Drug-target interaction prediction using high order nonlinear features via neural factorization machines

Abstract

Medication design and repositioning are sped up by the prediction of drug-target interactions (DTIs). Two main kinds of prediction methods are commonly used, which are based on chemical structure feature extraction and deep learning methods. However, on the one hand, the DTI prediction approaches based on chemical structural feature extraction may not wholly explore the possible network characteristics in the data. On the other hand, many deep learning methods call for numerous layers of neural networks to be layered to learn higher-order feature interaction information. To sum up, the existing computation methods often have the limitations of gradient disappearance and overfitting. This study presents a novel method (JRD-NFM) by calculating Jaccard similarities, getting an eigenvector through Restarted random walk (RWR), and generating low-dimensional feature vectors by Disposition Component Analysis (DCA). Besides decoding the topological features and similarity information of target and drug node, it can also get the context information of a single network. Considering the advantages of Neural Factorization Machines (NFM) in extracting high-order nonlinear features and processing sparse data, this study use NFM to classifier the collection data to integrate drug and target biochemical structure information. The experimental results demonstrate that JRD-NFM can outperform widely used deep learning methods and conventional chemical structure approaches. It could provide fresh ideas for combining molecular structure and heterogeneous network data to predict DTIs.