{ "protocol": { "lockedAtUTC": "2026-10-13T18:17:10.492578+00:00", "development": "Successful v2 MFASS development set plus all four previous external minigene cohorts, now explicitly development. Reserve SCN5A; prior v1 MFASS test remains unused.", "candidate": "M3 v3 research predictor combines SpliceAI/Pangolin scores, five aligned variant-location bins, transition status and reference/alternate GC indicators. Candidate HGB or spline calibration; no gene ID, assay ID or measured response feature.", "selection": "Leave one entire assay cohort out: MFASS, FAS, MST1R, POU1F1, WT1. Select lowest unweighted mean of five study Brier errors; worst-study Brier breaks exact ties. Training study-weight exponent grid 0,0.5,1 offered equally to candidate and baselines. OOF scores are development selection, not independent confirmation.", "baselines": "Retuned same-input ExtraTrees; score-only ExtraTrees; Pangolin plus context HGB; Pangolin spline/Platt/isotonic; ridge with all inputs. Retain frozen v1/v2 M3, ExtraTrees and Pangolin models as external comparators, not only retuned baselines.", "freshDataset": "ParSE-seq ONeill et al Nature Communications 2024; SCN5A. Primary iPSC-CM, secondary HEK assay. Same gene and overlapping variants; not two independent studies. Published normal/abnormal Outcome used unchanged; indeterminate/missing outcomes and non-SNVs excluded.", "freshFeatureContract": "SpliceAI max reconstructed from AG/AL/DG/DL, never substitute aggregate score. Published Pangolin column used as reported. Author code calls it Pangolin_Aggregate but aggregation implementation absent: only exploratory transfer qualification, not matched-score confirmation. Source scoring settings and assay definitions differ from development.", "freshPrimary": "iPSC-CM Brier on all common eligible SNVs. Log loss, AUROC, AP and ECE secondary. No test prevalence correction, calibration, thresholds or model changes. HEK is descriptive replication only.", "successRule": "Candidate must beat every retained/retuned baseline on primary Brier with positive Bonferroni-adjusted paired exon-cluster bootstrap lower limits. Do not assert across-study superiority from one fresh gene, even if primary test passes.", "uncertainty": "10000 paired whole-exon bootstrap draws; seed20261015; familywise alpha0.05 across all baselines. Assay cells not independent; one gene limits generalization.", "disclosure": "Public article aggregate findings and five example rows from figure source data were seen while locating predictor columns. No fresh numerical performance metrics used for model selection. All fresh inputs/labels parsed only after model freeze.", "limitations": [ "Previously tested cohorts now development, not independent validation.", "Development assay labels have heterogeneous biological definitions.", "Fresh SCN5A selection includes clinically ascertained variants and variants chosen using SpliceAI; not a population sample.", "Pangolin score aggregation is incompletely specified in deposited code.", "Pretrained SpliceAI/Pangolin training overlap with SCN5A is not ruled out.", "Research model requires Pangolin; not a standalone sequence model or clinical/patent validation." ], "sourceHashes": { "docs/validation/2026-10-13-m3-transfer-v2/development.csv": "f10187a0a68a24341c24953b07de81c177d34fff61a2a774b3a5c50719133ebb", "docs/validation/2026-10-13-m3-transfer-v2/external-inputs.csv": "d83db918402e85a58ed329cfa5157c91b9a897393d2328970a02c3575972e685", "docs/validation/2026-10-13-m3-transfer-v2/external-outcomes.csv": "794c70367451ccf5e64155c71152aec6de2635dfc0d99fa871e8ddfa855716d3", "docs/validation/2026-10-13-m3-multistudy-v3/41467_2024_52474_MOESM6_ESM.csv": "607814b68c05288e31ba221c964bee22daba0909d294beda55d307155246a06a", "docs/validation/2026-10-13-m3-multistudy-v3/41467_2024_52474_MOESM7_ESM.csv": "5b78c17cb06a737ff895cf2344bfa4133ce68dc4857c8d657c63da3803b4fd17" }, "promotion": "none" }, "qualification": { "status": "Exploratory independent-source transfer only: Pangolin aggregation provenance incomplete", "source": "https://www.nature.com/articles/s41467-024-52474-4", "sourceFiles": [ "41467_2024_52474_MOESM6_ESM.csv", "41467_2024_52474_MOESM7_ESM.csv" ], "totalAssayRows": 