Self-Attention Based Neural Network for Predicting RNA-Protein Binding Sites

Proteins binding to Ribonucleic Acid (RNA) inside cells are called RNA-binding proteins (RBP), which play a crucial role in gene regulation. The identification of RNA-protein binding sites helps to understand the function of RBP better. Although many computational methods have been developed to predict RNA-protein binding sites, their prediction accuracy on small sample datasets needs improvement. To overcome this limitation, we propose a novel model called SA-Net, which utilizes k-mer embedding to encode RNA sequences and a self-attention-based neural network to extract sequence features. K-mer embedding assists the model to discover significant subsequence fragments associated with binding sites. The self-attention mechanism captures contextual information from the entire input sequence globally, performing well in small sample sequence learning. Experimental results demonstrate that SA-Net attains state-of-the-art results on the RBP-24 dataset. We find that 4-mer embedding aids the model to achieve optimal performance. We also show that the self-attention network outperforms the commonly used CNN and CNN-BLSTM models in sequence feature extraction.