Skip to main content

Feature Selection Using Multi-Objective Optimization Technique for Supervised Cancer Classification

  • Chapter
  • First Online:
Multi-Objective Optimization

Abstract

In this chapter, a new multi-objective blended particle swarm optimization (MOBPSO) technique is proposed for the selection of significant and informative genes from the cancer datasets. As the basic optimization algorithm suffers from the local trapping, a blended Laplacian operator is integrated with it to overcome the drawback. The concept is also implemented for differential evolution, artificial bee colony, genetic algorithm and subsequently multi-objective blended differential evolution (MOBDE), multi-objective blended artificial bee colony (MOBABC) and multi-objective blended genetic algorithm (MOBGA) are proposed to extract the relevant genes from the cancer datasets. Proposed methodology utilizes two objective functions to sort out the genes which are differentially expressed from class to class as well as provides good results for the classification of disease. Experimental result reveals that the proposed methodology very efficiently selects differential and biologically relevant genes which are effective for the classification of disease which in turn offers more useful information about the gene–disease association.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • P. Agarwalla, S. Mukhopadhyay, Selection of relevant genes for pediatric leukemia using co-operative Multiswarm. Mater. Today Proc. 3(10), 3328–3336 (2016)

    Article  Google Scholar 

  • U. Alon, N. Barkai, D.A. Notterman, K. Gish, S. Ybarra, D. Mack, A.J. Levine, Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. 96(12), 6745–6750 (1999)

    Article  Google Scholar 

  • J. Apolloni, G. LeguizamĂ³n, E. Alba, Two hybrid wrapper-filter feature selection algorithms applied to high-dimensional microarray experiments. Appl. Soft Comput. 38, 922–932 (2016)

    Article  Google Scholar 

  • S. Bandyopadhyay, S. Mallik, A. Mukhopadhyay, A survey and comparative study of statistical tests for identifying differential expression from microarray data. IEEE/ACM Trans. Comput. Biol. Bioinform. 11(1), 95–115 (2014)

    Article  Google Scholar 

  • K.H. Chen, K.J. Wang, M.L. Tsai, K.M. Wang, A.M. Adrian, W.C. Cheng, K.S. Chang, Gene selection for cancer identification: a decision tree model empowered by particle swarm optimization algorithm. BMC Bioinform. 15(1), 49 (2014)

    Article  Google Scholar 

  • M.H. Cheok, W. Yang, C.H. Pui, J.R. Downing, C. Cheng, C.W. Naeve, W.E. Evans, Treatment-specific changes in gene expression discriminate in vivo drug response in human leukemia cells. Nat. Genet. 34(1), 85–90 (2003)

    Article  Google Scholar 

  • K. Deb, A. Pratap, S. Agarwal, T.A.M.T. Meyarivan, A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Trans. Evol. Comput. 6(2), 182–197 (2002)

    Article  Google Scholar 

  • T.R. Golub, D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J.P. Mesirov, C.D. Bloomfield, Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439), 531–537 (1999)

    Google Scholar 

  • A.O. Hero, G. Fluery, Pareto-optimal methods for gene filtering. J. Am. Stat. Assoc. (JASA) (2002)

    Google Scholar 

  • Y. Hippo, H. Taniguchi, S. Tsutsumi, N. Machida, J.M. Chong, M. Fukayama, H. Aburatani, Global gene expression analysis of gastric cancer by oligonucleotide microarrays. Cancer Res. 62(1), 233–240 (2002)

    Google Scholar 

  • D. Karaboga, B. Basturk, A powerful and efficient algorithm for numerical function optimization: artificial bee colony (ABC) algorithm. J. Glob. Optim. 39(3), 459–471 (2007)

    Article  MathSciNet  Google Scholar 

  • J. Kennedy, Particle swarm optimization. Encyclopedia of Machine Learning (Springer, US, 2011), pp. 760–766

    Google Scholar 

  • N. Khunlertgit, B.J. Yoon, Identification of robust pathway markers for cancer through rank-based pathway activity inference. Adv. Bioinform. (2013)

    Google Scholar 

  • S.B. Kotsiantis, I. Zaharakis, P. Pintelas, Supervised machine learning: a review of classification techniques (2007)

    Google Scholar 

  • L.K. Luo, D.F. Huang, L.J. Ye, Q.F. Zhou, G.F. Shao, H. Peng, Improving the computational efficiency of recursive cluster elimination for gene selection. IEEE/ACM Trans. Comput. Biol. Bioinform. 8(1), 122–129 (2011)

    Article  Google Scholar 

  • M.S. Mohamad, S. Omatu, S. Deris, M.F. Misman, M. Yoshioka, A multi-objective strategy in genetic algorithms for gene selection of gene expression data. Artif. Life Robot. 13(2), 410–413 (2009)

    Article  Google Scholar 

  • A. Mukhopadhyay, M. Mandal, Identifying non-redundant gene markers from microarray data: a multiobjective variable length PSO-based approach. IEEE/ACM Trans. Comput. Biol. Bioinform. (TCBB) 11(6), 1170–1183 (2014)

    Article  Google Scholar 

  • K. Price, R.M. Storn, J.A. Lampinen,  Differential Evolution: A Practical Approach to Global Optimization (Springer Science & Business Media, 2006)

    Google Scholar 

  • H. Salem, G. Attiya, N. El-Fishawy, Classification of human cancer diseases by gene expression profiles. Appl. Soft Comput. 50, 124–134 (2017)

    Article  Google Scholar 

  • N. Srinivas, K. Deb, Muiltiobjective optimization using nondominated sorting in genetic algorithms. Evol. Comput. 2(3), 221–248 (1994)

    Article  Google Scholar 

  • A.V. Ushakov, X. Klimentova, I. Vasilyev, Bi-level and bi-objective p-median type problems for integrative clustering: application to analysis of cancer gene-expression and drug-response data. IEEE/ACM Trans. Comput. Biol. Bioinform. (2016)

    Google Scholar 

  • J. Yang, V. Honavar, Feature subset selection using a genetic algorithm. IEEE Intell. Syst. Appl. 13(2), 44–49 (1998)

    Article  Google Scholar 

  • L. Zhang, J. Kuljis, X. Liu, Information visualization for DNA microarray data analysis: a critical review. IEEE Trans. Syst. Man Cybern. Part C Appl. Rev. 38(1), 42–54 (2008)

    Google Scholar 

  • Q. Zhang, H. Li, MOEA/D: a multiobjective evolutionary algorithm based on decomposition. IEEE Trans. Evol. Comput. 11(6), 712–731 (2007)

    Article  Google Scholar 

  • C.H. Zheng, W. Yang, Y.W. Chong, J.F. Xia, Identification of mutated driver pathways in cancer using a multi-objective optimization model. Comput. Biol. Med. 72, 22–29 (2016)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to P. Agarwalla .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Agarwalla, P., Mukhopadhyay, S. (2018). Feature Selection Using Multi-Objective Optimization Technique for Supervised Cancer Classification. In: Mandal, J., Mukhopadhyay, S., Dutta, P. (eds) Multi-Objective Optimization. Springer, Singapore. https://doi.org/10.1007/978-981-13-1471-1_9

Download citation

  • DOI: https://doi.org/10.1007/978-981-13-1471-1_9

  • Published:

  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-13-1470-4

  • Online ISBN: 978-981-13-1471-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics