Configuration

ESM-1v (single) [ProteinGym 144fe22b snapshot]

ESM-1v provides protein language models intended for zero-shot variant-effect scoring.

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

2 evaluations · 19 results

How it worksESM-1v workflow

Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation.

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Overview

Model type

Protein transformer for variant-effect scoring

Inputs

Protein amino-acid sequence and the specified sequence variation.

Outputs

Token probabilities used to calculate sequence-variant scores.

Access

Official project documentation and implementation: https://github.com/facebookresearch/esm

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

2 evaluations · 19 results. Different protocols are not a single leaderboard.

Sorted by Spearman (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	Spearman	Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays))	Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Prokaryote proteins: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman)	Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman)
ESM-1v (single) [ProteinGym 144fe22b snapshot]Evaluation	ProteinGym AMFR official zero-shot Spearman snapshot, ProteinGym AMFR 4G3O official snapshot cohort	0.07	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
ESM-1v (single) [ProteinGym 144fe22b snapshot]Evaluation	ProteinGym v1.3 zero-shot DMS substitutions, ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	Not reported	0.396	0.268	0.405	0.47	0.427	0.289	0.374	0.373	0.361	0.433	0.385	0.437	0.375	0.188	0.177	0.146	0.209	0.258

All 19 result rows with coverage, uncertainty and sources

Filter evaluations

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: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym AMFR official zero-shot Spearman snapshot Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort	0.07 Spearman unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single) AMFR official snapshot Not reported Aggregation: Not reported ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-1v (single)
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.374 Spearman (ProteinGym zero-shot DMS substitutions, mean over selection types of the per-type mean over proteins of assay-level Spearman (all 217 assays)) unitless · higher Uncertainty: SE 0.014. From compute_bootstrap_standard_error_functional_categories in performance_DMS_benchmarks.py at 144fe22 (default 10,000 resamples, lines 95-111 and 310-315); not an absolute standard error of the model's own average. Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Average_Spearman'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.375 Spearman (ProteinGym zero-shot DMS substitutions, variants with 1 substitution: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Depth_1'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.188 Spearman (ProteinGym zero-shot DMS substitutions, variants with 2 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Depth_2'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.177 Spearman (ProteinGym zero-shot DMS substitutions, variants with 3 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Depth_3'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.146 Spearman (ProteinGym zero-shot DMS substitutions, variants with 4 substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Depth_4'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.209 Spearman (ProteinGym zero-shot DMS substitutions, variants with 5 or more substitutions: mean over protein and selection-type groups of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Depth_5+'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.396 Spearman (ProteinGym zero-shot DMS substitutions, Activity assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Function_Activity'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.268 Spearman (ProteinGym zero-shot DMS substitutions, Binding assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Function_Binding'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.405 Spearman (ProteinGym zero-shot DMS substitutions, Expression assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Function_Expression'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.361 Spearman (ProteinGym zero-shot DMS substitutions, Organismal fitness assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Function_OrganismalFitness'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.437 Spearman (ProteinGym zero-shot DMS substitutions, Stability assays: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Function_Stability'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.47 Spearman (ProteinGym zero-shot DMS substitutions, High MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'High_MSA_depth'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.289 Spearman (ProteinGym zero-shot DMS substitutions, Low MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Low_MSA_depth'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.373 Spearman (ProteinGym zero-shot DMS substitutions, Medium MSA depth proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Medium_MSA_depth'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.427 Spearman (ProteinGym zero-shot DMS substitutions, Human proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Taxa_Human'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.433 Spearman (ProteinGym zero-shot DMS substitutions, Other eukaryote proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Taxa_Other_Eukaryote'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.385 Spearman (ProteinGym zero-shot DMS substitutions, Prokaryote proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Taxa_Prokaryote'
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]	Protocol: ProteinGym v1.3 zero-shot DMS substitutions Dataset subset: ProteinGym DMS substitution assays at commit 144fe22 (217 assays)	0.258 Spearman (ProteinGym zero-shot DMS substitutions, Virus proteins: mean over proteins of assay-level Spearman) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22) ProteinGym zero-shot DMS substitutions, Spearman summary Aggregation: Not reported ProteinGym zero-shot DMS substitutions Spearman summary at commit 144fe22 · benchmarks/DMS_zero_shot/substitutions/Spearman/Summary_performance_DMS_substitutions_Spearman.csv line 70, row 'ESM-1v (single)', column 'Taxa_Virus'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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How it works, versions and access

Related profile: ESM-1v. This page retains the exact record and its evaluation context.

This configuration

ESM-1v (single), from the ProteinGym reference scores at commit 144fe22b.

record: ESM-1v (single) [ProteinGym 144fe22b snapshot]
configuration: 144fe22b07dfaeec2b366f2346203a9838a55b4c
entity type: Configuration

How it works

Transformer architecture shared with ESM-1b, trained on UniRef90; multiple released model instances support the variant-scoring workflow. The documented inputs are protein amino-acid sequence and the specified sequence variation. The output consists of token probabilities used to calculate sequence-variant scores.

