iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features

Abstract

AbstractIdentification and classification of enhancers are highly significant because they play crucial roles in controlling gene transcription. Recently, several deep learning-based methods for identifying enhancers and their strengths have been developed. However, existing methods are usually limited because they use only local or only global features. The combination of local and global features is critical to further improve the prediction performance. In this work, we propose a novel deep learning-based method, called iEnhancer-DLRA, to identify enhancers and their strengths. iEnhancer-DLRA extracts local and multi-scale global features of sequences by using a residual convolutional network and two bidirectional long short-term memory networks. Then, a self-attention fusion strategy is proposed to deeply integrate these local and global features. The experimental results on the independent test dataset indicate that iEnhancer-DLRA performs better than nine existing state-of-the-art methods in both identification and classification of enhancers in almost all metrics. iEnhancer-DLRA achieves 13.8% (for identifying enhancers) and 12.6% (for classifying strengths) improvement in accuracy compared with the best existing state-of-the-art method. This is the first time that the accuracy of an enhancer identifier exceeds 0.9 and the accuracy of the enhancer classifier exceeds 0.8 on the independent test set. Moreover, iEnhancer-DLRA achieves superior predictive performance on the rice dataset compared with the state-of-the-art method RiceENN.