文章基本信息

标题：Revisiting the Parameterized Complexity of Maximum-Duo Preservation String Mapping
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作者：Christian Komusiewicz ; Mateus de Oliveira Oliveira ; Meirav Zehavi 等
期刊名称：LIPIcs : Leibniz International Proceedings in Informatics
电子版ISSN：1868-8969
出版年度：2017
卷号：78
页码：11:1-11:17
DOI：10.4230/LIPIcs.CPM.2017.11
出版社：Schloss Dagstuhl -- Leibniz-Zentrum fuer Informatik
摘要：In the Maximum-Duo Preservation String Mapping (Max-Duo PSM) problem, the input consists of two related strings A and B of length n and a nonnegative integer k. The objective is to determine whether there exists a mapping m from the set of positions of A to the set of positions of B that maps only to positions with the same character and preserves at least k duos, which are pairs of adjacent positions. We develop a randomized algorithm that solves Max-Duo PSM in time 4^k * n^{O(1)}, and a deterministic algorithm that solves this problem in time 6.855^k * n^{O(1)}. The previous best known (deterministic) algorithm for this problem has running time (8e)^{2k+o(k)} * n^{O(1)} [Beretta et al., Theor. Comput. Sci. 2016]. We also show that Max-Duo PSM admits a problem kernel of size O(k^3), improving upon the previous best known problem kernel of size O(k^6).
关键词：comparative genomics; parameterized complexity; kernelization