Integrating transformer and graph attention network for circRNA-miRNA interaction prediction

CircRNA-miRNA interaction (CMI) plays a crucial role in the gene regulatory network of the cell. Numerous experiments have shown that abnormalities in CMI can impact molecular functions and physiological processes, leading to the occurrence of specific diseases. Current computational models for predicting CMI typically focus on local molecular entity relationships, thereby neglecting inherent molecular attributes and global structural information. To address these limitations, we propose a multi-feature fusion prediction model based on the transformer and graph attention network, named EGATCMI. Specifically, EGATCMI combines the transformer architecture with Word2vec to pre-train the sequence of circRNA and miRNA, capturing their sequence feature representation and sequence similarity. By leveraging the self-attention mechanism, EGATCMI extracts global structural feature from the CMI network. EGATCMI effectively integrates the obtained multi-feature for prediction, achieving AUC values of 0.9106 and 0.9470 on the CMI-9905 and CircBank datasets, respectively, outperforming existing methods. In case studies that the prediction of interactions between three miRNAs that are closely related to diseases and circRNAs, 8 out of 10 pairs were accurately predicted and validated. Extensive experimental results demonstrate the potential of EGATCMI as a reliable tool for candidate screening in biological investigations.