Affiliation:
1. Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China
2. Department of Computer Science, Old Dominion University , Norfolk, VA 23529, USA
Abstract
Abstract
Motivation
Identifying drug–target interactions is a crucial step for drug discovery and design. Traditional biochemical experiments are credible to accurately validate drug–target interactions. However, they are also extremely laborious, time-consuming and expensive. With the collection of more validated biomedical data and the advancement of computing technology, the computational methods based on chemogenomics gradually attract more attention, which guide the experimental verifications.
Results
In this study, we propose an end-to-end deep learning-based method named IIFDTI to predict drug–target interactions (DTIs) based on independent features of drug–target pairs and interactive features of their substructures. First, the interactive features of substructures between drugs and targets are extracted by the bidirectional encoder–decoder architecture. The independent features of drugs and targets are extracted by the graph neural networks and convolutional neural networks, respectively. Then, all extracted features are fused and inputted into fully connected dense layers in downstream tasks for predicting DTIs. IIFDTI takes into account the independent features of drugs/targets and simulates the interactive features of the substructures from the biological perspective. Multiple experiments show that IIFDTI outperforms the state-of-the-art methods in terms of the area under the receiver operating characteristics curve (AUC), the area under the precision-recall curve (AUPR), precision, and recall on benchmark datasets. In addition, the mapped visualizations of attention weights indicate that IIFDTI has learned the biological knowledge insights, and two case studies illustrate the capabilities of IIFDTI in practical applications.
Availability and implementation
The data and codes underlying this article are available in Github at https://github.com/czjczj/IIFDTI.
Supplementary information
Supplementary data are available at Bioinformatics online.
Funder
National Key Research and Development Program of China
NSFC-Zhejiang Joint Fund for the Integration of Industrialization and Informatization
National Natural Science Foundation of China
Hunan Provincial Science and Technology Program
Publisher
Oxford University Press (OUP)
Subject
Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability
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