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Open Access Highly Accessed Methodology article

A balanced iterative random forest for gene selection from microarray data

Ali Anaissi1*, Paul J Kennedy1, Madhu Goyal1 and Daniel R Catchpoole2

Author Affiliations

1 Centre for Quantum Computation & Intelligent Systems (QCIS), Faculty of Engineering and Information Technology (FEIT), University of Technology, Sydney (UTS), Broadway New South Wales 2007, Australia

2 The Tumour Bank, Children’s Cancer Research Unit, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead New South Wales 2145, Australia

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BMC Bioinformatics 2013, 14:261  doi:10.1186/1471-2105-14-261

Published: 27 August 2013

Abstract

Background

The wealth of gene expression values being generated by high throughput microarray technologies leads to complex high dimensional datasets. Moreover, many cohorts have the problem of imbalanced classes where the number of patients belonging to each class is not the same. With this kind of dataset, biologists need to identify a small number of informative genes that can be used as biomarkers for a disease.

Results

This paper introduces a Balanced Iterative Random Forest (BIRF) algorithm to select the most relevant genes for a disease from imbalanced high-throughput gene expression microarray data. Balanced iterative random forest is applied on four cancer microarray datasets: a childhood leukaemia dataset, which represents the main target of this paper, collected from The Children’s Hospital at Westmead, NCI 60, a Colon dataset and a Lung cancer dataset. The results obtained by BIRF are compared to those of Support Vector Machine-Recursive Feature Elimination (SVM-RFE), Multi-class SVM-RFE (MSVM-RFE), Random Forest (RF) and Naive Bayes (NB) classifiers. The results of the BIRF approach outperform these state-of-the-art methods, especially in the case of imbalanced datasets. Experiments on the childhood leukaemia dataset show that a 7% ∼ 12% better accuracy is achieved by BIRF over MSVM-RFE with the ability to predict patients in the minor class. The informative biomarkers selected by the BIRF algorithm were validated by repeating training experiments three times to see whether they are globally informative, or just selected by chance. The results show that 64% of the top genes consistently appear in the three lists, and the top 20 genes remain near the top in the other three lists.

Conclusion

The designed BIRF algorithm is an appropriate choice to select genes from imbalanced high-throughput gene expression microarray data. BIRF outperforms the state-of-the-art methods, especially the ability to handle the class-imbalanced data. Moreover, the analysis of the selected genes also provides a way to distinguish between the predictive genes and those that only appear to be predictive.