DRONet: effectiveness-driven drug repositioning framework using network embedding and ranking learning
Kuo Yang, Yuxia Yang, Shuyue Fan, Jianan Xia, Qiguang Zheng, Xin Luna Dong, Jun Liu, Qiong Liu, Lei Lei, Yingying Zhang, Bing Li, Z Gao, Runshun Zhang, Baoyan Liu, Zhong Wang, Xuezhong Zhou
Abstract
As one of the most vital methods in drug development, drug repositioning emphasizes further analysis and research of approved drugs based on the existing large amount of clinical and experimental data to identify new indications of drugs. However, the existing drug repositioning methods didn't achieve enough prediction performance, and these methods do not consider the effectiveness information of drugs, which make it difficult to obtain reliable and valuable results. In this study, we proposed a drug repositioning framework termed DRONet, which make full use of effectiveness comparative relationships (ECR) among drugs as prior information by combining network embedding and ranking learning. We utilized network embedding methods to learn the deep features of drugs from a heterogeneous drug-disease network, and constructed a high-quality drug-indication data set including effectiveness-based drug contrast relationships. The embedding features and ECR of drugs are combined effectively through a designed ranking learning model to prioritize candidate drugs. Comprehensive experiments show that DRONet has higher prediction accuracy (improving 87.4% on Hit@1 and 37.9% on mean reciprocal rank) than state of the art. The case analysis also demonstrates high reliability of predicted results, which has potential to guide clinical drug development.