Protocol

real_test PPI held-out evaluation (protein-protein interaction prediction)

real_test PPI held-out evaluation · Table 3. Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.

Sources

ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3: Accuracy, real_test PPI held-out evaluation

3 evaluations · 18 results

Overview

Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.

limited source coverage · Automated source review, 2026-09-17. All specifications and missing details

Results

Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.

Evaluation scope and datasetMetric and reported setup

real_test PPI held-out evaluation · Table 3

Accuracy (fraction) · Higher values are better.

real_test PPI held-out evaluation (protein-protein interaction prediction) · real_test PPI held-out evaluation

Evidence origin: Author-reported evaluation.

ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3: Accuracy, real_test PPI held-out evaluation

Do not combine with Pan_dataset cross-validation.

Comparison details and limitations

Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.

No interval assigned unless printed in source cell.

Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.

Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.

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Tested configuration

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Reported score

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Evaluation in this paper

Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.

Sources

ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3: Accuracy, real_test PPI held-out evaluation

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Tasks

protein-protein interaction prediction

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Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

No reviewed evaluations with results linked in this release.

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

No source-reviewed explanatory claims are recorded here yet.

Profile review details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Stable record: paper-protocol-1edc32c80b0223fef1

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Datasets	Not extracted or verified for this record.
Organisms	Not extracted or verified for this record.
Assays	Not extracted or verified for this record.
Splits	Not extracted or verified for this record.
Allowed inputs	Not extracted or verified for this record.
Adaptation	Not extracted or verified for this record.
Metrics	Not extracted or verified for this record.
Baselines	Not extracted or verified for this record.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.

Paper or primary resource	Version	Reference
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery	version of record	Read source DOI: 10.1093/bib/bbaf434

Historical gaps recorded on 2026-09-17

The catalogue now holds 18 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.

Independent batch review before import; preserve existing observation identities.

Search and extraction details

complete comparison tables extracted pending publication review

Searches

ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery primary paper benchmark results

Evidence locations

Table 3: Accuracy, real_test PPI held-out evaluation

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.

3 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Evaluation in this paper Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Individual claims	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ Table 3: Accuracy, real_test PPI held-out evaluation Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Introduction real_test PPI held-out evaluation · Table 3. Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Individual claims	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ Table 3: Accuracy, real_test PPI held-out evaluation Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Relationship: evaluates task reported-task-09c3100b77dcc5 Individual claims	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ Table 3: Accuracy, real_test PPI held-out evaluation Version: version of record Retrieved: 2026-09-17T07:56:12.275470+00:00	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:reported-task-09c3100b77dcc5` Claim: paper-claim-0b3716556a8f360491 Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: needs review

1 source records and release history

ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Original source · version of record

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Technical metadata and extraction receipts

Stable ID: paper-protocol-1edc32c80b0223fef1

areas: molecular-interactions
tasks: protein-protein interaction prediction
entity level: protocol
protocol: Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.
comparison panels: id: part2-esm2-amp-2025-TB3-8efc06a1fc; title: real_test PPI held-out evaluation · Table 3; protocol id: paper-protocol-1edc32c80b0223fef1; dataset id: paper-dataset-a825ad55756b359150; metric: Accuracy; unit: fraction; direction: higher; result ids: paper-result-790e874858cc08f657; paper-result-99ad6e202a567da653; paper-result-6680db966a9d1e35b4; source ids: part2-esm2-amp-2025; source locator: Table 3: Accuracy, real_test PPI held-out evaluation; context: Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.; caveats: Do not combine with Pan_dataset cross-validation.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB3-43ece4a25b; title: real_test PPI held-out evaluation · Table 3; protocol id: paper-protocol-1edc32c80b0223fef1; dataset id: paper-dataset-a825ad55756b359150; metric: Recall; unit: fraction; direction: higher; result ids: paper-result-d6524b05023c42db9b; paper-result-f7a3d9ed37399b3a37; paper-result-ba3011fe28c284b86b; source ids: part2-esm2-amp-2025; source locator: Table 3: Recall, real_test PPI held-out evaluation; context: Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.; caveats: Do not combine with Pan_dataset cross-validation.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB3-639b23627b; title: real_test PPI held-out evaluation · Table 3; protocol id: paper-protocol-1edc32c80b0223fef1; dataset id: paper-dataset-a825ad55756b359150; metric: F1 Score; unit: fraction; direction: higher; result ids: paper-result-4f97fb035451eba1c6; paper-result-64ba0415593df539d7; paper-result-fa217cc5798f8af105; source ids: part2-esm2-amp-2025; source locator: Table 3: F1 Score, real_test PPI held-out evaluation; context: Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.; caveats: Do not combine with Pan_dataset cross-validation.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB3-8425c57523; title: real_test PPI held-out evaluation · Table 3; protocol id: paper-protocol-1edc32c80b0223fef1; dataset id: paper-dataset-a825ad55756b359150; metric: AUC; unit: fraction; direction: higher; result ids: paper-result-3753a3981ea1aeabec; paper-result-888e32ae1ab2ab63d6; paper-result-71f635574e69fdb267; source ids: part2-esm2-amp-2025; source locator: Table 3: AUC, real_test PPI held-out evaluation; context: Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.; caveats: Do not combine with Pan_dataset cross-validation.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB3-52c0496256; title: real_test PPI held-out evaluation · Table 3; protocol id: paper-protocol-1edc32c80b0223fef1; dataset id: paper-dataset-a825ad55756b359150; metric: MCC; unit: dimensionless; direction: higher; result ids: paper-result-c79f5ab35255cb8020; paper-result-4819f0b5707a3da216; paper-result-337efc2e5382ae31b9; source ids: part2-esm2-amp-2025; source locator: Table 3: MCC, real_test PPI held-out evaluation; context: Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.; caveats: Do not combine with Pan_dataset cross-validation.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB3-52c4c639e8; title: real_test PPI held-out evaluation · Table 3; protocol id: paper-protocol-1edc32c80b0223fef1; dataset id: paper-dataset-a825ad55756b359150; metric: Precision; unit: fraction; direction: higher; result ids: paper-result-3fe2b44a09889f8fb9; paper-result-f8339dba99e6d18757; paper-result-7361fa18276a31b368; source ids: part2-esm2-amp-2025; source locator: Table 3: Precision, real_test PPI held-out evaluation; context: Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.; caveats: Do not combine with Pan_dataset cross-validation.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17
benchmark research: review date: 2026-09-17; status: complete_comparison_tables_extracted_pending_publication_review; primary sources: part2-esm2-amp-2025; inspected locators: Table 3: Accuracy, real_test PPI held-out evaluation; searched queries: ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery primary paper benchmark results; gaps: Independent batch review before import; preserve existing observation identities.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
legacy kinds: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: part2-esm2-amp-2025; source locator: Table 3: Accuracy, real_test PPI held-out evaluation; ambiguities: None recorded

Related records

evaluates task: protein-protein interaction prediction
subject: real_test PPI held-out evaluation (protein-protein interaction prediction): links:evaluates_task:reported-task-09c3100b77dcc5
benchmark: ESM2_DPM: real_test PPI held-out evaluation
benchmark: ESM2_AMP_CSE: real_test PPI held-out evaluation
benchmark: ESM2_AMPS: real_test PPI held-out evaluation

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