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Gene selection and prediction for cancer classification using support vector machines with a reject option

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  • Choi, Hosik
  • Yeo, Donghwa
  • Kwon, Sunghoon
  • Kim, Yongdai

Abstract

In cancer classification based on gene expression data, it would be desirable to defer a decision for observations that are difficult to classify. For instance, an observation for which the conditional probability of being cancer is around 1/2 would preferably require more advanced tests rather than an immediate decision. This motivates the use of a classifier with a reject option that reports a warning in cases of observations that are difficult to classify. In this paper, we consider a problem of gene selection with a reject option. Typically, gene expression data comprise of expression levels of several thousands of candidate genes. In such cases, an effective gene selection procedure is necessary to provide a better understanding of the underlying biological system that generates data and to improve prediction performance. We propose a machine learning approach in which we apply the l1 penalty to the SVM with a reject option. This method is referred to as the l1 SVM with a reject option. We develop a novel optimization algorithm for this SVM, which is sufficiently fast and stable to analyze gene expression data. The proposed algorithm realizes an entire solution path with respect to the regularization parameter. Results of numerical studies show that, in comparison with the standard l1 SVM, the proposed method efficiently reduces prediction errors without hampering gene selectivity.

Suggested Citation

  • Choi, Hosik & Yeo, Donghwa & Kwon, Sunghoon & Kim, Yongdai, 2011. "Gene selection and prediction for cancer classification using support vector machines with a reject option," Computational Statistics & Data Analysis, Elsevier, vol. 55(5), pages 1897-1908, May.
  • Handle: RePEc:eee:csdana:v:55:y:2011:i:5:p:1897-1908
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    References listed on IDEAS

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    1. Peter Hall & J. S. Marron & Amnon Neeman, 2005. "Geometric representation of high dimension, low sample size data," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(3), pages 427-444, June.
    2. Lukas Meier & Sara Van De Geer & Peter Bühlmann, 2008. "The group lasso for logistic regression," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(1), pages 53-71, February.
    3. Hao Helen Zhang & Grace Wahba & Yi Lin & Meta Voelker & Michael Ferris & Ronald Klein & Barbara Klein, 2004. "Variable Selection and Model Building via Likelihood Basis Pursuit," Journal of the American Statistical Association, American Statistical Association, vol. 99, pages 659-672, January.
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    1. Drechsler, Jörg & Reiter, Jerome P., 2011. "An empirical evaluation of easily implemented, nonparametric methods for generating synthetic datasets," Computational Statistics & Data Analysis, Elsevier, vol. 55(12), pages 3232-3243, December.
    2. Pedro Duarte Silva, A., 2011. "Two-group classification with high-dimensional correlated data: A factor model approach," Computational Statistics & Data Analysis, Elsevier, vol. 55(11), pages 2975-2990, November.

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