Title

The application of wavelet-based neural network on DNA microarray data

Authors

Jack Lee¹ and Benny Zee^1, *

Affiliation

¹Centre for Clinical Trials, School of Public Health; Department of Clinical Oncology, the Chinese University of Hong Kong, Hong Kong

Email

bzee@cct.cuhk.edu.hk; *Corresponding author

Article Type

Hypothesis

Date

received May 05, 2008;  accepted December 05, 2008; accepted December 10, 2008; ;published December 31, 2008

Abstract

The advantage of using DNA microarray data when investigating human cancer gene expressions is its ability to generate enormous amount of information from a single assay in order to speed up the scientific evaluation process. The number of variables from the gene expression data coupled with comparably much less number of samples creates new challenges to scientists and statisticians. In particular, the problems include enormous degree of collinearity among genes expressions, likely violation of model assumptions as well as high level of noise with potential outliers. To deal with these problems, we propose a block wavelet shrinkage principal component (BWSPCA) analysis method to optimize the information during the noise reduction process. This paper firstly uses the National Cancer Institute database (NC160) as an illustration and shows a significant improvement in dimension reduction. Secondly we combine BWSPCA with an artificial neural network-based gene minimization strategy to establish a Block Wavelet-based Neural Network model in a robust and accurate cancer classification process (BWNN). Our extensive experiments on six public cancer datasets have shown that the method of BWNN for tumor classification performed well, especially on some difficult instances with large-class (more than two) expression data. This proposed method is extremely useful for data denoising and is competitiveness  with respect  to other methods such as BagBoost, RandomForest (RanFor), Support Vector Machines (SVM), K-Nearest Neighbor (KNN) and Artificial Neural Network (ANN).

Keywords

wavelet shrinkage; denoising; ANN; classification of cancer types

Citation

 Lee & Zee, Bioinformation 3(5): 223-229 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.