Active Learning Using Fuzzy-Rough Nearest Neighbor Classifier for Cancer Prediction from Microarray Gene Expression Data

Abstract

Cancer prediction from gene expression data is a very challenging area of research in the field of computational biology and bioinformatics. Conventional classifiers are often unable to achieve desired accuracy due to the lack of ‘sufficient’ training patterns in terms of clinically labeled samples. Active learning technique, in this respect, can be useful as it automatically finds only few most informative (or confusing) samples to get their class labels from the experts and those are added to the training set, which can improve the accuracy of the prediction consequently. A novel active learning technique using fuzzy-rough nearest neighbor classifier (ALFRNN) is proposed in this paper for cancer classification from microarray gene expression data. The proposed ALFRNN method is capable of dealing with the uncertainty, overlapping and indiscernibility often present in cancer subtypes (classes) of the gene expression data. The performance of the proposed method is tested using different real-life microarray gene expression cancer datasets and its performance is compared with five other state-of-the-art techniques (out of which three are active learning-based and two are traditional classification methods) in terms of percentage accuracy, precision, recall, [Formula: see text]-measures and kappa. Superiority of the proposed method over the other counterpart algorithms is established from experimental results for cancer prediction and results of the paired [Formula: see text]-test confirm statistical significance of the results in favor of the proposed method for almost all the datasets.