EKGDR: An End-to-End Knowledge Graph-Based Method for Computational Drug Repurposing

重新调整用途 药物重新定位 端到端原则 计算机科学 图形 分类 药品 机器学习 药物发现 数据挖掘 人工智能 医学 生物信息学 理论计算机科学 生物 生态学 精神科
作者
Javad Tayebi,Bagher BabaAli
出处
期刊:Journal of Chemical Information and Modeling [American Chemical Society]
卷期号:64 (6): 1868-1881 被引量:7
标识
DOI:10.1021/acs.jcim.3c01925
摘要

The lengthy and expensive process of developing new drugs from scratch, coupled with a high failure rate, has prompted the emergence of drug repurposing/repositioning as a more efficient and cost-effective approach. This approach involves identifying new therapeutic applications for existing approved drugs, leveraging the extensive drug-related data already gathered. However, the diversity and heterogeneity of data, along with the limited availability of known drug-disease interactions, pose significant challenges to computational drug design. To address these challenges, this study introduces EKGDR, an end-to-end knowledge graph-based approach for computational drug repurposing. EKGDR utilizes the power of a drug knowledge graph, a comprehensive repository of drug-related information that encompasses known drug interactions and various categorization information, as well as structural molecular descriptors of drugs. EKGDR employs graph neural networks, a cutting-edge graph representation learning technique, to embed the drug knowledge graph (nodes and relations) in an end-to-end manner. By doing so, EKGDR can effectively learn the underlying causes (intents) behind drug-disease interactions and recursively aggregate and combine relational messages between nodes along different multihop neighborhood paths (relational paths). This process generates representations of disease and drug nodes, enabling EKGDR to predict the interaction probability for each drug-disease pair in an end-to-end manner. The obtained results demonstrate that EKGDR outperforms previous models in all three evaluation metrics: area under the receiver operating characteristic curve (AUROC = 0.9475), area under the precision-recall curve (AUPRC = 0.9490), and recall at the top-200 recommendations (Recall@200 = 0.8315). To further validate EKGDR's effectiveness, we evaluated the top-20 candidate drugs suggested for each of Alzheimer's and Parkinson's diseases.
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