ProtTrans
ProtTrans protein language model family (T5-based).
Results are recorded on linked configurations and versions of this model. Their settings and evaluations are kept separate below.
Results on linked records
This model has no results of its own in this release. 7 linked records have results. They are not assigned to the underlying model: each record keeps its own settings and evaluations, and its scores are on its own page.
- GCN with ProtTrans protein embeddings (sequence) (PPI embeddings study) Configuration · uses this model · 4 evaluations · 4 results
- GraphSAGE with ProtTrans protein embeddings (sequence) (PPI embeddings study) Configuration · uses this model · 4 evaluations · 4 results
- MLP on concatenated protein embeddings (protein-only baseline, no network) with ProtTrans protein embeddings (sequence) (PPI embeddings study) Configuration · uses this model · 4 evaluations · 4 results
- NGNN with GCN combined with SEAL with ProtTrans protein embeddings (sequence) (PPI embeddings study) Configuration · uses this model · 4 evaluations · 4 results
- NGNN with GCN with ProtTrans protein embeddings (sequence) (PPI embeddings study) Configuration · uses this model · 4 evaluations · 4 results
- NGNN with GraphSAGE combined with SEAL with ProtTrans protein embeddings (sequence) (PPI embeddings study) Configuration · uses this model · 4 evaluations · 4 results
- NGNN with GraphSAGE with ProtTrans protein embeddings (sequence) (PPI embeddings study) Configuration · uses this model · 4 evaluations · 4 results
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
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How it works, versions and access
Strengths, limitations and unresolved questions
Evidence
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Evidence table
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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-model-prottrans
- areas
- molecular-interactions; proteins-complexes
- contexts
- research
- method types
- foundation_model
- reported name
- ProtTrans
- entity level
- family
- source locator
- Experimental design; Table 5 and 6 column headers
- missing metadata
- version: reason: unreported; note: No checkpoint or version printed in the main text; parameters are in Supplementary Table S3, not retrieved
Related records
- uses model: GCN with ProtTrans protein embeddings (sequence) (PPI embeddings study)
- uses model: GraphSAGE with ProtTrans protein embeddings (sequence) (PPI embeddings study)
- uses model: MLP on concatenated protein embeddings (protein-only baseline, no network) with ProtTrans protein embeddings (sequence) (PPI embeddings study)
- uses model: NGNN with GCN combined with SEAL with ProtTrans protein embeddings (sequence) (PPI embeddings study)
- uses model: NGNN with GCN with ProtTrans protein embeddings (sequence) (PPI embeddings study)
- uses model: NGNN with GraphSAGE combined with SEAL with ProtTrans protein embeddings (sequence) (PPI embeddings study)
- uses model: NGNN with GraphSAGE with ProtTrans protein embeddings (sequence) (PPI embeddings study)