circ2CBA: prediction of circRNA-RBP binding sites combining deep learning and attention mechanism

Circular RNAs(circRNAs)are RNAs with closed circular structure involved in many biological processes by key interactions with RNA binding proteins(RBPs).Existing methods for predicting these interactions have limitations in feature learning.In view of this,we propose a method named circ2CBA,which uses only sequence information of circRNAs to predict circRNA-RBP binding sites.We have constructed a data set which includes eight sub-datasets.First,circ2CBA encodes circRNA sequences using the one-hot method.Next,a two-layer convolutional neural network(CNN)is used to initially extract the features.After CNN,circ2CBA uses a layer of bidirectional long and short-term memory network(BiLSTM)and the self-attention mechanism to learn the features.The AUC value of circ2CBA reaches 0.8987.Comparison of circ2CBA with other three methods on our data set and an ablation experiment confirm that circ2CBA is an effective method to predict the binding sites between circRNAs and RBPs.