Update from task 88f3eb36-62ba-4bec-9478-f39c8275d593 - #7
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…kage Prevention** **Key features implemented:** - Added Layer 1 gene filtering functions (fit_layer1_gene_selector, transform_layer1_genes) for variance thresholding and mutual information selection on raw gene data only - Created Layer 2 domain-specific feature engineering (create_engineered_features) with pathway scores, clinical interactions, and graceful handling of missing genes in external validation - Implemented Layer 3 assembly function (assemble_layer3_features) for combining selected genes and engineered features with consistent alignment - Developed unified 3-layer strategy function (apply_3_layer_feature_engineering) supporting both training and external validation workflows with proper leakage prevention - Updated create_engineered_features to accept selected genes from Layer 1 and support lenient/strict modes for pathway scoring This refactoring enforces strict separation between feature selection and engineering phases, preventing data leakage by ensuring MI selection occurs only on training data while maintaining compatibility with both TCGA training and GSE70769 validation datasets.
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This PR was created by qwen-chat coder for task 88f3eb36-62ba-4bec-9478-f39c8275d593.