Systematic benchmarking of microarray data classification: assessing the role of non-linearity and dimensionality reduction

• Published in: Bioinformatics 2004-11, Vol.20 (17), p.3185-3195
• Main Authors: Pochet, Nathalie, De Smet, Frank, Suykens, Johan A. K., De Moor, Bart L. R.
• Format: Article
• Language: English
• Subjects: Algorithms; Benchmarking - methods; Benchmarking - standards; Biological and medical sciences; Computer Simulation; Data Interpretation, Statistical; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; Gene Expression Profiling - standards; General aspects; Linear Models; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Genetic; Nonlinear Dynamics; Oligonucleotide Array Sequence Analysis - methods; Oligonucleotide Array Sequence Analysis - standards; Reproducibility of Results; Sensitivity and Specificity; Software; Stochastic Processes
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/bth383

Motivation: Microarrays are capable of determining the expression levels of thousands of genes simultaneously. In combination with classification methods, this technology can be useful to support clinical management decisions for individual patients, e.g. in oncology. The aim of this paper is to systematically benchmark the role of non-linear versus linear techniques and dimensionality reduction methods. Results: A systematic benchmarking study is performed by comparing linear versions of standard classification and dimensionality reduction techniques with their non-linear versions based on non-linear kernel functions with a radial basis function (RBF) kernel. A total of 9 binary cancer classification problems, derived from 7 publicly available microarray datasets, and 20 randomizations of each problem are examined. Conclusions: Three main conclusions can be formulated based on the performances on independent test sets. (1) When performing classification with least squares support vector machines (LS-SVMs) (without dimensionality reduction), RBF kernels can be used without risking too much overfitting. The results obtained with well-tuned RBF kernels are never worse and sometimes even statistically significantly better compared to results obtained with a linear kernel in terms of test set receiver operating characteristic and test set accuracy performances. (2) Even for classification with linear classifiers like LS-SVM with linear kernel, using regularization is very important. (3) When performing kernel principal component analysis (kernel PCA) before classification, using an RBF kernel for kernel PCA tends to result in overfitting, especially when using supervised feature selection. It has been observed that an optimal selection of a large number of features is often an indication for overfitting. Kernel PCA with linear kernel gives better results. Availability: Matlab scripts are available on request. Supplementary information: http://www.esat.kuleuven.ac.be/~npochet/Bioinformatics/