Computational methods for the prediction of Major Histocompatibility Complex (MHC) class Ⅱ binding peptides play an important role in facilitating the understanding of immune recognition and the process of epitope discovery.To develop an effective computational method, we need to consider two important characteristics of the problem: (1) the length of binding peptides is highly flexible;and (2) MHC molecules are extremely polymorphic and for the vast majority of them there are no sufficient training data.