Abstract
We propose a genetic programming approach to extraction of glycan motifs by using tag tree patterns, which are tree structured patterns with structured variables. A structured variable in a tag tree pattern can be substituted by an arbitrary tree. Our experiments show that we have obtained tag tree patterns as the best individuals including similar substructures of glycan motifs obtained by the previous works.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Banzhaf, W., Nordin, P., Keller, R.E., Francone, F.D.: Genetic Programming: An Introduction: On the Automatic Evolution of Computer Programs and Its Applications. Morgan Kaufmann, San Francisco (1998)
Doubet, S., Albersheim, P.: Clycobiology. Data Mining and Knowledge Discovery 2(6), 505 (1992)
Yao, X. (ed.): Evolutionary Computation: Theory and Applications. World Scientific, Singapore (1999)
Hashimoto, K., Goto, S., Kawano, S., Aoki-Kinoshita, K.F., Ueda, N., Hamajima, M., Kawasaki, T., Kanehisa, M.: KEGG as a glycome informatics resource. Glycobiology 16, 63R–70R (2006)
Hizukuri, Y., Yamanishi, Y., Nakamura, O., Yagi, F., Goto, S., Kanehisa, M.: Extraction of leukemia specific glycan motifs in humans by computational glycomics. Carbohydrate Research 340, 2270–2278 (2005)
Inata, K., Miyahara, T., Ueda, H., Takahashi, K.: Evolution of characteristic tree structured patterns from semistructured documents. In: Sattar, A., Kang, B.H. (eds.) AI 2006. LNCS (LNAI), vol. 4304, pp. 1201–1207. Springer, Heidelberg (2006)
Koza, J.R.: Genetic Programming: On the Programming of Computers by Means of Natural Selection. MIT Press, Cambridge (1992)
Kuboyama, T., Hirata, K., Aoki-Kinoshita, K.F., Kashima, H., Yasuda, H.: A gram distribution kernel applied to glycan classification and motifextraction. Genome Informatics 17(2), 25–34 (2006)
Miyahara, T., Suzuki, Y., Shoudai, T., Uchida, T., Takahashi, K., Ueda, H.: Discovery of frequent tag tree patterns in semistructured web documents. In: Chen, M.-S., Yu, P.S., Liu, B. (eds.) PAKDD 2002. LNCS (LNAI), vol. 2336, pp. 341–355. Springer, Heidelberg (2002)
Suzuki, Y., Akanuma, R., Shoudai, T., Miyahara, T., Uchida, T.: Polynomial time inductive inference of ordered tree patterns with internal structured variables from positive data. In: Kivinen, J., Sloan, R.H. (eds.) COLT 2002. LNCS (LNAI), vol. 2375, pp. 169–184. Springer, Heidelberg (2002)
Tan, K.C., Lim, M.H., Yao, X., L. (eds.): Recent Advances in Simulated Evolution and Learning. World Scientific, Singapore (2004)
Watanabe, A., Miyahara, T., Takahashi, K., Ueda, H.: Application of genetic programming to discovery of characteristic tree structured patterns (in Japanese). IEICE Technical Report 101(502), 41–48 (2001)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Nagamine, M., Miyahara, T., Kuboyama, T., Ueda, H., Takahashi, K. (2007). A Genetic Programming Approach to Extraction of Glycan Motifs Using Tree Structured Patterns. In: Orgun, M.A., Thornton, J. (eds) AI 2007: Advances in Artificial Intelligence. AI 2007. Lecture Notes in Computer Science(), vol 4830. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-76928-6_17
Download citation
DOI: https://doi.org/10.1007/978-3-540-76928-6_17
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-76926-2
Online ISBN: 978-3-540-76928-6
eBook Packages: Computer ScienceComputer Science (R0)