Evaluating switching neural networks through artificial and real gene expression data

Abstract

OBJECTIVE DNA microarrays offer the possibility of analyzing the expression level for thousands of genes concerning a specific tissue. An important target of this analysis is to derive the subset of genes involved in a biological process of interest. Here, a new promising method for gene selection is proposed, which presents a good level of accuracy and reliability. METHODS AND MATERIALS The proposed technique adopts switching neural networks (SNN), a particular kind of connectionist models, to assign a relevance value to each gene, thus employing recursive feature addition (RFA) to derive the final list of relevant genes. To fairly evaluate the quality of the new approach, called SNN-RFA, its application on three real and three artificial gene expression datasets, generated according to a proper mathematical model that possesses biological and statistical plausibility, has been considered. In particular, a comparison with other two widely used gene selection methods, namely the signal to noise ratio (S2N) and support vector machines with recursive feature elimination (SVM-RFE), has been performed. RESULTS In all the considered cases SNN-RFA achieves the best performances, arriving to determine the whole collection of relevant genes in one of the three artificial datasets. The S2N method exhibits a quality similar to that of SNN-RFA, whereas SVM-RFE shows the worst behavior. CONCLUSION The quality of the proposed method SNN-RFA has been established together with the usefulness of the mathematical model adopted to generate the artificial datasets of gene expression levels.

DOI: 10.1016/j.artmed.2008.08.002

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@article{Muselli2009EvaluatingSN, title={Evaluating switching neural networks through artificial and real gene expression data}, author={Marco Muselli and Massimiliano Costacurta and Francesca Ruffino}, journal={Artificial intelligence in medicine}, year={2009}, volume={45 2-3}, pages={163-71} }