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ESM2_AMPS

ESM2_AMPS as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label

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ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMPS, column Accuracy; XML row2 column2

2 evaluations · 11 results

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

Evaluations and results

2 evaluations · 11 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM2_AMPS	Protocol: real_test PPI held-out evaluation (protein-protein interaction prediction) Dataset: real_test PPI held-out evaluation	0.793 AUC fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column AUC; XML row2 column5
Configuration: ESM2_AMPS	Protocol: real_test PPI held-out evaluation (protein-protein interaction prediction) Dataset: real_test PPI held-out evaluation	0.712 Precision fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column Precision; XML row2 column7
Configuration: ESM2_AMPS	Protocol: real_test PPI held-out evaluation (protein-protein interaction prediction) Dataset: real_test PPI held-out evaluation	0.804 F1 Score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column F1 Score; XML row2 column4
Configuration: ESM2_AMPS	Protocol: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction) Dataset: Pan_dataset five-fold PPI cross-validation	0.995 AUC fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: 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. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMPS, column AUC; XML row2 column5
Configuration: ESM2_AMPS	Protocol: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction) Dataset: Pan_dataset five-fold PPI cross-validation	0.955 MCC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: 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. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMPS, column MCC; XML row2 column6
Configuration: ESM2_AMPS	Protocol: real_test PPI held-out evaluation (protein-protein interaction prediction) Dataset: real_test PPI held-out evaluation	0.776 Accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column Accuracy; XML row2 column2
Configuration: ESM2_AMPS	Protocol: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction) Dataset: Pan_dataset five-fold PPI cross-validation	0.978 Accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: 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. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMPS, column Accuracy; XML row2 column2
Configuration: ESM2_AMPS	Protocol: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction) Dataset: Pan_dataset five-fold PPI cross-validation	0.978 F1 Score fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: 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. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMPS, column F1 Score; XML row2 column4
Configuration: ESM2_AMPS	Protocol: real_test PPI held-out evaluation (protein-protein interaction prediction) Dataset: real_test PPI held-out evaluation	0.579 MCC dimensionless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column MCC; XML row2 column6
Configuration: ESM2_AMPS	Protocol: real_test PPI held-out evaluation (protein-protein interaction prediction) Dataset: real_test PPI held-out evaluation	0.924 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: real_test PPI held-out evaluation Complete trained PPI pipelines evaluated on real_test. Paper real_test dataset; Table 3. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 3, row ESM2_AMPS, column Recall; XML row2 column3
Configuration: ESM2_AMPS	Protocol: Pan_dataset five-fold PPI cross-validation (protein-protein interaction prediction) Dataset: Pan_dataset five-fold PPI cross-validation	0.971 Recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESM2_AMPS: 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. Aggregation: Not reported ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMPS, column Recall; XML row2 column3

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Paper-specific evaluated pipeline; exact checkpoint not inferred from label

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ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery · Table 2, row ESM2_AMPS, column Accuracy; XML row2 column2

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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 Paper-specific evaluated pipeline; exact checkpoint not inferred from label Individual claims	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ Table 2, row ESM2_AMPS, column Accuracy; XML row2 column2 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 ESM2_AMPS as evaluated in the cited study. Paper-specific evaluated pipeline; exact checkpoint not inferred from label Individual claims	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ Table 2, row ESM2_AMPS, column Accuracy; XML row2 column2 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: uses model discovery-model-esm-2 Individual claims	ESM2_AMP: an interpretable framework for protein–protein interactions prediction and biological mechanism discovery Original source ↗ Methods: ESM2_AMPS and Transformer fusion of ESM2 segment features Version: version of record Retrieved: 2026-09-16T10:33:58.625Z	source checked automated source review · 2026-09-23 Audit details Source review establishes this relationship only. Exact evaluated configurations and original numerical review status remain unchanged. Source describes ESM-2 as an encoder/backbone/component of the evaluated estimator. Preserve the composite method as uses_model, not a family-equivalent ESM-2 score. Field: `links:uses_model:discovery-model-esm-2` Claim: model-evaluation-identity-81fa1c91c722f30e12dd Source artifact SHA-256: `8e7ad6efb72ca28d73037cdf465b0e62f99cd6d0ee4ca9eaf96a4c48da22fd6c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Stable ID: paper-model-1818d535d17a5ccea8

areas: molecular-interactions
tasks: protein-protein interaction prediction
entity level: method
configuration type: reported_configuration
version: Paper-specific evaluated pipeline; exact checkpoint not inferred from label
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: part2-esm2-amp-2025; source locator: Table 2, row ESM2_AMPS, column Accuracy; XML row2 column2; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

Related records

uses model: ESM-2
subject: ESM2_AMPS: uses model ESM-2
model: ESM2_AMPS: Pan_dataset five-fold PPI cross-validation
model: ESM2_AMPS: real_test PPI held-out evaluation

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