Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)
Enzyme-pair functional identity: original held-out test · Table 1. 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.
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1: ACC (%), Enzyme-pair functional identity: original held-out testOverview
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.
Enzyme-pair functional identity: original held-out test · Table 1
ACC (%) (percent) · Higher values are better.
Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction) · FUJISAN test sub-dataset
Evidence origin: Author-reported evaluation, Independent external evaluation.
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1: ACC (%), Enzyme-pair functional identity: original held-out test- Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.
- Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.
Comparison details and limitations
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.
- 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.
Showing 5 of 5 matching rows.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation in this paper
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.
Sources
Enhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1: ACC (%), Enzyme-pair functional identity: original held-out testEvaluation design
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Baseline coverage
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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
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Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
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Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-7088bcc2f0033b8a29Specifications
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. |
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 |
|---|---|---|
| Enhanced prediction of protein functional identity through the integration of sequence and structural features | PMC11609699.1 | Read source DOI: 10.1016/j.csbj.2024.11.028 |
Historical gaps recorded on 2026-09-17
The catalogue now holds 40 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
- Enhanced prediction of protein functional identity through the integration of sequence and structural features primary paper benchmark results
Evidence locations
- Table 1: ACC (%), Enzyme-pair functional identity: original held-out test
Evidence table
Inspect claims, sources and review details
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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 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. Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Table 1: ACC (%), Enzyme-pair functional identity: original held-out test Version: PMC11609699.1 | 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 Enzyme-pair functional identity: original held-out test · Table 1. 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. Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Table 1: ACC (%), Enzyme-pair functional identity: original held-out test Version: PMC11609699.1 | 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-1ebf9b408517f9 Individual claims | Enhanced prediction of protein functional identity through the integration of sequence and structural features Table 1: ACC (%), Enzyme-pair functional identity: original held-out test Version: PMC11609699.1 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-e1867c79e926ac2e28 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- Enhanced prediction of protein functional identity through the integration of sequence and structural features · Original source · PMC11609699.1
Technical metadata and extraction receipts
Stable ID: paper-protocol-7088bcc2f0033b8a29
- areas
- proteins-complexes
- tasks
- Enzyme functional identity prediction
- entity level
- protocol
- protocol
- 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.
- comparison panels
- id: part2-fujisan-2024-tbl0005-bac8a6d22a; title: Enzyme-pair functional identity: original held-out test · Table 1; protocol id: paper-protocol-7088bcc2f0033b8a29; dataset id: reported-dataset-5197cca532f89d; metric: ACC (%); unit: percent; direction: higher; result ids: paper-result-eaf1d6c59a5f36f4ce; paper-result-7a33f77a25091433d2; paper-result-357d8f3b2935e06e3d; paper-result-b621ec294f38d3f19c; paper-result-23786f6a1a92179f21; source ids: part2-fujisan-2024; source locator: Table 1: ACC (%), Enzyme-pair functional identity: original held-out test; context: 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.; caveats: Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.; Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-fujisan-2024-tbl0005-8cc77c9aa4; title: Enzyme-pair functional identity: original held-out test · Table 1; protocol id: paper-protocol-7088bcc2f0033b8a29; dataset id: reported-dataset-5197cca532f89d; metric: PRE (%); unit: percent; direction: higher; result ids: paper-result-989a4675188b8141c2; paper-result-003d7035891e68f095; paper-result-b6bde99a5fd8fcf312; paper-result-a18d074f2077ce82f8; paper-result-5c36a73bb7912f46bb; source ids: part2-fujisan-2024; source locator: Table 1: PRE (%), Enzyme-pair functional identity: original held-out test; context: 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.; caveats: Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.; Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-fujisan-2024-tbl0005-3714094960; title: Enzyme-pair functional identity: original