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A survey of kernels for structured data

Published: 01 July 2003 Publication History

Abstract

Kernel methods in general and support vector machines in particular have been successful in various learning tasks on data represented in a single table. Much 'real-world' data, however, is structured - it has no natural representation in a single table. Usually, to apply kernel methods to 'real-world' data, extensive pre-processing is performed to embed the data into areal vector space and thus in a single table. This survey describes several approaches of defining positive definite kernels on structured instances directly.

References

[1]
N. Aronszajn. Theory of reproducing kernels. Transactions of the American Mathematical Society, 68, 1950.]]
[2]
K. Bennett and C. Campbell. Support vector machines: Hype or hallelujah? SIGKDD Explorations, 2(2), 2000. http://www.acm.org/sigs/sigkdd/explorations/issue2-2/bennett.pdf.]]
[3]
B. E. Boser, I. M. Guyon, and V. N. Vapnik. A training algorithm for optimal margin classifiers. In D. Haussler, editor, Proceedings of the 5th Annual ACM Workshop on Computational Learning Theory, pages 144--152. ACM Press, July 1992.]]
[4]
M. Collins and N. Duffy. Convolution kernels for natural language. In T. G. Dietterich, S. Becker, and Z. Ghahramani, editors, Advances in Neural Information Processing Systems, volume 14. MIT Press, 2002.]]
[5]
N. Cristianini and J. Shawe-Taylor. An Introduction to Support Vector Machines (and Other Kernel-Based Learning Methods). Cambridge University Press, 2000.]]
[6]
T. G. Dietterich, R. H. Lathrop, and T. Lozano-Pérez. Solving the multiple instance problem with axis-parallel rectangles. Artificial Intelligence, 89(1--2):31--71, 1997.]]
[7]
R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.]]
[8]
S. Džeroski and N. Lavrač, editors. Relational Data Mining. Springer-Verlag, 2001.]]
[9]
S. Džeroski, S. Schulze-Kremer, K. Heidtke, K. Siems, D. Wettschereck, and H. Blockeel. Diterpene structure elucidation from 13C NMR spectra with inductive logic programming. Applied Artificial Intelligence, 12(5):363--383, July-Aug. 1998. Special Issue on First-Order Knowledge Discovery in Databases.]]
[10]
T. Gärtner. Exponential and geometric kernels for graphs. In NIPS Workshop on Unreal Data: Principles of Modeling Nonvectorial Data, 2002.]]
[11]
T. Gärtner, K. Driessens, and J. Ramon. Graph kernels and gaussian processes for relational reinforcement learning. In Proceedings of the 13th International Conference on Inductive Logic Programming, 2003.]]
[12]
T. Gärtner, P. A. Flach, A. Kowalczyk, and A. J. Smola. Multi-instance kernels. In C. Sammut and A. Hoffmann, editors, Proceedings of the 19th International Conference on Machine Learning, pages 179--186. Morgan Kaufmann, June 2002.]]
[13]
T. Gärtner, P. A. Flach, and S. Wrobel. On graph kernels: Hardness results and efficient alternatives. In Proceedings of the 16th Annual Conference on Computa tional Learning Theory and the 7th Kernel Workshop, 2003.]]
[14]
T. Gärtner, J. W. Lloyd, and P. A. Flach. Kernels for structured data. In Proceedings of the 12th International Conference on Inductive Logic Programming. Springer-Verlag, 2002.]]
[15]
D. Haussler. Convolution kernels on discrete structures. Technical report, Department of Computer Science, University of California at Santa Cruz, 1999.]]
[16]
T. Jaakkola, M. Diekhans, and D. Haussler. A discriminative framework for detecting remote protein homologies. Journal of Computational Biology, 7(1, 2), 2000.]]
[17]
T. Jaakkola and D. Haussler. Exploiting generative models in discriminative classifiers. In Advances in Neural Information Processing Systems, volume 10, 1999.]]
[18]
T. Jaakkola and D. Haussler. Probabilistic kernel regression models. In Proceedings of the 1999 Conference on AI and Statistics, 1999.]]
[19]
T. Joachims. Learning to Classify Text using Support Vector Machines. Kluwer Academic Publishers, 2002.]]
[20]
R. Karchin, K. Karplus, and D. Haussler. Classifying g-protein coupled receptors with support vector machines. Bioinformatics, 18(1):147--159, 2002.]]
[21]
H. Kashima and A. Inokuchi. Kernels for graph classification. In ICDM Workshop on Active Mining, 2002.]]
[22]
H. Kashima and T. Koyanagi. Kernels for semistructured data. In C. Sammut and A. Hoffmann, editors, Proceedings of the 19th International Conference on Machine Learning. Morgan Kaufmann, 2002.]]
[23]
H. Kashima, K. Tsuda, and A. Inokuchi. Marginalized kernels between labeled graphs. In Proceedings of the 20th International Conference on Machine Learning, 2003.]]
[24]
R. I. Kondor and J. Lafferty. Diffusion kernels on graphs and other discrete input spaces. In C. Sammut and A. Hoffmann, editors, Proceedings of the 19th International Conference on Machine Learning, pages 315--322. Morgan Kaufmann, 2002.]]
