Understanding the Prediction of Transmembrane Proteins by Support Vector Machine using Association Rule Mining

Abstract

With the efforts to understand protein structure, many computational approaches have been made recently. Among them, the support vector machine (SVM) methods have been recently applied and showed successful performance compared with other machine learning schemes. However, despite the high performance, the SVM approaches suffer from the problem of understandability since it is a black-box model. To overcome this limitation, this study attempted to combine the SVM with the association rule based classifier which can present the meaningful explanation about the prediction. To perform this task, a new association rule based classifier (PCPAR) was devised based on the existing classifier, CPAR, to handle the sequential data. PCPAR creates the patterns by merging the generated rules and then classifies the sequential data based on the pattern match. The experimental result presents the following: with sequential data, the PCPAR scheme shows better performance with respect to the accuracy and the number of generated patterns than CPAR method whether applied alone or combined with SVM. The combined scheme of SVMPCPAR generates more compact patterns than the combined scheme of SVM with decision tree, SVM DT, with similar performance. These patterns are easily understandable and biologically meaningful