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.

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

5 evaluations · 40 metric rows

At 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

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.

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

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Tasks

Enzyme functional identity prediction

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.

Comparison and metric

Enzyme-pair functional identity: original held-out test · Table 1

ACC (%) (percent) · Higher values are better for this metric.

Evaluation protocol · FUJISAN test sub-dataset

FUJISAN · Configuration · Author-reported evaluation87.05
E-value · Configuration · Author-reported evaluation81.91
DeepFRI · Configuration · Author-reported evaluation80.88
ESM2 · Configuration · Independent external evaluation71.33
Pfam · Configuration · Author-reported evaluation61.99

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.

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

Values, uncertainty and evidence

ACC (%): original source values
Tested entity	Printed value	Uncertainty	Evidence
FUJISAN · Configuration	87.05 percent	Not reported	Author-reported evaluation · source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row FUJISAN, column ACC (%); XML row2 column2
E-value · Configuration	81.91 percent	Not reported	Author-reported evaluation · source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column ACC (%); XML row3 column2
DeepFRI · Configuration	80.88 percent	Not reported	Author-reported evaluation · source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column ACC (%); XML row4 column2
ESM2 · Configuration	71.33 percent	Not reported	Independent external evaluation · source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column ACC (%); XML row5 column2
Pfam · Configuration	61.99 percent	Not reported	Author-reported evaluation · source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column ACC (%); XML row6 column2

Scope and limitations

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.

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 · 5 evaluations · 40 metric rows. Different protocols are not a single leaderboard.

Evaluation setupMetricEvidence origin

Results grouped by the exact reported evaluation
Metric and finding	Coverage and uncertainty	Evidence
FUJISAN: Enzyme functional identity prediction Configuration: FUJISANProtocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)Dataset: FUJISAN test sub-dataset 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. Author-reported evaluation · Evaluation metadata: needs review
0.9427 AUROC Unit: unitless · Direction: higher	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedEnhanced 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 Source checking is not independent reproduction.
87.05% REC (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row FUJISAN, column REC (%); XML row2 column4 Source checking is not independent reproduction.
0.7421 MCC Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row FUJISAN, column MCC; XML row2 column7 Source checking is not independent reproduction.
87.24% PRE (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row FUJISAN, column PRE (%); XML row2 column3 Source checking is not independent reproduction.
ESM2: Enzyme functional identity prediction Configuration: ESM2Protocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)Dataset: FUJISAN test sub-dataset 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. Independent external evaluation · Evaluation metadata: needs review
0.7991 AUROC Unit: unitless · Direction: higher	Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported	source checkedEnhanced 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 Source checking is not independent reproduction.
79.33% REC (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column REC (%); XML row5 column4 Source checking is not independent reproduction.
0.8147 AUPR Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column AUPR; XML row5 column9 Source checking is not independent reproduction.
0.4321 MCC Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column MCC; XML row5 column7 Source checking is not independent reproduction.
68.39% PRE (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row ESM2, column PRE (%); XML row5 column3 Source checking is not independent reproduction.
E-value: Enzyme-pair functional identity: original held-out test Configuration: E-valueProtocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)Dataset: FUJISAN test sub-dataset 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. Author-reported evaluation · Evaluation metadata: needs review
78.58% PRE (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column PRE (%); XML row3 column3 Source checking is not independent reproduction.
0.8291 F1 Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column F1; XML row3 column6 Source checking is not independent reproduction.
0.6427 MCC Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column MCC; XML row3 column7 Source checking is not independent reproduction.
23.92% FPR (%) Unit: percent · Direction: lower	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column FPR (%); XML row3 column5 Source checking is not independent reproduction.
87.75% REC (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column REC (%); XML row3 column4 Source checking is not independent reproduction.
81.91% ACC (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row E-value, column ACC (%); XML row3 column2 Source checking is not independent reproduction.
DeepFRI: Enzyme-pair functional identity: original held-out test Configuration: DeepFRIProtocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)Dataset: FUJISAN test sub-dataset 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. Author-reported evaluation · Evaluation metadata: needs review
83.16% REC (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column REC (%); XML row4 column4 Source checking is not independent reproduction.
80.88% ACC (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column ACC (%); XML row4 column2 Source checking is not independent reproduction.
0.6790 MCC Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column MCC; XML row4 column7 Source checking is not independent reproduction.
0.8143 F1 Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row DeepFRI, column F1; XML row4 column6 Source checking is not independent reproduction.
Pfam: Enzyme-pair functional identity: original held-out test Configuration: PfamProtocol: Enzyme-pair functional identity: original held-out test (Enzyme functional identity prediction)Dataset: FUJISAN test sub-dataset 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. Author-reported evaluation · Evaluation metadata: needs review
61.99% ACC (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column ACC (%); XML row6 column2 Source checking is not independent reproduction.
0.3520 MCC Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column MCC; XML row6 column7 Source checking is not independent reproduction.
56.92% PRE (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column PRE (%); XML row6 column3 Source checking is not independent reproduction.
0.7217 F1 Unit: dimensionless · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column F1; XML row6 column6 Source checking is not independent reproduction.
74.62% FPR (%) Unit: percent · Direction: lower	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column FPR (%); XML row6 column5 Source checking is not independent reproduction.
98.60% REC (%) Unit: percent · Direction: higher	Uncertainty: unreported Scored: Not reported · Eligible: Not reported	source checkedEnhanced prediction of protein functional identity through the integration of sequence and structural features · Table 1, row Pfam, column REC (%); XML row6 column4 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
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

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

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

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

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-7088bcc2f0033b8a29

Evidence 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

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
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 Original source ↗ Table 1: ACC (%), Enzyme-pair functional identity: original held-out test Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+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: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
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 Original source ↗ Table 1: ACC (%), Enzyme-pair functional identity: original held-out test Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+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: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Relationship: evaluates task reported-task-1ebf9b408517f9 Individual claims	Enhanced prediction of protein functional identity through the integration of sequence and structural features Original source ↗ Table 1: ACC (%), Enzyme-pair functional identity: original held-out test Version: PMC11609699.1 Retrieved: 2026-09-17T07:56:15.783679+00:00	source checked automated source review · 2026-09-17 Audit details Field: `links:evaluates_task:reported-task-1ebf9b408517f9` Claim: paper-claim-e1867c79e926ac2e28 Source artifact SHA-256: `db33e0542005ffae00cd644dfe697185b94c8823d5aee2768620a6db0c48e56f` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

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

Download this release

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

Suggest a correction