Inferring Drug-Target Interactions Based on Random Walk and Convolutional Neural Network

Computational strategies for identifying new drug–target interactions (DTIs) can guide the process of drug discovery, reduce the cost and time of drug development, and thus promote drug development. Most recently proposed methods predict DTIs via integration of heterogeneous data related to drugs and proteins. However, previous methods have failed to deeply integrate these heterogeneous data and learn deep feature representations of multiple original similarities and interactions related to drugs and proteins. We therefore constructed a heterogeneous network by integrating a variety of connection relationships about drugs and proteins, including drugs, proteins, and drug side effects, as well as their similarities, interactions, and associations. A DTI prediction method based on random walk and convolutional neural network was proposed and referred to as DTIPred. DTIPred not only takes advantage of various original features related to drugs and proteins, but also integrates the topological information of heterogeneous networks. The prediction model is composed of two sides and learns the deep feature representation of a drug–protein pair. On the left side, random walk with restart is applied to learn the topological vectors of drug and protein nodes. The topological representation is further learned by the constructed deep learning frame based on convolutional neural network. The right side of the model focuses on integrating multiple original similarities and interactions of drugs and proteins to learn the original representation of the drug–protein pair. The results of cross-validation experiments demonstrate that DTIPred achieves better prediction performance than several state-of-the-art methods. During the validation process, DTIPred can retrieve more actual drug–protein interactions within the top part of the predicted results, which may be more helpful to biologists. In addition, case studies on five drugs further demonstrate the ability of DTIPred to discover potential drug–protein interactions.