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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
Source PublicationAPPLIED SCIENCES-BASEL
ISSN2076-3417
Volume8Issue:1Pages:1-15
Abstract

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.

KeywordProtein-protein Interactions Position-specific Scoring Matrix Random Projection Ensemble Classifier Support Vector Machine
DOI10.3390/app8010089
Indexed BySCI
WOS IDWOS:000424388800089
Citation statistics
Cited Times:1[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.xjipc.cas.cn/handle/365002/5219
Collection多语种信息技术研究室
Corresponding AuthorYou, ZH (You, Zhu-Hong)
Affiliation1.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
Recommended Citation
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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