Joint embedding of biological networks for cross-species functional alignment

Lechuan Li, Ruth Dannenfelser, Yu Zhu, Nathaniel Hejduk, Santiago Segarra, Vicky Yao

Abstract: Model organisms are widely used to better understand the molecular causes of human disease. While sequence similarity greatly aids this cross-species transfer, sequence similarity does not imply functional similarity, and thus, several current approaches incorporate protein–protein interactions to help map findings between species. Existing transfer methods either formulate the alignment problem as a matching problem which pits network features against known orthology, or more recently, as a joint embedding problem.