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Commits on Sep 25, 2025

• Merge pull request #6 from stef1949/codex/evaluate-and-improve-neural-network-design

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• Merge pull request #5 from stef1949/codex/review-and-improve-the-code

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• Merge pull request #4 from stef1949/codex/create-visual-diagram-of-neural-network

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• Refine residual architecture for batch corrector

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• Update NN_batch_correct.py

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• Handle zero-count samples in CPM normalisation

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• Improve architecture diagram layout and annotations

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Commits on Sep 16, 2025

• Update output artifacts with new visualizations: logCPM boxplots, PCA before, and PCA after images have been modified.

  

  Stefan Ritchie

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• Refactor sweep_nn_residual_entry.py to reuse Python process and improve argument handling

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• Update output artifacts and adjust hyperparameters in wandb sweep configuration

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• Refactor project structure and update file paths

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• Add new tools and scripts for hyperparameter tuning and data generation

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Commits on Sep 14, 2025

• Implement Adversarial Autoencoder Components

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• Update model configuration and parameters in wandb_sweep_nn_residual.yaml

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• Update logo and PCA images

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• Remove unused PNG files: pca_after.png, pca_before.png, and pca_panel.png

  

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• Implement code changes to enhance functionality and improve performance

  

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• Merge pull request #1 from stef1949/copilot/fix-a3051515-197a-4122-b01a-8de3f2b93e55

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• Remove unused PNG files: logCPM_boxplots.png, pca_after.png, and pca_before.png

  

  Stefan Ritchie

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• Remove unused PNG files from VAEModel directory: logCPM_boxplots.png, pca_after.png, pca_before.png, and pca_panel.png.

  

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• Remove unused PNG files from VAEModel directory: logCPM_boxplots.png, pca_after.png, pca_before.png, and pca_panel.png.

  

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• Remove unused PNG files related to PCA and logCPM visualizations to clean up the repository.

  

  Stefan Ritchie

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• Refactor code structure for improved readability and maintainability

  

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• Enhance PCA visualization in _pca_panel function

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• Add W&B sweep configuration for legacy AE model with residual connections

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• Delete best_test_model.pt

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• Delete best_model_fallback_1756767710.pt

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• Delete best_model_fallback_1756770951.pt

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• Delete best_model_fallback_1756767711.pt

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• Delete best_model_fallback_1756767590.pt

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• Add GitHub Action to upload model on release

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• Merge pull request #3 from stef1949/copilot/fix-2

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• Add comprehensive documentation and finalize refactoring

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• Add comprehensive GitHub Copilot instructions for HarmonizeNN

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• Implement residual connections and enhanced checkpoint saving

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