Skip to main content

Analysis of Cancer Data Using Evolutionary Computation

  • Chapter
  • First Online:
Computational Biology
  • 1422 Accesses

Abstract

We present several methods based on evolutionary computation for classification of oncology data. The results in comparisons with other existing techniques show that our evolutionary computation-based methods are superior in most cases. Evolutionary computation is effective in this study because it can offer efficiency in searching in high-dimension space, particularly in nonlinear optimization and hard optimization problems. The first part of this chapter is the review of some previous work on cancer classification. The second part is an overview of evolutionary computation. The third part focuses on methods based on evolutionary computation and their applications on oncology data. Finally, this chapter concludes with some remarks and suggestions for further investigation.

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 179.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 229.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
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

  • Alba E., Laguna M., Luque G. (2005). “Workforce planning with a parallel genetic algorithm.” Proceedings of CEDI-MAEB’05: 911–919.

    Google Scholar 

  • Alon U., Barkai N., et al. (1999). “Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays.” Proc Natl Acad Sci USA 96: 6745–6750.

    Article  PubMed  CAS  Google Scholar 

  • Andre D., Koza J.R. (1996). “Parallel genetic programming: a scalable implementation using the transputer network architecture,” in Advances in Genetic Programming 2, Cambridge, MA, MIT Press.

    Google Scholar 

  • Bittner M., Meltzer P., Chen Y., et al. (2000). “Molecular classification of cutaneous malignant melanoma by gene expression profiling.” Nature 406, 536–540.

    Article  PubMed  CAS  Google Scholar 

  • Calegari P., Guidec F., Kuonen P., Kobler D. (1997). “Parallel island-based genetic algorithm for radio network design.” Journal of Parallel and Distributed Computing 47(1): 86–90.

    Article  Google Scholar 

  • Chong K.P.E., Zak H.S. (2001). An Introduction to Optimization. New York, John Wiley & Sons.

    Google Scholar 

  • Dettling M., Buhlmann P. (2003). “Boosting for tumor classification with gene expression data.” Bioinformatics 19: 1061–1069.

    Article  PubMed  CAS  Google Scholar 

  • Dudoit S., Fridlyand J., et al. (2002). “Comparison of discrimination methods for the classification of tumors using gene expression data.” Journal of the American Statistical Association 97: 77–87.

    Article  CAS  Google Scholar 

  • Erick Cantu-Paz (2001). Efficient and Accurate Parallel Genetic Algorithms. Kluwer Academic Publishers.

    Google Scholar 

  • Fernandez de Vega F. (2005). “Parallel genetic programming,” Workshop of the 2005 IEEE Congress on Evolutionary Computation.

    Google Scholar 

  • Freitas A.A. (2002). Data Mining and Knowledge Discovery with Evolutionary Algorithms. Berlin, Springer Verlag.

    Google Scholar 

  • Furey T.S., Cristianini N., et al. (2000). “Support vector machine classification and validation of cancer tissue samples using microarray expression data.” Bioinformatics 16: 906–914.

    Article  PubMed  CAS  Google Scholar 

  • Golub T.R., Slonim D.K., et al. (1999). “Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.” Science 286: 531–537.

    Article  PubMed  CAS  Google Scholar 

  • Gray H.F., Maxwell R.J., et al. (1996). “Genetic programming for classification of brain tumours from nuclear magnetic resonance biopsy spectra.” Genetic Programming 1996: Proceedings of the First Annual Conference: 28–31.

    Google Scholar 

  • Grunenfelder B., Rummel G., Vohradsky J., Roder D., Langen H., Jenal U. (2001). “Proteomic analysis of the bacterial cell cycle.” Proc Natl Acad Sci USA, 98(8):4681–4686.

    Article  PubMed  CAS  Google Scholar 

  • Guyon I., Weston J., et al. (2002). “Gene selection for cancer classification using support vector machines.” Machine Learning 46: 389–422.

