Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data

  • Authors:
  • Miguel GarcíA-Torres;RubéN ArmañAnzas;Concha Bielza;Pedro LarrañAga

  • Affiliations:
  • Área de Lenguajes y Sistemas Informáticos. Universidad Pablo de Olavide. Ctra de Utrera, km. 1, 41013 Sevilla, Spain;Computational Intelligence Group, Universidad Politécnica de Madrid. 28660, Boadilla del Monte, Madrid, Spain;Computational Intelligence Group, Universidad Politécnica de Madrid. 28660, Boadilla del Monte, Madrid, Spain;Computational Intelligence Group, Universidad Politécnica de Madrid. 28660, Boadilla del Monte, Madrid, Spain

  • Venue:
  • Information Sciences: an International Journal
  • Year:
  • 2013

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Abstract

Mass spectrometry (MS) data provide a promising strategy for biomarker discovery. For this purpose, the detection of relevant peakbins in MS data is currently under intense research. Data from mass spectrometry are challenging to analyze because of their high dimensionality and the generally low number of samples available. To tackle this problem, the scientific community is becoming increasingly interested in applying feature subset selection techniques based on specialized machine learning algorithms. In this paper, we present a performance comparison of some metaheuristics: best first (BF), genetic algorithm (GA), scatter search (SS) and variable neighborhood search (VNS). Up to now, all the algorithms, except for GA, have been first applied to detect relevant peakbins in MS data. All these metaheuristic searches are embedded in two different filter and wrapper schemes coupled with Naive Bayes and SVM classifiers.