468, "eligibleAssayRows": 366, "uniqueEligibleVariants": 224, "eligibleByAssay": { "HEK": 190, "iPSC-CM": 176 }, "rejectionCountsNonexclusive": { "non_SNV": 18, "indeterminate_or_missing_assay": 87, "missing_or_invalid_predictor": 6, "missing_location": 0, "missing_coordinate": 0, "reference_mismatch_or_nonSNV": 13, "historical_MFASS_variant_overlap": 0 }, "exonsByAssay": { "HEK": 19, "iPSC-CM": 19 }, "referenceMatchedEligibleRows": 366, "referenceURL": "https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chr3;start=38554271;end=38620972", "referenceSHA256": "a195aeb665a34ec2d76a44c0c1997291833626dcc9b1e90aaea1aa364f233f50", "historicalMFASSVariantOverlaps": 0, "v3TrainingGeneOverlap": [], "freshGene": "SCN5A", "scoreDefinition": "S0=max(AG,AL,DG,DL) only when all components present; P0=published Pangolin column, unchanged. Its aggregation implementation not deposited; cannot verify equivalence to development max-delta scores.", "secondaryAssayDependence": "HEK and iPSC-CM share SCN5A variants/exons and do not constitute two independent studies.", "clinicalIndependence": "Only published assay Outcome is used. Clinical classifications and protein function not used as target labels.", "selectionBias": "Some variants chosen with high SpliceAI scores; cannot extrapolate to unselected variants.", "sourceSHA256": { "41467_2024_52474_MOESM6_ESM.csv": "607814b68c05288e31ba221c964bee22daba0909d294beda55d307155246a06a", "41467_2024_52474_MOESM7_ESM.csv": "5b78c17cb06a737ff895cf2344bfa4133ce68dc4857c8d657c63da3803b4fd17" } }, "selection": { "lockedAtUTC": "2026-10-13T18:19:02.401235+00:00", "candidate": "M3_spline", "selected": { "M3_HGB": { "configuration": { "iterations": 150, "leaves": 3, "l2": 10, "studyWeightPower": 0.5 }, "meanStudyBrier": 0.18451744179667423, "worstStudyBrier": 0.45101422363009847, "studyBrier": { "FAS": 0.28280279567345773, "MFASS": 0.053721944064918495, "MST1R": 0.45101422363009847, "POU1F1": 0.08049566378724772, "WT1": 0.054552581827648855 } }, "M3_spline": { "configuration": { "knots": 3, "C": 1, "studyWeightPower": 1 }, "meanStudyBrier": 0.1825592528706601, 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0.17211182136987763, "worstStudyBrier": 0.39218631236440277, "studyBrier": { "FAS": 0.2393519299822101, "MFASS": 0.05653497518968719, "MST1R": 0.39218631236440277, "POU1F1": 0.09879024600705151, "WT1": 0.07369564330603658 } }, "Pangolin_spline": { "configuration": { "knots": 7, "C": 100, "studyWeightPower": 1 }, "meanStudyBrier": 0.16993395164748376, "worstStudyBrier": 0.38135032433979005, "studyBrier": { "FAS": 0.23628057897815272, "MFASS": 0.052444902828810744, "MST1R": 0.38135032433979005, "POU1F1": 0.10278572084725685, "WT1": 0.07680823124340826 } }, "Pangolin_Platt": { "configuration": { "C": 0.1, "studyWeightPower": 1 }, "meanStudyBrier": 0.17079385332616903, "worstStudyBrier": 0.3933697030180787, "studyBrier": { "FAS": 0.23817018723231748, "MFASS": 0.05207745461257717, "MST1R": 0.3933697030180787, "POU1F1": 0.09799903775799383, "WT1": 0.07235288400987797 } }, "Pangolin_isotonic": { "configuration": { "studyWeightPower": 1 }, "meanStudyBrier": 0.1707431197445482, "worstStudyBrier": 0.3840918556096234, "studyBrier": { "FAS": 0.2389724404295008, "MFASS": 0.05290464876558952, "MST1R": 0.3840918556096234, "POU1F1": 0.10175104422958386, "WT1": 0.07599560968844346 } }, "Ridge_context": { "configuration": { "alpha": 0.01, "studyWeightPower": 1 }, "meanStudyBrier": 0.204375530703152, "worstStudyBrier": 0.384280370117066, "studyBrier": { "FAS": 0.294023875153572, "MFASS": 0.0709221040278208, "MST1R": 0.384280370117066, "POU1F1": 0.12889928940216916, "WT1": 0.14375201481513203 } } }, "rows": 8031, "studyRows": { "MFASS": 5801, "POU1F1": 941, "MST1R": 598, "WT1": 502, "FAS": 189 }, "fits": 1080, "developmentSeconds": 88.026172875, "developmentSHA256": "4d091020de4746124fb3d73994f714c3155c90d7c273a6dfa679d93e878decaa", "checkpoint": "backend/models/m3-multistudy-v3/model.joblib", "checkpointSHA256": "bb4951fc6a571429aa987aa8e923e1bf1ca8c32e6b07b5e55e6f77d2eaa05251", "freshOutcomeMetricsComputed": false }, "assayCounts": { "HEK": { "rows": 190, "positives": 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