Published comparison of variant effect predictors; transcribed, not reproduced.
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1 evaluation · 5 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: VEST4 (Chen et al. 2020) | Protocol: OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) Dataset: OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral) | 0.69 accuracy fraction · higher Uncertainty: Not yet extracted: Printed as 'mean (lower-upper)' under the column header '(±2σ)': per Methods, the mean and two standard deviations over 100 random draws. That is not a confidence interval, and the schema's standard_deviation type would need a standard deviation derived from rounded bounds, so no structured uncertainty is recorded. The printed range is kept in printed_source_cell; every range is symmetric about the mean to rounding. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceVEST4 on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-oncokb-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) · Additional file 9 (sheet 'Additional_file_9'), B3; Algorithm 'VEST4'; column 'Accuracy (±2σ)' |
| Configuration: VEST4 (Chen et al. 2020) | Protocol: OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) Dataset: OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral) | 0.69 negative-predictive-value fraction · higher Uncertainty: Not yet extracted: Printed as 'mean (lower-upper)' under the column header '(±2σ)': per Methods, the mean and two standard deviations over 100 random draws. That is not a confidence interval, and the schema's standard_deviation type would need a standard deviation derived from rounded bounds, so no structured uncertainty is recorded. The printed range is kept in printed_source_cell; every range is symmetric about the mean to rounding. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceVEST4 on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-oncokb-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) · Additional file 9 (sheet 'Additional_file_9'), F3; Algorithm 'VEST4'; column 'NPV (±2σ)' |
| Configuration: VEST4 (Chen et al. 2020) | Protocol: OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) Dataset: OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral) | 0.69 precision fraction · higher Uncertainty: Not yet extracted: Printed as 'mean (lower-upper)' under the column header '(±2σ)': per Methods, the mean and two standard deviations over 100 random draws. That is not a confidence interval, and the schema's standard_deviation type would need a standard deviation derived from rounded bounds, so no structured uncertainty is recorded. The printed range is kept in printed_source_cell; every range is symmetric about the mean to rounding. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceVEST4 on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-oncokb-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) · Additional file 9 (sheet 'Additional_file_9'), E3; Algorithm 'VEST4'; column 'PPV (±2σ)' |
| Configuration: VEST4 (Chen et al. 2020) | Protocol: OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) Dataset: OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral) | 0.69 recall fraction · higher Uncertainty: Not yet extracted: Printed as 'mean (lower-upper)' under the column header '(±2σ)': per Methods, the mean and two standard deviations over 100 random draws. That is not a confidence interval, and the schema's standard_deviation type would need a standard deviation derived from rounded bounds, so no structured uncertainty is recorded. The printed range is kept in printed_source_cell; every range is symmetric about the mean to rounding. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceVEST4 on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-oncokb-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) · Additional file 9 (sheet 'Additional_file_9'), C3; Algorithm 'VEST4'; column 'Sensitivity (±2σ)' |
| Configuration: VEST4 (Chen et al. 2020) | Protocol: OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020 Additional file 9) Dataset: OncoKB-annotated somatic missense mutations (oncogenic, likely oncogenic and likely neutral) | 0.69 specificity fraction · higher Uncertainty: Not yet extracted: Printed as 'mean (lower-upper)' under the column header '(±2σ)': per Methods, the mean and two standard deviations over 100 random draws. That is not a confidence interval, and the schema's standard_deviation type would need a standard deviation derived from rounded bounds, so no structured uncertainty is recorded. The printed range is kept in printed_source_cell; every range is symmetric about the mean to rounding. Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceVEST4 on OncoKB benchmark (positive set not stated), median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-oncokb-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) · Additional file 9 (sheet 'Additional_file_9'), D3; Algorithm 'VEST4'; column 'Specificity (±2σ)' |
Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.
somatic-oncogenicity-20261009-protocol-chen2020-oncokb-median
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36 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation Not reported Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | 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 |
| attributes.comparison.adaptation Not reported Context-only references | Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | 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 |
| attributes.comparison.aggregation Mean over 100 draws Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | 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 |
| attributes.comparison.aggregation Mean over 100 draws Context-only references | Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | 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 |
| attributes.comparison.budget Not reported Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | 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 |
| attributes.comparison.budget Not reported Context-only references | Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | 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 |
| attributes.comparison.dataset_version Not reported Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | 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 |
| attributes.comparison.dataset_version Not reported Context-only references | Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | 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 |
| attributes.comparison.inputs Missense SNV scores Context-only references | Comprehensive assessment of computational algorithms in predicting cancer driver mutations Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML | 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 |
| attributes.comparison.inputs Missense SNV scores Context-only references | Chen et al. 2020, Additional file 9: Performance metrics of 33 algorithms, median-score threshold, benchmark 2 (OncoKB) Additional file 9, row 3 ('VEST4') Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 13059_2020_1954_MOESM9_ESM.xlsx | 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 2026-10-10-6e93f504adfc · Record review: source checked
Stable ID: somatic-oncogenicity-20261009-eval-chen2020-vest4-oncokb-median