A Unified String Kernel for Biology Sequence

Authors:
Dehui Yuan;Shengyun Yang;Guoming Lai
Affiliations:
Department of Mathematics and Information Technology, Hanshan Normal University, Guangdong Province, China 521041;Department of Mathematics and Information Technology, Hanshan Normal University, Guangdong Province, China 521041;Department of Mathematics and Information Technology, Hanshan Normal University, Guangdong Province, China 521041
Venue:
ICIC '08 Proceedings of the 4th international conference on Intelligent Computing: Advanced Intelligent Computing Theories and Applications - with Aspects of Artificial Intelligence
Year:
2008

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Abstract

In this paper, we introduce a unified String Kernel. Based on this unified string kernel, we construct improved sparse kernel and composite kernel. Using the same target families and the same test and training set splits as in the protein classification experiments from Weston, we do experiments with these new kernels. The results show that our kernels are superior to previously developed string kernel.