A Fast Bit-Parallel Algorithm for Gapped String Kernels

  • Chuanhuan Yin
  • Shengfeng Tian
  • Shaomin Mu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4232)


In this paper, we present a new kind of gapped string kernel, named length-weighted kernels, including p-length-weighted and all-length-weighted kernels. Moreover, we propose a dynamic programming algorithm based on suffix kernel to compute the length-weighted kernels. Given strings s and t, and a gap penalty λ, all-length-weighted kernel can be calculated in time O(|s||t|) using our algorithms. Based on the relationship between all-length and p-length kernels, the p-length-weighted can be computed in O(p|s||t|) time. Furthermore, a bit-parallel technique is used to reduce the complexity from O(p|s||t|) to O(⌈pk/w⌉|s||t|), where w is the word size of the machine (e.g. 32 or 64 in practice) and k is determined by the longest matching subsequence of two strings s and t. The empirical results suggest that this bit-parallel technique algorithm combined with dynamic programming and suffix kernel technique outperforms the other approaches in some cases where the necessary condition of using bit-parallel technique can be satisfied.


Dynamic Programming Intrusion Detection Weighted Kernel Suffix Tree Word Size 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Chuanhuan Yin
    • 1
  • Shengfeng Tian
    • 1
  • Shaomin Mu
    • 1
  1. 1.School of Computer and Information TechnologyBeijing Jiaotong UniversityBeijingChina

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