Cognitive Modeling Documentation

Welcome to the Cognitive Modeling documentation. This documentation is designed to be viewed in Obsidian for optimal navigation and knowledge linking.

[!info] Documentation Network This documentation works in conjunction with the [[agents/agentdocsreadme|Autonomous Agent Documentation Clearinghouse]] which contains comprehensive agent-specific documentation.

Directory Structure

```mermaid

graph TD

A[Documentation Root] --> B[concepts/]

A --> C[guides/]

A --> D[api/]

A --> E[examples/]

A --> F[tools/]

A --> G[templates/]

A --> H[agents/]

B --> B1[cognitive_modeling_concepts.md]

B --> B2[active_inference.md]

B --> B3[free_energy_principle.md]

C --> C1[implementation_guides.md]

C --> C2[installation_guide.md]

C --> C3[quickstart_guide.md]

D --> D1[api_documentation.md]

E --> E1[usage_examples.md]

E --> E2[quickstart_example.md]

F --> F1[development_tools.md]

G --> G1[documentation_templates.md]

H --> H1[agent_docs_readme.md]

style A fill:#f9d5e5,stroke:#333,stroke-width:1px

style H fill:#d5f5e3,stroke:#333,stroke-width:2px

style H1 fill:#d5f5e3,stroke:#333,stroke-width:2px

```

Core Documentation

• [[concepts/cognitivemodelingconcepts|Concepts]] - Core concepts and theoretical foundations

• [[guides/implementation_guides|Guides]] - Implementation guides and tutorials

• [[api/api_documentation|API]] - API reference documentation

• [[examples/usage_examples|Examples]] - Usage examples and tutorials

• [[tools/development_tools|Tools]] - Development tools and utilities

• [[templates/documentation_templates|Templates]] - Documentation templates

• [[agents/agentdocsreadme|Agent Documentation]] - Autonomous agent documentation clearinghouse

Getting Started

Essential Setup

• [[guides/installation_guide|Installation Guide]]

• [[guides/configuration_guide|Configuration Guide]]

• [[guides/quickstart_guide|Quick Start Guide]]

• [[guides/environment_setup|Environment Setup]]

• [[guides/dependency_management|Dependency Management]]

Core Concepts

• [[concepts/plaintextbenefits|Plain Text Benefits]]

• [[concepts/machine_readability|Machine Readability]]

• [[concepts/research_education|Research and Education]]

• [[concepts/active_inference|Active Inference]]

• [[concepts/freeenergyprinciple|Free Energy Principle]]

• [[concepts/predictive_processing|Predictive Processing]]

• [[concepts/variational_inference|Variational Inference]]

• [[concepts/message_passing|Message Passing]]

Documentation Usage

• [[guides/obsidian_linking|Obsidian Linking Guide]]

• [[guides/package_documentation|Package Documentation]]

• [[guides/pomdp_structure|POMDP Structure]]

• [[guides/mermaid_diagrams|Mermaid Diagram Guide]]

• [[guides/documentation_navigation|Documentation Navigation]]

Development

Implementation

• [[guides/model_implementation|Model Implementation]]

• [[guides/system_integration|System Integration]]

• [[guides/testing_guide|Testing Guide]]

• [[guides/performance_optimization|Performance Optimization]]

• [[guides/agent_development|Agent Development]]

• [[guides/environment_creation|Environment Creation]]

Architecture Overview

```mermaid

graph TB

subgraph "Core Framework"

    A[Abstract Base Classes]

    B[Common Utilities]

    C[Math Libraries]

    D[Config Management]

end

subgraph "Agent Models"

    E[POMDP Agents]

    F[Continuous Agents]

    G[Hybrid Agents]

    H[LLM Agents]

end

subgraph "Environments"

    I[Simulation Environments]

    J[Real-world Interfaces]

    K[Benchmarks]

end

A --> E

A --> F

A --> G

A --> H

B --> E

B --> F

B --> G

B --> H

C --> E

C --> F

C --> G

style A fill:#f9d5e5,stroke:#333,stroke-width:1px

style B fill:#f9d5e5,stroke:#333,stroke-width:1px

style C fill:#f9d5e5,stroke:#333,stroke-width:1px

style D fill:#f9d5e5,stroke:#333,stroke-width:1px

style E fill:#d5f5e3,stroke:#333,stroke-width:1px

style F fill:#d5f5e3,stroke:#333,stroke-width:1px

style G fill:#d5f5e3,stroke:#333,stroke-width:1px

style H fill:#d5f5e3,stroke:#333,stroke-width:1px

