ISLRWR: A network diffusion algorithm for drug–target interactions prediction

Abstract

Machine learning techniques and computer-aided methods are now widely used in the pre-discovery tasks of drug discovery, effectively improving the efficiency of drug development and reducing the workload and cost. In this study, we used multi-source heterogeneous network information to build a network model, learn the network topology through multiple network diffusion algorithms, and obtain compressed low-dimensional feature vectors for predicting drug–target interactions (DTIs). We applied the metropolis–hasting random walk (MHRW) algorithm to improve the performance of the random walk with restart (RWR) algorithm, forming the basis by which the self-loop probability of the current node is removed. Additionally, the propagation efficiency of the MHRW was improved using the improved metropolis–hasting random walk (IMRWR) algorithm, facilitating network deep sampling. Finally, we proposed a correction of the transfer probability of the entire network after increasing the self-loop rate of isolated nodes to form the ISLRWR algorithm. Notably, the ISLRWR algorithm improved the area under the receiver operating characteristic curve (AUROC) by 7.53 and 5.72%, and the area under the precision-recall curve (AUPRC) by 5.95 and 4.19% compared to the RWR and MHRW algorithms, respectively, in predicting DTIs performance. Moreover, after excluding the interference of homologous proteins (popular drugs or targets may lead to inflated prediction results), the ISLRWR algorithm still showed a significant performance improvement.