Prediction of drug target interaction based on under sampling strategy and random forest algorithm

Abstract

Drug target interactions (DTIs) play a crucial role in drug discovery and development. The prediction of DTIs based on computational method can effectively assist the experimental techniques for DTIs identification, which are time-consuming and expensive. However, the current computational models suffer from low accuracy and high false positive rate in the prediction of DTIs, especially for datasets with extremely unbalanced sample categories. To accurately identify the interaction between drugs and target proteins, a variety of descriptors that fully show the characteristic information of drugs and targets are extracted and applied to the integrated method random forest (RF) in this work. Here, the random projection method is adopted to reduce the feature dimension such that simplify the model calculation. In addition, to balance the number of samples in different categories, a down sampling method NearMiss (NM) which can control the number of samples is used. Based on the gold standard datasets (nuclear receptors, ion channel, GPCRs and enzymes), the proposed method achieves the auROC of 92.26%, 98.21%, 97.65%, 99.33%, respectively. The experimental results show that the proposed method yields significantly higher performance than that of state-of-the-art methods in predicting drug target interaction.