```

Tools

• [[tools/setup_tools|Setup Tools]]

• [[tools/development_tools|Development Tools]]

• [[tools/documentation_tools|Documentation Tools]]

• [[tools/experiment_tools|Experiment Tools]]

• [[tools/analysis_tools|Analysis Tools]]

• [[tools/visualization_tools|Visualization Tools]]

• [[tools/benchmark_tools|Benchmark Tools]]

• [[tools/simulation_tools|Simulation Tools]]

Examples

• [[examples/quickstart_example|Quick Start Example]]

• [[examples/basic_agent|Basic Agent]]

• [[examples/activeinferencebasic|Active Inference]]

• [[examples/multiagentsystem|Multi-Agent System]]

• [[examples/hierarchical_agent|Hierarchical Agent]]

• [[examples/belief_updating|Belief Updating Example]]

• [[examples/policy_selection|Policy Selection Example]]

Contributing

Guidelines

• [[guides/contribution_guide|Contribution Guide]]

• [[guides/documentation_guide|Documentation Guide]]

• [[guides/style_guide|Style Guide]]

• [[guides/code_standards|Code Standards]]

• [[guides/testing_guidelines|Testing Guidelines]]

• [[guides/review_process|Review Process]]

Development Workflow

```mermaid

stateDiagram-v2

[*] --> Development

Development --> Testing

Testing --> Review

Review --> Refinement

Refinement --> Testing

Review --> Documentation

Documentation --> Deployment

Deployment --> [*]

```

Templates

• [[templates/concept_template|Concept Template]]

• [[templates/guide_template|Guide Template]]

• [[templates/example_template|Example Template]]

• [[templates/api_template|API Documentation Template]]

• [[templates/implementation_template|Implementation Template]]

• [[templates/agent_template|Agent Template]]

• [[templates/research_template|Research Template]]

Additional Resources

References

• [[concepts/active_inference|Active Inference]]

• [[concepts/freeenergyprinciple|Free Energy Principle]]

• [[concepts/predictive_processing|Predictive Processing]]

• [[DOCUMENTATION_ROADMAP|Documentation Roadmap]]

• [[concepts/bibliography|Bibliography]]

• [[concepts/glossary|Glossary of Terms]]

Research Topics

• [[research/current_projects|Current Research Projects]]

• [[research/publications|Publications]]

• [[research/experimental_results|Experimental Results]]

• [[research/benchmarks|Benchmark Results]]

• [[research/future_directions|Future Research Directions]]

Related Projects

• [[related/similar_frameworks|Similar Frameworks]]

• [[related/complementary_tools|Complementary Tools]]

• [[related/partner_projects|Partner Projects]]

• [[related/community_extensions|Community Extensions]]

Support

Help

• [[guides/troubleshooting|Troubleshooting]]

• [[guides/faq|FAQ]]

• [[guides/support|Support]]

• [[guides/common_errors|Common Errors]]

• [[guides/performance_issues|Performance Issues]]

Community

• [[guides/community_guide|Community Guide]]

• [[guides/discussion|Discussion]]

• [[guides/feedback|Feedback]]

• [[guides/feature_requests|Feature Requests]]

• [[guides/bug_reporting|Bug Reporting]]

• [[guides/community_extensions|Community Extensions]]

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[!tip] Navigation Tip Use Obsidian's graph view and search functionality to explore connections between concepts. The [[agents/agentdocsreadme|Agent Documentation Clearinghouse]] provides comprehensive details on agent implementations.

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[!note] Open Source and Licensing Repository: ActiveInferenceInstitute/cognitive - Documentation and knowledge base content: CC BY-NC-SA 4.0 - Code and examples: MIT License (see LICENSE)