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Versions and reproducibility

esm1v_t33_650M_UR90S_1 through _5. The applicable input limits require configuration-specific checking.

Sources (2)

facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

The package provides a dedicated variant-prediction example without fitting a task-specific supervised classifier.
Sources (2)
facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Limitations and conditions

The five released instances are distinct models. A language-model score is not a calibrated clinical pathogenicity probability.
Sources (2)
facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models

Profile review details

Inspected pinned official documentation, relevant implementation files and named primary-paper sections. Claims are limited to those artifacts. Remaining field extraction and identity conflicts are explicit; no new performance claims, model runs or human review are implied.

Stable record: discovery-model-esm-1v

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Protein transformer for variant-effect scoring Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Architecture	Transformer architecture shared with ESM-1b, trained on UniRef90; multiple released model instances support the variant-scoring workflow. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Inputs	Protein amino-acid sequence and the specified sequence variation. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Outputs	Token probabilities used to calculate sequence-variant scores. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Parameters	650 million per model; 33 transformer layers. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Known versions	esm1v_t33_650M_UR90S_1 through _5. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Training data	UniRef90/S 2020_03, as reported in the pretrained-model table. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Training cutoff	The official model table identifies the UniRef90/S2020_03 training release; this is a corpus version rather than a verified latest-sequence deposition date. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Context limits	The inspected official esm1v_t33_650M_UR90S_1 config reserves 1,026 absolute positions. This includes model positions and is not a claim of 1,026-residue validated biological context. Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Weights licence	Separate checkpoint-distribution terms are not stated in the inspected release documentation and licence material. The source-code licence alone is not recorded as an explicit weight grant. · Not reported in inspected sources Sources (3) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json; facebookresearch/esm: LICENSE · README.md: Main models, Zero-shot variant prediction and Pre-trained Models; LICENSE: licence text
Access	Official project documentation and implementation: https://github.com/facebookresearch/esm Sources (2) facebookresearch/esm: README.md; facebook/esm1v_t33_650M_UR90S_1: config.json · README.md: Main models, Zero-shot variant prediction and Pre-trained Models
Code licence	MIT Sources facebookresearch/esm: LICENSE · LICENSE: licence text

Evidence

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Facets: method types 1 values foundation_model Individual claims	ProteinGym AMFR assay-level Spearman comparison Original source ↗ Proposer's report, ProteinGym AMFR: protein language and structure-conditioned models fit foundation_model Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-30	conflicting claim ["automated-source-review"] · 2026-10-12 Audit details Correct the method type from none to foundation_model (use-case baseline review 2026-10-12, table 2). Not source-checked in the review; this comparison has no baseline row. Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: `"[\"foundation_model\"]"`. Claim record status: source_checked. Field: `facets.method_types` Claim: metadata-correction-tags-20261012-655963c31ac51732fe2b Source artifact SHA-256: `f432423b87f79ac9778dfac86e3d95be041d246bc618dc0a406b35b0b7466437` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: configuration of discovery-model-esm-1v Individual claims	ProteinGym AMFR assay-level Spearman comparison Original source ↗ Pinned ProteinGym Spearman CSV header: ESM-1v (single) Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c Retrieved: 2026-09-30	source checked ["automated-source-review"] · 2026-09-30T21:40:59.576893+00:00 Audit details Field: `links:configuration_of:discovery-model-esm-1v` Claim: uc20260930-config-family-c2fcc670e1f30a3d Source artifact SHA-256: `f432423b87f79ac9778dfac86e3d95be041d246bc618dc0a406b35b0b7466437` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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ProteinGym AMFR assay-level Spearman comparison · Original source · 144fe22b07dfaeec2b366f2346203a9838a55b4c

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Technical metadata and extraction receipts

Stable ID: uc20260930-proteingym-amfr-config-esm-1v-single

areas: proteins-complexes
method types: foundation_model
source locator: See linked evaluation and result locators
missing metadata: checkpoint hash: reason: unextracted
review: method: automated-source-review; reviewer: codex; reviewed at: 2026-09-30T21:40:59.576893+00:00; scope: Primary-source transcription and catalogue applicability audit; not human scientific review or independent experimental reproduction.; reviewer note: role: experimental use-case curation
reported name: ESM-1v (single)
version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
provenance note: Exact official CSV source-label configuration; checkpoint and per-assay scoring details are not inferred from similarly named methods.

Related records

configuration of: ESM-1v
subject: ESM-1v (single) [ProteinGym 144fe22b snapshot]: facets.method_types
subject: ESM-1v (single) [ProteinGym 144fe22b snapshot] family identity
system: ESM-1v (single) AMFR official snapshot
system: ESM-1v (single): ProteinGym zero-shot DMS substitutions summary (144fe22)

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