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Prediction of Protein–Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures

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Abstract

Accurately predicting protein–protein interaction sites (PPIs) is currently a hot topic because it has been demonstrated to be very useful for understanding disease mechanisms and designing drugs. Machine-learning-based computational approaches have been broadly utilized and demonstrated to be useful for PPI prediction. However, directly applying traditional machine learning algorithms, which often assume that samples in different classes are balanced, often leads to poor performance because of the severe class imbalance that exists in the PPI prediction problem. In this study, we propose a novel method for improving PPI prediction performance by relieving the severity of class imbalance using a data-cleaning procedure and reducing predicted false positives with a post-filtering procedure: First, a machine-learning-based data-cleaning procedure is applied to remove those marginal targets, which may potentially have a negative effect on training a model with a clear classification boundary, from the majority samples to relieve the severity of class imbalance in the original training dataset; then, a prediction model is trained on the cleaned dataset; finally, an effective post-filtering procedure is further used to reduce potential false positive predictions. Stringent cross-validation and independent validation tests on benchmark datasets demonstrated the efficacy of the proposed method, which exhibits highly competitive performance compared with existing state-of-the-art sequence-based PPIs predictors and should supplement existing PPI prediction methods.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (No. 61373062, 61233011, and 61222306), the Jiangsu Postdoctoral Science Foundation (No. 1201027C), the Natural Science Foundation of Jiangsu (No. BK20141403), the China Postdoctoral Science Foundation (No. 2014T70526 and 2013 M530260), the Fundamental Research Funds for the Central Universities (No. 30920130111010), and “The Six Top Talents” of Jiangsu Province (No. 2013-XXRJ-022).

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Authors and Affiliations

  1. School of Computer Science and Engineering, Nanjing University of Science and Technology, Xiaolingwei 200, Nanjing, 210094, China

    Guang-Hui Liu & Dong-Jun Yu

  2. School of Information Engineering, Nanjing University of Finance & Economics, Nanjing, 210046, China

    Guang-Hui Liu

  3. Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, Dongchuan Road 800, Shanghai, 200240, China

    Hong-Bin Shen

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Liu, GH., Shen, HB. & Yu, DJ. Prediction of Protein–Protein Interaction Sites with Machine-Learning-Based Data-Cleaning and Post-Filtering Procedures. J Membrane Biol 249, 141–153 (2016). https://doi.org/10.1007/s00232-015-9856-z

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