AUTHOR=Zhao Lingling , Wang Junjie , Pang Long , Liu Yang , Zhang Jun TITLE=GANsDTA: Predicting Drug-Target Binding Affinity Using GANs JOURNAL=Frontiers in Genetics VOLUME=10 YEAR=2020 URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.01243 DOI=10.3389/fgene.2019.01243 ISSN=1664-8021 ABSTRACT=

The computational prediction of interactions between drugs and targets is a standing challenge in drug discovery. State-of-the-art methods for drug-target interaction prediction are primarily based on supervised machine learning with known label information. However, in biomedicine, obtaining labeled training data is an expensive and a laborious process. This paper proposes a semi-supervised generative adversarial networks (GANs)-based method to predict binding affinity. Our method comprises two parts, two GANs for feature extraction and a regression network for prediction. The semi-supervised mechanism allows our model to learn proteins drugs features of both labeled and unlabeled data. We evaluate the performance of our method using multiple public datasets. Experimental results demonstrate that our method achieves competitive performance while utilizing freely available unlabeled data. Our results suggest that utilizing such unlabeled data can considerably help improve performance in various biomedical relation extraction processes, for example, Drug-Target interaction and protein-protein interaction, particularly when only limited labeled data are available in such tasks. To our best knowledge, this is the first semi-supervised GANs-based method to predict binding affinity.