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 results

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

Inputs

Single amino-acid sequences.

Outputs

Residue embeddings, sequence representations and masked-token predictions.

Access

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

Sources (3)

limited source coverage · Automated source review, 2026-09-23. All specifications and missing details

Evaluations and results

1 evaluation · 5 results. 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	0.44 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 2026-09-25-8af07e960e5f.

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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 and considerations

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

Follow-up review of Reference checkpoint, Context limits, Training data release, Training cutoff. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied.

Stable record: discovery-model-esm-2

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-23. 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 inspected official table establishes an April 2021 UniRef release, but no separate latest-deposited-sequence date. Keep the corpus release distinct from a temporal leakage guarantee. · Not reported in inspected sources Sources facebookresearch/esm: README.md · README: Pre-trained Models and Pre-training Dataset Split
Context limits	The official extraction script truncates to 1,022 residues by default; --truncation_seq_length is configurable. This workflow default is not a universal architecture or validated biological-context limit. Sources esm2 extract: primary artifact · create_parser: --truncation_seq_length; run: get_batch_converter
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
Reference checkpoint	Example release: facebook/esm2_t33_650M_UR50D at 08e4846e537177426273712802403f7ba8261b6c. Its model.safetensors has registry-reported SHA-256 a08adabb949fa67ad3c14b509d04fd60368b35007b0095e3358f81200c4f4db0. This identifies a downloadable 650M checkpoint, not every ESM-2 evaluation. Sources esm2 release: primary artifact · sha; siblings[model.safetensors].lfs.sha256
Training data release	The official pretrained-model table labels ESM-2 training data UR50/D 2021_04. Sources facebookresearch/esm: README.md · README: Pre-trained Models table, ESM-2 rows

Evidence

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Evidence table

Inspect claims, sources and review details

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

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-25-8af07e960e5f
Property and statement	Original source and location	Review and provenance
Relationship: family catalog-model-esm-2 Individual claims	ESM-2 8M masked-marginal scoring: local execution report (20 September 2026) Original source ↗ report.json: model.checkpoint and artifacts checkpoint_url/checkpoint_sha256; esm2_t6_8M_UR50D Version: ca73fa47136d182f2d4ddb083d084712198fc0e2 Retrieved: 2026-09-20T20:54:03Z	source checked automated source review · 2026-09-23 Audit details Source review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Pinned run report explicitly identifies the 8M checkpoint and exact weight hash. Preserve masked-marginal ProteinGym assay protocol; this supports the size-qualified8M record without aliasing650M/15B variants. Field: `links:family:catalog-model-esm-2` Claim: model-evaluation-identity-e3db6ecc999ab32164a3 Source artifact SHA-256: `6a14b3866141d5779c76da8071d85c73b7cce0dc4e101c93122706873e847d26` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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 2026-09-25-8af07e960e5f · Record review: source checked

1 source records and release history

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: None recorded
method role: public model
training overlap: unreported; UniRef50 pretraining may overlap benchmark proteins

Related records

family: ESM-2
family: ESM-2
subject: ESM-2 8M masked-marginal scoring (ProteinGym v1.3 AMFR substitution assay): family ESM-2
subject: The executed esm2_t6_8M_UR50D checkpoint is an ESM-2 family member; only this exact scoring configuration is evaluated.
configuration: ESM-2 8M masked-marginal scoring on ProteinGym v1.3 AMFR substitution assay

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