LinearCytoVAE

Linear Conditional Variational Autoencoder for CyTOF data.

Scripts

• Linear_cytovae.py: Core model implementation
• cytovae_train_utils.py: Training utilities including optimizer setup, device management, and training loop
• FCLayers.py: Fully connected neural network layer components (used by core model)
• cytof_ann_loader.py: Data loader for AnnData objects containing CyTOF data

Subdirectories

• batch_correction/: Batch correction analysis (Figure 5)
• oncogene_screen_validation/: Signalling modules in oncogene screen (Figure 3)
• size_model/: Size factor modeling and analysis (Figure 4)
• test_hyperparameters/: Hyperparameter testing on oncogene screen data (Figure 2)