MLP protein-only PPI baseline
Binary PPI classifier: an MLP on concatenated protein embeddings, with no network information (ablation for RQ3).
Results are recorded on linked configurations and versions of this method. Their settings and evaluations are kept separate below.
Results on linked records
This method has no results of its own in this release. 11 linked records have results. They are not assigned to the underlying method: each record keeps its own settings and evaluations, and its scores are on its own page.
- MLP on concatenated protein embeddings (protein-only baseline, no network) with ComplEx protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with majority vote across the representations (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with ESM-2 protein embeddings (sequence) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with ESM-IF1 protein embeddings (structure) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with PiFold protein embeddings (structure) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with ProGen2 protein embeddings (sequence) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with ProstT5 protein embeddings (structure) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with ProtTrans protein embeddings (sequence) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with randomly initialised node features (baseline) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with RDF2Vec protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with TransE protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study) Configuration · configuration · 4 evaluations · 4 results
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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
Technical metadata and extraction receipts
Stable ID: lit-interactions-20261011-ppiemb-method-ppi-mlp-protein-only-baseline
- areas
- molecular-interactions; proteins-complexes
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- MLP
- entity level
- method
- source locator
- Experimental design; Tables 5 and 6 row labels
- missing metadata
- version: reason: unreported; note: GNN parameters are in Supplementary Table S7, not retrieved
Related records
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with ComplEx protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with majority vote across the representations (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with ESM-2 protein embeddings (sequence) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with ESM-IF1 protein embeddings (structure) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with PiFold protein embeddings (structure) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with ProGen2 protein embeddings (sequence) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with ProstT5 protein embeddings (structure) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with ProtTrans protein embeddings (sequence) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with randomly initialised node features (baseline) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with RDF2Vec protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)
- configuration of: MLP on concatenated protein embeddings (protein-only baseline, no network) with TransE protein embeddings (function (knowledge-graph embedding)) (PPI embeddings study)