Update from task 2cccf934-c853-4999-b18a-e8acb383cd90 - #3
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… BCR prediction Key features implemented: - New src/clinical_utility.py module with Decision Curve Analysis, confusion matrix with confidence intervals, and clinical impact curves - New src/survival_analysis.py module implementing Kaplan-Meier estimator, log-rank tests, and time-dependent ROC analysis - New src/batch_correction.py module with ComBat, z-score standardization, and quantile normalization for cross-study validation - Updated README.md with comprehensive repository overview and usage instructions - New requirements.txt with complete dependency list for reproducible installation - New CODE_AUDIT_REPORT.md with detailed performance recommendations and missing components analysis - Modified .gitignore with comprehensive file exclusion patterns for clean repository The changes significantly enhance the clinical utility analysis capabilities and address external validation performance through batch effect correction methods, while providing complete documentation and reproducibility infrastructure for publication-ready code.
- Added comprehensive troubleshooting guide in PIPELINE_CONSISTENCY_FIX.md with step-by-step solutions for missing artifacts - Updated .gitignore to properly exclude core data/processed and core/outputs directories - Enhanced verify_pipeline_consistency() function with detailed diagnostics showing missing/extra features - Improved error messages with actionable guidance pointing to Notebook 05 execution requirements - Added skipped checks tracking to identify which validations couldn't run due to missing prerequisites The changes resolve the feature count mismatch issue by providing clear guidance on generating required artifacts and implementing better diagnostic reporting for pipeline consistency failures.
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This PR was created by qwen-chat coder for task 2cccf934-c853-4999-b18a-e8acb383cd90.