feat: integrate auxiliary pathway loss and sparsity regularization#4
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BenjaminIsaac0111 merged 2 commits intomainfrom Feb 26, 2026
Merged
feat: integrate auxiliary pathway loss and sparsity regularization#4BenjaminIsaac0111 merged 2 commits intomainfrom
BenjaminIsaac0111 merged 2 commits intomainfrom
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Implement key mathematical and architectural improvements to the spatial transcriptomics pipeline, focusing on pathway-driven interpretability. Core Changes: - Add Auxiliary Pathway Loss to ground the model's latent space in biological priors using MSigDB pathway membership markers. - Introduce L1 sparsity regularization (--sparsity-lambda) on reconstruction weights to prune redundant pathway-to-gene mappings. - Implement --log-transform data strategy (log1p) to stabilize MSE against high-variance housekeeping gene expression. Architecture & Refactoring: - Update dataloader and train/predict scripts to support auxiliary objectives and log-transformed targets. - Refactor visualization modules to improve histology-pathway overlays. - Remove deprecated Bowel Cancer download script. Documentation & Compliance: - Formally document auxiliary loss and training objectives in the IP Statement. - Expand model documentation and training guides to reflect bottleneck transitions and latent discovery capabilities. - Add Future Directions and Clinical Collaborations to project README. - Resolve markdownlint error in LICENSE by adding a top-level H1 heading. Testing: - Add unit tests for pathway pruning logic and auxiliary loss calculation. - Strengthen visualization tests to ensure coordinate alignment integrity.
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Architecture & Refactoring:
Documentation & Compliance: