Techniques for the Cograph Editing Problem: Module Merge is equivalent to Editing P4s

Cographs are graphs in which no four vertices induce a simple connected path $P_4$. Cograph editing is to find for a given graph $G = (V,E)$ a set of at most $k$ edge additions and deletions that transform $G$ into a cograph. This combinatorial optimization problem is NP-hard. It has, recently found applications in the context of phylogenetics, hence good heuristics are of practical importance. It is well-known that the cograph editing problem can be solved independently on the so-called strong prime modules of the modular decomposition of $G$. We show here that editing the induced $P_4$'s of a given graph is equivalent to resolving strong prime modules by means of a newly defined merge operation on the submodules. This observation leads to a new exact algorithm for the cograph editing problem that can be used as a starting point for the construction of novel heuristics.

[1]  Michel Habib,et al.  Simpler Linear-Time Modular Decomposition Via Recursive Factorizing Permutations , 2008, ICALP.

[2]  Stephan Olariu,et al.  Recognizing P_4 Sparse Graphs in Linear Time , 1992, SIAM J. Comput..

[3]  Yunlong Liu,et al.  Cograph Editing: Complexity and Parameterized Algorithms , 2011, COCOON.

[4]  Lorna Stewart,et al.  A Linear Recognition Algorithm for Cographs , 1985, SIAM J. Comput..

[5]  Yong Gao,et al.  The cluster deletion problem for cographs , 2013, Discret. Math..

[6]  Yong Gao,et al.  Bounded Search Tree Algorithms for Parametrized Cograph Deletion: Efficient Branching Rules by Exploiting Structures of Special Graph Classes , 2012, Discret. Math. Algorithms Appl..

[7]  R. Möhring Algorithmic aspects of the substitution decomposition in optimization over relations, set systems and Boolean functions , 1985 .

[8]  F. Radermacher,et al.  Substitution Decomposition for Discrete Structures and Connections with Combinatorial Optimization , 1984 .

[9]  Jeremy P. Spinrad,et al.  Incremental modular decomposition , 1989, JACM.

[10]  Derek G. Corneil,et al.  Complement reducible graphs , 1981, Discret. Appl. Math..

[11]  Michel Habib,et al.  A Simple Linear-Time Modular Decomposition Algorithm for Graphs, Using Order Extension , 2004, SWAT.

[12]  Michel Habib,et al.  On the X-join decomposition for undirected graphs , 1979, Discret. Appl. Math..

[13]  Leizhen Cai,et al.  Fixed-Parameter Tractability of Graph Modification Problems for Hereditary Properties , 1996, Inf. Process. Lett..

[14]  Jeremy P. Spinrad,et al.  Ordered Vertex Partitioning , 2000, Discret. Math. Theor. Comput. Sci..

[15]  T. Gallai Transitiv orientierbare Graphen , 1967 .

[16]  Yunlong Liu,et al.  Complexity and parameterized algorithms for Cograph Editing , 2012, Theor. Comput. Sci..

[17]  Michel Habib,et al.  A survey of the algorithmic aspects of modular decomposition , 2009, Comput. Sci. Rev..

[18]  Michel Habib,et al.  A New Linear Algorithm for Modular Decomposition , 1994, CAAP.

[19]  Jeremy P. Spinrad,et al.  Linear-time modular decomposition and efficient transitive orientation of comparability graphs , 1994, SODA '94.

[20]  D. Seinsche On a property of the class of n-colorable graphs , 1974 .

[21]  Andrzej Ehrenfeucht,et al.  An O(n²) Divide-and-Conquer Algorithm for the Prime Tree Decomposition of Two-Structures and Modular Decomposition of Graphs , 1994, J. Algorithms.

[22]  S. Olariu,et al.  P4‐Reducible Graphs—Class of Uniquely Tree‐Representable Graphs , 1989 .

[23]  Jayme Luiz Szwarcfiter,et al.  Applying Modular Decomposition to Parameterized Cluster Editing Problems , 2008, Theory of Computing Systems.

[24]  Katharina T. Huber,et al.  Orthology relations, symbolic ultrametrics, and cographs , 2013, Journal of mathematical biology.

[25]  Martin Middendorf,et al.  Phylogenomics with paralogs , 2015, Proceedings of the National Academy of Sciences.

[26]  Jeremy P. Spinrad,et al.  Modular decomposition and transitive orientation , 1999, Discret. Math..

[27]  Jens Gustedt,et al.  Efficient and Practical Algorithms for Sequential Modular Decomposition , 2001, J. Algorithms.

[28]  Jens Gustedt,et al.  Efficient and practical modular decomposition , 1997, SODA '97.

[29]  Christophe Paul,et al.  On the (Non-)Existence of Polynomial Kernels for Pl-Free Edge Modification Problems , 2010, Algorithmica.

[30]  Laurent Viennot,et al.  Partition Refinement Techniques: An Interesting Algorithmic Tool Kit , 1999, Int. J. Found. Comput. Sci..

[31]  Peter F. Stadler,et al.  Spiders can be Recognized by Counting Their Legs , 2015, Math. Comput. Sci..

[32]  A. Brandstädt,et al.  Graph Classes: A Survey , 1987 .

[33]  Michel Habib,et al.  A Simple Linear Time LexBFS Cograph Recognition Algorithm , 2003, WG.

[34]  Andreas Blass,et al.  Graphs with unique maximal clumpings , 1978, J. Graph Theory.