[go: up one dir, main page]
More Web Proxy on the site http://driver.im/ skip to main content
10.5555/1786194.1786337guideproceedingsArticle/Chapter ViewAbstractPublication PagesConference Proceedingsacm-pubtype
Article

A parallel classification and feature reduction method for biomedical applications

Published: 09 September 2007 Publication History

Abstract

Classification is one of the most widely used methods in data mining, with numerous applications in biomedicine. The scope and the resolution of data involved in many real life applications require very efficient implementations of classification methods, developed to run on parallel or distributed computational systems. In this study we describe SVD-ReGEC, a fully parallel implementation, for distributed memory multicomputers, of a classification algorithm with a feature reduction. The classification is based on Regularized Generalized Eigenvalue Classifier (ReGEC) and the preprocessing stage is a filter method algorithm based on Singular Value Decomposition (SVD), that reduces the dimension of the space in which classification is accomplished. The implementation is tested on random datasets and results are discussed using standard parameters.

References

[1]
Cannataro, M., Talia, D., Srimani, P.: Parallel data intensive computing in scientific and commercial applications. Par. Comp. 28(5), 673-704 (2002).
[2]
Oja, E.: A simplified neuron model as a principal component analyzer. Journal of Mathematical Biology 15, 267-273 (1982).
[3]
Wall, M., Dyck, P., Brettin, T.: SVDMAN - Singular Value Decomposition analysis of microarray data. Bioinformatics 17(6), 566-568 (2001).
[4]
Golub, T., et al.: Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286, 531-537 (1999).
[5]
Vapnik, V.: The Nature of Statistical Learning Theory. Springer, Heidelberg (1995).
[6]
Osuna, R., Girosi, F.: An improved training algorithm for support vector machines. In: IEEE Workshop on Neural Networks for Signal Processing, pp. 276-285 (1997).
[7]
Platt, J.: Fast training of SVMs using sequential minimal optimization. In: Advances in Kernel Methods: Support Vector Learning, pp. 185-208. MIT press, Cambridge (1999).
[8]
Graf, H., Cosatto, E., Bottou, L., Dourdanovic, I., Vapnik Parallel, V.: support vector machines: the cascade SVM. In: Press, M. (ed.) Proc. of Neural Information Processing Systems (NIPS), vol. 17 (2004).
[9]
Mangasarian, O., Wild, E.: Multisurface proximal support vector classification via generalized eigenvalues. Technical Report 04-03, Data Mining Institute (September 2004).
[10]
Guarracino, M.R., Cifarelli, C., Seref, O., Pardalos, P.M.: A classification algorithm based on generalized eigenvalue problems. Opt. Meth. Soft. 22(1), 73-81 (2007).
[11]
Duda, R., Hart, P., Stork, D.: Pattern Classification. Wiley-Interscience Publication, Chichester (2000).
[12]
Yan, R.: A matlab package for classification algorithms (2006), http://finalfantasyxi.inf.cs.cmu.edu/tmp/MATLABArsenal.zip
[13]
Hedenfalk, I., et al.: Gene-expression profiles in hereditary breast cancer. The New England Journal of Medicine 344, 539-548 (2001).
[14]
Nutt, C., et al.: Oligonucleotide microarray for prediction of early intrahepatic recurrence of hepatocelllaur carcinoma after curative resection. The Lancet 63(7), 1602-1607 (2003).
[15]
Blake, C., Merz, C.: Uci repository of machine learning databases (1998), www.ics.uci.edu/~mlearn/MLRepository.html
[16]
Dongarra, J., Whaley, R.: A user's guide to the blacs v1.1. Technical Report UT-CS-95-281, Dept. of CS, U. of Tennessee, Knoxville (1995).
[17]
Gropp, W., Lusk, E., Skjellum, A.: Using MPI: Portable Parallel Programming with the Message Passing Interface, 2nd edn. The MIT Press, Cambridge (1999).
[18]
Choi, J., Demmel, J., Dhillon, I., Dongarra, J., Ostrouchov, S., Petitet, A., Stanley, K., Walker, D., Whaley, R.: Scalapack: A portable linear algebra library for distributed memory computers - design and performance. Comp. Phys. Comm. (97), 1-15 (1996).
[19]
Choi, J., Dongarra, J., Ostrouchov, S., Petitet, A., Walker, D., Whaley, R.: A proposal for a set of parallel basic linear algebra subprograms. Technical Report UT-CS-95-292, Dept. of CS, U. of Tennessee, Knoxville (1995).
[20]
Anderson, E., Bai, Z., Bischof, C., Demmel, J., Dongarra, J., Croz, J.D., Greenbaum, A., Hammarling, S., McKenney, A., Ostrouchov, S., Sorensen, D.: LAPACK Users Guide, 2nd edn. SIAM, Philadelphia (1995).
  1. A parallel classification and feature reduction method for biomedical applications

    Recommendations

    Comments

    Please enable JavaScript to view thecomments powered by Disqus.

    Information & Contributors

    Information

    Published In

    cover image Guide Proceedings
    PPAM'07: Proceedings of the 7th international conference on Parallel processing and applied mathematics
    September 2007
    1413 pages
    ISBN:3540681051
    • Editors:
    • Roman Wyrzykowski,
    • Konrad Karczewski,
    • Jack Dongarra,
    • Jerzy Wasniewski

    Sponsors

    • Microsoft Corp.
    • Intel: Intel
    • Action S.A.
    • SIAM: Society for Industrial and Applied Mathematics
    • IBM Corporation

    Publisher

    Springer-Verlag

    Berlin, Heidelberg

    Publication History

    Published: 09 September 2007

    Author Tags

    1. binary classification
    2. feature transformation
    3. generalized eigenvalue classifier

    Qualifiers

    • Article

    Contributors

    Other Metrics

    Bibliometrics & Citations

    Bibliometrics

    Article Metrics

    • 0
      Total Citations
    • 3
      Total Downloads
    • Downloads (Last 12 months)0
    • Downloads (Last 6 weeks)0
    Reflects downloads up to 10 Dec 2024

    Other Metrics

    Citations

    View Options

    View options

    Login options

    Media

    Figures

    Other

    Tables

    Share

    Share

    Share this Publication link

    Share on social media