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GCN with PiFold protein embeddings (structure) (PPI embeddings 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

GCN with PiFold protein embeddings (structure): GCN; node features: PiFold protein embeddings (structure).

4 evaluations · 4 results

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Evaluations and results

4 evaluations · 4 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (HuRI PPI link prediction) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Accuracy (HuRI PPI link prediction)	Accuracy (OGBl-ppa PPI link prediction)	Hits at 100 (HuRI PPI link prediction)	Hits at 100 (OGBl-ppa PPI link prediction)
GCN with PiFold protein embeddings (structure) (PPI embeddings study)Evaluation	HuRI PPI link prediction, Accuracy (Table 6), HuRI PPI graph (embedding study)	0.704	Not reported	Not reported	Not reported
GCN with PiFold protein embeddings (structure) (PPI embeddings study)Evaluation	HuRI PPI link prediction, Hits@100 (Table 5), HuRI PPI graph (embedding study)	Not reported	Not reported	0.457	Not reported
GCN with PiFold protein embeddings (structure) (PPI embeddings study)Evaluation	OGBl-ppa PPI link prediction, Accuracy (Table 6), OGBl-ppa PPI graph (embedding study)	Not reported	0.899	Not reported	Not reported
GCN with PiFold protein embeddings (structure) (PPI embeddings study)Evaluation	OGBl-ppa PPI link prediction, Hits@100 (Table 5), OGBl-ppa PPI graph (embedding study)	Not reported	Not reported	Not reported	0.189

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Tested configuration	Protocol and dataset	Finding	Evidence and details
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 PiFold protein embeddings (structure) (PPI embeddings study)	Protocol: OGBl-ppa PPI link prediction, Accuracy (Table 6) Dataset: OGBl-ppa PPI graph (embedding study)	0.899 Accuracy (OGBl-ppa 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 OGBl-ppa (Accuracy) lit-interactions-20261011-ppiemb-protocol-ogbl-ppa-accuracy Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 6, block 'OGBl-ppa', row 'GCN', column 'PiFold'
Configuration: GCN with PiFold protein embeddings (structure) (PPI embeddings study)	Protocol: OGBl-ppa PPI link prediction, Hits@100 (Table 5) Dataset: OGBl-ppa PPI graph (embedding study)	0.189 Hits at 100 (OGBl-ppa 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 OGBl-ppa (Hits@100) lit-interactions-20261011-ppiemb-protocol-ogbl-ppa-hits-100 Aggregation: Not reported The role of protein embeddings for protein-protein interaction prediction with graph neural networks · Table 5, block 'OGBl-ppa', row 'GCN', column 'PiFold'

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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-config-gcn-pifold

areas: molecular-interactions; proteins-complexes
contexts: research
method types: foundation_model
reported name: GCN / PiFold
foundation model eligible: true
parameters: GCN; node features: PiFold protein embeddings (structure). Leaderboard hyperparameters reproduced for OGBl-ppa (Experimental design).
source locator: Tables 5 and 6, row 'GCN', column 'PiFold'
access reuse: Not stated in the source
missing metadata: version: reason: unreported; note: Embedding and GNN parameters are in Supplementary Tables S3, S5-S7, not retrieved
provenance note: GCN using PiFold protein embeddings (structure), as evaluated for PPI prediction.

Related records

configuration of: GCN
uses model: PiFold
system: GCN / PiFold on HuRI (Accuracy)
system: GCN / PiFold on HuRI (Hits@100)
system: GCN / PiFold on OGBl-ppa (Accuracy)
system: GCN / PiFold on OGBl-ppa (Hits@100)

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