F-score with Pareto Front Analysis for Multiclass Gene Selection

Authors:
Piyushkumar A. Mundra;Jagath C. Rajapakse
Affiliations:
Bioinformatics Research Center, School of Computer Engineering, Nanyang Technological University, Singapore;Bioinformatics Research Center, School of Computer Engineering, Nanyang Technological University, Singapore and Singapore-MIT Alliance, Singapore and Department of Biological Engineering, Massachu ...
Venue:
EvoBIO '09 Proceedings of the 7th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics
Year:
2009

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Abstract

F-score is a widely used filter criteria for gene selection in multiclass cancer classification. This ranking criterion may become biased towards classes that have surplus of between-class sum of squares, resulting in inferior classification performance. To alleviate this problem, we propose to compute individual class wise between-class sum of squares with Pareto frontal analysis to rank genes. We tested our approach on four multiclass cancer gene expression datasets and the results show improvement in classification performance.