Abstract
Let \({\cal C}\) be a finite set of n elements and \({\cal R}=\{r_1,r_2, \ldots , r_m\}\) a family of m subsets of \({\cal C}\). A subset \({\cal X}\) of \({\cal R}\) satisfies the Consecutive Ones Property (C1P) if there exists a permutation P of \({\cal C}\) such that each r i in \({\cal X}\) is an interval of P. A Minimal Conflicting Set (MCS) \({\cal S} \subseteq{\cal R}\) is a subset of \({\cal R}\) that does not satisfy the C1P, but such that any of its proper subsets does. In this paper, we present a new simpler and faster algorithm to decide if a given element \(r \in{\cal R}\) belongs to at least one MCS. Our algorithm runs in O(n 2 m 2 + nm 7), largely improving the current O(m 6 n 5 (m + n)2 log(m + n)) fastest algorithm of [Blin et al, CSR 2011]. The new algorithm is based on an alternative approach considering minimal forbidden induced subgraphs of interval graphs instead of Tucker matrices.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Bergeron, A., Blanchette, M., Chateau, A., Chauve, C.: Reconstructing Ancestral Gene Orders Using Conserved Intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 14–25. Springer, Heidelberg (2004)
Blin, G., Rizzi, R., Vialette, S.: A Faster Algorithm for Finding Minimum Tucker Submatrices. In: Ferreira, F., Löwe, B., Mayordomo, E., Mendes Gomes, L. (eds.) CiE 2010. LNCS, vol. 6158, pp. 69–77. Springer, Heidelberg (2010)
Blin, G., Rizzi, R., Vialette, S.: A Polynomial-Time Algorithm for Finding a Minimal Conflicting Set Containing a Given Row. In: Kulikov, A., Vereshchagin, N. (eds.) CSR 2011. LNCS, vol. 6651, pp. 373–384. Springer, Heidelberg (2011)
Chauve, C., Haus, U.-U., Stephen, T., You, V.P.: Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction. In: Ciccarelli, F.D., Miklós, I. (eds.) RECOMB-CG 2009. LNCS, vol. 5817, pp. 48–58. Springer, Heidelberg (2009)
Chauve, C., Tannier, E.: A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput. Biol. 4(11), 11 (2008)
Dom, M.: Algorithmic aspects of the consecutive-ones property. Bulletin of the Eur. Assoc. for Theor. Comp. Science (EATCS) 98, 27–59 (2009)
Lekkerkerker, C.G., Boland, J.C.: Representation of a finite graph by a set of intervals on the real line. Fund. Math. 51, 45–64 (1962)
Nishizeki, T., Rahman, M.S.: Planar Graph Drawing. World Scientific (2004)
Ouangraoua, A., Raffinot, M.: Faster and Simpler Minimal Conflicting Set Identification. In: Kärkkäinen, J., Stoye, J. (eds.) CPM 2012. LNCS, vol. 7354, pp. 41–55. Springer, Heidelberg (2012)
Stoye, J., Wittler, R.: A unified approach for reconstructing ancient gene clusters. IEEE/ACM Trans. Comput. Biol. Bioinf. 6(3), 387–400 (2009)
Tucker, A.C.: A structure theorem for the consecutive 1s property. Journal of Combinatorial Theory. Series B 12, 153–162 (1972)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Ouangraoua, A., Raffinot, M. (2012). Faster and Simpler Minimal Conflicting Set Identification. In: Kärkkäinen, J., Stoye, J. (eds) Combinatorial Pattern Matching. CPM 2012. Lecture Notes in Computer Science, vol 7354. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31265-6_4
Download citation
DOI: https://doi.org/10.1007/978-3-642-31265-6_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-31264-9
Online ISBN: 978-3-642-31265-6
eBook Packages: Computer ScienceComputer Science (R0)