The paper titled “Bio-JOIE: Joint Representation Learning of Biological Knowledge Bases,” by Junheng Hao, Chelsea Ju, Muhao Chen, Yizhou Sun, Carlo Zaniolo, and Wei Wang from the UCLA Scalable Analytics Institute (ScAi), has been recognized with the Best Student Paper Award at the 11th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB 2020).
The paper proposes Bio-JOIE, a transferred multi-relational embedding based model for representation learning on biological knowledge bases. It jointly captures the knowledge of protein-protein interaction (PPI) networks and gene ontology. By leveraging structured knowledge in both domains, Bio-JOIE significantly outperforms existing state-of-the-art methods in PPI type prediction on multiple species. Bio-JOIE can accurately identify PPIs between the SARS-CoV-2 proteins and human proteins, providing valuable insights for advancing research on this new widespread disease.