Robust twin boosting for feature selection from high-dimensional omics data with label noise

Shan He, Huanhuan Chen, Zexuan Zhu, Douglas G. Ward, Helen J. Cooper, Mark R. Viant, John K. Heath, Xin Yao

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)
568 Downloads (Pure)

Abstract

Omics data such as microarray transcriptomic and mass spectrometry proteomic data are typically characterized by high dimensionality and relatively small sample sizes. In order to discover biomarkers for diagnosis and prognosis from omics data, feature selection has become an indispensable step to find a parsimonious set of informative features. However, many previous studies report considerable label noise in omics data, which will lead to unreliable inferences to select uninformative features. Yet, to the best of our knowledge, very few feature selection methods are proposed to address this problem. This paper proposes a novel ensemble feature selection algorithm, robust twin boosting feature selection (RTBFS), which is robust to label noise in omics data. The algorithm has been validated on an omics feature selection test bed and seven real-world heterogeneous omics datasets, of which some are known to have label noise. Compared with several state-of-the-art ensemble feature selection methods, RTBFS can select more informative features despite label noise and obtain better classification results. RTBFS is a general feature selection method and can be applied to other data with label noise. MATLAB implementation of RTBFS and sample datasets are available at: http://www.cs.bham.ac.uk/∼szh/TReBFSMatlab.zip.
Original languageEnglish
Pages (from-to)1-18
Number of pages18
JournalInformation Sciences
Volume291
Early online date30 Aug 2014
DOIs
Publication statusPublished - 1 Jan 2015

Keywords

  • Boosting
  • Ensemble learning
  • Feature selection

ASJC Scopus subject areas

  • Artificial Intelligence
  • Software
  • Control and Systems Engineering
  • Theoretical Computer Science
  • Computer Science Applications
  • Information Systems and Management

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