An efficient pruning strategy for approximate string matching over suffix tree

作者：Hu, Huan; Wang, Hongzhi^*; Li, Jianzhong; Gao, Hong

来源：Knowledge and Information Systems, 2016, 49(1): 121-141.

DOI：10.1007/s10115-015-0896-6

• Approximate string matching
• Suffix tree
• Depth-first
• Backtracking
• Dynamic programming
• Bit-parallelism

Approximate string matching over suffix tree with depth-first search (ASM_ST_DFS), a classical algorithm in the field of approximate string matching, was originally proposed by Ricardo A. Baeza-Yates and Gaston H. Gonnet in 1990. The algorithm is one of the most excellent algorithms for approximate string matching if combined with other indexing techniques. However, its time complexity is sensitive to the length of pattern string because it searches characters on each path from the root before backtracking. In this paper, we propose an efficient pruning strategy to solve this problem. We prove its correctness and efficiency in theory. Particularly, we proved that if the pruning strategy is adopted, it averagely searches O(k) characters on each path before backtracking instead of O(m). Considering each internal node of suffix tree has multiple branches, the pruning strategy should work very well. We also experimentally show that when k is much smaller than m, the efficiency improves hundreds of times, and when k is not much smaller than m, it is still several times faster. This is the first paper that tries to solve the backtracking problem of ASM_ST_DFS in both theory and practice.

• 出版日期2016-10
• 单位哈尔滨工业大学