Active Inference framework | ✅ All templates | POMDP, Multi-agent |
| RxInfer | gnn_rxinfer.md | Julia Bayesian inference | ✅ All templates | Hierarchical, Multi-agent |
| DisCoPy | gnn_discopy.md | Category theory and quantum computing | ✅ Advanced templates | Category Theory Models |
| DSPy | gnn_dspy.md | AI prompt programming | 🔄 LLM integration | LLM Pipeline |
| AutoGenLib | gnn_autogenlib.md | Dynamic code generation | 🔄 Code generation | Tool Development |
| MCP | gnn_mcp.md | Model Context Protocol | ✅ API integration | MCP Guide, FastMCP |
| PoE-World | poe-world_gnn.md | Compositional world modeling | 🔄 Research integration | PoE-World Overview, Program Synthesis |
🔗 Cross-References: API Documentation | Pipeline Integration | Performance Comparison
- SAPF - Structured Audio Processing Framework for sonification
- Pedalboard - Audio effects framework for model representation
- Axiom - Formal verification and theorem proving
- Petri Nets - Workflow modeling and process analysis
- Nock - Formal specification language integration
- GUI-Oxdraw - Visual model construction interface
- OneFileLLM - Single-file LLM wrapper for analysis
- Vec2Text - Vector-to-text model interpretation
- ARC-AGI - Abstract reasoning benchmark integration
- D2 - Scriptable diagram generation
- Glowstick - Interactive visualization framework
- Klong - Array programming language integration
- TimEP - Performance profiling and temporal analysis
- POMDP - POMDP analytical framework
- SPM - Statistical Parametric Mapping for neuroscience
- Pkl - Configuration-as-code language integration
- Muscle-Mem - Behavior caching for performance optimization
- SymPy - Symbolic mathematics and MCP integration
- Kit - Code intelligence and developer tools
- ActiveInference.jl - High-performance Julia framework
- Quadray - Geometric coordinate system for spatial modeling
📈 Progressive Complexity | 🎯 Learning Path: Basic → Intermediate → Advanced
⏱️ Time to Complete: 30 minutes | Prerequisites: Syntax Guide
- Static Perception - Simplest GNN model
- Template: Basic GNN Template
- Frameworks: PyMDP Tutorial, RxInfer Basics
- Dynamic Perception - Adding time dynamics
- See Also: Time Modeling, POMDP Template
⏱️ Time to Complete: 1-2 hours | Prerequisites: Basic examples + Implementation Guide
- Butterfly Agent - POMDP navigation
- Template: POMDP Template
- Frameworks: PyMDP POMDP, RxInfer Navigation
- Trading Agent - Decision making under uncertainty
- See Also: Decision Theory, Economic Models
⏱️ Time to Complete: 2-4 hours | Prerequisites: Intermediate examples + Advanced Patterns
- Language Model - Multi-level linguistic processing
- Template: Hierarchical Template
- See Also: LLM Integration, Cognitive Phenomena
- Learning Agent - Parameter learning in JAX
- See Also: Advanced Patterns, Performance Guide
- Poetic Muse - Creative Bayesian network
- See Also: Multi-modal Models
🔬 Learning Path: Theory → Specification → Applications → Research (Full Advanced Path)
🧠 Specialized Applications | 🔗 Related: Cognitive Phenomena
- Advanced Modeling Patterns - Sophisticated modeling techniques
- Cross-refs: Implementation Guide, Templates
- Applications: Cognitive Phenomena, Multi-agent
- Ontology System - Active Inference Ontology integration
- Cross-refs: About GNN, Academic Paper
- Related: Pipeline Step 8
- Resource Metrics - Computational resource estimation
- Cross-refs: Performance Guide, Type Checker
- Related: Pipeline Step 4
- GNN Kit - Comprehensive toolkit documentation
- Cross-refs: Tools Guide, API Documentation
- Cerebrum Integration - Advanced cognitive architectures
- Cross-refs: Cognitive Phenomena, Hierarchical Template
- Audio Sonification - Auditory representation of model dynamics
- Cross-refs: SAPF, Pedalboard
