Predicting interactions between drugs and target proteins has become an essential task in the drug discovery process. Although the method of validation via wet-lab experiments has become available, experimental methods for drug-target interaction (DTI) identification remain either time consuming or heavily dependent on domain expertise. Therefore, various computational models have been proposed to predict possible interactions between drugs and target proteins. However, most prediction methods do not consider the topological structures characteristics of the relationship. In this paper, we propose a relational topology- based heterogeneous network embedding method to predict drug-target interactions, abbreviated as RTHNE_ DTI. We first construct a heterogeneous information network based on the interaction between different types of nodes, to enhance the ability of association discovery by fully considering the topology of the network. Then drug and target protein nodes can be represented by the other types of nodes. According to the different topological structure of the relationship between the nodes, we divide the relationship in the heterogeneous network into two categories and model them separately. Extensive experiments on the real- world drug datasets, RTHNE_DTI produces high efficiency and outperforms other state-of-the-art methods. RTHNE_DTI can be further used to predict the interaction between unknown interaction drug-target pairs.

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