Dataset

FUJISAN test sub-dataset

Evaluation results

5 evaluations · 40 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: FUJISAN	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.943 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FUJISAN: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features; Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, FUJISAN row, AUROC column
Configuration: ESM2	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.799 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM2: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features; Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, ESM2 row, AUROC column
Configuration: E-value	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	78.6% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source E-value: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column PRE (%); XML row3 column3
Configuration: FUJISAN	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	87% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FUJISAN: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row FUJISAN, column REC (%); XML row2 column4
Configuration: ESM2	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	79.3% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM2: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column REC (%); XML row5 column4
Configuration: E-value	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.829 F1 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source E-value: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column F1; XML row3 column6
Configuration: ESM2	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.815 AUPRC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM2: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column AUPR; XML row5 column9
Configuration: FUJISAN	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.742 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FUJISAN: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row FUJISAN, column MCC; XML row2 column7
Configuration: DeepFRI	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	83.2% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepFRI: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column REC (%); XML row4 column4
Configuration: Pfam	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	62% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pfam: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column ACC (%); XML row6 column2
Configuration: E-value	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.643 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source E-value: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column MCC; XML row3 column7
Configuration: DeepFRI	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	80.9% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepFRI: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column ACC (%); XML row4 column2
Configuration: ESM2	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.432 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM2: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column MCC; XML row5 column7
Configuration: DeepFRI	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.679 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepFRI: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column MCC; XML row4 column7
Configuration: Pfam	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.352 MCC unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pfam: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column MCC; XML row6 column7
Configuration: Pfam	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	56.9% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pfam: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column PRE (%); XML row6 column3
Configuration: E-value	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	23.9% False positive rate percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source E-value: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column FPR (%); XML row3 column5
Configuration: E-value	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	87.8% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source E-value: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column REC (%); XML row3 column4
Configuration: Pfam	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.722 F1 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pfam: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column F1; XML row6 column6
Configuration: E-value	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	81.9% Accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source E-value: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column ACC (%); XML row3 column2
Configuration: DeepFRI	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	0.814 F1 unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepFRI: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column F1; XML row4 column6
Configuration: Pfam	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	74.6% False positive rate percent · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pfam: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column FPR (%); XML row6 column5
Configuration: FUJISAN	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	87.2% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FUJISAN: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row FUJISAN, column PRE (%); XML row2 column3
Configuration: Pfam	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	98.6% Recall percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Pfam: Enzyme-pair functional identity: original held-out test LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column REC (%); XML row6 column4
Configuration: ESM2	Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) Dataset: FUJISAN test sub-dataset	68.4% Precision percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ESM2: Enzyme functional identity prediction LightGBM FUJISAN and comparison methods; predictions thresholded to maximizeF 1. Protein-pair splitting is not evidence of disjoint proteins or families. 41,600 protein pairs; balanced functional-identity classes; random 56.25/18.75/25% training/validation/test split. Aggregation: Not reported Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column PRE (%); XML row5 column3

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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
Description No value recorded Context-only references	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-16T10:33:35.728Z	missing or unspecified No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name FUJISAN test sub-dataset Context-only references	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ No field-specific location recorded Version: PMC11609699.1 Retrieved: 2026-09-16T10:33:35.728Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Enhanced prediction of protein functional identity through the integration of sequence and structural features · Original source · PMC11609699.1

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Stable ID: reported-dataset-5197cca532f89d

areas: proteins-complexes
missing metadata: accession: reason: unextracted; split: reason: unextracted; version: reason: unextracted
entity classification: review date: 2026-09-17; rationale: This record identifies a biological data collection or source-labelled evaluation cohort. Keep its dataset identity; split, assay, taxonomic level, candidate restrictions and comparison context remain attributes rather than automatically becoming new entity kinds.; source ids: fujisan-2024; source locator: Methods: Dataset construction; classification and metrics; Results: model comparison; cached text lines 10–11, 25, 28, 52, 55; uncertainty/repeat-run/statistical-comparison passages; ambiguities: The name suggests a selected cohort, but this record has no verified parent-dataset relationship or independently pinned membership manifest. Retain dataset rather than infer a new parent/subset identity from its name alone.

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