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Dealing with large diagonals in kernel matrices

  • Special Section on New Trends in Statistical Information Processing
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Abstract

In kernel methods, all the information about the training data is contained in the Gram matrix. If this matrix has large diagonal values, which arises for many types of kernels, then kernel methods do not perform well: We propose and test several methods for dealing with this problem by reducing the dynamic range of the matrix while preserving the positive definiteness of the Hessian of the quadratic programming problem that one has to solve when training a Support Vector Machine, which is a common kernel approach for pattern recognition.

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References

  • Alizadeh, A. A.et al (2000). Distinct types of diffuse large b-cell lymphoma identified by gene expression profiling,Nature,403, 503–511 (Data available from http://llmpp.nih.gov/lymphoma)

    Article  Google Scholar 

  • Alon, U., Barkai, N., Notterman, D., Gish, K., Ybarra, S., Mack, D. and Levine, A. (1999). Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon cancer tissues probed by oligonucleotide arrays,Cell Biology,96, 6745–6750.

    Google Scholar 

  • Berg, C., Christensen, J. P. R. and Ressel, P. (1984).Harmonic Analysis on Semigroups, Springer, New York.

    MATH  Google Scholar 

  • Boser, B. E., Guyon, I. M. and Vapnik, V. (1992). A training algorithm for optimal margin classifiers (ed. D. Haussler),Proceedings of the 5th Annual ACM Workshop on Computational Learning Theory, 144–152, ACM Press, Pittsburgh, Pensylvania.

    Chapter  Google Scholar 

  • Brown, M. P. S., Grundy, W. N., Lin, D., Cristianini, N., Sugnet, C., Furey, T. S., Ares, M. and Haussler, D. (2000). Knowledge-based analysis of microarray gene expression data using support vector machines,Proc. Nat. Acad. Sci. U.S.A.,97(1), 262–267.

    Article  Google Scholar 

  • Cortes, C. and Vapnik, V. (1995). Support vector networks,Machine Learning,20, 273–297.

    Google Scholar 

  • Guyon, I., Weston, J., Barnhill, S. and Vapnik, V. (2002). Gene selection for cancer classification using support vector machines,Machine Learning,46, 389–422.

    Article  Google Scholar 

  • Hastie, T. J. and Tibshirani, R. J. (1990).Generalized Additive Models, Monographs on Statistics and Applied Probability, Vol. 43, Chapman & Hall, London.

    MATH  Google Scholar 

  • Haussler, D. (1999). Convolutional kernels on discrete structures, Tech. Report, UCSC-CRL-99-10, Computer Science Department, University of California at Santa Cruz.

  • Jaakkola, T. S. and Haussler, D. (1999). Exploiting generative models in discriminative classifiers (eds. M. S. Kearns, S. A. Solla and D. A. Cohn),Advances in Neural Information Processing Systems 11, MIT Press, Cambridge, Massachusetts.

    Google Scholar 

  • Jaakkola, T. S., Diekhans, M. and Haussler, D. (2000). A discriminative framework for detecting remote protein homologies,Journal of Computational Biology,7, 95–114.

    Article  Google Scholar 

  • Leslie, C., Eskin, E. and Noble, W. S. (2002). The spectrum kernel: A string kernel for SVM protein classification,Proceedings of the Pacific Symposium on Biocomputing, 564–575.

  • Liao, L. and Noble, W. S. (2002). Combining pairwise sequence similarity and support vector machines for remote protein homology detection,Proceedings of the Sixth International Conference on Computational Molecular Biology.

  • Lodhi, H., Saunders, C., Shawe-Taylor, J., Cristianini, N. and Watkins, C. (2002). Text classification using string kernels,Journal of Machine Learning Research,2, 419–444.

    Article  Google Scholar 

  • Murzin, A. G., Brenner, S. E., Hubbard, T. and Chothia, C. (1995). SCOP: A structural classification of proteins database for the investigation of sequences and structures,Journal of Molecular Biology,247, 536–540.

    Article  Google Scholar 

  • Schölkopf, B. and Smola, A. J. (2002).Learning with Kernels, MIT Press, Cambridge, Massachusetts.

    Google Scholar 

  • Schölkopf, B., Weston, J., Eskin, E., Leslie, C. and Noble, W. S. (2002). A kernel approach for learning from almost orthogonal patterns,Proceedings ECML’2002, Helsinki (to appear).

  • Tsuda, K. (1999). Support vector classifier with asymmetric kernel function (ed. M. Verleysen),Proceedings ESANN, 183–188, D Facto, Brussels.

    Google Scholar 

  • Tsuda, K., Kawanabe, M., Rätsch, G., Sonnenburg, S. and Müller, K. (2002). A new discriminative kernel from probabilistic models (eds. t. Dietterich, S. Becker and Z. Ghahramani).Advances in Neural Information Processing Systems,14, MIT Press, Cambridge, Massachusetts.

    Google Scholar 

  • Vapnik, V. (1979).Estimation of Dependences Based on Empirical Data, Nauka, Moscow (in Russian) (English translation: Springer Verlag, New York 1982).

    Google Scholar 

  • Vapnik, V. (1998).Statistical Learning Theory, Wiley, New York.

    MATH  Google Scholar 

  • Watkins, C. (2000). Dynamic alignment kernels (eds. A. J. Smola, P. L. Bartlett, B. Schölkopf and D. Schuurmans),Advances in Large Margin Classifiers, 39–50, MIT Press, Cambridge, Massachusetts.

    Google Scholar 

  • Weston, J., Elisseff, A. and Schölkopf, B. (2001). Use of the ℓ0 with linear models and kernel methods, Tech. Report, Biowulf Technologies, New York.

    Google Scholar 

  • Weston, J., Pérez-Cruz, F., Bousquet, O., Chapelle, O., Elisseeff A. and Schölkopf, B. (2002). Feature selection and transduction for prediction of molecular bioactivity for drug design, http://www. conclu.de/≈jason/kdd/kdd.html

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Weston, J., Schölkopf, B., Eskin, E. et al. Dealing with large diagonals in kernel matrices. Ann Inst Stat Math 55, 391–408 (2003). https://doi.org/10.1007/BF02530507

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  • DOI: https://doi.org/10.1007/BF02530507

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