Model type
Protein sequence transformer; this record is the paper-specific evaluated configuration.
Pipeline
ESM2_AMPS
ESM2_AMPS predicts binary protein–protein interactions by combining segment-level ESM-2 features.
Sources
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Construction of dual models based on feature integration (paragraph 3); Results/Attention mechanism reveal protein–protein interaction mechanism (paragraph 1)How 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
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Interpretability analysis utilizing attention mechanisms (paragraph 1); Methods/Construction of dual models based on feature integration (paragraph 3)At a glance
Biological inputs
Pairs of protein sequences
Sources
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Results/Attention mechanism reveal protein–protein interaction mechanism (paragraph 1); Results/Benchmarking evaluation for ESM2_AMP on PPIs prediction (paragraph 1)Outputs
Binary protein–protein interaction predictions
Sources
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Overview of ESM2_AMP framework (paragraph 1); Results/Benchmarking evaluation for ESM2_AMP on PPIs prediction (paragraph 1)limited 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_AMPS: protein-protein interaction prediction ESM2-derived embeddings plus paper interaction predictor Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.68 AUROC Unit: fraction · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 4, ESM2_AMPS row, AUROC column Source checking is not independent reproduction. |
How it works
How the evaluated method works
ESM-2 produces representations of sequence segments; a transformer fuses the segment information for interaction prediction. AMPS is the segment-feature variant and is distinct from the special-token-combination variant.
Sources
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Interpretability analysis utilizing attention mechanisms (paragraph 1); Methods/Construction of dual models based on feature integration (paragraph 3)Underlying 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_AMPS: protein-protein interaction prediction. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-b4-024Strengths and limitations
Strengths and considerations
- Segment attention can be inspected alongside known functional regions.
Sources
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Identification and computational methods of functional amino acid regions (paragraph 4); Results/Correlation between feature attribution value and functional amino acid regions (paragraph 7)
Limitations and conditions
- Attention alignment with annotated domains is an association, not proof of the causal interaction mechanism; random-pair and strict-protein splits are different evaluations.
Sources
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Feature extraction and fusion method (paragraph 4); Methods/Construction of dual models based on feature integration (paragraph 2)
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-67ea6bd77b2ed1Specifications
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 | ESM-2 produces representations of sequence segments; a transformer fuses the segment information for interaction prediction. AMPS is the segment-feature variant and is distinct from the special-token-combination variant.SourcesESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Interpretability analysis utilizing attention mechanisms (paragraph 1); Methods/Construction of dual models based on feature integration (paragraph 3) |
| Biological inputs | Pairs of protein sequencesSourcesESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Results/Attention mechanism reveal protein–protein interaction mechanism (paragraph 1); Results/Benchmarking evaluation for ESM2_AMP on PPIs prediction (paragraph 1) |
| Outputs | Binary protein–protein interaction predictionsSourcesESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Overview of ESM2_AMP framework (paragraph 1); Results/Benchmarking evaluation for ESM2_AMP on PPIs prediction (paragraph 1) |
| Parameters | An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sourcesSources (2)ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery; facebookresearch/esm README.md · Methods/Protein–protein interaction datasets; Methods/Overview of ESM2_AMP framework; Methods/Feature extraction and fusion method; Methods/Construction of dual models based on feature integration; Methods/Methodology for model training and performance evaluation; Methods/Interpretability analysis utilizing attention mechanisms; Methods/Autoencoder model construction and feature importance calculation methods; Methods/Identification and computational methods of functional amino acid regions; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision |
| Known versions / configuration | ESM2_AMPS is the comparison-table label; that label does not specify an immutable weight revision. · Not reported in inspected sourcesSourcesESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Model identification in the comparison table and corresponding Methods; immutable checkpoint revision is not supplied by the table label. |
| Training data / fitting | Pan and Bernett human PPI datasets with separate evaluation schemes, plus a curated real_test set; similarity filtering is described for independence checks.SourcesESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Protein–protein interaction datasets (paragraph 1); Methods/Protein–protein interaction datasets (paragraph 2) |
