Published comparison transcribed from the pinned source; not reproduced.
1 evaluation · 2 results. Different protocols are not a single leaderboard.
Protocol: HGMD/gnomAD missense pathogenicity, ESM1b head to head with one other method on the variants both score (Brandes et al. 2023 Fig. 2g,h, Supplementary Table 2) · Dataset subset: HGMD/gnomAD missense variants scored by both ESM1b and GERP++ (Brandes et al. 2023)
Sorted by AUPRC (balanced PRC-AUC over the variants both methods score: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | AUPRC (balanced PRC-AUC over the variants both methods score: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) | AUROC (global ROC-AUC over the variants both methods score; zero-shot) |
|---|---|---|
| GERP++ (Brandes et al. 2023 clinical benchmarks)Evaluation | 0.762 | 0.809 |
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38 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation zero-shot Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
| Comparison: adaptation zero-shot Context-only references | Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz |
| Comparison: aggregation Pooled over variants Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
| Comparison: aggregation Pooled over variants Context-only references | Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz |
| Comparison: budget Not reported Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
| Comparison: budget Not reported Context-only references | Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz |
| Comparison: dataset version Not reported Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
| Comparison: dataset version Not reported Context-only references | Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz |
| Comparison: inputs Precomputed per-variant scores Context-only references | Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-pmc10484790.xml.gz |
| Comparison: inputs Precomputed per-variant scores Context-only references | Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods Supplementary Table 2 sheet 'Table_of_results_HGMD' row 15 ('GERP++'), columns E-I Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10) | 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 Archive member: artifacts/brandes2023-supplementary-table-2.xlsx.gz |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: gfm-guides-20261014-esm1b-eval-hgmd-h2h-gerp-vep