Skip to main content

Dimensionality Reduction for Microarray Data Using Local Mean Based Discriminant Analysis

  • Conference paper

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 7996))

Abstract

In this paper we propose a new method for finding a low dimensional subspace of high dimensional microarray data. We developed a new criterion for constructing the weight matrix by using local neighborhood information to discover the intrinsic discriminant structure in the data. Also this approach applies regularized least square technique to extract relevant features. We assess the performance of the proposed methodology by applying it to four publicly available tumor datasets. In a low dimensional subspace, the proposed method classified these tumors accurately and reliably. Also, through a comparison study, the reliability of the dimensionality reduction and discrimination results is verified.

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

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   54.99
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

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Wang, H.Q., Huang, D.S.: A Gene Selection Algorithm based on the Gene Regulation Probability using Maximal Likelihood Estimation. Bitotechnol. Lett. 27, 597–603 (2005)

    Article  Google Scholar 

  2. Payton, P., Kottapalli, K.R., Kebede, H., Mahan, J.R., Wright, R.J., Allen, R.D.: Examining the Drought Stress Transcriptome in Cotton Leaf And Root Tissue. Bitotechnol. Lett. 33, 821–828 (2011)

    Article  Google Scholar 

  3. Joliffe, I.: Principal Component Analysis. Springer (1986)

    Google Scholar 

  4. Fukunnaga, K.: Introduction to Statistical Pattern Recognition, 2nd edn. Academic Press (1991)

    Google Scholar 

  5. Roweis, S.T., Saul, L.K.: Nonlinear Dimensionality Reduction by Locally Linear Embedding. Science 290, 2323–2326 (2000)

    Article  Google Scholar 

  6. He, X., Niyogi, P.: Locality Preserving Projections. In: Adv. Neural Inf. Process Syst. MIT Press (2004)

    Google Scholar 

  7. Ye, J.: Characterization of a Family of Algorithms for Generalized Discriminant Analysis on Undersampled Problems. J. Mach. Learn. Res. 6, 483–502 (2005)

    MathSciNet  MATH  Google Scholar 

  8. Golub, T.R., Slonim, D.K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J.P., Coller, H., Loh, M.L., Downing, J.R., Caligiuri, M.A., Bloomfield, C.D., Lander, E.S.: Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. Science 286, 531–537 (1999)

    Article  Google Scholar 

  9. Singh, D., Febbo, P.G., Ross, K., Jackson, D.G., Manola, J., Ladd, C., Tamayo, P., Renshaw, A.A., D’Amico, A.V., Richie, J.P., Lander, E.S., Loda, M., Kantoff, P.W., Golub, T.R., Sellers, W.R.: Gene Expression Correlates of Clinical Prostate Cancer Behavior. Cancer Cell 1, 203–209 (2002)

    Article  Google Scholar 

  10. Khan, J., Wei, J.S., Ringner, M., Saal, L.H., Ladanyi, M., Westermann, F., Berthold, F., Schwab, M., Antonescu, C.R., Peterson, C., Meltzer, P.S.: Classification and Diagnostic Prediction of Cancers using Gene Expression Profiling and Artificial Neural Networks. Nat. Med. 7, 673–679 (2001)

    Article  Google Scholar 

  11. Bhattacharjee, A., Richards, W.G., Staunton, J., Li, C., Monti, S., Vasa, P., Ladd, C., Beheshti, J., Bueno, R., Gillette, M.: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Subclasses. Proc. Natl. Acad. Sci. USA 98, 13790–13795 (2001)

    Article  Google Scholar 

  12. Zelnik-Manor, L., Perona, P.: Self-tuning Spectral Clustering. In: Adv. Neural. Inf. Process Syst., vol. 17, pp. 1601–1608. MIT Press, Cambridge (2005)

    Google Scholar 

  13. Golub, G.H., Loan, C.F.V.: Matrix Computations, 3rd edn. Johns Hopkins University Press (1996)

    Google Scholar 

  14. Cai D., He X., Han J.: Spectral Regression for Dimensionality Reduction. UIUCDCS-R-2007-2856 (2007)

    Google Scholar 

  15. Paige, C.C., Saunders, M.A.: LSQR: An Algorithm for Sparse Linear Equations and Sparse Least Squares. ACM Trans. Math. Softw. 8, 43–71 (1982)

    Article  MathSciNet  MATH  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Cui, Y., Zheng, CH., Yang, J. (2013). Dimensionality Reduction for Microarray Data Using Local Mean Based Discriminant Analysis. In: Huang, DS., Jo, KH., Zhou, YQ., Han, K. (eds) Intelligent Computing Theories and Technology. ICIC 2013. Lecture Notes in Computer Science(), vol 7996. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-39482-9_31

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-39482-9_31

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-39481-2

  • Online ISBN: 978-3-642-39482-9

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics