Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction)
Pan_dataset five-fold PPI cross-validation · Table 2. ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2: Accuracy, Pan_dataset five-fold PPI cross-validationAt a glance
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.
How it works
Evaluation in this paper
ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.
ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2: Accuracy, Pan_dataset five-fold PPI cross-validationEvaluation 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.
Pan_dataset five-fold PPI cross-validation · Table 2
Accuracy (fraction) · Higher values are better for this metric.
ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.
Evaluation protocol · Pan_dataset five-fold PPI cross-validation
- ESM2_AMPS · Configuration · Author-reported evaluation0.9776
- ESM2_AMP_CSE · Configuration · Author-reported evaluation0.9787
- ESM2_DPM · Configuration · Author-reported evaluation0.9802
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 2: Accuracy, Pan_dataset five-fold PPI cross-validationValues, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| ESM2_AMPS · Configuration | 0.9776 fraction | Not reported | Author-reported evaluation · source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMPS, column Accuracy; XML row2 column2 |
| ESM2_AMP_CSE · Configuration | 0.9787 fraction | Not reported | Author-reported evaluation · source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMP_CSE, column Accuracy; XML row3 column2 |
| ESM2_DPM · Configuration | 0.9802 fraction | Not reported | Author-reported evaluation · source checkedESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_DPM, column Accuracy; XML row4 column2 |
Scope and limitations
- Do not combine with real_test or Bernett splits.
- 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 · 15 metric rows. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| ESM2_DPM: Pan_dataset five-fold PPI cross-validation Configuration: ESM2_DPMProtocol: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction)Dataset: Pan_dataset five-fold PPI cross-validation ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.9801 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 2, row ESM2_DPM, column F1 Score; XML row4 column4 Source checking is not independent reproduction. |
| 0.9959 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 2, row ESM2_DPM, column AUC; XML row4 column5 Source checking is not independent reproduction. |
| 0.9605 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 2, row ESM2_DPM, column MCC; XML row4 column6 Source checking is not independent reproduction. |
| 0.9802 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 2, row ESM2_DPM, column Accuracy; XML row4 column2 Source checking is not independent reproduction. |
| 0.9738 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 2, row ESM2_DPM, column Recall; XML row4 column3 Source checking is not independent reproduction. |
| ESM2_AMP_CSE: Pan_dataset five-fold PPI cross-validation Configuration: ESM2_AMP_CSEProtocol: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction)Dataset: Pan_dataset five-fold PPI cross-validation ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.9937 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 2, row ESM2_AMP_CSE, column AUC; XML row3 column5 Source checking is not independent reproduction. |
| 0.974 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 2, row ESM2_AMP_CSE, column Recall; XML row3 column3 Source checking is not independent reproduction. |
| 0.9574 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 2, row ESM2_AMP_CSE, column MCC; XML row3 column6 Source checking is not independent reproduction. |
| 0.9786 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 2, row ESM2_AMP_CSE, column F1 Score; XML row3 column4 Source checking is not independent reproduction. |
| 0.9787 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 2, row ESM2_AMP_CSE, column Accuracy; XML row3 column2 Source checking is not independent reproduction. |
| ESM2_AMPS: Pan_dataset five-fold PPI cross-validation Configuration: ESM2_AMPSProtocol: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction)Dataset: Pan_dataset five-fold PPI cross-validation ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.9949 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 2, row ESM2_AMPS, column AUC; XML row2 column5 Source checking is not independent reproduction. |
| 0.9553 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 2, row ESM2_AMPS, column MCC; XML row2 column6 Source checking is not independent reproduction. |
| 0.9776 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 2, row ESM2_AMPS, column Accuracy; XML row2 column2 Source checking is not independent reproduction. |
| 0.9775 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 2, row ESM2_AMPS, column F1 Score; XML row2 column4 Source checking is not independent reproduction. |
| 0.9708 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 2, row ESM2_AMPS, column Recall; XML row2 column3 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 2: Accuracy, Pan_dataset five-fold PPI cross-validation
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-be1c9eab950fb814ecEvidence table
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 ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation. Individual claims | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Table 2: Accuracy, Pan_dataset five-fold PPI cross-validation 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 Pan_dataset five-fold PPI cross-validation · Table 2. ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation. Individual claims | ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Table 2: Accuracy, Pan_dataset five-fold PPI cross-validation 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 2: Accuracy, Pan_dataset five-fold PPI cross-validation Version: version of record | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-614dda00c2d286b40f Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: needs review
- 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-be1c9eab950fb814ec
- areas
- molecular-interactions
- tasks
- protein-protein interaction prediction
- entity level
- protocol
- protocol
- ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.
- comparison panels
- id: part2-esm2-amp-2025-TB2-bcfa7fd935; title: Pan_dataset five-fold PPI cross-validation · Table 2; protocol id: paper-protocol-be1c9eab950fb814ec; dataset id: paper-dataset-1de23e14845ef72241; metric: Accuracy; unit: fraction; direction: higher; result ids: paper-result-849a689bb863da7b89; paper-result-ad1bca4f43523769b0; paper-result-95b8985c40d7060b18; source ids: part2-esm2-amp-2025; source locator: Table 2: Accuracy, Pan_dataset five-fold PPI cross-validation; context: ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.; caveats: Do not combine with real_test or Bernett splits.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB2-080c760521; title: Pan_dataset five-fold PPI cross-validation · Table 2; protocol id: paper-protocol-be1c9eab950fb814ec; dataset id: paper-dataset-1de23e14845ef72241; metric: Recall; unit: fraction; direction: higher; result ids: paper-result-d7ca453d8394415cf3; paper-result-6596ff3ab5a5186dd5; paper-result-d9f6f8b8dce18dabdc; source ids: part2-esm2-amp-2025; source locator: Table 2: Recall, Pan_dataset five-fold PPI cross-validation; context: ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.; caveats: Do not combine with real_test or Bernett splits.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB2-34516e10b1; title: Pan_dataset five-fold PPI cross-validation · Table 2; protocol id: paper-protocol-be1c9eab950fb814ec; dataset id: paper-dataset-1de23e14845ef72241; metric: F1 Score; unit: fraction; direction: higher; result ids: paper-result-b95e4f473396a4ec4a; paper-result-a7f701de866be03f45; paper-result-080bcca9522a063c76; source ids: part2-esm2-amp-2025; source locator: Table 2: F1 Score, Pan_dataset five-fold PPI cross-validation; context: ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.; caveats: Do not combine with real_test or Bernett splits.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB2-a76b0f5e92; title: Pan_dataset five-fold PPI cross-validation · Table 2; protocol id: paper-protocol-be1c9eab950fb814ec; dataset id: paper-dataset-1de23e14845ef72241; metric: AUC; unit: fraction; direction: higher; result ids: paper-result-65a00f3c782a024fa3; paper-result-29145ccafb7fa248fb; paper-result-4138022a44ce806e42; source ids: part2-esm2-amp-2025; source locator: Table 2: AUC, Pan_dataset five-fold PPI cross-validation; context: ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.; caveats: Do not combine with real_test or Bernett splits.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-esm2-amp-2025-TB2-c4db9319dd; title: Pan_dataset five-fold PPI cross-validation · Table 2; protocol id: paper-protocol-be1c9eab950fb814ec; dataset id: paper-dataset-1de23e14845ef72241; metric: MCC; unit: dimensionless; direction: higher; result ids: paper-result-7158b83512c200c2b8; paper-result-7317681be4f0a4ac94; paper-result-5695f2aceef2d88e83; source ids: part2-esm2-amp-2025; source locator: Table 2: MCC, Pan_dataset five-fold PPI cross-validation; context: ESM 2_AMPS, ESM 2_AMP_CSE and ESM 2_DPM evaluated as complete PPI pipelines. Pan_dataset; Table 2 five-fold cross-validation.; caveats: Do not combine with real_test or Bernett splits.; 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 2: Accuracy, Pan_dataset five-fold PPI cross-validation; 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 2: Accuracy, Pan_dataset five-fold PPI cross-validation; ambiguities: None recorded
Related records
- evaluates task: protein-protein interaction prediction
- subject: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction): links:evaluates_task:reported-task-09c3100b77dcc5
- benchmark: ESM2_DPM: Pan_dataset five-fold PPI cross-validation
- benchmark: ESM2_AMPS: Pan_dataset five-fold PPI cross-validation
- benchmark: ESM2_AMP_CSE: Pan_dataset five-fold PPI cross-validation