EvoAug2 Documentation

Evolution-Inspired Data Augmentation for Genomic Sequences - DataLoader Version

Welcome to EvoAug2, a Python package that provides evolution-inspired data augmentation techniques for genomic sequence analysis using deep learning. This package implements the two-stage training approach described in the EvoAug2 paper, combining robust augmentation during training with fine-tuning on original data.

Getting Started

• Installation
  • Installation from PyPI
  • Installation with Optional Dependencies
  • Installation from Source
  • System Requirements
  • Dependencies
  • Verification
  • Troubleshooting
  • Next Steps
• Quick Start Guide
  • Basic Usage
  • Integration with PyTorch DataLoader
  • Using RobustLoader (Recommended)
  • Two-Stage Training Approach
  • Complete Example
  • Next Steps
• Examples
  • Available Examples
  • Example Categories
  • Running the Examples
  • Example Outputs
  • Customizing Examples
  • Troubleshooting Examples
  • Next Steps

API Reference

• EvoAug2 Core API
  • Augmentation Module
  • Training Module
  • Usage Examples
• EvoAug2 API Reference
  • Package Overview
  • Core Modules
  • Augmentation Classes
  • Training Utilities
  • Model Architectures
  • Utility Functions
  • Usage Examples
  • Configuration
  • Error Handling
  • Performance Considerations
• EvoAug2 Examples API
  • Lightning Module Example
  • Vanilla PyTorch Example
  • Running Examples

Examples

• PyTorch Lightning Integration Example
  • Overview
  • Key Features
  • File Structure
  • Usage
  • Training Stages
  • DataModule Implementation
  • Checkpoint Management
  • Performance Evaluation
  • Visualization
  • Output Structure
  • Customization
  • Troubleshooting
  • Next Steps
• Vanilla PyTorch Integration Example
  • Overview
  • Key Features
  • File Structure
  • Usage
  • Code Walkthrough
  • Augmentation Application
  • Customization Examples
  • Data Handling
  • Training Configuration
  • Evaluation and Metrics
  • Comparison with Lightning Example
  • Troubleshooting
  • Next Steps

Indices and tables

• Index

• Module Index

• Search Page

Note

This documentation is for EvoAug2 version 2.0.3. For older versions, please refer to the GitHub releases.

Tip

If you're new to EvoAug2, start with the Quick Start Guide and then explore the Examples section.