Skip to main content

Analysis of Gene Expression Data: Application of Quantum-Inspired Evolutionary Algorithm to Minimum Sum-of-Squares Clustering

  • Conference paper
Book cover Rough Sets, Fuzzy Sets, Data Mining, and Granular Computing (RSFDGrC 2005)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 3642))

Abstract

Microarray experiments have produced a huge amount of gene expression data. So it becomes necessary to develop effective clustering techniques to extract the fundamental patterns inherent in the data. In this paper, we propose a novel evolutionary algorithm so called quantum-inspired evolutionary algorithm (QEA) for minimum sum-of-squares clustering. We use a new representation form and add an additional mutation operation in QEA. Experiment results show that the proposed algorithm has better global search ability and is superior to some conventional clustering algorithms such as k-means and self-organizing maps.

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 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
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. Eisen, M., Spellman, P., Botstein, D.: Cluster Analysis and Display of Genome-wide Expression Patterns. In: Proceedings of the National Academy of Sciences, pp. 14863–14867 (1998)

    Google Scholar 

  2. Kohonen, T.: Self-Organizing Maps. Springer, Berlin (1997)

    MATH  Google Scholar 

  3. Tavazoie, S., et al.: Systematic Determination of Genetic Network Architecture. Nat. Genet. 22, 281–285 (1999)

    Article  Google Scholar 

  4. Shamir, R., Sharan, R.: Algorithmic Approaches to Clustering Gene Expression Data. In: Jiang, T., et al. (eds.) Current Topics in Computational Molecular Biology, pp. 269–299. MIT Press, Cambridge (2002)

    Google Scholar 

  5. Xu, Y., Olman, V., Xu, D.: Clustering Gene Expression Data Using a Graph-theoretic Approach: An Application of Minimum Spanning Trees. Bioinformatics 18, 536–545 (2002)

    Article  Google Scholar 

  6. Merz, P.: Analysis of Gene Expression Profiles: An Application of Memetic Algorithms to the Minimum Sum-of-squares Clustering Problem. Biosystem 72, 99–109 (2003)

    Article  Google Scholar 

  7. Brucker, P.: On the Complexity of Clustering Problems. Lecture Notes in Economics and Mathematical Systems, vol. 157, pp. 45–54 (1978)

    Google Scholar 

  8. Han, K., Kim, J.: Quantum-inspired Evolutionary Algorithm for a Class of Combinatorial Problem. IEEE transactions on evolutionary computation 6, 580–593 (2002)

    Article  Google Scholar 

  9. Han, K., Kim, J.: Genetic Quantum Algorithm and Its Application to Combinatorial Optimization Problem. In: Proceedings of the Congress on Evolutionary Computation, pp. 1354–1360 (2000)

    Google Scholar 

  10. Hey, T.: Quantum Computing: An Introduction. Computing & Control Engineering Journal 10, 105–112 (1999)

    Article  Google Scholar 

  11. Tamayo, P., Slonim, D., et al.: Interpreting Patterns of Gene Expression with Self-organizing Maps: Methods and Application to Hematopoietic Differentiation. In: Proceedings of the National Academy of Sciences, pp. 2907–2912 (1999)

    Google Scholar 

  12. Cho, R.J., Winzeler, E.A., Davis, R.W.: A Genome-wide Transcriptional Analysis of the Mitotic Cell Cycle. Mol. Cell 2, 65–73 (1998)

    Article  Google Scholar 

  13. Han, K., Kim, J.: On Setting the Parameters of Quantum-inspired Evolutionary Algorithm for Practical Applications. In: Proceedings of the Congress on Evolutionary Computation, pp. 178–184 (2003)

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2005 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Zhou, W., Zhou, C., Huang, Y., Wang, Y. (2005). Analysis of Gene Expression Data: Application of Quantum-Inspired Evolutionary Algorithm to Minimum Sum-of-Squares Clustering. In: Ślęzak, D., Yao, J., Peters, J.F., Ziarko, W., Hu, X. (eds) Rough Sets, Fuzzy Sets, Data Mining, and Granular Computing. RSFDGrC 2005. Lecture Notes in Computer Science(), vol 3642. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11548706_40

Download citation

  • DOI: https://doi.org/10.1007/11548706_40

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-28660-8

  • Online ISBN: 978-3-540-31824-8

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics