Configuration

ESM-2 8M masked-marginal scoring (ProteinGym v1.3 AMFR substitution assay)

ESM-2 is a family of protein sequence encoders that produce representations for downstream protein analyses.

Sources (3)

facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json

1 evaluation · 5 metric rows

How it worksESM-2 workflow

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

Sources (3)

Overview

Model type

Masked-token protein transformer encoder

Sources (3)

Inputs

Single amino-acid sequences.

Sources (3)

Outputs

Residue embeddings, sequence representations and masked-token predictions.

Sources (3)

Access

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

Sources (3)

Source reviewed · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

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

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM-2 8M masked-marginal scoring (ProteinGym v1.3 AMFR substitution assay)	Protocol: ProteinGym v1.3 AMFR substitution assay Dataset subset: ProteinGym v1.3 AMFR substitution assay full assay	0.394 AUC dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972	Rewire evaluation · source checked Methods, coverage and source ESM-2 8M masked-marginal scoring on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported ESM-2 8M masked-marginal scoring: local execution report (20 September 2026); ESM-2 8M masked-marginal scoring: automated execution audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.AUC
Configuration: ESM-2 8M masked-marginal scoring (ProteinGym v1.3 AMFR substitution assay)	Protocol: ProteinGym v1.3 AMFR substitution assay Dataset subset: ProteinGym v1.3 AMFR substitution assay full assay	-0.139 MCC dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972	Rewire evaluation · source checked Methods, coverage and source ESM-2 8M masked-marginal scoring on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported ESM-2 8M masked-marginal scoring: local execution report (20 September 2026); ESM-2 8M masked-marginal scoring: automated execution audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.MCC
Configuration: ESM-2 8M masked-marginal scoring (ProteinGym v1.3 AMFR substitution assay)	Protocol: ProteinGym v1.3 AMFR substitution assay Dataset subset: ProteinGym v1.3 AMFR substitution assay full assay	0.440 NDCG dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972	Rewire evaluation · source checked Methods, coverage and source ESM-2 8M masked-marginal scoring on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported ESM-2 8M masked-marginal scoring: local execution report (20 September 2026); ESM-2 8M masked-marginal scoring: automated execution audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.NDCG
Configuration: ESM-2 8M masked-marginal scoring (ProteinGym v1.3 AMFR substitution assay)	Protocol: ProteinGym v1.3 AMFR substitution assay Dataset subset: ProteinGym v1.3 AMFR substitution assay full assay	-0.209 Spearman dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972	Rewire evaluation · source checked Methods, coverage and source ESM-2 8M masked-marginal scoring on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported ESM-2 8M masked-marginal scoring: local execution report (20 September 2026); ESM-2 8M masked-marginal scoring: automated execution audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.Spearman
Configuration: ESM-2 8M masked-marginal scoring (ProteinGym v1.3 AMFR substitution assay)	Protocol: ProteinGym v1.3 AMFR substitution assay Dataset subset: ProteinGym v1.3 AMFR substitution assay full assay	0.057 Top_recall dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972	Rewire evaluation · source checked Methods, coverage and source ESM-2 8M masked-marginal scoring on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported ESM-2 8M masked-marginal scoring: local execution report (20 September 2026); ESM-2 8M masked-marginal scoring: automated execution audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.Top_recall

Source checking is not independent reproduction. Release 2026-09-22-f58a0f1d267f.

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How it works, versions and access

Related profile: ESM-2. This page retains the exact record and its evaluation context.

This configuration

unreported; UniRef50 pretraining may overlap benchmark proteins

record: ESM-2 8M masked-marginal scoring (ProteinGym v1.3 AMFR substitution assay)
configuration: Not reported
entity type: Configuration

How it works

ESM-2 tokenizes an amino-acid sequence and uses a transformer encoder trained to recover masked residues. Self-attention lets each residue representation depend on its sequence context. The released model returns token probabilities and embeddings; a specified pooling rule, task head or complete folding pipeline is needed for a particular biological prediction.

Sources (3)

Versions and reproducibility

ESM-2 checkpoint identifiers encode layer count, parameter scale and training-data tag. The checked esm2_t33_650M_UR50D configuration lists max_position_embeddings=1,026. This configuration field includes model positions and is not a claim of training or validated inference on 1,026 amino acids.

