BMC Bioinformatics | |
Comparing methods for drug–gene interaction prediction on the biomedical literature knowledge graph: performance versus explainability | |
Research | |
Georgios Paliouras1  Fotis Aisopos1  | |
[1] Institute of Informatics and Telecommunications, National Centre for Scientific Research Demokritos, Athens, Greece; | |
关键词: Drug–target interaction; Knowledge graph; Graph embeddings; Deep learning; | |
DOI : 10.1186/s12859-023-05373-2 | |
received in 2023-04-07, accepted in 2023-06-01, 发布年份 2023 | |
来源: Springer | |
【 摘 要 】
This paper applies different link prediction methods on a knowledge graph generated from biomedical literature, with the aim to compare their ability to identify unknown drug-gene interactions and explain their predictions. Identifying novel drug–target interactions is a crucial step in drug discovery and repurposing. One approach to this problem is to predict missing links between drug and gene nodes, in a graph that contains relevant biomedical knowledge. Such a knowledge graph can be extracted from biomedical literature, using text mining tools. In this work, we compare state-of-the-art graph embedding approaches and contextual path analysis on the interaction prediction task. The comparison reveals a trade-off between predictive accuracy and explainability of predictions. Focusing on explainability, we train a decision tree on model predictions and show how it can aid the understanding of the prediction process. We further test the methods on a drug repurposing task and validate the predicted interactions against external databases, with very encouraging results.
【 授权许可】
CC BY
© The Author(s) 2023
【 预 览 】
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