Model type
Protein sequence transformer; this record is the paper-specific evaluated configuration.
Pipeline
ESM2 OFS pseudo-perplexity
One Fell Swoop approximates ESM-2 pseudo-perplexity from a single unmasked-sequence embedding pass.
Sources
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluationHow it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluationAt a glance
Biological inputs
Protein sequence and unmasked ESM-2 residue embeddings
Sources
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluationOutputs
Approximate residue probability profiles and OFS pseudo-perplexity
Sources
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluationlimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ESM2 OFS pseudo-perplexity: protein variant fitness prediction Pipeline: ESM2 OFS pseudo-perplexityTask: protein variant fitness predictionDataset: ProteinGym substitutions authors’ zero-shot ESM2 OFS pseudo-perplexity evaluation; aggregate mean across ProteinGym substitution assays Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.403 Spearman rho Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedPseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Published PDF page 6 (033014-6), Table I, ESM2: OFS PP row, Aggregate mean column Source checking is not independent reproduction. |
How it works
How the evaluated method works
Eight multilayer perceptrons map last-layer ESM-2 650M residue embeddings to the masked residue probability profiles that would otherwise require repeated model passes.
Sources
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluationUnderlying method and version boundaries
ESM-2 is a transformer protein language-model family. The official repository exposes residue embeddings, sequence-level pooling and models at several sizes; the study configuration determines which of these is evaluated.
Sources
facebookresearch/esm README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies ESM2 OFS pseudo-perplexity: protein variant fitness prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-b2-esm2-ofs-fitness-2025Strengths and limitations
Strengths and considerations
- Reduces repeated encoder passes while retaining an approximation to the sequence-wide masked profile.
Sources
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation
Limitations and conditions
- The output is an approximation, not exact pseudo-perplexity; the paper reports task-specific trade-offs against other mutation-scoring heuristics.
Sources
Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-40ce004270dee4Specifications
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.
| Property | Description and evidence |
|---|---|
| Model type | Protein sequence transformer; this record is the paper-specific evaluated configuration.Sourcesfacebookresearch/esm README.md · README.md model description |
| Architecture / procedure | Eight multilayer perceptrons map last-layer ESM-2 650M residue embeddings to the masked residue probability profiles that would otherwise require repeated model passes.SourcesPseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation |
| Biological inputs | Protein sequence and unmasked ESM-2 residue embeddingsSourcesPseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation |
| Outputs | Approximate residue probability profiles and OFS pseudo-perplexitySourcesPseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation |
| Parameters | 650-million-parameter ESM-2 encoder plus a 7-million-parameter OFS ensemble.SourcesPseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation |
| Known versions / configuration | ESM2 OFS pseudo-perplexity is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesPseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | Cluster-representative sequences provide one-at-a-time masked profiles for a cross-entropy distillation objective.SourcesPseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation |
| Context limits | A maximum input/context length for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation; facebookresearch/esm README.md · Complete primary text and named comparison table; inspected for explicit maximum input length (dataset lengths and family-wide limits are not substituted); README.md at pinned repository revision |
| Access | Official upstream implementation and usage documentation: https://github.com/facebookresearch/esm/blob/2b369911bb5b4b0dda914521b9475cad1656b2ac/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourcesfacebookresearch/esm README.md · README.md; installation, model download and usage instructions |
| Code licence | MIT (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourcesfacebookresearch/esm LICENSE · LICENSE; complete licence text |
| Weights licence | The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. · Not reported in inspected sourcesSourcesfacebookresearch/esm README.md · README.md; checkpoint/access documentation and licence scope |
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.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation Version: PRX Life 2025 journal article | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Protein sequence and unmasked ESM-2 residue embeddings","ESM2 OFS pseudo-perplexity","Approximate residue probability profiles and OFS pseudo-perplexity"] Individual claims | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation Version: PRX Life 2025 journal article | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation Version: PRX Life 2025 journal article | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type Protein sequence transformer; this record is the paper-specific evaluated configuration. Individual claims | facebookresearch/esm README.md README.md model description Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure Eight multilayer perceptrons map last-layer ESM-2 650M residue embeddings to the masked residue probability profiles that would otherwise require repeated model passes. Individual claims | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation Version: PRX Life 2025 journal article | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence The inspected model-access documentation does not explicitly identify terms for this exact evaluated checkpoint or fitted head; repository code terms are shown separately. Individual claims | facebookresearch/esm README.md README.md; checkpoint/access documentation and licence scope Version: 2b369911bb5b4b0dda914521b9475cad1656b2ac | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Protein sequence and unmasked ESM-2 residue embeddings Individual claims | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation Version: PRX Life 2025 journal article | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Approximate residue probability profiles and OFS pseudo-perplexity Individual claims | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation Version: PRX Life 2025 journal article | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters 650-million-parameter ESM-2 encoder plus a 7-million-parameter OFS ensemble. Individual claims | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation Version: PRX Life 2025 journal article | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Known versions / configuration ESM2 OFS pseudo-perplexity is the comparison-table label; that label does not specify an immutable weight revision. Individual claims | Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. Version: PRX Life 2025 journal article | unreported automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation · Original source · PRX Life 2025 journal article
- facebookresearch/esm README.md · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
- facebookresearch/esm LICENSE · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
Technical metadata and extraction receipts
Stable ID: reported-model-40ce004270dee4
- areas
- proteins-complexes
- entity level
- method
- version
- not stated in table
- reported name
- ESM2 OFS pseudo-perplexity
- historical missing metadata
- checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: not_reported_in_legacy_extract
- 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.
- legacy kinds
- model
- entity classification
- review date: 2026-09-17; rationale: This record identifies a composed analysis workflow with separately identifiable upstream models, representations or tools and a downstream prediction/scoring procedure. Results belong to that complete composition rather than to an upstream model alone.; source ids: esm2-ofs-fitness-2025; evidence-reported-base-esm-readme-md; source locator: Section III, One Fell Swoop; Figure 1; Section IV fitness evaluation | README.md model description; ambiguities: This is the paper-specific pipeline identity; unspecified component checkpoints or implementation versions are not inferred from its name.