Metasample-based sparse representation for tumor classification

Chun Hou Zheng, Lei Zhang, Vincent To Yee Ng, Chi Keung Simon Shiu, De Shuang Huang

Research output: Journal article publicationJournal articleAcademic researchpeer-review

96 Citations (Scopus)

Abstract

A reliable and accurate identification of the type of tumors is crucial to the proper treatment of cancers. In recent years, it has been shown that sparse representation (SR) by l1-norm minimization is robust to noise, outliers and even incomplete measurements, and SR has been successfully used for classification. This paper presents a new SR-based method for tumor classification using gene expression data. A set of metasamples are extracted from the training samples, and then an input testing sample is represented as the linear combination of these metasamples by l1-regularized least square method. Classification is achieved by using a discriminating function defined on the representation coefficients. Since l1-norm minimization leads to a sparse solution, the proposed method is called metasample-based SR classification (MSRC). Extensive experiments on publicly available gene expression data sets show that MSRC is efficient for tumor classification, achieving higher accuracy than many existing representative schemes.
Original languageEnglish
Article number5708133
Pages (from-to)1273-1282
Number of pages10
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume8
Issue number5
DOIs
Publication statusPublished - 21 Jun 2011

Keywords

  • gene expression data
  • metasample
  • sparse representation
  • Tumors classification

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Applied Mathematics
  • Medicine(all)

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