Abstract
In 2000, T. Uno and M. Yagiura published an algorithm that computes all the K common intervals of two given permutations of length n in \(\mathcal{O}(n+ K)\) time. Our paper first presents a decomposition approach to obtain a compact encoding for common intervals of d permutations. Then, we revisit T. Uno and M. Yagiura’s algorithm to yield a linear time algorithm for finding this encoding. Besides, we adapt the algorithm to obtain a linear time modular decomposition of an undirected graph, and thereby propose a formal invariant-based proof for all these algorithms.
Full version available at http://www.lirmm.fr/~buixuan as RR-LIRMM-05049
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
Béal, M.-P., Bergeron, A., Corteel, S., Raffinot, M.: An algorithmic view of gene teams. Theoretical Computer Science 320(2-3), 395–418 (2004)
Bérard, S., Bergeron, A., Chauve, C.: Conservation of combinatorial structures in evolution scenarios. In: Lagergren, J. (ed.) RECOMB-WS 2004. LNCS (LNBI), vol. 3388, pp. 1–14. Springer, Heidelberg (2005)
Bergeron, A., Chauve, C., de Montgolfier, F., Raffinot, M.: Computing common intervals of k permutations, with applications to modular decomposition of graphs. In: Brodal, G.S., Leonardi, S. (eds.) ESA 2005. LNCS, vol. 3669, pp. 779–790. Springer, Heidelberg (2005)
Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, pp. 68–79. Springer, Heidelberg (2003)
Bogart, K.P., Fishburn, P.C., Isaak, G., Langley, L.: Proper and unit tolerance graphs. Discrete Applied Mathematics 60, 99–117 (1995)
Capelle, C.: Block decomposition of inheritance hierarchies. In: Möhring, R.H. (ed.) WG 1997. LNCS, vol. 1335, pp. 118–131. Springer, Heidelberg (1997)
Capelle, C., Habib, M., de Montgolfier, F.: Graph decomposition and factorizing permutations. Discrete Mathematics and Theoretical Computer Science 5(1), 55–70 (2002)
Chein, M., Habib, M., Maurer, M.C.: Partitive hypergraphs. Discrete Mathematics 37(1), 35–50 (1981)
Cournier, A., Habib, M.: A new linear algorithm for modular decomposition. In: Tison, S. (ed.) CAAP 1994. LNCS, vol. 787, pp. 68–84. Springer, Heidelberg (1994)
Dahlhaus, E.: Parallel algorithms for hierarchical clustering, and applications to split decomposition and parity graph recognition. Journal of Algorithms 36(2), 205–240 (2000)
de Berg, M., van Kreveld, M., Overmars, M., Schwarzkopf, O.: Computational geometry. Springer, Heidelberg (1991)
de Montgolfier, F.: Décomposition modulaire des graphes. Théorie, extensions et algorithmes. PhD thesis, Université Montpellier II (2003)
Felsner, S.: Tolerance graphs and orders. Journal of Graph Theory 28(3), 129–140 (1998)
Figeac, M., Varré, J.-S.: Sorting by reversals with common intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 26–37. Springer, Heidelberg (2004)
Habib, M., de Montgolfier, F., Paul, C.: A simple linear-time modular decomposition algorithm. In: Hagerup, T., Katajainen, J. (eds.) SWAT 2004. LNCS, vol. 3111, pp. 187–198. Springer, Heidelberg (2004)
Habib, M., Huchard, M., Spinrad, J.P.: A linear algorithm to decompose inheritance graphs into modules. Algorithmica 13(6), 573–591 (1995)
Heber, S., Stoye, J.: Finding all common intervals of k permutations. In: Amir, A., Landau, G.M. (eds.) CPM 2001. LNCS, vol. 2089, pp. 207–218. Springer, Heidelberg (2001)
Hsu, W.-L., Ma, T.-M.: Substitution decomposition on chordal graphs and applications. In: Hsu, W.-L., Lee, R.C.T. (eds.) ISA 1991. LNCS, vol. 557, pp. 52–60. Springer, Heidelberg (1991)
Landau, G.M., Parida, L., Weimann, O.: Using pq trees for comparative genomics. In: Apostolico, A., Crochemore, M., Park, K. (eds.) CPM 2005. LNCS, vol. 3537, pp. 128–143. Springer, Heidelberg (2005)
McConnell, R.M., de Montgolfier, F.: Algebraic Operations on PQ Trees and Modular Decomposition Trees. In: Kratsch, D. (ed.) WG 2005. LNCS, vol. 3787, pp. 421–432. Springer, Heidelberg (2005)
McConnell, R.M., Spinrad, J.P.: Modular decomposition and transitive orientation. Discrete Mathematics 201, 189–241 (1999)
Möhring, R.H., Radermacher, F.J.: Substitution decomposition for discrete structures and connections with combinatorial optimization. Annals of Discrete Mathematics 19, 257–356 (1984)
Uno, T., Yagiura, M.: Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26(2), 290–309 (2000)
Welsh, D.J.A.: Matroids: Fundamental concepts. In: Handbook of Combinatorics, vol. 1, pp. 481–526. North-Holland, Amsterdam (1995)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Xuan, BM.B., Habib, M., Paul, C. (2005). Revisiting T. Uno and M. Yagiura’s Algorithm. In: Deng, X., Du, DZ. (eds) Algorithms and Computation. ISAAC 2005. Lecture Notes in Computer Science, vol 3827. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11602613_16
Download citation
DOI: https://doi.org/10.1007/11602613_16
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-30935-2
Online ISBN: 978-3-540-32426-3
eBook Packages: Computer ScienceComputer Science (R0)