Evaluation

BayesDel: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense

Independent benchmark by Livesey and Marsh 2025; transcribed, not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BayesDel (Livesey and Marsh 2025)	Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins)	66.9% Pairwise win rate (average pairwise win rate against all other VEPs, per-protein AUROC on shared variants, ClinVar P/LP versus gnomAD v4.1 missense, proteins with at least 10 of each) percent · higher Uncertainty: Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed Coverage: 814/819 proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP scored ('proteins' column, cell CJ22)	Independent external evaluation · Source checked Methods, coverage and source BayesDel: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense Aggregation: Not reported Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8); Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Supplementary Material 2, sheet 'Table S8', cell CI22 (row 'BayesDel', column 'rank_score')

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense

Configuration: BayesDel (Livesey and Marsh 2025)
Protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
Dataset: Livesey and Marsh 2025 clinical set: ClinVar pathogenic versus gnomAD v4.1 missense (819 proteins)

origin: Independent external evaluation
configuration: Not reported
protocol id: vep-lit-20261014-protocol-livesey2025-clinical-auroc
dataset version: ClinVar 06/08/2024 and gnomAD v4.1, 819 proteins
split: Not reported
population: Proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants; variants scored by both VEPs of a pair
inputs: BayesDel predictions from dbNSFP
adaptation: None; precomputed or locally run predictions
metric implementation: sklearn roc_auc_score (0.18.1) per protein
aggregation: Win rate of each VEP pair across proteins (wins divided by times the pair was tested), averaged over all other VEPs (Methods, 'Spearman's correlation and rank score')
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Not reported
Adaptation: None; precomputed or locally run predictions
Scoring implementation: sklearn roc_auc_score (0.18.1) per protein

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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34 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation None; precomputed or locally run predictions Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Comparison: adaptation None; precomputed or locally run predictions Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Comparison: aggregation Win rate of each VEP pair across proteins (wins divided by times the pair was tested), averaged over all other VEPs (Methods, 'Spearman's correlation and rank score') Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Comparison: aggregation Win rate of each VEP pair across proteins (wins divided by times the pair was tested), averaged over all other VEPs (Methods, 'Spearman's correlation and rank score') Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Comparison: budget Not reported Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Comparison: budget Not reported Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	missing or unspecified No individual claim review recorded independent paper Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Comparison: dataset version ClinVar 06/08/2024 and gnomAD v4.1, 819 proteins Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Comparison: dataset version ClinVar 06/08/2024 and gnomAD v4.1, 819 proteins Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record
Comparison: inputs BayesDel predictions from dbNSFP Context-only references	Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: PMC12016141 (published 2025-04-22; Genome Biol 26:104) Retrieved: 2026-10-14T13:36:01Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `1735ee461ef192d9de67c914e9ad73d72d8aa255ea0e3479eb68cd8631d99fa2` Hash scope: Hash scope not separately documented; inspect source record
Comparison: inputs BayesDel predictions from dbNSFP Context-only references	Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Original source ↗ Supplementary Material 2, Table S8, row 'BayesDel' Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141 Retrieved: 2026-10-14T13:36:25Z	not individually reviewed No individual claim review recorded independent paper Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70` Hash scope: Hash scope not separately documented; inspect source record

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) · Original source · 13059_2025_3575_MOESM2_ESM.xlsx as published with PMC12016141
Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) · Original source · PMC12016141 (published 2025-04-22; Genome Biol 26:104)

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Technical metadata and extraction receipts

Stable ID: vep-lit-20261014-eval-livesey2025-clinical-auroc-bayesdel

areas: dna-genomes; proteins-complexes
contexts: clinical_research
origin: independent_paper
protocol: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
comparison: protocol id: vep-lit-20261014-protocol-livesey2025-clinical-auroc; dataset version: ClinVar 06/08/2024 and gnomAD v4.1, 819 proteins; split: Not reported; population: Proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants; variants scored by both VEPs of a pair; inputs: BayesDel predictions from dbNSFP; adaptation: None; precomputed or locally run predictions; metric implementation: sklearn roc_auc_score (0.18.1) per protein; aggregation: Win rate of each VEP pair across proteins (wins divided by times the pair was tested), averaged over all other VEPs (Methods, 'Spearman's correlation and rank score'); budget: Not reported
source locator: Supplementary Material 2, Table S8, row 'BayesDel'
missing metadata: budget: reason: unreported; split: reason: inapplicable; note: Zero-shot comparison with no training split
review: reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T15:30:00Z; artifact sha256: 1b0d792d1a5d3daa95545a7973cabb131c45e42c952e7e5a447a72deef1d1e70; retrieval url: https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-025-03575-w/MediaObjects/13059_2025_3575_MOESM2_ESM.xlsx; method: source-hash-verification; deterministic-table-parse; scope-review; method note: Links, origin and comparison fields checked against the source and the linked protocol; results checked by review/check_values.py.; note: Origin independent_paper checked: no VEP reference in the workbook's References sheet lists Livesey or Marsh (one DMS dataset, PAX6, reference 5, is co-authored by Livesey).

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