Explaining Drug Repositioning: A Case-Based Reasoning Graph Neural Network Approach

Drug repositioning, the identification of novel uses of existing therapies, has become an attractive strategy to accelerate drug development. Recently, knowledge graphs (KGs) have emerged as a powerful representation of interconnected data within the biomedical domain. While biomedical KGs can be used to predict new connections between compounds and diseases, most approaches only state whether two nodes are related. Yet, they fail to explain why two nodes are related. In this project, we introduce an implementation of the semi-parametric Case-Based Reasoning over subgraphs approach (CBR-SUBG), designed to derive the underlying mechanisms for a drug query by gathering graph patterns of similar entities. We show that our adaptation outperforms existing KG link prediction models on a drug repositioning task. Furthermore, our findings demonstrate that CBR-SUBG strategy can not only rank potential repositioning candidates but also provide interpretable biological paths, leading to more informed decisions.