Add AML blast triage reports and presentations#178
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Set up the STAMP crossvalidation experiment for AML bone marrow response prediction (RESPONSE_CR) using UNI2 features with ViT MIL. Includes: - Config YAML with all paths for crossval, statistics, and heatmaps - Per-split heatmap generation script that correctly matches test-set slides to their corresponding crossval checkpoint (avoids data leakage) - Self-contained HTML report generator combining ROC/PR curves, per-fold stats, and GradCAM heatmap gallery with top/bottom tiles 5-fold crossval achieved mean AUROC 0.870 (95% CI: 0.804-0.936). Heatmaps generated for 17 available WSI slides across all 5 splits. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
…figs and report Three new STAMP experiments derived from BLAST_PERCENT column: - BLAST_PERCENT regression (Pearson r=0.680, MAE=12.4%) - BLAST_SEVERITY 3-class classification (AUROC: high=0.912, int=0.783, low=0.864) - HIGH_BLAST binary classification (AUROC=0.929, AUPRC=0.845) Includes experiment YAML configs, generalized heatmap runner (--experiment flag), and combined HTML report generator with cross-experiment comparison, statistics plots, per-fold tables, and sampled heatmap gallery. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add RESPONSE_CR (treatment response, binary classification) as the first experiment in the combined report alongside BLAST_PERCENT, BLAST_SEVERITY, and HIGH_BLAST. Updated TOC, overview comparison table, heatmap gallery colors, discussion section, and heatmap coverage stats. Report output renamed to aml_crossval_report.html. Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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.venv/bin/ruff check scripts/analyze_blast_enrichment_triage.py scripts/analyze_cell_resolution_qc.py scripts/pilot_cell_resolution.py scripts/build_analysis_figs.py scripts/build_presentation_assets.py scripts/build_presentations.pygit diff --cached --check