Inferring protein interactions from sequence using support vector machine

Ming Guang Shi, Min Wu, De Shuang Huang, Xue Ling Li

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Data of protein-protein interactions derived from High-throughput technologies are often incomplete and fairly noisy. Therefore, it is very important to develop computational methods for predicting protein-protein interactions. A sequence-based method is proposed by combining support vector machine and a new feature representation using Geary autocorrelation. SVM model trained with Geary autocorrelation of amino acid sequence yielded the best performance with a high accuracy of 82.9% using gold standard positives (GSPs) PRS and gold standard negatives (GSNs) RRS datasets. Meanwhile, the SVM model has been successfully employed to predict the single core PPI network.

Original languageEnglish (US)
Title of host publication2009 International Joint Conference on Neural Networks, IJCNN 2009
Pages2903-2907
Number of pages5
DOIs
StatePublished - 2009
Externally publishedYes
Event2009 International Joint Conference on Neural Networks, IJCNN 2009 - Atlanta, GA, United States
Duration: Jun 14 2009Jun 19 2009

Other

Other2009 International Joint Conference on Neural Networks, IJCNN 2009
CountryUnited States
CityAtlanta, GA
Period6/14/096/19/09

Fingerprint

Support vector machines
Proteins
Autocorrelation
Computational methods
Amino acids
Throughput

ASJC Scopus subject areas

  • Software
  • Artificial Intelligence

Cite this

Shi, M. G., Wu, M., Huang, D. S., & Li, X. L. (2009). Inferring protein interactions from sequence using support vector machine. In 2009 International Joint Conference on Neural Networks, IJCNN 2009 (pp. 2903-2907). [5178660] https://doi.org/10.1109/IJCNN.2009.5178660

Inferring protein interactions from sequence using support vector machine. / Shi, Ming Guang; Wu, Min; Huang, De Shuang; Li, Xue Ling.

2009 International Joint Conference on Neural Networks, IJCNN 2009. 2009. p. 2903-2907 5178660.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Shi, MG, Wu, M, Huang, DS & Li, XL 2009, Inferring protein interactions from sequence using support vector machine. in 2009 International Joint Conference on Neural Networks, IJCNN 2009., 5178660, pp. 2903-2907, 2009 International Joint Conference on Neural Networks, IJCNN 2009, Atlanta, GA, United States, 6/14/09. https://doi.org/10.1109/IJCNN.2009.5178660
Shi MG, Wu M, Huang DS, Li XL. Inferring protein interactions from sequence using support vector machine. In 2009 International Joint Conference on Neural Networks, IJCNN 2009. 2009. p. 2903-2907. 5178660 https://doi.org/10.1109/IJCNN.2009.5178660
Shi, Ming Guang ; Wu, Min ; Huang, De Shuang ; Li, Xue Ling. / Inferring protein interactions from sequence using support vector machine. 2009 International Joint Conference on Neural Networks, IJCNN 2009. 2009. pp. 2903-2907
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