Predicting Drug Repurposing Candidates and Their Mechanisms from A Biomedical Knowledge Graph

Chunyu Ma, Zhihan Zhou, Han Liu, David Koslicki

Keywords: Drug Repurposing, Reinforcement Learning, Biomedical Knowledge Graph

TL;DR: We predict drug repurposing candidates and their path-based mechanisms of action based on a large biomedical knowledge graph.

Abstract: Computational drug repurposing is a cost- and time-efficient method to identify new indications of approved or experimental drugs/compounds. It is especially critical for emerging and/or orphan diseases due to its cheaper investment and shorter research cycle compared with traditional wet-lab drug discovery approaches. However, the underlying mechanisms of action between repurposed drugs and their target diseases remain largely unknown, which is still an unsolved issue in existing repurposing methods. As such, computational drug repurposing has not been widely adopted in clinical settings. In this work, based on a massive biomedical knowledge graph, we propose a computational drug repurposing framework that not only predicts the treatment probabilities between drugs and diseases but also predicts the path-based, testable mechanisms of action (MOAs) as their biomedical explanations. Specifically, we utilize the GraphSAGE model in an unsupervised manner to integrate each entity’s neighborhood information and employ a Random Forest model to predict the treatment probabilities between pairs of drugs and diseases. Moreover, we train an adversarial actor-critic reinforcement learning model to predict the potential MOA for explaining drug purposing. To encourage the model to find biologically reasonable paths, we utilize the curated molecular interactions of drugs and a PubMed-publication-based concept distance to extract potential drug MOA paths from the knowledge graph as ”demonstration paths” to guide the model during the process of path-finding. Comprehensive experiments and case studies show that the proposed framework outperforms state-of-the-art baselines in both predictive performance of drug repurposing and explanatory performance of recapitulating human-curated DrugMechDB-based paths.

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