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A Fast Bit-Parallel Algorithm for Gapped String Kernels

Authors: Chuanhuan Yin; Shengfeng Tian; Shaomin Mu;

A Fast Bit-Parallel Algorithm for Gapped String Kernels

Abstract

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.

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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