TY - GEN

T1 - Common structured patterns in linear graphs

T2 - 18th Annual Symposium on Combinatorial Pattern Matching, CPM 2007

AU - Fertin, Guillaume

AU - Hermelin, Danny

AU - Rizzi, Romeo

AU - Vialette, Stéphane

PY - 2007/1/1

Y1 - 2007/1/1

N2 - A linear graph is a graph whose vertices are linearly ordered. This linear ordering allows pairs of disjoint edges to be either preceding (<), nesting (square subset) or crossing (between). Given a family of linear graphs, and a non-empty subset R ⊆ {<, square subset, between}, we are interested in the MCSP problem: Find a maximum size edge-disjoint graph, with edge-pairs all comparable by one of the relations in R, that occurs as a subgraph in each of the linear graphs of the family. In this paper, we generalize the framework of Davydov and Batzoglou by considering patterns comparable by all possible subsets T ⊆ {<, square subset, between}. This is motivated by the fact that many biological applications require considering crossing structures, and by the fact that different combinations of the relations above give rise to different generalizations of natural combinatorial problems. Our results can be summarized as follows: We give tight hardness results for the MCSP problem for {<, between}-structured patterns and {square subset, between}-structured patterns. Furthermore, we prove that the problem is approximable within ratios: (i) 2 ℋ(k) for {<, between}-structured patterns, (ii) k1/2 for {square subset, between}-structured patterns, and (iii) Ο(y√k lg k) for {<, square subset, between}-structured patterns, where k is the size of the optimal solution and ℋ(k) = Σi=1k 1/i is the k-th harmonic number.

AB - A linear graph is a graph whose vertices are linearly ordered. This linear ordering allows pairs of disjoint edges to be either preceding (<), nesting (square subset) or crossing (between). Given a family of linear graphs, and a non-empty subset R ⊆ {<, square subset, between}, we are interested in the MCSP problem: Find a maximum size edge-disjoint graph, with edge-pairs all comparable by one of the relations in R, that occurs as a subgraph in each of the linear graphs of the family. In this paper, we generalize the framework of Davydov and Batzoglou by considering patterns comparable by all possible subsets T ⊆ {<, square subset, between}. This is motivated by the fact that many biological applications require considering crossing structures, and by the fact that different combinations of the relations above give rise to different generalizations of natural combinatorial problems. Our results can be summarized as follows: We give tight hardness results for the MCSP problem for {<, between}-structured patterns and {square subset, between}-structured patterns. Furthermore, we prove that the problem is approximable within ratios: (i) 2 ℋ(k) for {<, between}-structured patterns, (ii) k1/2 for {square subset, between}-structured patterns, and (iii) Ο(y√k lg k) for {<, square subset, between}-structured patterns, where k is the size of the optimal solution and ℋ(k) = Σi=1k 1/i is the k-th harmonic number.

UR - http://www.scopus.com/inward/record.url?scp=37849026538&partnerID=8YFLogxK

U2 - 10.1007/978-3-540-73437-6_25

DO - 10.1007/978-3-540-73437-6_25

M3 - Conference contribution

AN - SCOPUS:37849026538

SN - 9783540734369

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 241

EP - 252

BT - Combinatorial Pattern Matching - 18th Annual Symposium, CPM 2007, Proceedings

PB - Springer Verlag

Y2 - 9 July 2007 through 11 July 2007

ER -