Pool PaRTI: a PageRank-based pooling method for identifying critical residues and enhancing protein sequence representations
Pool PaRTI is implemented in Python with PyTorch and is available at github.com/Helix-Research-Lab/Pool_PaRTI.git. The Pool PaRTI sequence embeddings and residue importance values for all human proteins on UniProt are available at zenodo.org/records/15036725 for ESM2 and protBERT.
Authors
- Gowri Nayar (ORCID: https://orcid.org/0000-0001-5819-7115)
- Russ B. Altman (ORCID: https://orcid.org/0000-0003-3859-2905)
- Alp Tartici
Institutions
- Palo Alto University (US)
- Stanford University (US)
Publication Details
- Journal
- Bioinformatics
- Published
- 2025-05-31
- DOI
- https://doi.org/10.1093/bioinformatics/btaf330
- Citations
- 4
- Primary Topic
- Machine Learning in Bioinformatics
- Type
- article
- Field-Weighted Citation Impact
- 3.22
Funders
- National Institutes of Health
- Stanford Research Computing Center, Stanford University