TY - GEN
T1 - Revisiting the parameterized complexity of maximum-duo preservation string mapping
AU - Komusiewicz, Christian
AU - De Oliveira Oliveira, Mateus
AU - Zehavi, Meirav
N1 - Publisher Copyright: © Christian Komusiewicz, Mateus de Oliveira Oliveira, and Meirav Zehavi.
PY - 2017/7/1
Y1 - 2017/7/1
N2 - 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 MAXDUO PSM in time 4k · nO(1) a deterministic algorithm that solves this problem in time 6.855k · nO(1). The previous best known (deterministic) algorithm for this problem has running time (8e)2k+o(k) · nO(1) [Beretta et al., Theor. Comput. Sci. 2016]. We also show that MAX-DUO PSM admits a problem kernel of size O(k3), improving upon the previous best known problem kernel of size O(k6).
AB - 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 MAXDUO PSM in time 4k · nO(1) a deterministic algorithm that solves this problem in time 6.855k · nO(1). The previous best known (deterministic) algorithm for this problem has running time (8e)2k+o(k) · nO(1) [Beretta et al., Theor. Comput. Sci. 2016]. We also show that MAX-DUO PSM admits a problem kernel of size O(k3), improving upon the previous best known problem kernel of size O(k6).
KW - Comparative genomics
KW - Kernelization
KW - Parameterized complexity
UR - http://www.scopus.com/inward/record.url?scp=85027246850&partnerID=8YFLogxK
U2 - 10.4230/LIPIcs.CPM.2017.11
DO - 10.4230/LIPIcs.CPM.2017.11
M3 - Conference contribution
T3 - Leibniz International Proceedings in Informatics, LIPIcs
BT - 28th Annual Symposium on Combinatorial Pattern Matching, CPM 2017
A2 - Radoszewski, Jakub
A2 - Karkkainen, Juha
A2 - Rytter, Wojciech
PB - Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
T2 - 28th Annual Symposium on Combinatorial Pattern Matching, CPM 2017
Y2 - 4 July 2017 through 6 July 2017
ER -