Protein subnuclear localization based on a new effective representation and intelligent kernel linear discriminant analysis by dichotomous greedy genetic algorithm

Abstract

A wide variety of methods have been proposed in protein subnuclear localization to improve the prediction accuracy. However, one important trend of these means is to treat fusion representation by fusing multiple feature representations, of which, the fusion process takes a lot of time. In view of this, this paper novelly proposed a method by combining a new single feature representation and a new algorithm to obtain good recognition rate. Specifically, based on the position-specific scoring matrix (PSSM), we proposed a new expression, correlation position-specific scoring matrix (CoPSSM) as the protein feature representation. Based on the classic nonlinear dimension reduction algorithm, kernel linear discriminant analysis (KLDA), we added a new discriminant criterion and proposed a dichotomous greedy genetic algorithm (DGGA) to intelligently select its kernel bandwidth parameter. Two public datasets with Jackknife test and KNN classifier were used for the numerical experiments. The results showed that the overall success rate (OSR) with single representation CoPSSM is larger than that with many relevant representations. The OSR of the proposed method can reach as high as 87.444% and 90.3361% for these two datasets, respectively, outperforming many current methods. To show the generalization of the proposed algorithm, two extra standard datasets of protein subcellular were chosen to conduct the expending experiment, and the prediction accuracy by Jackknife test and Independent test is still considerable.