- Formal Verification - Provably correct model specification
- Cross-refs: Petri Nets, Nock
- Visual Model Construction - Interactive GUI for model building
⚡ Fast Access | 🎯 Common Tasks | 🔗 Related: Troubleshooting
- Creating your first model: Start with Static Perception Example
- Tools: Basic Template → Type Checker → PyMDP Rendering
- Understanding syntax: Check GNN Syntax Reference
- Practice: Examples → Templates → Implementation
- Validating models: Use Type Checker Guide
- Troubleshooting: Common Errors → FAQ
- Converting to code: See Rendering Documentation
- Visualizing models: Follow Visualization Guide
- Pipeline: Step 6 Visualization → Step 12 Website
📋 Production-Ready Templates | 📊 Total: 4 comprehensive templates (49KB)
- Template System Overview - Complete template documentation
- Cross-refs: Examples, Implementation
- Basic GNN Template - Simple model starting point
- Use Cases: Learning, prototyping, static models
- Next Steps: POMDP Template or Examples
- POMDP Template - Comprehensive POMDP modeling template
- Use Cases: Navigation, perception, decision-making
- Frameworks: PyMDP POMDP, RxInfer POMDP
- Multi-agent Template - Multi-agent systems template
- Use Cases: Coordination, communication, social modeling
- Examples: Multi-agent Systems, RxInfer Multi-agent
- Hierarchical Template - Hierarchical architectures template
- Use Cases: Cognitive architectures, multi-scale modeling, complex systems
- Related: Advanced Patterns, Cerebrum
⚙️ 25-Step Processing Pipeline | 📈 Complete Workflow Coverage
- Complete Pipeline Guide - All 25 steps explained (0-24)
- Architecture: Pipeline Architecture
- Configuration: Configuration Guide
- Pipeline Architecture - Technical architecture
- Development: Development Guide
- API Integration: API Documentation
🔌 Programming Interfaces | 📚 36KB Documentation | 🎯 103 Functions
- Complete API Documentation - All classes, functions, and interfaces
- Development: Development Guide
- Examples: Tool Development
- MCP Integration Guide - Model Context Protocol APIs
- FastMCP: FastMCP Guide
- Pipeline: Step 7 MCP
- Tool Development - Creating new MCP tools
- Cross-refs: API Documentation, DSL Manual
- Interactive GUI Tools - Visual model construction interfaces
- GUI 1: Form-based constructor (localhost:7860)
- GUI 2: Visual matrix editor (localhost:7861)
- GUI 3: State space design studio (localhost:7862)
- Pipeline: Step 22 GUI Processing
📖 Progressive Learning System | 🎯 Beginner to Expert
- Tutorial System - Step-by-step learning guides from beginner to expert
- Start Here: Quickstart → Examples
- Configuration Guide - Complete configuration reference
- Examples: Configuration Examples
- Deployment: Deployment Guide
- Testing Guide - Testing strategies and best practices
- Pipeline: Step 3 Testing
- Quality: Style Guide and Testing Guide
🔒 Enterprise Security | 📊 Production-Ready
- Security Guide - Comprehensive security documentation
- LLM Security: Prompt injection prevention and API security
- MCP Security: Model Context Protocol security measures
- Production Security: Deployment and infrastructure security
- Development Security: Secure coding practices and testing
🚀 Professional Release Process | 📋 Version Control
- Release Management - Complete release process documentation
- Versioning: Semantic versioning strategy and guidelines
- Release Cycles: Regular and emergency release procedures
- Quality Assurance: Testing and validation requirements
- Security Releases: Critical vulnerability response process
- Releases - Release management and version history
- Current Version: v1.3.0 with comprehensive feature additions
- Version History: Detailed change tracking since project inception
- Upgrade Guides: Migration assistance between major versions
📝 Contribution Guidelines | ✅ Quality Assurance