| Context limits | Proteins between 15 and 4,000 residues are retained in the Pan dataset preparation.SourcesESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Methods/Identification and computational methods of functional amino acid regions (paragraph 1); Methods/Protein–protein interaction datasets (paragraph 1) |
| 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 | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Methods/Interpretability analysis utilizing attention mechanisms (paragraph 1); Methods/Construction of dual models based on feature integration (paragraph 3) Version: version of record | 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 ["Pairs of protein sequences","ESM2_AMPS","Binary protein–protein interaction predictions"] Individual claims | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Methods/Interpretability analysis utilizing attention mechanisms (paragraph 1); Methods/Construction of dual models based on feature integration (paragraph 3) Version: version of record | 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 | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Methods/Interpretability analysis utilizing attention mechanisms (paragraph 1); Methods/Construction of dual models based on feature integration (paragraph 3) Version: version of record | 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 ESM-2 produces representations of sequence segments; a transformer fuses the segment information for interaction prediction. AMPS is the segment-feature variant and is distinct from the special-token-combination variant. Individual claims | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Methods/Interpretability analysis utilizing attention mechanisms (paragraph 1); Methods/Construction of dual models based on feature integration (paragraph 3) Version: version of record | 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 Pairs of protein sequences Individual claims | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Results/Attention mechanism reveal protein–protein interaction mechanism (paragraph 1); Results/Benchmarking evaluation for ESM2_AMP on PPIs prediction (paragraph 1) Version: version of record | 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 Binary protein–protein interaction predictions Individual claims | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Methods/Overview of ESM2_AMP framework (paragraph 1); Results/Benchmarking evaluation for ESM2_AMP on PPIs prediction (paragraph 1) Version: version of record | 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 An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Methods/Protein–protein interaction datasets; Methods/Overview of ESM2_AMP framework; Methods/Feature extraction and fusion method; Methods/Construction of dual models based on feature integration; Methods/Methodology for model training and performance evaluation; Methods/Interpretability analysis utilizing attention mechanisms; Methods/Autoencoder model construction and feature importance calculation methods; Methods/Identification and computational methods of functional amino acid regions; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: version of record | 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 |
| Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims | facebookresearch/esm README.md Methods/Protein–protein interaction datasets; Methods/Overview of ESM2_AMP framework; Methods/Feature extraction and fusion method; Methods/Construction of dual models based on feature integration; Methods/Methodology for model training and performance evaluation; Methods/Interpretability analysis utilizing attention mechanisms; Methods/Autoencoder model construction and feature importance calculation methods; Methods/Identification and computational methods of functional amino acid regions; inspected for aggregate parameter count (component sizes are not added without an exact configuration); README.md at pinned repository revision Shared locator for this statement’s cited sources; not a separate locator for each citation. 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 |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
3 source records and release history
- ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Original source · version of record
- facebookresearch/esm README.md · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
- facebookresearch/esm LICENSE · Original source · 2b369911bb5b4b0dda914521b9475cad1656b2ac
Technical metadata and extraction receipts
Stable ID: reported-model-67ea6bd77b2ed1
- areas
- molecular-interactions
- entity level
- method
- version
- Not reported
- reported name
- ESM2_AMPS
- historical missing metadata
- version: not_reported_in_legacy_extract; 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-amp-2025; evidence-reported-base-esm-readme-md; source locator: Methods/Interpretability analysis utilizing attention mechanisms (paragraph 1); Methods/Construction of dual models based on feature integration (paragraph 3) | README.md model description | Methods/Construction of dual models based on feature integration (paragraph 3); Results/Attention mechanism reveal protein–protein interaction mechanism (paragraph 1); ambiguities: This is the paper-specific pipeline identity; unspecified component checkpoints or implementation versions are not inferred from its name.