期刊
FRONTIERS IN GENETICS
卷 10, 期 -, 页码 -出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fgene.2019.00459
关键词
drug-target interaction prediction; class imbalance; ensemble learning; path category-based features; gradient boosting decision tree
资金
- Natural Science Foundation of China [61702296, 61302139]
- Natural Science Foundation of Heilongjiang Province [LH2019F049, LH2019A029]
- China Postdoctoral Science Foundation [2019M650069]
- Heilongjiang Postdoctoral Scientific Research Staring Foundation [BHL-Q18104]
- Fundamental Research Foundation of Universities in Heilongjiang Province for Technology Innovation [KJCX201805]
- Fundamental Research Foundation of Universities in Heilongjiang Province for Youth Innovation Team [RCYJTD201805]
- Foundation of Graduate Innovative Research [YJSCX2018-047HLJU, YJSCX2018-139HLJU]
Determining the target genes that interact with drugs- drug-target interactions- plays an important role in drug discovery. Identification of drug-target interactions through biological experiments is time consuming, laborious, and costly. Therefore, using computational approaches to predict candidate targets is a good way to reduce the cost of wet-lab experiments. However, the known interactions (positive samples) and the unknown interactions (negative samples) display a serious class imbalance, which has an adverse effect on the accuracy of the prediction results. To mitigate the impact of class imbalance and completely exploit the negative samples, we proposed a new method, named DTIGBDT, based on gradient boosting decision trees, for predicting candidate drug-target interactions. We constructed a drug-target heterogeneous network that contains the drug similarities based on the chemical structures of drugs, the target similarities based on target sequences, and the known drug-target interactions. The topological information of the network was captured by random walks to update the similarities between drugs or targets. The paths between drugs and targets could be divided into multiple categories, and the features of each category of paths were extracted. We constructed a prediction model based on gradient boosting decision trees. The model establishes multiple decision trees with the extracted features and obtains the interaction scores between drugs and targets. DTIGBDT is a method of ensemble learning, and it effectively reduces the impact of class imbalance. The experimental results indicate that DTIGBDT outperforms several state-of-the-art methods for drug-target interaction prediction. In addition, case studies on Quetiapine, Clozapine, Olanzapine, Aripiprazole, and Ziprasidone demonstrate the ability of DTIGBDT to discover potential drug-target interactions.
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