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Using ABC Algorithm with Shrinkage Estimator to Identify Biomarkers of Ovarian Cancer from Mass Spectrometry Analysis

  • Syarifah Adilah Mohamed Yusoff
  • Rosni Abdullah
  • Ibrahim Venkat
Part of the Lecture Notes in Computer Science book series (LNCS, volume 8073)

Abstract

Biomarker discovery through mass spectrometry analysis has continuously intrigued researchers from various fields such as analytical researchers, computer scientists and mathematicians. The uniqueness of this study relies on the ability of the proteomic patterns to detect particular disease especially at the early stage. However, identification through high-throughput mass spectrometry analysis raises some challenges. Typically, it suffers from high dimensionality of data with tens of thousands attributes and high level of redundancy and noises. Hence this study will focus on two stages of mass spectrometry pipelines; firstly we propose shrinkage estimation of covariance to evaluate the discriminant characteristics among peaks of mass spectrometry data for feature extraction; secondly a sophisticated computational technique that mimic survival and natural processing which is called as Artificial Bee Colony (ABC) as feature selection is integrated with linear SVM classifier for this biomarker discovery analysis. The proposed method is tested with real-world ovarian cancer dataset to evaluate the discrimination power, accuracy, sensitivity and also specificity.

Keywords

metaheuristic feature selection swarm algorithm bio-inspired algorithm classification feature extraction 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Syarifah Adilah Mohamed Yusoff
    • 1
    • 2
  • Rosni Abdullah
    • 1
  • Ibrahim Venkat
    • 1
  1. 1.School of Computer SciencesUniversiti Sains MalaysiaMalaysia
  2. 2.Dept Computer Sciences and MathematicsUniversiti Teknologi MARA Pulau PinangMalaysia

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