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22nd International Workshop on Combinatorial Algorithms

作者： Beal, Richard Adjeroh, Donald W Virginia Univ Lane Dept Comp Sci & Elect Engn Morgantown WV 26506 USA

ISBN: (纸本)9783642250101

The challenge of direct parameterized suffix sorting (p-suffix sorting) for a parameterized string (p-string) is the dynamic nature of parameterized suffixes (p-suffixes). In this work, we propose transformative approaches to direct p-suffix sorting by generating and sorting lexicographically numeric fingerprints and arithmetic codes that correspond to individual p-suffixes. Our algorithm to p-suffix sort via fingerprints is the first theoretical linear time algorithm for p-suffix sorting for non-binary parameter alphabets, which assumes that each code is represented by a practical integer. We eliminate the key problems of fingerprints by introducing an algorithm that exploits the ordering of arithmetic codes to sort p-suffixes in linear time on average.

关键词： parameterized suffix array parameterized suffix sorting arithmetic coding fingerprints p-string p-match

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p-suffix sorting as arithmetic coding

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JOURNAL OF DISCRETE ALGORITHMS 2012年 16卷 151-169页

作者： Beal, Richard Adjeroh, Donald West Virginia Univ Lane Dept Comp Sci & Elect Engn Morgantown WV 26506 USA

The challenge of direct parameterized suffix sorting (p-suffix sorting) for a parameterized string (p-string), say T of length-n, is the dynamic nature of the n parameterized suffixes (p-suffixes) of T. In this work, we propose transformative approaches to direct p-suffix sorting by generating and sorting lexicographically numeric fingerprints and arithmetic codes that correspond to individual p-suffixes. Our algorithm to p-suffix sort via fingerprints is the first theoretical linear time algorithm for p-suffix sorting for nonbinary parameter alphabets, which assumes that, in practice, all codes are within the range of an integral data type. We eliminate the key problems of fingerprints by introducing an algorithm that exploits the ordering of arithmetic codes to sort p-suffixes in linear time on average. The arithmetic coding approach is further extended to handle p-strings in the worst case. This algorithm is the first direct p-suffix sorting approach in theory to execute in o(n(2)) time in the worst case, which improves on the best known theoretical result on this problem that sorts p-suffixes based on p-suffix classifications in O(n(2)) time. We show that, based on the algorithmic parameters and the input data, our algorithm does indeed execute in linear time in various cases, which is confirmed with experimental results. (C) 2012 Elsevier B. V. All rights reserved.

关键词： parameterized suffix array parameterized suffix sorting Arithmetic coding Fingerprints p-string p-match

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