Skip to main content

Ensemble Neural Networks with Novel Gene-Subsets for Multiclass Cancer Classification

  • Conference paper
Neural Information Processing (ICONIP 2007)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4985))

Included in the following conference series:

  • 1154 Accesses

Abstract

Multiclass gene selection and classification of cancer are rapidly gaining attention in recent years, while conventional rank-based gene selection methods depend on predefined ideal marker genes that basically devised for binary classification. In this paper, we propose a novel gene selection method based on a gene’s local class discriminability, which does not require any ideal marker genes for multiclass classification. An ensemble classifier with multiple NNs is trained with the gene subsets. The Global Cancer Map (GCM) cancer dataset is used to verify the proposed method for comparisons with the conventional approaches.

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 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight 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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Hong, J.-H., Cho, S.-B.: Efficient huge-scale feature selection with speciated genetic algorithm. Pattern Recognition Letter 27(2), 143–150 (2006)

    Article  Google Scholar 

  2. Deutsch, J.: Evolutionary algorithms for finding optimal gene sets in microarray prediction. Bioinformatics 19(1), 45–52 (2003)

    Article  Google Scholar 

  3. Lee, Y., Lee, C.-K.: Classification of multiple cancer types by multicategory support vector machines using gene expression data. Bioinformatics 19(9), 1132–1139 (2003)

    Article  Google Scholar 

  4. Li, T., Zhang, C., Ogihara, M.: A comparative study of feature selection and multiclass classification methods for tissue classification based on gene expression. Bioinformatics 20(15), 2429–2437 (2004)

    Article  Google Scholar 

  5. Yeang, C.-H., Ramaswamy, S., Tamayo, P., Mukherjee, S., Rifkin, R., Angelo, M., Reich, M., Lander, E., Mesirov, J., Golub, T.: Molecular classification of multiple tumor types. Bioinformatics 17(1), 316–322 (2001)

    Google Scholar 

  6. Wang, Y., Makedon, F., Ford, J., Pearlman, J.: HykGene: A hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data. Bioinformatics 21(8), 1530–1537 (2005)

    Article  Google Scholar 

  7. Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J., Poggio, T., Gerald, W., Loda, M., Lander, E., Golub, T.: Multiclass cancer diagnosis using tumor gene expression signatures. Proc. National Academy of Science 98(26), 15149–15154 (2001)

    Article  Google Scholar 

  8. Hsu, A., Tang, S.-L., Halgamuge, S.: An unsupervised hierarchical dynamic self-organized approach to cancer class discovery and marker gene identification in microarray data. Bioinformatics 19(16), 2131–2140 (2003)

    Article  Google Scholar 

  9. Ooi, C., Tan, P.: Genetic algorithms applied to multi-class prediction for the analysis of gene expression data. Bioinformatics 19(1), 37–44 (2003)

    Article  Google Scholar 

  10. Zhou, X., Liu, K.-Y., Wong, S.: Cancer classification and prediction using logistic regression with Bayesian gene selection. J. Biomedical Informatics 37(4), 249–259 (2004)

    Article  Google Scholar 

  11. Liu, J., Cutler, G., Li, W., Pan, Z., Peng, S., Hoey, T., Chen, L., Ling, X.: Multiclass cancer classification and biomarker discovery using GA-based algorithms. Bioinformatics 21(11), 2691–2697 (2005)

    Article  Google Scholar 

  12. Statnikov, A., Aliferis, C., Tsamardinos, L., Hardin, D., Levy, S.: A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis. Bioinformatics 21(5), 631–643 (2005)

    Article  Google Scholar 

  13. Tan, A., Naiman, D., Xu, L., Winslow, R., Geman, D.: Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics 21(20), 3896–3904 (2005)

    Article  Google Scholar 

  14. Yeung, K.-Y., Bumgarner, R., Raftery, A.: Bayesian model averaging: Development of an improved multi-class, gene selection and classification tool for microarray data. Bioinformatics 21(10), 2394–2402 (2005)

    Article  Google Scholar 

  15. Hong, J.-H., Cho, S.-B.: Multi-class cancer classification with OVR-support vector machines selected by naive Bayes classifier. In: King, I., Wang, J., Chan, L.-W., Wang, D. (eds.) ICONIP 2006. LNCS, vol. 4234, pp. 155–164. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

  16. Zhang, W., Rekaya, R., Bertrand, K.: A method for predicting disease subtypes in presence of misclassification among training samples using gene expression: Application to human breast cancer. Bioinformatics 22(3), 317–325 (2006)

    Article  Google Scholar 

  17. Cho, S.-B., Ryu, J.-W.: Classifying gene expression data of cancer using classifier ensemble with mutually exclusive features. Proceedings of the IEEE 90(11), 1744–1753 (2002)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Masumi Ishikawa Kenji Doya Hiroyuki Miyamoto Takeshi Yamakawa

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Hong, JH., Cho, SB. (2008). Ensemble Neural Networks with Novel Gene-Subsets for Multiclass Cancer Classification. In: Ishikawa, M., Doya, K., Miyamoto, H., Yamakawa, T. (eds) Neural Information Processing. ICONIP 2007. Lecture Notes in Computer Science, vol 4985. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69162-4_89

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-69162-4_89

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-69159-4

  • Online ISBN: 978-3-540-69162-4

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics