Independent benchmark by Livesey and Marsh 2025; transcribed, not reproduced.
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: FathmmXF (Livesey and Marsh 2025) | Protocol: Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions only Dataset: Livesey and Marsh 2025 human DMS benchmark set (36 proteins) | 24.5% Pairwise win rate (average pairwise win rate against all other VEPs, |Spearman| with DMS on shared variants, SNV-accessible substitutions only) percent · higher Uncertainty: Not reported by the source: Bootstrap standard deviations appear only as Figure 2 error bars; not printed Coverage: 36/36 human DMS datasets (one per protein) with predictions for this VEP scored ('proteins' column, cell C80) | Independent external evaluation · Source checkedMethods, coverage and sourceLivesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions only 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 S6', cell B80 (row 'FathmmXF', column 'rank_score') |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
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Livesey and Marsh 2025 DMS benchmark: pairwise |Spearman| win rate, SNV-accessible substitutions only
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34 evidence rows matching the loaded filters
| 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) Supplementary Material 2, Table S6, row 'FathmmXF' 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) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: 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) Supplementary Material 2, Table S6, row 'FathmmXF' 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: 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) Supplementary Material 2, Table S6, row 'FathmmXF' 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) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: 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) Supplementary Material 2, Table S6, row 'FathmmXF' 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: 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) Supplementary Material 2, Table S6, row 'FathmmXF' 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) | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: 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) Supplementary Material 2, Table S6, row 'FathmmXF' 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 | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version 36 human DMS sets of Table S1 Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Supplementary Material 2, Table S6, row 'FathmmXF' 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) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: dataset version 36 human DMS sets of Table S1 Context-only references | Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Supplementary Material 2, Table S6, row 'FathmmXF' 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs FathmmXF predictions from dbNSFP Context-only references | Livesey and Marsh 2025, Genome Biology 26:104 (Europe PMC full text XML) Supplementary Material 2, Table S6, row 'FathmmXF' 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) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Comparison: inputs FathmmXF predictions from dbNSFP Context-only references | Livesey and Marsh 2025, Supplementary Material 2 (Tables S1-S8) Supplementary Material 2, Table S6, row 'FathmmXF' 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 | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: vep-lit-20261014-eval-livesey2025-dms-snv-fathmm-xf