Hybrid biogeography based simultaneous feature selection and MHC class I peptide binding prediction using support vector machines and random forests

作者：Srivastava Atulji; Ghosh Shameek; Anantharaman N; Jayaraman V K^*

来源：Journal of Immunological Methods, 2013, 387(1-2): 284-292.

DOI：10.1016/j.jim.2012.09.013

• MHC class I peptide binding prediction
• CoEPrA classification and regression
• Feature selection
• Weighted heuristics
• Biogeography based optimization
• SVM and random forests

Accurate detection of peptides binding to specific Major Histocompatibility Complex Class I (MHC-I) molecules is extremely important for understanding the underlying process of the immune system, as well as for effective vaccine design and developing immunotherapies. Development of learning algorithms and their application for binding predictions have thus speeded up the state-of-the-art in immunological research, in a cost-effective manner. In this work, we propose the application of a hybrid filter-wrapper algorithm employing concepts from the recently developed biogeography based optimization algorithm, in conjunction with SVM and Random Forests for identification of MIC-I binding peptides. In the process, we demonstrate the effectiveness of this evolutionary technique, coupled with weighted heuristics, for the construction of improved prediction models. The experiments have been carried out for the CoEPrA competition datasets (accessible online at: http://www.coepra.org) and the results show a marked improvement over the winner results in some situations and comparably good with regard to others. We thus hope to initiate further research on the application of this new bio-inspired methodology for immunological research.

• 出版日期2013-1