SELECTING GENES FROM GENE EXPRESSION DATA BY USING AN ENHANCEMENT OF BINARY PARTICLE SWARM OPTIMIZATION FOR CANCER CLASSIFICATION

Mohd Saberi Mohamad, Sigeru Omatu, Michifumi Yoshioka, Safaai Deris

Abstract

In order to select a small subset of informative genes from gene expression data for cancer classification, recently, many researchers are analyzing gene expression data using various computational intelligence methods. However, due to the small number of samples compared to the huge number of genes (high-dimension), irrelevant genes, and noisy genes, many of the computational methods face difficulties to select the small subset. Thus, we propose an enhancement of binary particle swarm optimization to select a small subset of informative genes that is relevant for classifying cancer samples more accurately. In this proposed method, three approaches have been introduced to increase the probability of bits in particle’s positions to be zero. By performing experiments on three different gene expression data sets, we have found that the performance of the proposed method is superior to other previous related works, including the conventional version of binary particle swarm optimization (BPSO) in terms of classification accuracy and the number of selected genes. The proposed method also produces lower running times compared to BPSO.

References

  1. Chuang, L. Y., Chang, H. W., Tu, C. J. and Yang, C. H. (2008). Improved Binary PSO for Feature Selection Using Gene Expression Data. Computational Biology and Chemistry, 32, 29-38.
  2. doi:10.1016/j.compbiolchem.2007.09.005
  3. Kennedy, J. and Eberhart, R. 1995. Particle swarm optimization. In Proceeding of the 1995 IEEE International Conference on Neural Networks, 4, 1942-1948. IEEE Press. Retrieved from: IEEE Xplore Digital Library.
  4. Kennedy, J. and Eberhart, R. 1997. A discrete binary version of the particle swarm algorithm. In Proceeding of the 1997 IEEE International. Conference on Systems, Man, and Cybernetics, 5, 4104-4108. IEEE Press. Retrieved from: IEEE Xplore Digital Library.
  5. Knudsen, S. (2002). A Biologist's Guide to Analysis of DNA Microarray Data (1st ed.). New York: John Wiley & Sons.
  6. Li, S., Wu, X. and Tan, M. (2008). Gene Selection Using Hybrid Particle Swarm Optimization and Genetic Algorithm. Soft Computing, 12, 1039-1048. doi:10.1007/s00500-007-0272-x
  7. Mohamad, M. S., Omatu, S., Yoshioka, M. and Deris, S. (2009). A Cyclic Hybrid Method to Select a Smaller Subset of Informative Genes for Cancer Classification. International Journal of Innovative Computing, Information and Control, 5(8), 2189-2202.
  8. Shen, Q., Shi, W. M. and Kong, W. Hybrid Particle Swarm Optimization and Tabu Search Approach for Selecting Genes for Tumor Classification Using Gene Expression Data. Computational Biology and Chemistry, 32, 53-60. doi:10.1016/j.compbiolchem. 2007.10.001
Download


Paper Citation


in Harvard Style

Saberi Mohamad M., Omatu S., Yoshioka M. and Deris S. (2010). SELECTING GENES FROM GENE EXPRESSION DATA BY USING AN ENHANCEMENT OF BINARY PARTICLE SWARM OPTIMIZATION FOR CANCER CLASSIFICATION . In Proceedings of the 2nd International Conference on Agents and Artificial Intelligence - Volume 1: ICAART, ISBN 978-989-674-021-4, pages 82-89. DOI: 10.5220/0002732300820089


in Bibtex Style

@conference{icaart10,
author={Mohd Saberi Mohamad and Sigeru Omatu and Michifumi Yoshioka and Safaai Deris},
title={SELECTING GENES FROM GENE EXPRESSION DATA BY USING AN ENHANCEMENT OF BINARY PARTICLE SWARM OPTIMIZATION FOR CANCER CLASSIFICATION},
booktitle={Proceedings of the 2nd International Conference on Agents and Artificial Intelligence - Volume 1: ICAART,},
year={2010},
pages={82-89},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0002732300820089},
isbn={978-989-674-021-4},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 2nd International Conference on Agents and Artificial Intelligence - Volume 1: ICAART,
TI - SELECTING GENES FROM GENE EXPRESSION DATA BY USING AN ENHANCEMENT OF BINARY PARTICLE SWARM OPTIMIZATION FOR CANCER CLASSIFICATION
SN - 978-989-674-021-4
AU - Saberi Mohamad M.
AU - Omatu S.
AU - Yoshioka M.
AU - Deris S.
PY - 2010
SP - 82
EP - 89
DO - 10.5220/0002732300820089