Feature Selection from Microarray Data via an Ordered Search with Projected Margin

Abstract

Microarray experiments are capable of measuring the expression level of thousands of genes simultaneously. Dealing with this enormous amount of information requires complex computation. Support Vector Machines (SVM) have been widely used with great efficiency to solve classification problems that have high dimension. In this sense, it is plausible to develop new feature selection strategies for microarray data that are associated with this type of classifier. Therefore, we propose, in this paper, a new method for feature selection based on an ordered search process to explore the space of possible subsets. The algorithm, called Admissible Ordered Search (AOS), uses as evaluation function the margin values estimated for each hypothesis by a SVM classifier. An important theoretical contribution of this paper is the development of the projected margin concept. This value is computed as the margin vector projection on a lower dimensional subspace and is used as an upper bound for the current value of the hypothesis in the search process. This enables great economy in runtime and consequently efficiency in the search process as a whole. The algorithm was tested using five different microarray data sets yielding superior results when compared to three representative feature selection methods.