3 years ago

Identification of DNA–protein binding sites by bootstrap multiple convolutional neural networks on sequence information

Yongqing Zhang, Shaojie Qiao, Shengjie Ji, Nan Han, Dingxiang Liu, Jiliu Zhou

Publication date: March 2019

Source: Engineering Applications of Artificial Intelligence, Volume 79

Author(s): Yongqing Zhang, Shaojie Qiao, Shengjie Ji, Nan Han, Dingxiang Liu, Jiliu Zhou


Identification of DNA–protein binding sites in protein sequence plays an essential role in a wide variety of biological processes. In particular, there are huge volumes of protein sequences accumulated in the post-genomic era. In this study, we propose a new prediction approach appropriate for imbalanced DNA–protein binding sites data. Specifically, motivated by the imbalanced problem of the distribution of DNA–protein binding and non-binding sites, we employ the Adaptive Synthetic Sampling (ADASYN) approach to over-sample the positive data and Bootstrap strategy to under-sample the negative data to balance the number of the binding and non-binding samples. Furthermore, we employ the three types of features: the position specific scoring matrix, one-hot encoding and predicted solvent accessibility, to encode the sequence-based feature of each protein residue. In addition, we design an ensemble convolutional neural network classifier to handle the imbalance problem between binding and non-binding sites in protein sequence. Extensive experiments were conducted on the real DNA–protein binding sites dataset, PDNA-543, PDNA-224 and PDNA-316, in order to validate the effectiveness of our method on predicting the binding sites by ten-fold cross-validation metric. The experimental results demonstrate that our method achieves a high prediction performance and outperforms the state-of-the-art sequence-based DNA–protein binding sites predictors in terms of the Sensitivity, Specificity, Accuracy, Precision and Mathew’s Correlation Coefficient (MCC). Our method can obtain the MCC values of 0.63, 0.48 and 0.67 on PDNA-543, PDNA-224 and PDNA-316 datasets, respectively. Compared with the state-of-the art prediction models, the MCC values for our method are increased by at least 0.24, 0.13 and 0.23 on PDNA-543, PDNA-224 and PDNA-316 datasets, respectively.

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