Predicting miRNA-drug interactions via dual-channel network based on TCN and BiLSTM

Abstract

Discovering new drugs is a complicated, time-consuming, costly, risky and failure-prone process. However, about 80% of the drugs that have been approved so far are targeted at protein targets, and 99% of them only target specific proteins. This means that there are still a large number of protein targets that are considered “useless”. By exploring miRNA as a potential therapeutic target, we can expand the range of target selection and improve the efficiency of drug development. Therefore, it is of great significance to search for potential miRNA-drug interactions (MDIs) through reasonable computational methods. In this paper, a dual-channel network model, MDIDCN, based on Temporal Convolutional Network (TCN) and Bi-directional Long Short-Term Memory (BiLSTM), was proposed to predict MDIs. Specifically, we first used a known bipartite network to represent the interaction between miRNAs and drugs, and the graph embedding technique of BiNE was applied to learn the topological features of both. Secondly, we used TCN to learn the MACCS fingerprints of drugs, BiLSTM to learn the k-mer of miRNA, and concatenated the topological and structural features of the two together as their fusion features. Finally, the fusion features of miRNA and drug underwent max-pooling, and they were input into the Softmax layer to obtain the predicted scores of both, so as to obtain the potential miRNA-drug interaction pairs. In this paper, the prediction performance of the model was evaluated on three different datasets by using 5-fold cross-validation, and the average AUC were 0.9567, 0.9365, and 0.8975, respectively. In addition, case studies on the drugs Gemcitabine and hsa-miR-155-5p were also conducted in this paper, and the results showed that the model had high accuracy and reliability. In conclusion, the MDIDCN model can accurately and efficiently predict MDIs, which has important implications for drug development.

Graphical abstract

Keywords

miRNA-drug interactions / BiNE / temporal convolutional network / bi-directional long short-term memory

Xiaoxuan Zhang received the BS degree in School of Computer Science from Shaanxi Normal University, China in 2022, where she is currently pursuing the MS degree. Her current research interests include bioinformatics and deep learning

Xiujuan Lei is a professor and PhD Supervisor at Shaanxi Normal University, China. Her research interests include intelligent computing, bioinformatics and deep learning. She serves as a standing committee member of the Bioinformatics and Artificial Life Committee of the Chinese Association for Artificial Intelligence (CAAI), a standing committee member of the Bioinformatics Committee of the China Computer Federation (CCF), etc. She is also a distinguished member of CCF, a senior member of CAAI, a member of IEEE, ACM, SIGBIO, etc

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Acknowledgements

This work was supported by the National Natural Science Foundation of China (Grant No. 62272288), the Fundamental Research Funds for the Central Universities, and Shaanxi Normal University (GK202302006).

Competing interests

The authors declare that they have no competing interests or financial conflicts to disclose.

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