Configuration

ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)

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 · 2 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 · 2 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-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)	Protocol: FLIP2 Rhomax by_wild_type Dataset subset: FLIP2 Rhomax by_wild_type test subset	0.907 ndcg dimensionless · higher Uncertainty: Not reported Coverage: 184/184	Rewire evaluation · Source checked Methods, coverage and source ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) on FLIP2 Rhomax by_wild_type FLIP2 Rhomax by_wild_type Aggregation: Not reported ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report; ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): audit · metrics.ndcg
Configuration: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)	Protocol: FLIP2 Rhomax by_wild_type Dataset subset: FLIP2 Rhomax by_wild_type test subset	-0.222 spearman dimensionless · higher Uncertainty: Not reported Coverage: 184/184	Rewire evaluation · Source checked Methods, coverage and source ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) on FLIP2 Rhomax by_wild_type FLIP2 Rhomax by_wild_type Aggregation: Not reported ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report; ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): audit · metrics.spearman

Source checking is not independent reproduction. Release 2026-09-28-c7b5ac6d34f2.

Use this model

How it works, versions and access

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

This configuration

Frozen features with a fixed alpha-10 ridge head fitted only on training rows; all 184 Rhomax by_wild_type held-out proteins scored. This selected split is not a whole FLIP2 score.

record: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)
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

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-28-c7b5ac6d34f2
Property and statement	Original source and location	Review and provenance
Relationship: family discovery-model-esm-2 Individual claims	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report Original source ↗ model_configuration.checkpoint; model.name Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	source checked automated execution evidence review · 2026-09-22T21:18:22Z Audit details Field: `links:family:discovery-model-esm-2` Claim: rewire-local-20260921-configuration-esm2-35m-family Source artifact SHA-256: `29d7c0ae7f47d45861a769eb8813bf8c650c9a95b3a6821c524b216b0b907ef0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

Release 2026-09-28-c7b5ac6d34f2 · Record review: source checked

2 source records and release history

ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): audit · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191

Download this release

Technical metadata and extraction receipts

Stable ID: rewire-local-20260921-configuration-esm2-35m

areas: proteins-complexes
source locator: model; model_configuration; protocol_configuration.embedding_probe; execution
configuration: checkpoint: esm2_t12_35M_UR50D; device: cpu; dimension: 480; encoder frozen: true; head: alpha: 10; feature scaling: none; fit intercept: true; max iter: 1000000; name: rewire-frozen-embedding-ridge-v1; refit: train only; relationship to published baseline: Frozen-embedding extension of upstream alpha-10 ridge. The published baseline uses one-hot features and scales targets using train plus validation rows. This extension is not that published baseline.; solver: auto; target scaling: StandardScaler fitted only on train labels; tol: 0.00001; validation use: none; fixed hyperparameters; pooling: mean over residues excluding BOS/EOS and padding; representation layer: 12; scope: one complete Rhomax split, not FLIP2 suite; torch seed: 0; torch threads: 4; validation used: false
execution: adapter: ESM2Embeddings; adapter provenance: checkpoint sha256: 7f21e80e61d16a71735163ef555d3009afb0c98da74c48e29df08606973cc55e; checkpoint url: https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t12_35M_UR50D.pt; device: cpu; fair esm version: 2.0.0; implementation sha256: bb46676af95050012cf0bf8a8309581b400f660d2722519889693f4084559d73; maximum sequence length: 1022; model: esm2_t12_35M_UR50D; published result reproduction: false; reference: https://github.com/facebookresearch/esm/blob/2b369911bb5b4b0dda914521b9475cad1656b2ac/README.md#usage; representation layer: 12; strategy: frozen_final_layer_residue_mean_excluding_special_tokens; training overlap: unreported; UniRef50 pretraining may overlap benchmark proteins; batch size: 4; fitting: protocol_owned_probe; inference and fit seconds: 64.14407666699844; mode: local_adapter; prediction type: embedding
model: name: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire); training overlap: UniRef50 pretraining overlap is unreported; the linear head fits only archived training rows
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: 08cbbaac2aa8f60af5c43af7a83410e9690b44c5e4d162fbe1e5766885952fce; sif sha256: unreported
training overlap: UniRef50 pretraining overlap is unreported; the linear head fits only archived training rows
method role: frozen pretrained encoder plus trained regression head

Related records

family: ESM-2
subject: Evaluated ESM-2 checkpoint belongs to ESM-2
configuration: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) on FLIP2 Rhomax by_wild_type

Suggest a correction