Model

ESM-1v

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

1 evaluation · 5 results · 5 evaluated configurations using this model

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

1 evaluation · 5 results. Different protocols are not a single leaderboard.

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 (ensemble)	Task: ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.723 auc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, AUC)
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.32 mcc correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, MCC)
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.749 ndcg fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, NDCG@10%)
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.211 recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, top 10% recall)
Configuration: ESM-1v (ensemble)	Task: ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.407 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM-1v (ensemble) on ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(ESM-1v (ensemble)), column(Zero-shot substitutions, Spearman)

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Related configurations, pipelines and services

These configurations, services and pipelines use this model within their own configurations. Their results, where available, are not assigned to the underlying model.

ESM-1v (mean) Configuration · 13 results
ESM-1v (mut mean) Configuration · 10 results
ESM-1v (per AA) Configuration · 14 results
Embed. ESM-1v Configuration · 8 results
OHE ESM-1v Configuration · 8 results

Use this model

How it works, versions and access

Versions and evaluated configurations

ESM-1v (ensemble) · family

How it works

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

Applicable tests and references

Applicability is distinct from a completed evaluation.

ProteinGym · Proposed association

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

40 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram caption Conceptual summary of the documented data flow; optional inputs and configured downstream stages must be reported for a reproducible evaluation. Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Reference protein sequence ESM-1v token predictions Specified variant scoring rule Variant score Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram steps Reference protein sequence ESM-1v token predictions Specified variant scoring rule Variant score Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title ESM-1v workflow Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Diagram title ESM-1v workflow Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Protein transformer for variant-effect scoring Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Model type Protein transformer for variant-effect scoring Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Transformer architecture shared with ESM-1b, trained on UniRef90; multiple released model instances support the variant-scoring workflow. Individual claims	facebook/esm1v_t33_650M_UR90S_1: config.json Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8 Retrieved: 2026-09-16T20:12:20.912868+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `6c4b576e2e73ad85fc51a4fa75d4e350532b773e04551307a74643c3fc3c5d59` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact
Architecture Transformer architecture shared with ESM-1b, trained on UniRef90; multiple released model instances support the variant-scoring workflow. Individual claims	facebookresearch/esm: README.md Original source ↗ README.md: Main models, Zero-shot variant prediction and Pre-trained Models Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac Retrieved: 2026-09-16T19:46:19.090082+00:00	source checked automated source review · 2026-09-16 Audit 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. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `8b273c21a322fc9473d1b68d0dd40c8166ab2f89e4a190aa26ca87251b97cba9` Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Inspected artifact

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Release 2026-09-29-06401fd5b220 · Record review: discovered

4 source records and release history

facebookresearch/esm official source · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
facebookresearch/esm: README.md · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
facebook/esm1v_t33_650M_UR90S_1: config.json · Original source · 8bfdb1892536cc77bd0760b9c25ddced2cd0b4c8
facebookresearch/esm: LICENSE · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac

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Technical metadata and extraction receipts

Stable ID: discovery-model-esm-1v

areas: protein-function
access: official_source_linked
benchmark applicability: candidate; not evidence of a reported evaluation
candidate benchmark ids: discovery-benchmark-proteingym
entity level: family
reported name: ESM-1v
version: Not reported
historical missing metadata: checkpoint: unextracted; code licence: unextracted; parameters: unextracted; training cutoff: unextracted; training data: unextracted; version: unextracted; weights licence: unextracted
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
entity classification: review date: 2026-09-17; rationale: The cited profile describes a named learned biological predictor or representation model/family. Preserve this identity separately from task-specific fitting, individual checkpoints, pipelines and hosted access.; source ids: evidence-official-29d4b229a3aa426a6dfb; evidence-official-137a3a936ffa4673b3d3; source locator: README.md: Main models, Zero-shot variant prediction and Pre-trained Models; ambiguities: None recorded

Related records

applicable to: ProteinGym
uses model: ESM-1v (mean)
uses model: ESM-1v (mut mean)
uses model: ESM-1v (per AA)
uses model: Embed. ESM-1v
family: ESM-1v (ensemble)
uses model: OHE ESM-1v

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