Feature weight estimation for gene selection: A local hyperlinear learning approach

Hongmin Cai*, Peiying Ruan, Kwok Po NG, Tatsuya Akutsu

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

42 Citations (Scopus)


Background: Modeling high-dimensional data involving thousands of variables is particularly important for gene expression profiling experiments, nevertheless,it remains a challenging task. One of the challenges is to implement an effective method for selecting a small set of relevant genes, buried in high-dimensional irrelevant noises. RELIEF is a popular and widely used approach for feature selection owing to its low computational cost and high accuracy. However, RELIEF based methods suffer from instability, especially in the presence of noisy and/or high-dimensional outliers.Results: We propose an innovative feature weighting algorithm, called LHR, to select informative genes from highly noisy data. LHR is based on RELIEF for feature weighting using classical margin maximization. The key idea of LHR is to estimate the feature weights through local approximation rather than global measurement, which is typically used in existing methods. The weights obtained by our method are very robust in terms of degradation of noisy features, even those with vast dimensions. To demonstrate the performance of our method, extensive experiments involving classification tests have been carried out on both synthetic and real microarray benchmark datasets by combining the proposed technique with standard classifiers, including the support vector machine (SVM), k-nearest neighbor (KNN), hyperplane k-nearest neighbor (HKNN), linear discriminant analysis (LDA) and naive Bayes (NB).Conclusion: Experiments on both synthetic and real-world datasets demonstrate the superior performance of the proposed feature selection method combined with supervised learning in three aspects: 1) high classification accuracy, 2) excellent robustness to noise and 3) good stability using to various classification algorithms.

Original languageEnglish
Article number70
JournalBMC Bioinformatics
Issue number1
Publication statusPublished - 14 Mar 2014

Scopus Subject Areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

User-Defined Keywords

  • Classification
  • Feature weighting
  • KNN
  • Local hyperplane


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