    Article  Google Scholar 

  • Juille H., Pollack J.B. (1995). “Parallel genetic programming and fine-grained SIMD architecture” in Working Notes for The AAAI Symp. 31–37.

    Google Scholar 

  • Khan J., Wei J.S., et al. (2001). “Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks.” Nature Medicine 7: 673–679.

    Article  PubMed  CAS  Google Scholar 

  • Koza J.R. (1992). Genetic Programming: on the Programming of Computers by Means of Natural Selection. London, MIT Press.

    Google Scholar 

  • Lee Y., Lee C.-K. (2003). “Classification of multiple cancer types by multicategory support vector machines using gene expression data.” Bioinformatics 19: 1132–1139.

    Article  PubMed  CAS  Google Scholar 

  • Liu J.J., Cutler G., et al. (2005). “Multiclass cancer classification and biomarker discovery using GA-based algorithms.” Bioinformatics 21: 2691–2697.

    Article  PubMed  CAS  Google Scholar 

  • Mangasarian O.L., Street W.N., Wolberg W.H. (1995). “Breast cancer diagnosis and prognosis via linear programming.” Operations Research, 43(4), pages 570–577.

    Google Scholar 

  • Mitchell M. (2001). An Introduction to Genetic Algorithm. London, MIT Press.

    Google Scholar 

  • Nguyen D.V., Rocke D.M. (2002). “Tumor classification by partial least squares using microarray gene expression data.” Bioinformatics 18: 39–50.

    Article  PubMed  CAS  Google Scholar 

  • Perou C.M., Jeffery S.S., et al. (1999). “Distinctive gene expression patterns in human mammary epithelial cells and breast cancers.” Proc Natl Acad Sci USA 96: 9212–9217.

    Article  PubMed  CAS  Google Scholar 

  • Petricoin E.F., Ardekani A.M., et al. (2002). “Use of proteomic patterns in serum to identify ovarian cancer.” The Lancet 359: 9306, 572–577.

    Article  CAS  Google Scholar 

  • Pham T.D. (2008). “Computational prediction models for cancer classification using mass spectrometry data.” Int. J. Data Mining and Bioinformatics, Vol. 2, No. 4: 405–422.

    Article  Google Scholar 

  • Punch W.F. (1998). “How effective are multiple populations in genetic programming.” Proceedings of the Third Annual Genetic Programming Conference: 313–318.

    Google Scholar 

  • Scholkopf B., Smola J.A. (2002). Learning with Kernels. MIT Press.

    Google Scholar 

  • Street W.N., Wolberg W.H., Mangasarian O.L. (1993). “Nuclear feature extraction for breast tumor diagnosis.” IS&T/SPIE 1993 International Symposium on Electronic Imaging: Science and Technology 1905: 861–870.

    Google Scholar 

  • Su M., Basu M., et al. (2002). “Multi-domain gating network for classification of cancer cells using gene expression data.” Proceedings of the International Joint Conference on Neural Networks 1: 286–289.

    Google Scholar 

  • Toure A., Basu M. (2001). “Application of neural network to gene expression data for cancer classification.” Proceedings of the International Joint Conference on Neural Networks 1: 583–587.

    Google Scholar 

  • Vohradsky J., Janda I., Grunenfelder B., Berndt P., Roder D., Langen H., Weiser J., Jenal U. (2003). “Proteome of Caulobacter crescentus cell cycle publicly accessible on SWICZ server.” Proteomics, 3(10):1874–1882.

    Article  PubMed  CAS  Google Scholar 

  • Zhang H., Yu C.-Y., et al. (2001). “Recursive partitioning for tumor classification with gene expression microarray data.” Proc Natl Acad Sci USA 98: 6730–6735.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Cuong C. To .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

To, C.C., Pham, T. (2009). Analysis of Cancer Data Using Evolutionary Computation. In: Pham, T. (eds) Computational Biology. Applied Bioinformatics and Biostatistics in Cancer Research. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-0811-7_6

Download citation

Publish with us

Policies and ethics