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DTI-CDF: a CDF model towards the prediction of DTIs based on hybrid features

By Yan-Yi Chu, Yu-Fang Zhang, Wei Wang, Xian-Geng Wang, Xiao-Qi Shan, Yi Xiong, Dong-Qing Wei

Posted 03 Jun 2019
bioRxiv DOI: 10.1101/657973

Drug-target interactions play a crucial role in target-based drug discovery and exploitation. Computational prediction of DTIs has become a popular alternative strategy to the experimental methods for identification of DTIs of which are both time and resource consuming. However, the performances of the current DTIs prediction approaches suffer from a problem of low precision and high false positive rate. In this study, we aimed to develop a novel DTIs prediction method, named DTI-CDF, for improving the prediction precision based on a cascade deep forest model which integrates hybrid features, including multiple similarity-based features extracted from the heterogeneous graph, fingerprints of drugs, and evolution information of target protein sequences. In the experiments, we built five replicates of 10 fold cross-validations under three different experimental settings of data sets, namely, corresponding DTIs values of certain drugs (S\_D), targets (S\_T), or drug-target pairs (S_P) in the training set are missed, but existed in the test set. The experimental results show that our proposed approach DTI-CDF achieved significantly higher performance than the state-of-the-art methods.

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