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genomic_scorer.py

@@ -26,9 +26,11 @@ PATHO_THRESH = 0.564  # AlphaMissense likely-pathogenic cut (Cheng et al., Scien
 # Validated VEP performance on REAL ClinVar variants (coords verified vs GRCh37).
 # Scaled benchmark: 451 variants across 20 rare-disease genes (236 path/215 benign);
 # see benchmark/results/evo2_bench_multigene.json. (FBN1-only pilot: n=30.)
-VEP_VALIDATION = {"benchmark": "ClinVar missense, 20 genes", "n": 451,
-                  "alphamissense_auroc": 0.928, "evo2_7b_auroc": 0.816,
+VEP_VALIDATION = {"missense_benchmark": "ClinVar, 20 genes, n=451",
+                  "alphamissense_auroc": 0.928,            # missense
+                  "evo2_7b_auroc": 0.816,                  # coding/global, zero-shot
                   "evo2_per_gene_median_auroc": 0.854,
+                  "alphagenome_splice_auroc": 0.734,       # splice (ClinVar splice, n=40)
                   "fbn1_pilot": {"n": 30, "alphamissense_auroc": 0.96, "evo2_7b_auroc": 0.88}}