Skip to main content

Kernels Based on Distributions of Agreement Subtrees

  • Conference paper
AI 2008: Advances in Artificial Intelligence (AI 2008)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 5360))

Included in the following conference series:

Abstract

The MAST (maximum agreement subtrees) problem has been extensively studied, and the size of the maximum agreement subtrees between two trees represents their similarity. This similarity measure, however, only takes advantage of a very small portion of the agreement subtrees, that is, the maximum agreement subtrees, and agreement subtrees of smaller size are neglected at all. On the other hand, it is reasonable to consider that the distributions of the sizes of the agreement subtrees may carry useful information with respect to similarity. Based on the notion of the size-of-index-structure-distribution kernel introduced by Shin and Kuboyama, the present paper introduces positive semidefinite tree-kernels, which evaluate distributional features of the sizes of agreement subtrees, and shows efficient dynamic programming algorithms to calculate the kernels. In fact, the algorithms are of O(|x| ยท|y|)-time for labeled and ordered trees x and y. In addition, the algorithms are designed so that the agreement subtrees have roots and leaves with labels from predetermined sub-domains of an alphabet. This design will be very useful for important applications such as the XML documents.

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. Shin, K., Kuboyama, T.: A generalization of hausslerโ€™s convolution kernel - mapping kernel. In: Proc. of The 25th International Conference On Machine Learning, ICML (2008)

    Google Scholarย 

  2. Kashima, H., Koyanagi, T.: Kernels for Semi-Structured Data. In: Proc. of The 9th International Conference on Machine Learning (ICML), pp. 291โ€“298 (2002)

    Google Scholarย 

  3. Berry, V., Nicolas, F.: Maximum Agreement and Compatible Supertrees (Extended Abstract). In: Sahinalp, S.C., Muthukrishnan, S.M., Dogrusoz, U. (eds.) CPM 2004. LNCS, vol.ย 3109, pp. 205โ€“219. Springer, Heidelberg (2004)

    Chapterย  Google Scholarย 

  4. Hein, J., Jiang, T., Wang, L., Zhang, K.: On the complexity of comparing evolutionary trees. Discrete Applied Mathematicsย 71, 153โ€“169 (1996)

    Articleย  MathSciNetย  MATHย  Google Scholarย 

  5. Amir, A., Keselman, D.: Maximum agreement subtree in a set of evolutionary trees: Metrics and efficient algorithm. SIAM J. Computingย 26(6), 1656โ€“1669 (1997)

    Articleย  MathSciNetย  MATHย  Google Scholarย 

  6. Kao, M.Y., Lam, T.W., Sung, W.-K., Ting, H.F.: An even faster and more unifying algorithm for comparing trees via unbalanced bipartite matching. J. Algorithmsย 40(2), 212โ€“233 (2001)

    Articleย  MathSciNetย  MATHย  Google Scholarย 

  7. Kao, M.Y., Lam, T.W., Sung, W.-K., Ting, H.F.: A decomposition theorem for maximum weight bipartite matching with applications to evolutionary trees. SIAM J. Computingย 31(1), 18โ€“26 (2001)

    Articleย  MATHย  Google Scholarย 

  8. Cristianini, N., Shawe-Taylor, J.: An Introduction to Support Vector Machines and other kernel-based learning methods. Cambridge University Press, Cambridge (2000)

    Bookย  MATHย  Google Scholarย 

  9. Chang, C.-C., Lin, C.-J.: LIBSVM: a library for support vector machines, Software (2001), http://www.csie.ntu.edu.tw/~cjlin/libsvm/

  10. Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N.: KEGG as a glycome informatics resource. Glycobiologyย 16, 63Rโ€“70R (2006)

    Articleย  Google Scholarย 

  11. Doubet, S., Albersheim, P.: CarbBank. Glycobiologyย 2(6), 505 (1992)

    Articleย  Google Scholarย 

  12. Yamanishi, Y., Bach, F., Vert, J.-P.: Glycan classification with tree kernels. Bioinformaticsย 23(10), 1211โ€“1216 (2007)

    Articleย  Google Scholarย 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

ยฉ 2008 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Shin, K., Kuboyama, T. (2008). Kernels Based on Distributions of Agreement Subtrees. In: Wobcke, W., Zhang, M. (eds) AI 2008: Advances in Artificial Intelligence. AI 2008. Lecture Notes in Computer Science(), vol 5360. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-89378-3_23

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-89378-3_23

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-89377-6

  • Online ISBN: 978-3-540-89378-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics