IsoGraph Documentation

IsoGraph documentation is split by user need:

• The GitHub README.md is the project landing page.

• This documentation tree is the reference layer intended for Read the Docs.

• The GitHub Wiki is the tutorial layer for step-by-step, own-data walkthroughs.

Guide

• Overview
  • Documentation Map
  • Current Scope
• Installation
  • PyPI (recommended)
  • Optional Backends
  • Documentation
  • Development
• Quickstart
  • 1. Activate the Environment
  • 2. Run a Toy Benchmark
  • 3. Inspect the Result
  • 4. Next Steps
• CLI Reference
  • Overrides
  • benchmark
  • freeze-real
  • fit
  • explain-module
  • annotate-structure
  • compare
  • export
• Own-Data Data Model
  • Minimum Practical Bundle
  • Required Alignment Rules
  • Building a Bundle
  • Running the VAE Backend from the CLI
  • Running Backends from Python
• Module Explanation
  • Quick Start
  • Python API
  • Inputs
  • Outputs
  • Publication-Ready Plots
  • Structural Annotation
  • VAE Decoder Attribution
  • Captum Integrated Gradients
• Multiplex and Stress Benchmarks
  • Standard Multiplex Suite
  • Explain Compatibility
  • Extra-Large Multiplex Stress Fixture
  • Understanding Role-Aware Recall
  • Artifact Policy
• Configuration Reference
  • Command Configs
  • Backend Configs
  • Real-Data and Stability Configs
  • Default Config Files
  • Multiplex-Specific Fields
  • Per-Fixture Overrides
• Outputs and Artifacts
  • Dataset Bundles
  • Benchmark Outputs
  • Fit Outputs
  • Explain Outputs
  • Compare Outputs
  • Export Outputs
• Backend Reference
  • Baseline
  • Latent
  • Graph
  • VAE (default)
  • WGCNA
  • Important Notes
• Limitations and Reproducibility
  • Current Product Boundaries
  • Data Assumptions
  • Scale Considerations
  • Reproducibility Design
• Acknowledgements
• API Reference
  • isograph.workflow.config
  • isograph.io.artifacts
  • isograph.validation
  • isograph.evaluation.runner
  • isograph.evaluation.selection