Configuration

ESM1b (Brandes et al. 2023 clinical benchmarks)

Configuration of ESM-1b: esm1b_t33_650M_UR50S; missense effect score is the log-likelihood ratio of the alternate versus reference amino acid; proteins longer than 1,022 aa tiled with 1,022 aa windows overlapping by at least 511 aa and combined by a weighted average.

92 evaluations · 184 results

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

Evaluations and results

92 evaluations · 184 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: ClinVar missense pathogenic vs benign, primary isoforms (Brandes et al. 2023, from the EVE portal)	0.884 AUPRC (balanced PRC-AUC: mean over 100 random downsamples to equal pathogenic and benign counts (80% of the minority class); zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-all-19-methods Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell C2, row 'ESM1b', column 'AUC_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2) Dataset: ClinVar missense pathogenic vs benign, primary isoforms (Brandes et al. 2023, from the EVE portal)	0.892 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-all-19-methods Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell B2, row 'ESM1b', column 'AUC_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and BayesDel (no AF) (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against BayesDel (no AF) (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H21, row 'BayesDel (no AF)', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and BayesDel (no AF) (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against BayesDel (no AF) (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F21, row 'BayesDel (no AF)', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and BayesDel (with AF) (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against BayesDel (with AF) (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H22, row 'BayesDel (with AF)', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and BayesDel (with AF) (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against BayesDel (with AF) (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F22, row 'BayesDel (with AF)', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and bStatistic (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against bStatistic (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H19, row 'bStatistic', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and bStatistic (Brandes et al. 2023)	0.905 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against bStatistic (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F19, row 'bStatistic', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and CADD (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against CADD (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H23, row 'CADD', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and CADD (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against CADD (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F23, row 'CADD', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and ClinPred (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against ClinPred (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H24, row 'ClinPred', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and ClinPred (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against ClinPred (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F24, row 'ClinPred', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and DANN (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against DANN (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H25, row 'DANN', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and DANN (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against DANN (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F25, row 'DANN', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and DEOGEN2 (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against DEOGEN2 (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H26, row 'DEOGEN2', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and DEOGEN2 (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against DEOGEN2 (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F26, row 'DEOGEN2', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and Eigen (Brandes et al. 2023)	0.907 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against Eigen (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H27, row 'Eigen', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and Eigen (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against Eigen (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F27, row 'Eigen', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and Eigen-PC (Brandes et al. 2023)	0.907 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against Eigen-PC (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H28, row 'Eigen-PC', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and Eigen-PC (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against Eigen-PC (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F28, row 'Eigen-PC', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and EVE (Brandes et al. 2023)	0.905 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against EVE (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H3, row 'EVE', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and EVE (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against EVE (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F3, row 'EVE', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and FATHMM (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against FATHMM (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H29, row 'FATHMM', column 'head2head_ESM1b_auc_Balanced_AUPRC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and FATHMM (Brandes et al. 2023)	0.906 AUROC (global ROC-AUC over the variants both methods score; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against FATHMM (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell F29, row 'FATHMM', column 'head2head_ESM1b_auc_AUROC'
Configuration: ESM1b (Brandes et al. 2023 clinical benchmarks)	Protocol: ClinVar 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: ClinVar missense variants scored by both ESM1b and FATHMM-MKL (Brandes et al. 2023)	0.906 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM1b on ClinVar missense, head to head against FATHMM-MKL (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-head-to-head Aggregation: Not reported Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Supplementary Table 2 sheet 'Table_of_results_ClinVar' cell H30, row 'FATHMM-MKL', column 'head2head_ESM1b_auc_Balanced_AUPRC'

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Genome-wide prediction of disease variant effects with a deep protein language model (Brandes et al., Nature Genetics 2023) · Original source · Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10)
Brandes et al. 2023 Supplementary Table 2: full benchmark evaluations of ESM1b and all other methods · Original source · Version of record, Nature Genetics 55, 1512-1522 (published 2023-08-10)

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Stable ID: gfm-guides-20261014-esm1b-config-esm1b

areas: protein-function
contexts: clinical_research
method types: foundation_model
reported name: ESM1b
version: esm1b_t33_650M_UR50S
parameters: esm1b_t33_650M_UR50S; missense effect score is the log-likelihood ratio of the alternate versus reference amino acid; proteins longer than 1,022 aa tiled with 1,022 aa windows overlapping by at least 511 aa and combined by a weighted average
foundation model eligible: true
source locator: Supplementary Table 2 column vep_name 'ESM1b'; Methods 'ESM1b' and 'Other VEP methods'
provenance note: ESM1b as scored in the Brandes et al. 2023 clinical missense benchmarks.

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