Parallel Dynamic Programming for Solving the String Editing Problem on a CGM/BSP

摘要

In this paper we present a coarse-grained parallel algorithm for solving the string edit distance problem for a string A and all substrings of a string C. Our method is based on a novel CGM/BSP parallel dynamic programming technique for computing all highest scoring paths in a weighted grid graph. The algorithm requires log p rounds/supersteps and O((n~2)/p log m) local computation, where p is the number of processors, p~2 ≤ m ≤ n. To our knowledge, this is the first efficient CGM/BSP algorithm for the alignment of all substrings of C with A. Furthermore, the CGM/BSP parallel dynamic programming technique presented is of interest in its own right and we expect it to lead to other parallel dynamic programming methods for the CGM/BSP.