A heterogeneous network-based method with attentive meta-path extraction for predicting drug–target interactions

Abstract

Abstract Predicting drug–target interactions (DTIs) is crucial at many phases of drug discovery and repositioning. Many computational methods based on heterogeneous networks (HNs) have proved their potential to predict DTIs by capturing extensive biological knowledge and semantic information from meta-paths. However, existing methods manually customize meta-paths, which is overly dependent on some specific expertise. Such strategy heavily limits the scalability and flexibility of these models, and even affects their predictive performance. To alleviate this limitation, we propose a novel HN-based method with attentive meta-path extraction for DTI prediction, named HampDTI, which is capable of automatically extracting useful meta-paths through a learnable attention mechanism instead of pre-definition based on domain knowledge. Specifically, by scoring multi-hop connections across various relations in the HN with each relation assigned an attention weight, HampDTI constructs a new trainable graph structure, called meta-path graph. Such meta-path graph implicitly measures the importance of every possible meta-path between drugs and targets. To enable HampDTI to extract more diverse meta-paths, we adopt a multi-channel mechanism to generate multiple meta-path graphs. Then, a graph neural network is deployed on the generated meta-path graphs to yield the multi-channel embeddings of drugs and targets. Finally, HampDTI fuses all embeddings from different channels for predicting DTIs. The meta-path graphs are optimized along with the model training such that HampDTI can adaptively extract valuable meta-paths for DTI prediction. The experiments on benchmark datasets not only show the superiority of HampDTI in DTI prediction over several baseline methods, but also, more importantly, demonstrate the effectiveness of the model discovering important meta-paths.