EvoAug2

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
      • AugmentBase
        • AugmentBase.__call__()
      • RandomDeletion
        • RandomDeletion.__init__()
        • RandomDeletion.__call__()
      • RandomInsertion
        • RandomInsertion.__init__()
        • RandomInsertion.__call__()
      • RandomTranslocation
        • RandomTranslocation.__init__()
        • RandomTranslocation.__call__()
      • RandomInversion
        • RandomInversion.__init__()
        • RandomInversion.__call__()
      • RandomMutation
        • RandomMutation.__init__()
        • RandomMutation.__call__()
      • RandomRC
        • RandomRC.__init__()
        • RandomRC.__call__()
      • RandomNoise
        • RandomNoise.__init__()
        • RandomNoise.__call__()
    • Training Module
      • Classes
      • AugmentedGenomicDataset
        • AugmentedGenomicDataset.__init__()
        • AugmentedGenomicDataset.__len__()
        • AugmentedGenomicDataset.__getitem__()
        • AugmentedGenomicDataset.enable_augmentations()
        • AugmentedGenomicDataset.disable_augmentations()
      • RobustLoader
        • RobustLoader.__init__()
        • RobustLoader.enable_augmentations()
        • RobustLoader.disable_augmentations()
        • RobustLoader.set_augmentations()
    • Usage Examples
  • EvoAug2 API Reference
    • Package Overview
    • Core Modules
    • Augmentation Classes
      • RandomMutation
        • RandomMutation.__init__()
        • RandomMutation.__call__()
      • RandomDeletion
        • RandomDeletion.__init__()
        • RandomDeletion.__call__()
      • RandomInsertion
        • RandomInsertion.__init__()
        • RandomInsertion.__call__()
      • RandomTranslocation
        • RandomTranslocation.__init__()
        • RandomTranslocation.__call__()
      • RandomRC
        • RandomRC.__init__()
        • RandomRC.__call__()
      • RandomNoise
        • RandomNoise.__init__()
        • RandomNoise.__call__()
    • Training Utilities
      • RobustLoader
        • RobustLoader.__init__()
        • RobustLoader.enable_augmentations()
        • RobustLoader.disable_augmentations()
        • RobustLoader.set_augmentations()
    • Model Architectures
      • DeepSTARR
        • DeepSTARR.__init__()
        • DeepSTARR.get_which_conv_layers_transferred()
        • DeepSTARR.forward()
      • DeepSTARRModel
        • DeepSTARRModel.__init__()
        • DeepSTARRModel.forward()
        • DeepSTARRModel.training_step()
        • DeepSTARRModel.validation_step()
        • DeepSTARRModel.test_step()
        • DeepSTARRModel.configure_optimizers()
      • Basset
        • Basset.__init__()
        • Basset.get_which_conv_layers_transferred()
        • Basset.forward()
      • CNN
        • CNN.__init__()
        • CNN.forward()
    • Utility Functions
      • H5DataModule
        • H5DataModule.data_path
        • H5DataModule.batch_size
        • H5DataModule.x
        • H5DataModule.y
        • H5DataModule.transpose
        • H5DataModule.downsample
        • H5DataModule.x_train
        • H5DataModule.y_train
        • H5DataModule.x_valid
        • H5DataModule.y_valid
        • H5DataModule.x_test
        • H5DataModule.y_test
        • H5DataModule.A
        • H5DataModule.L
        • H5DataModule.num_classes
        • H5DataModule.__init__()
        • H5DataModule.setup()
        • H5DataModule.train_dataloader()
        • H5DataModule.val_dataloader()
        • H5DataModule.test_dataloader()
      • evaluate_model()
      • get_predictions()
      • calculate_auroc()
      • calculate_aupr()
      • calculate_mse()
      • calculate_pearsonr()
      • calculate_spearmanr()
      • configure_optimizer()
      • get_fmaps()
      • make_directory()
    • 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
EvoAug2
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