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ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery

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DOI: 10.1093/bib/bbaf434 Original source

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3 configurations
1 task
2 protocols
2 datasets
6 evaluations
33 results
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Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction): links:evaluates_task:reported-task-09c3100b77dcc5: Evaluates task protein-protein interaction prediction (Table 2: Accuracy, Pan_dataset five-fold PPI cross-validation)
real_test PPI held-out evaluation (protein-protein interaction prediction): links:evaluates_task:reported-task-09c3100b77dcc5: Evaluates task protein-protein interaction prediction (Table 3: Accuracy, real_test PPI held-out evaluation)

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Configurations (3)

Tasks (1)

protein-protein interaction prediction

Protocols (2)

Datasets (2)

Evaluations (6)

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Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Artifact SHA-256 8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12392411/fullTextXML Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Doi 10.1093/bib/bbaf434 Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Hash scope Exact retrieved primary paper artifact bytes. Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.hash_scope` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Retrieved at 2026-09-17T07:56:12.275470+00:00 Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review method 1 values automated-source-review Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.method` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Review: scope Source identification and table transcription; no independent experimental reproduction. Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.review.scope` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12392411/fullTextXML Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Version version of record Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Primary reference; inspect retrieval status and review scope. Source metadata	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ No field-specific location recorded Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	catalogued No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Stable ID: part2-esm2-amp-2025

url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12392411/fullTextXML
doi: 10.1093/bib/bbaf434
version: version of record
retrieved at: 2026-09-17T07:56:12.275470+00:00
artifact sha256: 8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c
artifact url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12392411/fullTextXML
hash scope: Exact retrieved primary paper artifact bytes.
review: scope: Source identification and table transcription; no independent experimental reproduction.; method: automated-source-review

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Model or configuration	Metric	Value	Dataset	Evaluation
ESM2_AMP_CSE	Accuracy	0.9787 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_AMP_CSE: Pan_dataset five-fold PPI cross-validation
ESM2_AMP_CSE	AUROC	0.9937 unitless	Pan_dataset five-fold PPI cross-validation	ESM2_AMP_CSE: Pan_dataset five-fold PPI cross-validation
ESM2_AMP_CSE	F1	0.9786 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_AMP_CSE: Pan_dataset five-fold PPI cross-validation
ESM2_AMP_CSE	MCC	0.9574 unitless	Pan_dataset five-fold PPI cross-validation	ESM2_AMP_CSE: Pan_dataset five-fold PPI cross-validation
ESM2_AMP_CSE	Recall	0.974 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_AMP_CSE: Pan_dataset five-fold PPI cross-validation
ESM2_AMP_CSE	Accuracy	0.7665 fraction	real_test PPI held-out evaluation	ESM2_AMP_CSE: real_test PPI held-out evaluation
ESM2_AMP_CSE	AUROC	0.8064 unitless	real_test PPI held-out evaluation	ESM2_AMP_CSE: real_test PPI held-out evaluation
ESM2_AMP_CSE	F1	0.7981 fraction	real_test PPI held-out evaluation	ESM2_AMP_CSE: real_test PPI held-out evaluation
ESM2_AMP_CSE	MCC	0.5628 unitless	real_test PPI held-out evaluation	ESM2_AMP_CSE: real_test PPI held-out evaluation
ESM2_AMP_CSE	Precision	0.7014 fraction	real_test PPI held-out evaluation	ESM2_AMP_CSE: real_test PPI held-out evaluation
ESM2_AMP_CSE	Recall	0.9258 fraction	real_test PPI held-out evaluation	ESM2_AMP_CSE: real_test PPI held-out evaluation
ESM2_AMPS	Accuracy	0.9776 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_AMPS: Pan_dataset five-fold PPI cross-validation
ESM2_AMPS	AUROC	0.9949 unitless	Pan_dataset five-fold PPI cross-validation	ESM2_AMPS: Pan_dataset five-fold PPI cross-validation
ESM2_AMPS	F1	0.9775 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_AMPS: Pan_dataset five-fold PPI cross-validation
ESM2_AMPS	MCC	0.9553 unitless	Pan_dataset five-fold PPI cross-validation	ESM2_AMPS: Pan_dataset five-fold PPI cross-validation
ESM2_AMPS	Recall	0.9708 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_AMPS: Pan_dataset five-fold PPI cross-validation
ESM2_AMPS	Accuracy	0.7761 fraction	real_test PPI held-out evaluation	ESM2_AMPS: real_test PPI held-out evaluation
ESM2_AMPS	AUROC	0.7932 unitless	real_test PPI held-out evaluation	ESM2_AMPS: real_test PPI held-out evaluation
ESM2_AMPS	F1	0.8045 fraction	real_test PPI held-out evaluation	ESM2_AMPS: real_test PPI held-out evaluation
ESM2_AMPS	MCC	0.5785 unitless	real_test PPI held-out evaluation	ESM2_AMPS: real_test PPI held-out evaluation
ESM2_AMPS	Precision	0.7123 fraction	real_test PPI held-out evaluation	ESM2_AMPS: real_test PPI held-out evaluation
ESM2_AMPS	Recall	0.9242 fraction	real_test PPI held-out evaluation	ESM2_AMPS: real_test PPI held-out evaluation
ESM2_DPM	Accuracy	0.9802 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_DPM: Pan_dataset five-fold PPI cross-validation
ESM2_DPM	AUROC	0.9959 unitless	Pan_dataset five-fold PPI cross-validation	ESM2_DPM: Pan_dataset five-fold PPI cross-validation
ESM2_DPM	F1	0.9801 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_DPM: Pan_dataset five-fold PPI cross-validation
ESM2_DPM	MCC	0.9605 unitless	Pan_dataset five-fold PPI cross-validation	ESM2_DPM: Pan_dataset five-fold PPI cross-validation
ESM2_DPM	Recall	0.9738 fraction	Pan_dataset five-fold PPI cross-validation	ESM2_DPM: Pan_dataset five-fold PPI cross-validation
ESM2_DPM	Accuracy	0.7703 fraction	real_test PPI held-out evaluation	ESM2_DPM: real_test PPI held-out evaluation
ESM2_DPM	AUROC	0.7767 unitless	real_test PPI held-out evaluation	ESM2_DPM: real_test PPI held-out evaluation
ESM2_DPM	F1	0.8024 fraction	real_test PPI held-out evaluation	ESM2_DPM: real_test PPI held-out evaluation
ESM2_DPM	MCC	0.5733 unitless	real_test PPI held-out evaluation	ESM2_DPM: real_test PPI held-out evaluation
ESM2_DPM	Precision	0.7023 fraction	real_test PPI held-out evaluation	ESM2_DPM: real_test PPI held-out evaluation
ESM2_DPM	Recall	0.9358 fraction	real_test PPI held-out evaluation	ESM2_DPM: real_test PPI held-out evaluation