Prediction of drug–disease associations by integrating common topologies of heterogeneous networks and specific topologies of subnets

Abstract Motivation The development process of a new drug is time-consuming and costly. Thus, identifying new uses for approved drugs, named drug repositioning, is helpful for speeding up the drug development process and reducing development costs. Existing drug-related disease prediction methods mainly focus on single or multiple drug–disease heterogeneous networks. However, heterogeneous networks, and drug subnets and disease subnet contained in heterogeneous networks cover the common topology information between drug and disease nodes, the specific information between drug nodes and the specific information between disease nodes, respectively. Results We design a novel model, CTST, to extract and integrate common and specific topologies in multiple heterogeneous networks and subnets. Multiple heterogeneous networks composed of drug and disease nodes are established to integrate multiple kinds of similarities and associations among drug and disease nodes. These heterogeneous networks contain multiple drug subnets and a disease subnet. For multiple heterogeneous networks and subnets, we then define the common and specific representations of drug and disease nodes. The common representations of drug and disease nodes are encoded by a graph convolutional autoencoder with sharing parameters and they integrate the topological relationships of all nodes in heterogeneous networks. The specific representations of nodes are learned by specific graph convolutional autoencoders, respectively, and they fuse the topology and attributes of the nodes in each subnet. We then propose attention mechanisms at common representation level and specific representation level to learn more informative common and specific representations, respectively. Finally, an integration module with representation feature level attention is built to adaptively integrate these two representations for final association prediction. Extensive experimental results confirm the effectiveness of CTST. Comparison with six latest methods and case studies on five drugs further verify CTST has the ability to discover potential candidate diseases.