A PSO-based rank aggregation algorithm for ranking genes from microarray data

  • Authors:
  • Monalisa Mandal;Anirban Mukhopadhyay

  • Affiliations:
  • University of Kalyani, West Bengal, India;University of Kalyani, West Bengal, India

  • Venue:
  • Proceedings of the 17th Panhellenic Conference on Informatics
  • Year:
  • 2013

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Abstract

In microarray analysis, gene relevance is measured according to the level of differential expression of the gene and this level of differential expression decides the rank of that gene. Ranking the disease-related genes has major impact on disease classification and prediction. Several statistical tests exist in literature for ranking the genes with respect to their abilities to distinguish different classes of samples. However, none of these methods can perform well for all kinds of datasets. Therefore the scientists have applied rank aggregation techniques to obtain a consensus ranking of the genes from the rankings produced by different methods. In this article, we have posed the problem of rank aggregation as an optimization problem for minimizing the average distance of the output ranking from the input rankings. In this regard, a novel particle swarm optimization (PSO)-based algorithm is proposed for minimizing this distance. The well-known Kendall's Tau distance measure has been used for this purpose. The performance of the proposed algorithm is compared with that of different existing rank aggregation methods and evaluated using one artificial and two real-life datasets.