DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding

Yang Yue, Shan He

Research output: Contribution to journalArticlepeer-review

162 Downloads (Pure)


BACKGROUND: Prediction of the drug-target interaction (DTI) is a critical step in the drug repurposing process, which can effectively reduce the following workload for experimental verification of potential drugs' properties. In recent studies, many machine-learning-based methods have been proposed to discover unknown interactions between drugs and protein targets. A recent trend is to use graph-based machine learning, e.g., graph embedding to extract features from drug-target networks and then predict new drug-target interactions. However, most of the graph embedding methods are not specifically designed for DTI predictions; thus, it is difficult for these methods to fully utilize the heterogeneous information of drugs and targets (e.g., the respective vertex features of drugs and targets and path-based interactive features between drugs and targets).

RESULTS: We propose a DTI prediction method DTI-HeNE (DTI based on Heterogeneous Network Embedding), which is specifically designed to cope with the bipartite DTI relations for generating high-quality embeddings of drug-target pairs. This method splits a heterogeneous DTI network into a bipartite DTI network, multiple drug homogeneous networks and target homogeneous networks, and extracts features from these sub-networks separately to better utilize the characteristics of bipartite DTI relations as well as the auxiliary similarity information related to drugs and targets. The features extracted from each sub-network are integrated using pathway information between these sub-networks to acquire new features, i.e., embedding vectors of drug-target pairs. Finally, these features are fed into a random forest (RF) model to predict novel DTIs.

CONCLUSIONS: Our experimental results show that, the proposed DTI network embedding method can learn higher-quality features of heterogeneous drug-target interaction networks for novel DTIs discovery.

Original languageEnglish
Article number418
JournalBMC Bioinformatics
Issue number1
Publication statusPublished - 3 Sept 2021

Bibliographical note

© 2021. The Author(s).


  • Drug Development
  • Drug Interactions
  • Drug Repositioning
  • Machine Learning
  • Pharmaceutical Preparations


Dive into the research topics of 'DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding'. Together they form a unique fingerprint.

Cite this