Pancreatic cancer biomarker detection using recursive feature elimination based on Support Vector Machine and large margin distribution machine

Abstract

Pancreatic cancer acts as one of the leading causes of cancer-connective deaths. Its five-year overall survival rate being reported is about 7.7% from 2006 to 2012 by the National Cancer Institute. One of the main causes for its poor prognosis is because its non-typical symptoms make early diagnosis very challenging. Therefore, a predominant strategy for early accurate detection and prognostication on pancreatic cancer is vital to the whole course of comprehensive therapy. In this research, we proposed a method which combined Recursive Feature Elimination (RFE) method based on Support Vector Machine (SVM) and Large Margin Distribution Machine (LDM) to identify potential biomarkers for pancreatic cancer. In our experiments, we have strengthened the process of RFE to achieve better performance. The dataset GSE15471 we adopted are from GEO database with 39 pairs of pancreatic ductal carcinoma and adjacent control pancreatic tissues. Through experiments, a panel of twelve genes was identified as biomarkers in pancreatic cancer with 91.28% classification accuracy. The universality of the candidate genes was examined on another dataset GSE28735 and the classification accuracy was higher than 80%. In addition, by using the SVM, LDM and BP classifiers, we compared the ordered feature sets generated by our proposed method with T-test, SVM-RFE and LDM-RFE, and the results indicated our proposed method obtained higher average classification accuracy.