LM-DTI: a tool of predicting drug-target interactions using the node2vec and network path score methods

Abstract

Introduction: Drug-target interaction (DTI) prediction is a key step in drug function discovery and repositioning. The emergence of large-scale heterogeneous biological networks provides an opportunity to identify drug-related target genes, which led to the development of several computational methods for DTI prediction. Methods: Considering the limitations of conventional computational methods, a novel tool named LM-DTI based on integrated information related to lncRNAs and miRNAs was proposed, which adopted the graph embedding (node2vec) and the network path score methods. First, LM-DTI innovatively constructed a heterogeneous information network containing eight networks composed of four types of nodes (drug, target, lncRNA, and miRNA). Next, the node2vec method was used to obtain feature vectors of drug as well as target nodes, and the path score vector of each drug-target pair was calculated using the DASPfind method. Finally, the feature vectors and path score vectors were merged and input into the XGBoost classifier to predict potential drug-target interactions. Results and Discussion: The 10-fold cross validations evaluate the classification accuracies of the LM-DTI. The prediction performance of LM-DTI in AUPR reached 0.96, which showed a significant improvement compared with those of conventional tools. The validity of LM-DTI has also been verified by manually searching literature and various databases. LM-DTI is scalable and computing efficient; thus representing a powerful drug relocation tool that can be accessed for free at http://www.lirmed.com:5038/lm_dti.

Keywords: XGBoost; drug-target interaction; heterogeneous information network; network path score; node2vec.