[25]
S. Kramer, N. Lavrač, and P. A. Flach. Propositionalization approaches to relational data mining. In Džeroski and Lavrač {8}, chapter 11.]]
[26]
M.-A. Krogel and S. Wrobel. Transformation-based learning using multirelational aggregation. In C. Rouveirol and M. Sebag, editors, Proceedings of the 11th International Conference on Inductive Logic Programming. Springer-Verlag, 2001.]]
[27]
C. Leslie, E. Eskin, andW. Noble. The spectrum kernel: A string kernel for svm protein classification. In Proceedings of the Pacific Symposium on Biocomputing, pages 564--575, 2002.]]
[28]
C. Leslie, E. Eskin, J. Weston, and W. Noble. Mismatch string kernels for svm protein classification. In S. Becker, S. Thrun, and K. Obermayer, editors, Advances in Neural Information Processing Systems, volume 15. MIT Press, 2003.]]
[29]
J. W. Lloyd. Logic for Learning. Springer-Verlag, 2002.]]
[30]
H. Lodhi, C. Saunders, J. Shawe-Taylor, N. Cristianini, and C. Watkins. Text classification using string kernels. Journal of Machine Learning Research, 2, 2002.]]
[31]
H. Lodhi, J. Shawe-Taylor, N. Christianini, and C. Watkins. Text classification using string kernels. In T. Leen, T. Dietterich, and V. Tresp, editors, Advances in Neural Information Processing Systems, volume 13. MIT Press, 2001.]]
[32]
K.-R. Müller, S. Mika, G. Rätsch, K. Tsuda, and B. Schölkopf. An introduction to kernel-based learning algorithms. IEEE Transactions on Neural Networks, 2(2), 2001.]]
[33]
G. Paass, E. Leopold, M. Larson, J. Kindermann, and S. Eickeler. Svm classification using sequences of phonemes and syllables. In T. Elomaa, H. Mannila, and H. Toivonen, editors, Proceedings of the 6th European Conference on Principles of Data Mining and Knowledge Discovery, pages 373--384. Springer-Verlag, 2002.]]
[34]
P. Pavlidis, T. Furey, M. Liberto, D. Haussler, and W. Grundy. Promoter region-based classification of genes. In Proceedings of the Pacific Symposium on Biocomputing, pages 151--163, 2001.]]
[35]
L. R. Rabiner. A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE, 77(2):257--285, Feb. 1989.]]
[36]
C. Saunders, J. Shawe-Taylor, and A. Vinokourov. String kernels, fisher kernels and finite state automata. In S. Becker, S. Thrun, and K. Obermayer, editors, Advances in Neural Information Processing Systems, volume 15. MIT Press, 2003.]]
[37]
B. Schölkopf and A. J. Smola. Learning with Kernels. MIT Press, 2002.]]
[38]
N. Smith and M. Gales. Speech recognition using SVMs. In T. Dietterich, S. Becker, and Z. Ghahramani, editors, Advances in Neural Information Processing Systems, volume 14. MIT Press, 2002.]]
[39]
K. Tsuda, M. Kawanabe, G. Rätsch, S. Sonnenburg, and K.-R. Müller. A new discriminative kernel from probabilistic models. In T. Dietterich, S. Becker, and Z. Ghahramani, editors, Advances in Neural Information Processing Systems, volume 14. MIT Press, 2002.]]
[40]
K. Tsuda, T. Kin, and K. Asai. Marginalized kernels for biological sequences. Bioinformatics, 2002.]]
[41]
V. Vapnik. The Nature of Statistical Learning Theory. Springer-Verlag, 1995.]]
[42]
J.-P. Vert. A tree kernel to analyze phylogenetic profiles. Bioinformatics, 2002.]]
[43]
J.-P. Vert and M. Kanehisa. Graph driven features extraction from microarray data using diffusion kernels and kernel cca. In S. Becker, S. Thrun, and K. Ober mayer, editors, Advances in Neural Information Processing Systems, volume 15. MIT Press, 2003.]]
[44]
S. Vishwanathan and A. Smola. Fast kernels for string and tree matching. In S. Becker, S. Thrun, and K. Obermayer, editors, Advances in Neural Information Processing Systems, volume 15. MIT Press, 2003.]]
[45]
C. Watkins. Dynamic alignment kernels. Technical report, Department of Computer Science, Royal Holloway, University of London, 1999.]]
[46]
C. Watkins. Kernels from matching operations. Technical report, Department of Computer Science, Royal Holloway, University of London, 1999.]]
[47]
A, Zien, G. Ratsch, S. Mika, B. Schölkopf, T. Lengauer, and K.-R. Muller. Engineering support vector machine kernels that recognize translation initiation sites. Bioinforrnatics, 16(9):799--807, 2000.]]

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    Published In

    cover image ACM SIGKDD Explorations Newsletter
    ACM SIGKDD Explorations Newsletter  Volume 5, Issue 1
    July 2003
    101 pages
    ISSN:1931-0145
    EISSN:1931-0153
    DOI:10.1145/959242
    Issue’s Table of Contents

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    Association for Computing Machinery

    New York, NY, United States

    Publication History

    Published: 01 July 2003
    Published in SIGKDD Volume 5, Issue 1

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    Author Tags

    1. inductive logic programming
    2. kernel methods
    3. multi-relational data mining
    4. structured data

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