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A Comprehensive Study of Tree Kernels

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Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 8417))

Abstract

Tree kernels are an effective method to capture the structural information of tree data of various applications and many algorithms have been proposed. Nevertheless, we do not have sufficient knowledge about how to select good kernels. To answer this question, we focus on 32 tree kernel algorithms defined within a certain framework to engineer positive definite kernels, and investigate them under two different parameter settings. The result is amazing. Three of the 64 tree kernels outperform the others, and their superiority proves statistically significant through t-tests. These kernels include the benchmark tree kernels proposed in the literature, while many of them are introduced and tested for the first time in this paper.

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References

  1. Augsten, N., Böhlen, M.H., Gamper, J.: The pq-gram distance between ordered labeled trees. ACM Trans. Database Syst. 35(1), 1–36 (2010)

    Article  Google Scholar 

  2. Collins, M., Duffy, N.: Convolution kernels for natural language. In: Proceedings of Advances in Neural Information Processing Systems 14 (NIPS), pp. 625–632 (2001)

    Google Scholar 

  3. Cristianini, N., Shawe-Taylor, J.: An introduction to Support Vector Machines and Other Kernel-Based Learning Methods. Cambridge University Press, Cambridge (2000)

    Book  Google Scholar 

  4. Demaine, E.D., Mozes, S., Rossman, B., Weimann, O.: An optimal decomposition algorithm for tree edit distance. ACM Trans. Algorithms (TALG) 6(1), 2:1–2:19 (2009)

    MathSciNet  MATH  Google Scholar 

  5. Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N.: Kegg as a glycome informatics resource. Glycobiology 16, 63R–70R (2006)

    Article  Google Scholar 

  6. Haussler, D.: Convolution kernels on discrete structures. UCSC-CRL 99–10, Department of Computer Science, University of California at Santa Cruz (1999)

    Google Scholar 

  7. Kashima, H., Koyanagi, T.: Kernels for semi-structured data. In: Proceedings of the 9th International Conference on Machine Learning (ICML), pp. 291–298 (2002)

    Google Scholar 

  8. Kimura, D., Kashima, H.: Computation of subpath kernel for trees. In: Proceedings of the 29th International Conference on Machine Learning (ICML) (2012)

    Google Scholar 

  9. Kuboyama, T., Shin, K., Kashima, H.: Flexible tree kernels based on counting the number of tree mappings. In Proceedings of the Machine Learning with Graphs (MLG) (2006)

    Google Scholar 

  10. Kuboyama, T., Hirata, K., Aoki-Kinoshita, K.F.: An efficient unordered tree kernel and its application to glycan classification. In: Washio, T., Suzuki, E., Ting, K.M., Inokuchi, A. (eds.) PAKDD 2008. LNCS (LNAI), vol. 5012, pp. 184–195. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  11. Kuboyama, T., Hirata, K., Aoki-Kinoshita, K.F., Kashima, H., Yasuda, H.: A gram distribution kernel applied to glycan classification and motif extraction. Genome Inform. Ser. 17(2), 25–34 (2006)

    Google Scholar 

  12. Kuboyama, T., Hirata, K., Kashima, H., Aoki-Kinoshita, K.F., Yasuda, H.: A spectrum tree kernel. Inf. Media Technol. 2(1), 292–299 (2007)

    Google Scholar 

  13. Lu, C.L., Su, Z.-Y., Tang, C.Y.: A new measure of edit distance between labeled trees. In: Wang, J. (ed.) COCOON 2001. LNCS, vol. 2108, pp. 338–348. Springer, Heidelberg (2001)

    Chapter  Google Scholar 

  14. Lu, S.Y.: A tree-to-tree distance and its application to cluster analysis. EEE Trans. Pattern Anal. Mach. Intell. (PAMI) 1, 219–224 (1979)

    Article  Google Scholar 

  15. Moschitti, A.: Example data for Tree Kernels in SVM-light. http://disi.unitn.it/moschitti/Tree-Kernel.htm

  16. Pyysalo, S., Airola, A., Heimonen, J., Bjorne, J., Ginter, F., Salakoski, T.: Comparative analysis of five protein-protein interaction corpora. BMC Bioinform. 9(S–3), S6 (2008)

    Article  Google Scholar 

  17. Shin, K., Cuturi, M., Kuboyama, T.: Mapping kernels for trees. In: Proceedings of the 28th International Conference on Machine Learning ICML (2011)

    Google Scholar 

  18. K. Shin and T. Kuboyama. A generalization of Haussler’s convolution kernel - mapping kernel. In: Proceedings of the 25th International Conference on Machine Learning ICML (2008)

    Google Scholar 

  19. Taï, K.C.: The tree-to-tree correction problem. JACM 26(3), 422–433 (1979)

    Article  MathSciNet  Google Scholar 

  20. Zaki, M.J., Aggarwal, C.C.: Xrules: an effective algorithm for structural classification of XML data. Mach. Learn. 62, 137–170 (2006)

    Article  Google Scholar 

  21. Zhang, K.: Algorithms for the constrained editing distance between ordered labeled trees and related problems. Pattern Recogn. 28(3), 463–474 (1995)

    Article  Google Scholar 

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Correspondence to Tetsuji Kuboyama .

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Shin, K., Kuboyama, T. (2014). A Comprehensive Study of Tree Kernels. In: Nakano, Y., Satoh, K., Bekki, D. (eds) New Frontiers in Artificial Intelligence. JSAI-isAI 2013. Lecture Notes in Computer Science(), vol 8417. Springer, Cham. https://doi.org/10.1007/978-3-319-10061-6_22

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  • DOI: https://doi.org/10.1007/978-3-319-10061-6_22

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-10060-9

  • Online ISBN: 978-3-319-10061-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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