Evaluation

GraphSAGE / PiFold on OGBl-ppa (Hits@100)

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

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GraphSAGE 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)	0.209 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 GraphSAGE / 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 'GS', column 'PiFold'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Evaluation procedure

OGBl-ppa PPI link prediction, Hits@100 (Table 5)

Configuration: GraphSAGE 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)

origin: Independent external evaluation
configuration: Primary source as retrieved 2026-10-11
protocol id: lit-interactions-20261011-ppiemb-protocol-ogbl-ppa-hits-100
dataset version: bbag313
split: Benchmark test edges
population: Not reported
inputs: PPI graph with structure node features
adaptation: Trained by the study authors
metric implementation: Hits@100 as printed
aggregation: Not reported
budget: Not reported

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Benchmark test edges
Adaptation: Trained by the study authors
Scoring implementation: Hits@100 as printed

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

18 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Comparison: adaptation Trained by the study authors Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: aggregation Not reported Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: budget Not reported Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: dataset version bbag313 Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: inputs PPI graph with structure node features Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: metric implementation Hits@100 as printed Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: population Not reported Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	missing or unspecified No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: protocol id lit-interactions-20261011-ppiemb-protocol-ogbl-ppa-hits-100 Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison: split Benchmark test edges Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Origin independent_paper Context-only references	The role of protein embeddings for protein-protein interaction prediction with graph neural networks Original source ↗ Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold' Version: Briefings in Bioinformatics 2026, bbag313; PMC13280947 full-text XML Retrieved: 2026-10-11T21:27:23Z	not individually reviewed No individual claim review recorded independent paper Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.origin` Source artifact SHA-256: `360d4f17b779e07f170c3f0c3755bfbfddd064831bf5a81d2642a4cfffd4866c` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

How to read the evidence

Sources and history

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

1 source record and release history

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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Technical metadata and extraction receipts

Stable ID: lit-interactions-20261011-ppiemb-eval-gs-pifold-ogbl-ppa-hits-100

areas: molecular-interactions; proteins-complexes
contexts: research
origin: independent_paper
protocol: lit-interactions-20261011-ppiemb-protocol-ogbl-ppa-hits-100
version: Primary source as retrieved 2026-10-11
comparison: protocol id: lit-interactions-20261011-ppiemb-protocol-ogbl-ppa-hits-100; dataset version: bbag313; split: Benchmark test edges; population: Not reported; inputs: PPI graph with structure node features; adaptation: Trained by the study authors; metric implementation: Hits@100 as printed; aggregation: Not reported; budget: Not reported
source locator: Table 5, block 'OGBl-ppa', row 'GS', column 'PiFold'
missing metadata: comparison.aggregation: reason: unreported; comparison.budget: reason: unreported; comparison.population: reason: unreported

Related records

system: GraphSAGE with PiFold protein embeddings (structure) (PPI embeddings study)
assessment: OGBl-ppa PPI link prediction, Hits@100 (Table 5)
data: OGBl-ppa PPI graph (embedding study)
evaluation: GS PiFold OGBl-ppa Hits@100

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