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An Ensemble Classifier with Random Projection for Predicting Protein-Protein Interactions Using Sequence and Evolutionary Information
Song, XY (Song, Xiao-Yu); Chen, ZH (Chen, Zhan-Heng); Sun, XY (Sun, Xiang-Yang); You, ZH (You, Zhu-Hong); Li, LP (Li, Li-Ping); Zhao, Y (Zhao, Yang)
2018
发表期刊APPLIED SCIENCES-BASEL
ISSN2076-3417
卷号8期号:1页码:1-15
摘要

Identifying protein-protein interactions (PPIs) is crucial to comprehend various biological processes in cells. Although high-throughput techniques generate many PPI data for various species, they are only a petty minority of the entire PPI network. Furthermore, these approaches are costly and time-consuming and have a high error rate. Therefore, it is necessary to design computational methods for efficiently detecting PPIs. In this study, a random projection ensemble classifier (RPEC) was explored to identify novel PPIs using evolutionary information contained in protein amino acid sequences. The evolutionary information was obtained from a position-specific scoring matrix (PSSM) generated from PSI-BLAST. A novel feature fusion scheme was then developed by combining discrete cosine transform (DCT), fast Fourier transform (FFT), and singular value decomposition (SVD). Finally, via the random projection ensemble classifier, the performance of the presented approach was evaluated on Yeast, Human, and H. pylori PPI datasets using 5-fold cross-validation. Our approach achieved high prediction accuracies of 95.64%, 96.59%, and 87.62%, respectively, effectively outperforming other existing methods. Generally speaking, our approach is quite promising and supplies a practical and effective method for predicting novel PPIs.

关键词Protein-protein Interactions Position-specific Scoring Matrix Random Projection Ensemble Classifier Support Vector Machine
DOI10.3390/app8010089
收录类别SCI
WOS记录号WOS:000424388800089
引用统计
文献类型期刊论文
条目标识符http://ir.xjipc.cas.cn/handle/365002/5219
专题多语种信息技术研究室
通讯作者You, ZH (You, Zhu-Hong)
作者单位1.Lanzhou Jiaotong Univ, Sch Elect & Informat Engn, Lanzhou 730070, Gansu, Peoples R China
2.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi 830011, Xinjiang, Peoples R China
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GB/T 7714
Song, XY ,Chen, ZH ,Sun, XY ,et al. An Ensemble Classifier with Random Projection for Predicting Protein-Protein Interactions Using Sequence and Evolutionary Information[J]. APPLIED SCIENCES-BASEL,2018,8(1):1-15.
APA Song, XY ,Chen, ZH ,Sun, XY ,You, ZH ,Li, LP ,&Zhao, Y .(2018).An Ensemble Classifier with Random Projection for Predicting Protein-Protein Interactions Using Sequence and Evolutionary Information.APPLIED SCIENCES-BASEL,8(1),1-15.
MLA Song, XY ,et al."An Ensemble Classifier with Random Projection for Predicting Protein-Protein Interactions Using Sequence and Evolutionary Information".APPLIED SCIENCES-BASEL 8.1(2018):1-15.
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