DeepA-rbpbs: A Hybrid Convolution and Recurrent Neural Network Combined with Attention Mechanism for Predicting RBP Binding Site
Document Type
Article
Publication Date
2022
Keywords
Rna-binding Proteins, Deep Learning, Attention Mechanism, Clip-seq
Digital Object Identifier (DOI)
https://doi.org/10.1080/07391102.2020.1854861
Abstract
It’s important to infer the binding site of RNA-binding proteins (RBP) for understanding the interaction between RBP and its RNA targets and decipher the mechanisms of transcriptional regulation. However, experimental detection of RBP binding sites is still time-intensive and expensive. Algorithms based on machine learning can speed up detection of RBP binding sites. In this article, we propose a new deep learning method, DeepA-RBPBS, which can use RNA sequences and structural features to predict RBP binding site. DeepA-RBPBS uses CNN and BiGRU to extract sequences and structural features without long-term dependence issues. It also utilizes an attention mechanism to enhance the contribution of key features. The comparison shows that the performance of DeepA-RBPBS is better than that of the state-of-the-art predictors. In the testing on 31 datasets of CLIP-seq experiments over 19 proteins, MCC (AUC) is 8% (5%) higher than those of the latest method based on deep learning, iDeepS. We also apply DeepA-RBPBS to the target RNA data of RBPs related to diabetes (LIN28, RBFOX2, FTO, IGF2BP2, CELF1 and HuR). The results show that DeepA-RBPBS correctly predicted 41,693 samples, where iDeepS predicted 31,381 samples.
Was this content written or created while at USF?
Yes
Citation / Publisher Attribution
Journal of Biomolecular Structure and Dynamics, v. 40, issue 9, p. 4250-4258
Scholar Commons Citation
Du, Zhihua; Xiao, Xiangdong; and Uversky, Vladimir N., "DeepA-rbpbs: A Hybrid Convolution and Recurrent Neural Network Combined with Attention Mechanism for Predicting RBP Binding Site" (2022). Molecular Medicine Faculty Publications. 970.
https://digitalcommons.usf.edu/mme_facpub/970