held-out test · Table 1; protocol id: paper-protocol-7088bcc2f0033b8a29; dataset id: reported-dataset-5197cca532f89d; metric: REC (%); unit: percent; direction: higher; result ids: paper-result-0081b12c9bb122c13a; paper-result-71abecaef7ab30d471; paper-result-21390f8f107e3d5169; paper-result-0d3498cab7dbd41b99; paper-result-9907ce062be9dbd488; source ids: part2-fujisan-2024; source locator: Table 1: REC (%), Enzyme-pair functional identity: original held-out test; context: 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.; caveats: Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.; Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-fujisan-2024-tbl0005-a129b9c665; title: Enzyme-pair functional identity: original held-out test · Table 1; protocol id: paper-protocol-7088bcc2f0033b8a29; dataset id: reported-dataset-5197cca532f89d; metric: FPR (%); unit: percent; direction: lower; result ids: paper-result-ff3b35eac39b7fa2ed; paper-result-6e46bf4f05ccae3dff; paper-result-a36c2ff5211b482ac8; paper-result-c478bf21db79f9c0fa; paper-result-95850ea0b3b65d0a9f; source ids: part2-fujisan-2024; source locator: Table 1: FPR (%), Enzyme-pair functional identity: original held-out test; context: 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.; caveats: Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.; Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-fujisan-2024-tbl0005-0b4696dd22; title: Enzyme-pair functional identity: original held-out test · Table 1; protocol id: paper-protocol-7088bcc2f0033b8a29; dataset id: reported-dataset-5197cca532f89d; metric: F1; unit: dimensionless; direction: higher; result ids: paper-result-ef58d0787535e7e9a5; paper-result-113e4214c6249dc3c8; paper-result-895a3e38bb00f10f4a; paper-result-b5897e7fb2d9f17e8c; paper-result-73d717fd51d9b2682a; source ids: part2-fujisan-2024; source locator: Table 1: F1, Enzyme-pair functional identity: original held-out test; context: 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.; caveats: Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.; Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-fujisan-2024-tbl0005-d782fec4a4; title: Enzyme-pair functional identity: original held-out test · Table 1; protocol id: paper-protocol-7088bcc2f0033b8a29; dataset id: reported-dataset-5197cca532f89d; metric: MCC; unit: dimensionless; direction: higher; result ids: paper-result-1ebedcb0adb7517e54; paper-result-3559edcbf93633cc0d; paper-result-58038afdc07c1aada5; paper-result-46452dcfe78a4f3d04; paper-result-5ac77bcc4aed51f516; source ids: part2-fujisan-2024; source locator: Table 1: MCC, Enzyme-pair functional identity: original held-out test; context: 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.; caveats: Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.; Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-fujisan-2024-tbl0005-d1fced1a9c; title: Enzyme-pair functional identity: original held-out test · Table 1; protocol id: paper-protocol-7088bcc2f0033b8a29; dataset id: reported-dataset-5197cca532f89d; metric: AUROC; unit: unitless; direction: higher; result ids: lit-019; paper-result-d2f325ea0c890b170d; paper-result-b0dd968f641a7e8f16; lit-020; paper-result-b29f561ff4e41c3215; source ids: part2-fujisan-2024; source locator: Table 1: AUROC, Enzyme-pair functional identity: original held-out test; context: 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.; caveats: Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.; Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.; No interval assigned unless printed in source cell.; review: method: automated_source_review; date: 2026-09-17; id: part2-fujisan-2024-tbl0005-f8b070cff8; title: Enzyme-pair functional identity: original held-out test · Table 1; protocol id: paper-protocol-7088bcc2f0033b8a29; dataset id: reported-dataset-5197cca532f89d; metric: AUPR; unit: dimensionless; direction: higher; result ids: paper-result-baae3f4bd4e7d2eb06; paper-result-c9d11b0a9461bd483c; paper-result-ddfb253a50cc5308a8; paper-result-1dc6f9c6ff21f4263a; paper-result-f9f63e4d253b1af323; source ids: part2-fujisan-2024; source locator: Table 1: AUPR, Enzyme-pair functional identity: original held-out test; context: 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.; caveats: Input information differs: sequence similarity, protein embeddings, structure-aware descriptors and domain annotations.; Table1 reports point values;50bootstrap iterations described elsewhere do not establish a Table1 interval.; 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-fujisan-2024; inspected locators: Table 1: ACC (%), Enzyme-pair functional identity: original held-out test; searched queries: Enhanced prediction of protein functional identity through the integration of sequence and structural features 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-fujisan-2024; source locator: Table 1: ACC (%), Enzyme-pair functional identity: original held-out test; ambiguities: None recorded
Related records
- evaluates task: Enzyme functional identity prediction
- benchmark: FUJISAN: Enzyme functional identity prediction
- benchmark: ESM2: Enzyme functional identity prediction
- subject: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction): links:evaluates_task:reported-task-1ebf9b408517f9
- benchmark: E-value: Enzyme-pair functional identity: original held-out test
- benchmark: DeepFRI: Enzyme-pair functional identity: original held-out test
- benchmark: Pfam: Enzyme-pair functional identity: original held-out test