1
|
Tu R, Sinha M, González C, Hu E, Dhuliawala S, McCallum A, Su AI. Drug Repurposing using consilience of Knowledge Graph Completion methods. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.12.540594. [PMID: 39149283 PMCID: PMC11326126 DOI: 10.1101/2023.05.12.540594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
While link prediction methods in knowledge graphs have been increasingly utilized to locate potential associations between compounds and diseases, they suffer from lack of sufficient evidence to explain why a drug and a disease may be indicated. This is especially true for knowledge graph embedding (KGE) based methods where a drug-disease indication is linked only by information gleaned from a vector representation. Complementary pathwalking algorithms can increase the confidence of drug repurposing candidates by traversing a knowledge graph. However, these methods heavily weigh the relatedness of drugs, through their targets, pharmacology or shared diseases. Furthermore, these methods can rely on arbitrarily extracted paths as evidence of a compound to disease indication and lack the ability to make predictions on rare diseases. In this paper, we evaluate seven link prediction methods on a vast biomedical knowledge graph for drug repurposing. We follow the principle of consilience, and combine the reasoning paths and predictions provided by path-based reasoning approaches with those of KGE methods to identify putative drug repurposing indications. Finally, we highlight the utility of our approach through a potential repurposing indication.
Collapse
Affiliation(s)
- Roger Tu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Meghamala Sinha
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Carolina González
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Eric Hu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| | - Shehzaad Dhuliawala
- College of Information of Computer Sciences, University of Massachusetts Amherst, Amherst, MA 01003, United States of America
| | - Andrew McCallum
- College of Information of Computer Sciences, University of Massachusetts Amherst, Amherst, MA 01003, United States of America
| | - Andrew I. Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States of America
| |
Collapse
|