New Algorithms for Efficient Parallel String Comparison
Krusche, P. and Tiskin, A. (2010) New Algorithms for Efficient Parallel String Comparison. In: 22nd ACM symposium on Parallelism in algorithms and architectures.
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Official URL: http://dx.doi.org/10.1145/1810479.1810521
In this paper, we show new parallel algorithms for a set of classical string comparison problems: computation of string alignments, longest common subsequences (LCS) or edit distances, and longest increasing subsequence computation. These problems have a wide range of applications, in particular in computational biology and signal processing. We discuss the scalability of our new parallel algorithms in computation time, in memory, and in communication. Our new algorithms are based on an efficient parallel method for (min,+)-multiplication of distance matrices. The core result of this paper is a scalable parallel algorithm for multiplying implicit simple unit-Monge matrices of size n x n on p processors using time O( n log n ‾ p). communication O(n log p) ‾ p) and O(log p) supersteps. This algorithm allows us to implement scalable LCS computation for two strings of length n using time O(n2 ‾ p) and communication O(n ‾ √ p), requiring local memory of size O(n ‾ √ p) on each processor. Furthermore, our algorithm can be used to obtain the first generally work-scalable algorithm for computing the longest increasing subsequence (LIS). Our algorithm for LIS computation requires computation O(n log2 n ‾ p), communication O(n log p)/ p), and O(log2 p) supersteps for computing the LIS of a sequence of length n. This is within a log n factor of work-optimality for the LIS problem, which can be solved sequentially in time O(n log n) in the comparison-based model. Our LIS algorithm is also within a log p-factor of achieving perfectly scalable communication and furthermore has perfectly scalable memory size requirements of O(n ‾ p) per processor.
|Item Type:||Conference or Workshop Item (Paper)|
|Uncontrolled Keywords:||focs BSP algorithms longest common subsequences longest increasing subsequences|
|Subjects:||Q Science > QA Mathematics > QA75 Electronic computers. Computer science|
|Divisions:||Faculty of Science > Computer Science|
|Depositing User:||Ms Saima Arif|
|Date Deposited:||07 Dec 2010 15:16|
|Last Modified:||26 Jul 2011 11:15|
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