MaER: A New Ensemble Based Multiclass Classifier for Binding Activity Prediction of HLA Class II Proteins

Human Leukocyte Antigen class II (HLA II) proteins are crucial for the activation of adaptive immune response. In HLA class II molecules, high rate of polymorphisms has been observed. Hence, the accurate prediction of HLA II-peptide interactions is a challenging task that can both improve the understanding of immunological processes and facilitate decision-making in vaccine design. In this regard, during the last decade various computational tools have been developed, which were mainly focused on the binding activity prediction of different HLA II isotypes (such as DP, DQ and DR) separately. This fact motivated us to make a humble contribution towards the prediction of isotypes binding propensity as a multiclass classification task. In this regard, we have analysed a binding affinity dataset, which contains the interactions of 27 HLA II proteins with 636 variable length peptides, in order to prepare new multiclass datasets for strong and weak binding peptides. Thereafter, a new ensemble based multiclass classifier, called Meta EnsembleR (MaER) is proposed to predict the activity of weak/unknown binding peptides, by integrating the results of various heterogeneous classifiers. It pre-processes the training and testing datasets by making feature subsets, bootstrap samples and creates diverse datasets using principle component analysis, which are then used to train and test the MaER. The performance of MaER with respect to other existing state-of-the-art classifiers, has been estimated using validity measures, ROC curves and gain value analysis. Finally, a statistical test called Friedman test has been conducted to judge the statistical significance of the results produced by MaER.