Protocol

Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21)

Accuracy, sensitivity, specificity, PPV and NPV of 33 predictors using median-score threshold.

Overview

Accuracy, sensitivity, specificity, PPV and NPV of 33 predictors using median-score threshold.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

33 recorded evaluations, 165 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

33 evaluations · 165 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CADD (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.59 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 checked Methods, coverage and source CADD on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), B23; Algorithm 'CADD'; column 'Accuracy (±2σ)'
Configuration: CADD (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.59 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 checked Methods, coverage and source CADD on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), F23; Algorithm 'CADD'; column 'NPV (±2σ)'
Configuration: CADD (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.59 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 checked Methods, coverage and source CADD on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), E23; Algorithm 'CADD'; column 'PPV (±2σ)'
Configuration: CADD (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.59 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 checked Methods, coverage and source CADD on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), C23; Algorithm 'CADD'; column 'Sensitivity (±2σ)'
Configuration: CADD (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.59 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 checked Methods, coverage and source CADD on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), D23; Algorithm 'CADD'; column 'Specificity (±2σ)'
Configuration: CanDrA (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.67 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	Author-reported evaluation · Source checked Methods, coverage and source CanDrA on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), B5; Algorithm 'CanDrA'; column 'Accuracy (±2σ)'
Configuration: CanDrA (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.67 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	Author-reported evaluation · Source checked Methods, coverage and source CanDrA on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), F5; Algorithm 'CanDrA'; column 'NPV (±2σ)'
Configuration: CanDrA (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.67 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	Author-reported evaluation · Source checked Methods, coverage and source CanDrA on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), E5; Algorithm 'CanDrA'; column 'PPV (±2σ)'
Configuration: CanDrA (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.67 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	Author-reported evaluation · Source checked Methods, coverage and source CanDrA on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), C5; Algorithm 'CanDrA'; column 'Sensitivity (±2σ)'
Configuration: CanDrA (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.67 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	Author-reported evaluation · Source checked Methods, coverage and source CanDrA on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), D5; Algorithm 'CanDrA'; column 'Specificity (±2σ)'
Configuration: CHASM (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	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 checked Methods, coverage and source CHASM on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), B4; Algorithm 'CHASM'; column 'Accuracy (±2σ)'
Configuration: CHASM (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	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 checked Methods, coverage and source CHASM on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), F4; Algorithm 'CHASM'; column 'NPV (±2σ)'
Configuration: CHASM (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	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 checked Methods, coverage and source CHASM on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), E4; Algorithm 'CHASM'; column 'PPV (±2σ)'
Configuration: CHASM (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	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 checked Methods, coverage and source CHASM on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), C4; Algorithm 'CHASM'; column 'Sensitivity (±2σ)'
Configuration: CHASM (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	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 checked Methods, coverage and source CHASM on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), D4; Algorithm 'CHASM'; column 'Specificity (±2σ)'
Configuration: CTAT-cancer (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.7 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 checked Methods, coverage and source CTAT-cancer on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), B2; Algorithm 'CTAT-cancer'; column 'Accuracy (±2σ)'
Configuration: CTAT-cancer (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.7 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 checked Methods, coverage and source CTAT-cancer on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), F2; Algorithm 'CTAT-cancer'; column 'NPV (±2σ)'
Configuration: CTAT-cancer (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.7 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 checked Methods, coverage and source CTAT-cancer on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), E2; Algorithm 'CTAT-cancer'; column 'PPV (±2σ)'
Configuration: CTAT-cancer (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.7 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 checked Methods, coverage and source CTAT-cancer on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), C2; Algorithm 'CTAT-cancer'; column 'Sensitivity (±2σ)'
Configuration: CTAT-cancer (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.7 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 checked Methods, coverage and source CTAT-cancer on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), D2; Algorithm 'CTAT-cancer'; column 'Specificity (±2σ)'
Configuration: CTAT-population (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.64 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 checked Methods, coverage and source CTAT-population on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), B11; Algorithm 'CTAT-population'; column 'Accuracy (±2σ)'
Configuration: CTAT-population (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.64 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 checked Methods, coverage and source CTAT-population on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), F11; Algorithm 'CTAT-population'; column 'NPV (±2σ)'
Configuration: CTAT-population (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.64 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 checked Methods, coverage and source CTAT-population on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), E11; Algorithm 'CTAT-population'; column 'PPV (±2σ)'
Configuration: CTAT-population (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.64 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 checked Methods, coverage and source CTAT-population on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), C11; Algorithm 'CTAT-population'; column 'Sensitivity (±2σ)'
Configuration: CTAT-population (Chen et al. 2020)	Protocol: Cell viability drivers versus neutral, median-score threshold (Chen et al. 2020 Additional file 21) Dataset: Missense mutations with Ba/F3 and MCF10A cell viability calls (published and new)	0.64 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 checked Methods, coverage and source CTAT-population on cell viability drivers versus neutral, median-score threshold (Chen et al. 2020) somatic-oncogenicity-20261009-protocol-chen2020-viability-median Aggregation: Not reported Comprehensive assessment of computational algorithms in predicting cancer driver mutations; Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Additional file 21 (sheet 'Additional_file_21'), D11; Algorithm 'CTAT-population'; column 'Specificity (±2σ)'

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Comprehensive assessment of computational algorithms in predicting cancer driver mutations · Original source · Genome Biology 21:43, published 2020-02-20; PMC7033911 full-text XML
Chen et al. 2020, Additional file 21: Performance metrics of 33 algorithms, median-score threshold, benchmark 5 (cell viability) · Original source · 13059_2020_1954_MOESM21_ESM.xlsx

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Stable ID: somatic-oncogenicity-20261009-protocol-chen2020-viability-median

areas: dna-genomes
contexts: clinical_research
protocol: Binary predictions by median-score threshold (each algorithm's median score on the benchmark) compared with the truth labels with reportROC; 400 positives and 400 negatives sampled 100 times; mean and two standard deviations reported.
version: Additional file 21
metric: accuracy
limitations: Binary metrics are means over 100 random draws of 400 positives and 400 negatives; the bracketed range is the mean plus or minus two standard deviations, not a confidence interval.; Predictor scores date from dbNSFP v4.0 and 2019 web servers; current releases (for example AlphaMissense, CHASMplus, BoostDM) are not included.; The threshold is each algorithm's median score on the benchmark draw, which is not available when classifying a new variant; with balanced draws it makes sensitivity, specificity, PPV and NPV nearly equal, so the table ranks tools rather than measuring a usable operating point.; Functional calls come from the authors' own Ba/F3 and MCF10A screens; a growth effect in either cell model counts as positive.; Activating and inactivating variants are pooled, so oncogene and tumour-suppressor mechanisms are not separated.; The combined cell viability set has 376 positives (Results), yet Methods say 400 positives were drawn per repeat, so positives were drawn with replacement or the counts differ; the source does not say.; Two authors (H. Liang, G.B. Mills) co-developed CanDrA (reference 7), and the cell viability labels come from the same group's assays; CanDrA rows are author_reported.
source locator: Additional file 21; Methods 'Calculation of five evaluation metrics based on categorical predictions'

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