Hierarchical Attention Network for Predicting DNA-Protein Binding Sites

Abstract

Discovering DNA-protein binding sites, also known as motif discovery, is the foundation for further analyses of transcription factors (TFs). Deep learning algorithms such as convolutional neural networks (CNN) and recurrent neural networks (RNN) are introduced to motif discovery task and have achieved state-of–art performance. However, these methods still have limitations such as neglecting the context information in large-scale sequencing data. Thus, inspired by the similarity between DNA sequence and human language, in this paper we propose a hierarchical attention network for predicting DNA-protein binding sites which is based on a natural language processing method for document classification. The proposed method is tested on real ChIP-seq datasets and the experimental results show a considerable improvement compared with two well-tested deep learning-based sequence model, DeepBind and Deepsea.