An Encoding-Decoding Framework Based on CNN for circRNA-RBP Binding Sites Prediction

Predicting RNA binding protein (RBP) binding sites on circular RNAs (circRNAs) is a fundamental step to understand their interaction mechanism. Numerous computational methods are developed to solve this problem, but they cannot fully learn the features. Therefore, we propose circ-CNNED, a convolutional neural network (CNN)-based encoding and decoding framework. We first adopt two encoding methods to obtain two original matrices. We preprocess them using CNN before fusion. To capture the feature dependencies, we utilize temporal convolutional network (TCN) and CNN to construct encoding and decoding blocks, respectively. Then we introduce global expectation pooling to learn latent information and enhance the robustness of circ-CNNED. We perform circ-CNNED across 37 datasets to evaluate its effect. The comparison and ablation experiments demonstrate that our method is superior. In addition, motif enrichment analysis on four datasets helps us to explore the reason for performance improvement of circ-CNNED.