Interactive Semi-Supervised Learning for Microarray Analysis

Yijuan Lu, Qi Tian, Feng Liu, Maribel Sanchez, Yufeng Wang

Research output: Contribution to journalArticle

Abstract

Microarray technology has generated vast amounts of gene expression data with distinct patterns. Based on the premise that genes of correlated functions tend to exhibit similar expression patterns, various machine learning methods have been applied to capture these specific patterns in microarray data. However, the discrepancy between the rich expression profiles and the limited knowledge of gene functions has been a major hurdle to the understanding of cellular networks. To bridge this gap so as to properly comprehend and interpret expression data, we introduce Relevance Feedback to microarray analysis and propose an interactive learning framework to incorporate the expert knowledge into the decision module. In order to find a good learning method and solve two intrinsic problems in microarray data: high dimensionality and small sample size, we also propose a semi-supervised learning algorithm: Kernel Discriminant-EM (KDEM). This algorithm efficiently utilizes a large set of unlabeled data to compensate for the insufficiency of a small set of labeled data and it extends linear algorithm in Discriminant-EM (DEM) to kernel algorithm to handle nonlinearly separable data in a lower dimensional space. Relevance Feedback technique and KDEM together construct an efficient and effective interactive semi-supervised learning framework for microarray analysis. Extensive experiments on the yeast cell cycle regulation data set and Plasmodium falciparum red blood cell cycle data set show the promise of this approach.

Original languageEnglish (US)
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
DOIs
StateAccepted/In press - Jan 1 2018

Keywords

  • Bridges
  • Cells (biology)
  • Feedback
  • Fungi
  • Gene expression
  • Kernel
  • Kernel DEM
  • Land mobile radio cellular systems
  • Learning systems
  • microarray analysis
  • Red blood cells
  • Relevance Feedback
  • semi-supervised learning
  • Semisupervised learning

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics

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