LoGoPPI enables fast and accurate protein protein interaction mapping at scale
- 1Yonsei University
Abstract
Graph-based protein function analysis is powerful, but protein-protein interaction (PPI) networks exist for only a small fraction of animal and plant genomes. We present LoGoPPI, which infers PPIs from sequence by combining bi-encoder global protein representation with local residue-level late interaction. LoGoPPI matches or exceeds state-of-the-art PLM-based cross-encoders while achieving orders-of-magnitude faster inference, up to ~1,500-fold, and its local branch provides residue-level signals associated with interaction interfaces and structurally flexible regions. This efficiency enables practical proteome-wide PPI reconstruction at scales prohibitive for cross-encoder models, potentially extending interactome mapping to tens of thousands of animal and plant species. LoGoPPI thus provides a scalable framework for comparative and functional analysis of protein networks across diverse taxa.
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BibTeX
@misc{lee2026logoppi,
title = {{LoGoPPI enables fast and accurate protein protein interaction mapping at scale}},
author = {H. B. Lee and J. Ma and H.-J. Kim and K. Song and I. Lee},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.20.753039},
url = {https://www.biorxiv.org/content/10.64898/2026.09.20.753039v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - LoGoPPI enables fast and accurate protein protein interaction mapping at scale
AU - H. B. Lee
AU - J. Ma
AU - H.-J. Kim
AU - K. Song
AU - I. Lee
PY - 2026
DA - 2026/09/20
PB - bioRxiv
DO - 10.64898/2026.09.20.753039
UR - https://www.biorxiv.org/content/10.64898/2026.09.20.753039v1
AB - Graph-based protein function analysis is powerful, but protein-protein interaction (PPI) networks exist for only a small fraction of animal and plant genomes. We present LoGoPPI, which infers PPIs from sequence by combining bi-encoder global protein representation with local residue-level late interaction. LoGoPPI matches or exceeds state-of-the-art PLM-based cross-encoders while achieving orders-of-magnitude faster inference, up to ~1,500-fold, and its local branch provides residue-level signals associated with interaction interfaces and structurally flexible regions. This efficiency enables practical proteome-wide PPI reconstruction at scales prohibitive for cross-encoder models, potentially extending interactome mapping to tens of thousands of animal and plant species. LoGoPPI thus provides a scalable framework for comparative and functional analysis of protein networks across diverse taxa.
ER -