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Open Access Highly Accessed Methodology article

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

Hongmin Cai1*, Peiying Ruan2, Michael Ng3 and Tatsuya Akutsu2

Author Affiliations

1 School of Computer Science and Engineering, South China University of Technology, Guangdong, China

2 Institute for Chemical Research, Kyoto University, Kyoto, Japan

3 Department of Mathematics, Hong Kong Baptist University, Hong Kong, China

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BMC Bioinformatics 2014, 15:70  doi:10.1186/1471-2105-15-70

Published: 14 March 2014

Abstract

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.

Keywords:
Feature weighting; Local hyperplane; Classification; RELIEF; KNN