Configuration

ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)

ESM-1b in-frame indel score: the absolute value of the pseudo-log-likelihood ratio between the mutated and wild-type protein sequences, so likelihood gains and losses both count as damaging.

4 evaluations · 4 results

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Evaluations and results

4 evaluations · 4 results. Different protocols are not a single leaderboard.

Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2)

Sorted by AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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	Protocol and dataset	AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; zero-shot)	AUROC (ROC-AUC, pathogenic versus benign ClinVar deletion-insertions; zero-shot)	AUROC (ROC-AUC, pathogenic versus benign ClinVar deletions; zero-shot)	AUROC (ROC-AUC, pathogenic versus benign ClinVar insertions; zero-shot)
ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.874	Not reported	Not reported	Not reported
ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame deletions (Brandes et al. 2023)	Not reported	Not reported	0.875	Not reported
ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame deletion-insertions (Brandes et al. 2023)	Not reported	0.887	Not reported	Not reported
ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)Evaluation	ClinVar in-frame insertions (Brandes et al. 2023)	Not reported	Not reported	Not reported	0.831

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame deletions (Brandes et al. 2023)	0.875 AUROC (ROC-AUC, pathogenic versus benign ClinVar deletions; 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-aPLLR on deletions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell D2, row 'ESM1b-aPLLR', column 'AUC_del'
Configuration: ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame deletion-insertions (Brandes et al. 2023)	0.887 AUROC (ROC-AUC, pathogenic versus benign ClinVar deletion-insertions; 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-aPLLR on deletion-insertions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell E2, row 'ESM1b-aPLLR', column 'AUC_delins'
Configuration: ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset: ClinVar in-frame indels, pathogenic vs benign (Brandes et al. 2023)	0.874 AUROC (ROC-AUC, pathogenic versus benign ClinVar all in-frame indels; 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-aPLLR on all in-frame indels (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell B2, row 'ESM1b-aPLLR', column 'AUC_indels'
Configuration: ESM1b absolute-valued PLLR indel score (Brandes et al. 2023)	Protocol: ClinVar in-frame indel pathogenicity, ROC-AUC (Brandes et al. 2023 Fig. 6b, Supplementary Table 2) Dataset subset: ClinVar in-frame insertions (Brandes et al. 2023)	0.831 AUROC (ROC-AUC, pathogenic versus benign ClinVar insertions; 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-aPLLR on insertions (Brandes et al. 2023) gfm-guides-20261014-esm1b-protocol-clinvar-inframe-indels 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_indels' cell C2, row 'ESM1b-aPLLR', column 'AUC_ins'

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

2 source records and release history

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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Technical metadata and extraction receipts

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

areas: protein-function
contexts: clinical_research
method types: foundation_model
reported name: ESM1b-aPLLR
version: esm1b_t33_650M_UR50S
parameters: esm1b_t33_650M_UR50S; sequences longer than 1,022 amino acids scored on a 1,022-residue window around the variant; |PLL(mut) - PLL(WT)|
foundation model eligible: true
source locator: Methods 'Generalized effect scores for indels and stop-gain variants' paragraph 3; Supplementary Table 2 sheet 'Table_of_results_indels' row 'ESM1b-aPLLR'

Related records

configuration of: ESM-1b
system: ESM1b-aPLLR on deletions (Brandes et al. 2023)
system: ESM1b-aPLLR on deletion-insertions (Brandes et al. 2023)
system: ESM1b-aPLLR on all in-frame indels (Brandes et al. 2023)
system: ESM1b-aPLLR on insertions (Brandes et al. 2023)

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