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v0.2.2 - reviewer-requested analyses

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@SharoonSharif SharoonSharif released this 23 Sep 19:28
· 17 commits to master since this release

Adds to v0.2.1 (same protocol, same 180-run campaign) the analyses reviewers ask for, all archived under pod_results/pull_0923 and tabled in results/final/:

  • Seed-averaged paired tests over 25 (cohort, fold) units: PathQ-Former +0.037 vs SurvPath (t p 0.020, Wilcoxon p 0.020); aux variant +0.036 (t p 0.074, Wilcoxon p 0.030).
  • RNA / WSI permutation test, three seeds, five cohorts (scripts/eval_missing_impute.py --permute): permuting RNA costs PathQ-Former + aux 0.023 C-index and SurvPath 0.001; permuting WSI costs both ~0.067.
  • Mean-imputation missing-modality columns for all three seeds; learned null codes match or beat imputation.
  • Single-modality PathQ-Former for a second seed (BRCA seed 2 pending) and per-seed late fusion: joint fusion +0.011 over the ensemble (n.s.), ensemble +0.027 over SurvPath (n.s.).
  • Risk-score correlations (scripts/risk_correlation.py) and a three-seed missing-modality table (scripts/missing_modality_table.py).
  • Hyper-parameter grid configs for SurvPath (lr x alpha) and PathQ-Former (lr) in configs/grid/ with scripts/pod/batch9.sh; 1/35 cells run so far.

REPORT.md, EXPERIMENT_LOG.md and paper/draft.md are updated accordingly.