RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks.

Authors:
Zhen Shen
Zhen Shen
Nanjing University
China
Su-Ping Deng
Su-Ping Deng
Ocean University of China
China
De-Shuang Huang
De-Shuang Huang
Hefei Institute of Intelligent Machines
China

IEEE/ACM Trans Comput Biol Bioinform 2019 Apr 11. Epub 2019 Apr 11.

RNA-Protein binding plays important roles in the field of gene expression. With the development of high throughput sequencing, several conventional methods and deep learning-based methods have been proposed to predict the binding preference of RNA-protein binding. These methods can hardly meet the need of consideration of the dependencies between subsequence and the various motif lengths of different translation factors (TFs). To overcome such limitations, we propose a predictive model that utilizes a combination of multi-scale convolutional layers and bidirectional gated recurrent unit (GRU) layer. Multi-scale convolution layer has the ability to capture the motif features of different lengths, and bidirectional GRU layer is able to capture the dependencies among subsequence. Experimental results show that the proposed method performs better than four art-of-the-state methods in this field. In addition, we investigate the effect of model structure on model performance by performing our proposed method with different convolution layer and different number of kernel size. We also demonstrate the effectiveness of bidirectional GRU in improving model performance through comparative experiments.

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Source
http://dx.doi.org/10.1109/TCBB.2019.2910513DOI Listing
April 2019

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