Dataset

HuRI PPI graph (embedding study)

Evidence concern: excluded from comparisons

The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6

Human Reference Interactome (HuRI) PPI graph (8,248 nodes, 51,813 edges).

Evaluation results

154 evaluations · 154 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GCN with ComplEx protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.792 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ComplEx on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'ComplEx'
Configuration: GCN with ComplEx protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.606 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ComplEx on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'ComplEx'
Configuration: GCN with majority vote across the representations (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.671 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / Ensemble on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'Ensemble'
Configuration: GCN with majority vote across the representations (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.529 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / Ensemble on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'Ensemble'
Configuration: GCN with ESM-2 protein embeddings (sequence) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.702 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ESM-2 on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'ESM-2'
Configuration: GCN with ESM-2 protein embeddings (sequence) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.444 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ESM-2 on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'ESM-2'
Configuration: GCN with ESM-IF1 protein embeddings (structure) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.76 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ESM-IF1 on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'ESM-IF1'
Configuration: GCN with ESM-IF1 protein embeddings (structure) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.497 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ESM-IF1 on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'ESM-IF1'
Configuration: GCN with PiFold protein embeddings (structure) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.704 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / PiFold on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'PiFold'
Configuration: GCN with PiFold protein embeddings (structure) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.457 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / PiFold on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'PiFold'
Configuration: GCN with ProGen2 protein embeddings (sequence) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.715 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ProGen2 on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'ProGen2'
Configuration: GCN with ProGen2 protein embeddings (sequence) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.454 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ProGen2 on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'ProGen2'
Configuration: GCN with ProstT5 protein embeddings (structure) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.65 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ProstT5 on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'ProstT5'
Configuration: GCN with ProstT5 protein embeddings (structure) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.447 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ProstT5 on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'ProstT5'
Configuration: GCN with ProtTrans protein embeddings (sequence) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.675 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ProtTrans on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'ProtTrans'
Configuration: GCN with ProtTrans protein embeddings (sequence) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.45 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / ProtTrans on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'ProtTrans'
Configuration: GCN with randomly initialised node features (baseline) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.7 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / Random on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'Random'
Configuration: GCN with randomly initialised node features (baseline) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.435 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / Random on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'Random'
Configuration: GCN with RDF2Vec protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.799 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / RDF2Vec on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'RDF2Vec'
Configuration: GCN with RDF2Vec protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.651 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / RDF2Vec on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'RDF2Vec'
Configuration: GCN with TransE protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.515 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / TransE on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GCN', column 'TransE'
Configuration: GCN with TransE protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.432 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GCN / TransE on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GCN', column 'TransE'
Configuration: GraphSAGE with ComplEx protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.772 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GraphSAGE / ComplEx on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GS', column 'ComplEx'
Configuration: GraphSAGE with ComplEx protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)	Protocol: HuRI PPI link prediction, Hits@100 (Table 5) Dataset: HuRI PPI graph (embedding study)	0.562 Hits at 100 (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GraphSAGE / ComplEx on HuRI (Hits@100) lit-interactions-20261011-ppiemb-protocol-huri-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'HuRI', row 'GS', column 'ComplEx'
Configuration: GraphSAGE with majority vote across the representations (PPI embeddings study)	Protocol: HuRI PPI link prediction, Accuracy (Table 6) Dataset: HuRI PPI graph (embedding study)	0.622 Accuracy (HuRI PPI link prediction) fraction · higher Uncertainty: Not reported by the source: Only a table-wide maximum SD is printed (Table 5/6 footnote) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons The text's summary does not match the tables: it lists ProtT5 among structure embeddings while the tables print ProstT5; it reports a GraphSAGE with DistMult result (+38% Hits@100 on HuRI) although DistMult is not a column; and the stated gains (for example ESM-2 with GraphSAGE +6% Hits@100 on OGBl-ppa) cannot be reproduced from the printed table values (GS random 0.0104, ESM-2 0.2421). Values are kept as printed; comparisons should rely on the tables only after a reviewer has judged this. Random-feature baselines on OGBl-ppa (GCN 0.0588, GS 0.0104 Hits@100) look far below the public OGB leaderboard values the authors say they reproduced (Supplementary Table S2, not retrieved; reviewer did not verify the leaderboard values).The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Results and discussion, first paragraph; Tables 5 and 6 Methods, coverage and source GraphSAGE / Ensemble on HuRI (Accuracy) lit-interactions-20261011-ppiemb-protocol-huri-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'HuRI', row 'GS', column 'Ensemble'

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Population 8248 nodes; 51 813 edges Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 4; Datasets Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.population` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Table 4; Datasets Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 4; Datasets Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Version HuRI as used in bbag313; release and file in Supplementary Table S1 (not retrieved) Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 4; Datasets Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.version` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Human Reference Interactome (HuRI) PPI graph (8,248 nodes, 51,813 edges). Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 4; Datasets Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name HuRI PPI graph (embedding study) Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 4; Datasets Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `name` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Original source · Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML

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Stable ID: lit-interactions-20261011-ppiemb-data-huri

areas: molecular-interactions; proteins-complexes
contexts: research
version: HuRI as used in bbag313; release and file in Supplementary Table S1 (not retrieved)
population: 8248 nodes; 51 813 edges
source locator: Table 4; Datasets
missing metadata: split: reason: unreported; note: Main text does not describe the HuRI train/test edge split

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