| Configuration: SiPhy (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) | 0.666 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 | Independent external evaluation · Source checkedMethods, coverage and sourceSiPhy 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 C11, row 'SiPhy', column 'AUC_Balanced_AUPRC' |
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| Configuration: SiPhy (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) | 0.738 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSiPhy 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 B11, row 'SiPhy', column 'AUC_AUROC' |
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| Configuration: SiPhy (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 SiPhy (Brandes et al. 2023) | 0.702 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 | Independent external evaluation · Source checkedMethods, coverage and sourceSiPhy on ClinVar missense, head to head against ESM1b (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 G11, row 'SiPhy', column 'head2head_VEP_auc_Balanced_AUPRC' |
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| Configuration: SiPhy (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 SiPhy (Brandes et al. 2023) | 0.772 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 | Independent external evaluation · Source checkedMethods, coverage and sourceSiPhy on ClinVar missense, head to head against ESM1b (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 E11, row 'SiPhy', column 'head2head_VEP_auc_AUROC' |
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| Configuration: SiPhy (Brandes et al. 2023 clinical benchmarks) | Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2)
Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023) | 0.671 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 | Independent external evaluation · Source checkedMethods, coverage and sourceSiPhy on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-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_HGMD' cell C11, row 'SiPhy', column 'AUC_Balanced_AUPRC' |
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| Configuration: SiPhy (Brandes et al. 2023 clinical benchmarks) | Protocol: HGMD/gnomAD missense pathogenicity, variants scored by all 19 eligible methods (Brandes et al. 2023 Fig. 2e-f, Supplementary Table 2)
Dataset: HGMD disease-causing vs gnomAD common missense variants, primary isoforms (Brandes et al. 2023) | 0.743 AUROC (global ROC-AUC over all variants; zero-shot) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSiPhy on HGMD/gnomAD missense, variants scored by all 19 methods (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-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_HGMD' cell B11, row 'SiPhy', column 'AUC_AUROC' |
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| Configuration: SiPhy (Brandes et al. 2023 clinical benchmarks) | 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 SiPhy (Brandes et al. 2023) | 0.791 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 | Independent external evaluation · Source checkedMethods, coverage and sourceSiPhy on HGMD/gnomAD missense, head to head against ESM1b (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-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_HGMD' cell G11, row 'SiPhy', column 'head2head_VEP_auc_Balanced_AUPRC' |
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| Configuration: SiPhy (Brandes et al. 2023 clinical benchmarks) | 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 SiPhy (Brandes et al. 2023) | 0.833 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 | Independent external evaluation · Source checkedMethods, coverage and sourceSiPhy on HGMD/gnomAD missense, head to head against ESM1b (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-hgmd-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_HGMD' cell E11, row 'SiPhy', column 'head2head_VEP_auc_AUROC' |
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