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Bioinformatics Vol. 19 no. 17 2003
pages 2246-2253
© 2003 Oxford University Press

A simple and efficient algorithm for gene selection using sparse logistic regression

S. K. Shevade 1 and S. S. Keerthi 2,*

1 Department of Computer Science and Automation, Indian Institute of Science, Bangalore 560012, India and 2 Control Division, Department of Mechanical Engineering, National University of Singapore, Singapore 117576, Republic of Singapore

Received on November 30, 2002 ; revised on March 12, 2003 ; accepted on May 29, 2003

Motivation: This paper gives a new and efficient algorithm for the sparse logistic regression problem. The proposed algorithm is based on the Gauss–Seidel method and is asymptotically convergent. It is simple and extremely easy to implement; it neither uses any sophisticated mathematical programming software nor needs any matrix operations. It can be applied to a variety of real-world problems like identifying marker genes and building a classifier in the context of cancer diagnosis using microarray data.

Results: The gene selection method suggested in this paper is demonstrated on two real-world data sets and the results were found to be consistent with the literature.

Availability: The implementation of this algorithm is available at the site http://guppy.mpe.nus.edu.sg/~mpessk/SparseLOGREG.shtml

Supplementary Information: Supplementary material is available at the site http://guppy.mpe.nus.edu.sg/~mpessk/SparseLOGREG.shtml

Contact: mpessk{at}nus.edu.sg

* To whom correspondence should be addressed.


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