Sources (3)

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths supported by sources

Released checkpoints span several sizes and can be used without constructing a multiple sequence alignment.
Sources (3)
facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json

Limitations and conditions

A general embedding is not a directly measured function or structure. Fine-tuning, pooling and downstream heads remain part of each evaluated configuration.
Sources (3)
facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json

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-2

Specifications

Inputs, training, access and other details

Explanatory profile: source reviewed · 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	Masked-token protein transformer encoder Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Architecture	Masked-token protein transformer encoder; the checked 650M checkpoint has 33 layers, hidden width 1,280, 20 attention heads and rotary positional encoding. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Inputs	Single amino-acid sequences. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Outputs	Residue embeddings, sequence representations and masked-token predictions. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Parameters	Released scales: 8M, 35M, 150M, 650M, 3B and 15B. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Known versions	ESM-2 checkpoint identifiers encode layer count, parameter scale and training-data tag. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Training data	UniRef50 clusters with UniRef90 sampling; the pretrained-model table labels UR50/D 2021_04. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Training cutoff	The pretrained-model table identifies training-data release UR50/D 2021_04; a corpus release date is not necessarily a last-deposited-sequence cutoff. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Context limits	The checked esm2_t33_650M_UR50D configuration lists max_position_embeddings=1,026. This configuration field includes model positions and is not a claim of training or validated inference on 1,026 amino acids. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Weights licence	The official facebook/esm2_t33_650M_UR50D model card declares MIT; this is the inspected checkpoint, not a licence inference from source code. Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Access	Official project documentation and implementation: https://github.com/facebookresearch/esm Sources (3) facebookresearch/esm: README.md; facebook/esm2_t33_650M_UR50D: README.md; facebook/esm2_t33_650M_UR50D: config.json · ESM README: Pre-trained Models and Main models; official facebook/esm2_t33_650M_UR50D README licence metadata and config.json
Code licence	MIT Sources facebookresearch/esm: LICENSE · LICENSE: licence text

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Claims, original sources and review scope · Release 2026-09-22-f58a0f1d267f
Property and statement	Original source and location	Review and provenance
Relationship: family discovery-model-esm-2 Individual claims	ESM-2 8M masked-marginal scoring: local execution report (20 September 2026) Original source ↗ model; model_configuration; execution Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	source checked automated execution evidence review · 2026-09-20T20:54:03Z Audit details Field: `links:family:discovery-model-esm-2` Claim: rewire-local-20260920-configuration-proteingym-esm2-family-discovery-model-esm-2 Source artifact SHA-256: `6a14b3866141d5779c76da8071d85c73b7cce0dc4e101c93122706873e847d26` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-09-22-f58a0f1d267f · Record review: source checked

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ESM-2 8M masked-marginal scoring: local execution report (20 September 2026) · Original source · ca73fa47136d182f2d4ddb083d084712198fc0e2

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Technical metadata and extraction receipts

Stable ID: rewire-local-20260920-configuration-proteingym-esm2

areas: proteins-complexes
source locator: model; model_configuration; execution; environment
configuration: checkpoint: esm2_t6_8M_UR50D; device: cpu; seed: 0; strategy: masked_marginals; threads: 1
execution: adapter: ESM2Adapter; adapter provenance: checkpoint sha256: 46f002a9870c9bdecd0ea887acb1f9a38a6b561e8f8bf8a6990b679b9d31b928; checkpoint url: https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t6_8M_UR50D.pt; device: cpu; fair esm version: 2.0.0; implementation sha256: 4ff38cfbb91d718b52a44da53aa5594fe73d9d1d4d0ce43724807597c3929889; maximum sequence length: 1022; model: esm2_t6_8M_UR50D; published result reproduction: false; strategy: masked_marginals_wild_type_context_sum_log_odds; training overlap: unreported; UniRef50 pretraining may overlap benchmark proteins; batch size: 32; fitting: none; inference and fit seconds: 0.18779424999956973; mode: local_adapter; prediction type: scalar
model: name: ESM-2 esm2_t6_8M_UR50D masked marginals; training overlap: unreported; UniRef50 pretraining may overlap benchmark proteins
environment: architecture: arm64; container digest: unreported; container runtime: unreported; platform: macOS-26.6.2-arm64-arm-64bit; python: 3.11.13; rewirebench: 0.4.0; sdk code sha256: fcc5ab65e6753cf29aabbdae231cbb5cdf72a3dd40ba8f109802c33223b33536; sif sha256: unreported
packages
method role: public model
training overlap: unreported; UniRef50 pretraining may overlap benchmark proteins

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