Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
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 evaluationAt a glance
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.
| 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. |
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 evaluationEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.
real_test PPI held-out evaluation · Table 3
Accuracy (fraction) · Higher values are better for this metric.
Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3.
- ESM2_AMPS · Configuration · Author-reported evaluation0.7761
- ESM2_AMP_CSE · Configuration · Author-reported evaluation0.7665
- ESM2_DPM · Configuration · Author-reported evaluation0.7703
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3: Accuracy, real_test PPI held-out evaluationValues, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| ESM2_AMPS · Configuration | 0.7761 fraction | Not reported | Author-reported evaluation · source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column Accuracy; XML row2 column2 |
| ESM2_AMP_CSE · Configuration | 0.7665 fraction | Not reported | Author-reported evaluation · source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMP_CSE, column Accuracy; XML row3 column2 |
| ESM2_DPM · Configuration | 0.7703 fraction | Not reported | Author-reported evaluation · source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_DPM, column Accuracy; XML row4 column2 |
Scope and limitations
- Do not combine with Pan_dataset cross-validation.
- No interval assigned unless printed in source cell.
Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 3 evaluations · 18 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ESM2_DPM: real_test PPI held-out evaluation Configuration: ESM2_DPMProtocol: real_test PPI held-out evaluation (protein-protein interaction prediction)Dataset: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.5733 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_DPM, column MCC; XML row4 column6 Source checking is not independent reproduction. |
| 0.7703 Accuracy Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_DPM, column Accuracy; XML row4 column2 Source checking is not independent reproduction. |
| 0.7767 AUC Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_DPM, column AUC; XML row4 column5 Source checking is not independent reproduction. |
| 0.7023 Precision Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_DPM, column Precision; XML row4 column7 Source checking is not independent reproduction. |
| 0.9358 Recall Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_DPM, column Recall; XML row4 column3 Source checking is not independent reproduction. |
| 0.8024 F1 Score Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_DPM, column F1 Score; XML row4 column4 Source checking is not independent reproduction. |
| ESM2_AMPS: real_test PPI held-out evaluation Configuration: ESM2_AMPSProtocol: real_test PPI held-out evaluation (protein-protein interaction prediction)Dataset: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.7932 AUC Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column AUC; XML row2 column5 Source checking is not independent reproduction. |
| 0.7123 Precision Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column Precision; XML row2 column7 Source checking is not independent reproduction. |
| 0.8045 F1 Score Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column F1 Score; XML row2 column4 Source checking is not independent reproduction. |
| 0.7761 Accuracy Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column Accuracy; XML row2 column2 Source checking is not independent reproduction. |
| 0.5785 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column MCC; XML row2 column6 Source checking is not independent reproduction. |
| 0.9242 Recall Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column Recall; XML row2 column3 Source checking is not independent reproduction. |
| ESM2_AMP_CSE: real_test PPI held-out evaluation Configuration: ESM2_AMP_CSEProtocol: real_test PPI held-out evaluation (protein-protein interaction prediction)Dataset: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.5628 MCC Unit: dimensionless · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMP_CSE, column MCC; XML row3 column6 Source checking is not independent reproduction. |
| 0.7981 F1 Score Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMP_CSE, column F1 Score; XML row3 column4 Source checking is not independent reproduction. |
| 0.8064 AUC Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMP_CSE, column AUC; XML row3 column5 Source checking is not independent reproduction. |
| 0.7665 Accuracy Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMP_CSE, column Accuracy; XML row3 column2 Source checking is not independent reproduction. |
| 0.9258 Recall Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMP_CSE, column Recall; XML row3 column3 Source checking is not independent reproduction. |
| 0.7014 Precision Unit: fraction · Direction: higher | Uncertainty: unreported Scored: Not reported · Eligible: Not reported | source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMP_CSE, column Precision; XML row3 column7 Source checking is not 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 |
What is still missing
- 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
Strengths and limitations
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-1edc32c80b0223fef1Evidence 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
| 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 Table 3: Accuracy, real_test PPI held-out evaluation Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| 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 Table 3: Accuracy, real_test PPI held-out evaluation Version: version of record | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: evaluates task reported-task-09c3100b77dcc5 Individual claims | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Table 3: Accuracy, real_test PPI held-out evaluation Version: version of record | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-0b3716556a8f360491 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-d277315f7d76 · 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
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