Prediction of MHC II-binding peptides using rough set-based rule sets ensemble

摘要

Peptide binding to Major Histocompatibility Complex (MHC) is a prerequisite for any T cell-mediated immune response. Predicting which peptides can bind to a specific MHC molecule is indispensable to minimizing the number of peptides required to synthesize, to the development of vaccines and immunotherapy of cancer, and to aiding to understand the specificity of T-cell mediated immunity. At present, although predictions based on machine learning methods have good prediction performance, they cannot acquire understandable knowledge and prediction performance can be further improved. Thereupon, the Rule Sets ENsemble (RSEN) algorithm, which takes advantage of diverse attribute and attribute value reduction algorithms based on rough set (RS) theory, is proposed as the initial trial to acquire understandable rules along with enhancement of prediction performance. Finally, the RSEN is applied to predict the peptides that bind to HLA-DR4(B1* 0401). Experimentation results show: (1) prepositional rules for predicting the peptides that bind to HLA-DR4 (B1* 0401) are obtained; (2) compared with individual RS-based algorithms, the RSEN has a significant decrease (13%–38%) in prediction error rate; (3) compared with the Back-Propagation Neural Networks (BPNN), prediction error rate of the RSEN decreases by 4%–16%. The acquired rules have been applied to help experts make molecules modeling.