ANMM4CBR: a case-based reasoning method for gene expression data classification

Abstract

Abstract Background Accurate classification of microarray data is critical for successful clinical diagnosis and treatment. The "curse of dimensionality" problem and noise in the data, however, undermines the performance of many algorithms. Method In order to obtain a robust classifier, a novel Additive Nonparametric Margin Maximum for Case-Based Reasoning (ANMM4CBR) method is proposed in this article. ANMM4CBR employs a case-based reasoning (CBR) method for classification. CBR is a suitable paradigm for microarray analysis, where the rules that define the domain knowledge are difficult to obtain because usually only a small number of training samples are available. Moreover, in order to select the most informative genes, we propose to perform feature selection via additively optimizing a nonparametric margin maximum criterion, which is defined based on gene pre-selection and sample clustering. Our feature selection method is very robust to noise in the data. Results The effectiveness of our method is demonstrated on both simulated and real data sets. We show that the ANMM4CBR method performs better than some state-of-the-art methods such as support vector machine (SVM) and k nearest neighbor (kNN), especially when the data contains a high level of noise. Availability The source code is attached as an additional file of this paper.</p