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) of BayesDel (Livesey and Marsh 2025) on 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)
Methods
- Tested 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)
- Procedure
- Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- Evaluation
- BayesDel: Livesey and Marsh 2025 clinical benchmark: pairwise AUROC win rate, ClinVar pathogenic versus gnomAD missense
- 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)
- Uncertainty
- Not reported by the source: Figure 3 error bars (standard error across comparisons) are not printed
- Evidence
- Independent external evaluation · source checkedLivesey 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')
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- Not reported
- Adaptation
- None; precomputed or locally run predictions
- Scoring implementation
- sklearn roc_auc_score (0.18.1) per protein
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
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
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 66.8625108589117 Individual claims | 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') 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) | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-14T15:30:00Z independent paper Audit detailsExtracted by extract/extract_vep.py; independently re-checked by review/check_values.py. Hand-checked sample in the dated review. Value, metric and identity match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
| Reported result 66.8625108589117 Individual claims | Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Supplementary Material 2, sheet 'Table S8', cell CI22 (row 'BayesDel', column 'rank_score') 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 | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-14T15:30:00Z independent paper Audit detailsExtracted by extract/extract_vep.py; independently re-checked by review/check_values.py. Hand-checked sample in the dated review. Value, metric and identity match the source. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
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)
Technical metadata and extraction receipts
Stable ID: vep-lit-20261014-result-livesey2025-clinical-auroc-bayesdel-rank-score
- metric
- pairwise-win-rate
- metric direction
- higher
- unit
- percent
- metric qualifier
- 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
- printed value
- 66.8625108589117
- numeric value
- 66.8625108589117
- raw xml value
- 66.862510858911705
- workbook number format
- General
- source locator
- Supplementary Material 2, sheet 'Table S8', cell CI22 (row 'BayesDel', column 'rank_score')
- missing metadata
- uncertainty: reason: unreported; note: Figure 3 error bars (standard error across comparisons) are not printed
- 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; independent-cell-check; method note: Re-downloaded the Springer workbook and matched the pinned SHA-256. review/check_values.py re-read the sheet XML with its own parser and checked printed value (shortest round-trip decimal of the General-format cell), numeric value, raw cell, cell reference, row label, column header, metric, qualifier, unit, direction, coverage and the linked configuration, protocol and dataset; all 667 workbook results matched.; note: Extracted by extract/extract_vep.py; independently re-checked by review/check_values.py. Hand-checked sample in the dated review. Value, metric and identity match the source.
- coverage
- scored: 814; eligible: 819; unit: proteins with at least 10 ClinVar P/LP and 10 gnomAD missense variants scored by this VEP; note: 'proteins' column, cell CJ22