- Documentation Style Guide - Comprehensive writing and formatting standards
- Writing Standards: Voice, tone, and clarity guidelines
- Technical Guidelines: Code examples, mathematical notation, GNN syntax
- Quality Assurance: Review processes and automated validation
- Content Guidelines: Structure, cross-references, and accessibility
🚀 Production Deployment | 📊 46KB Operational Documentation
- Deployment Guide - Local development to enterprise deployment
- Configuration: Configuration Guide
- Testing: Testing Guide
- Performance Guide - Optimization strategies and benchmarking
- Troubleshooting: Performance Issues
- Resource Metrics: Resource Estimation
- Development Guide - Contributing and extending GNN
- Contributing: Contributing Guide
- API Development: API Documentation
🆘 Comprehensive Problem Solving | 📊 56KB Support Documentation
- Troubleshooting Guide - Comprehensive problem-solving guide
- Common Issues: Common Errors
- Performance: Performance Issues
- Common Errors - Detailed error scenarios and solutions
- FAQ: Frequently Asked Questions
- Validation: Type Checker
- FAQ - Extensive frequently asked questions
- Learning: Learning Resources
- Community: Getting Help
📝 Community Contributions Welcome | 📋 Standards & Guidelines
We welcome contributions! See our Contributing Guide and Documentation Style Guide for:
- Writing standards and conventions
- Style: Style Guide
- Quality: Style Guide and Testing Guide
- Documentation templates and examples
- Templates: Template System
- Examples: Example Gallery
- Review process and quality criteria
- Process: Contributing Guide
- Quality: Testing Guide
- How to add new examples and tutorials
- Development: Development Guide
- Templates: Template Creation
🌐 Community Support Channels
- Issues: Report problems on GitHub Issues
- Before Posting: Check Common Errors and FAQ
- Discussions: Join conversations in GitHub Discussions
- Topics: Research, development, applications, best practices
- Community: Connect with the Active Inference Institute
- Resources: Papers, workshops, collaborations
🔗 Related Support: Support Guide | Troubleshooting | Contributing
🏷️ Machine-Readable Navigation Data
document_type: navigation_hub
primary_audience: [beginners, practitioners, developers, researchers]
learning_paths:
beginner: [about_gnn.md, quickstart_tutorial.md, gnn_examples_doc.md, gnn_syntax.md]
practitioner: [gnn_syntax.md, gnn_file_structure_doc.md, gnn_implementation.md, templates/README.md]
developer: [api/README.md, gnn/reference/architecture_reference.md, development/README.md]
researcher: [gnn/gnn_paper.md, advanced_modeling_patterns.md, cognitive_phenomena/README.md, poe-world/poe-world.md]
cross_references:
setup: [SETUP.md, configuration/README.md, deployment/README.md]
frameworks: [pymdp/gnn_pymdp.md, rxinfer/gnn_rxinfer.md, discopy/gnn_discopy.md, poe-world/poe-world_gnn.md]
templates: [templates/README.md, templates/basic_gnn_template.md, templates/pomdp_template.md, templates/multiagent_template.md, templates/hierarchical_template.md]
support: [troubleshooting/README.md, troubleshooting/common_errors.md, troubleshooting/faq.md]
research_integration: [poe-world/poe-world.md, gnn/advanced/gnn_llm_neurosymbolic_active_inference.md, dspy/gnn_dspy.md]
coverage_metrics:
total_documents: 70+
total_content: 1.3MB+
template_count: 4
framework_integrations: 12+
research_integrations: 5+
pipeline_steps: 25
cognitive_phenomena: 22+
test_status: 1,522+ tests passing
status: production_ready
quality_level: gold_standard
recent_additions: [poe-world_integration, enhanced_cross_references, improved_research_pathways, 100%_signposting_coverage]Status: Comprehensive and Production-Ready
Documentation Version: Compatible with GNN v1.x
Cross-Reference Network: ✅ Fully Integrated