Finding Good Decompositions for Dynamic Programming on Dense Graphs

It is well-known that for graphs with high edge density the tree-width is always high while the clique-width can be low. Boolean-width is a new parameter that is never higher than tree-width or clique-width and can in fact be as small as logarithmic in clique-width. Boolean-width is defined using a decomposition tree by evaluating the number of neighborhoods across the resulting cuts of the graph. Several NP-hard problems can be solved efficiently by dynamic programming when given a decomposition of boolean-width k, e.g. Max Weight Independent Set in time O(n2k22k) and Min Weight Dominating Set in time O(n2+nk23k). Finding decompositions of low boolean-width is therefore of practical interest. There is evidence that computing boolean-width is hard, while the existence of a useful approximation algorithm is still open. In this paper we introduce and study a heuristic algorithm that finds a reasonably good decomposition to be used for dynamic programming based on boolean-width. On a set of graphs of practical relevance, specifically graphs in TreewidthLIB, the best known upper bound on their tree-width is compared to the upper bound on their boolean-width given by our heuristic. For the large majority of the graphs on which we made the tests, the tree-width bound is at least twice as big as the boolean-width bound, and boolean-width compares better the higher the edge density. This means that, for problems like Dominating Set, using boolean-width should outperform dynamic programming by tree-width, at least for graphs of edge density above a certain bound. In view of the amount of previous work on heuristics for tree-width these results indicate that boolean-width could in the future outperform tree-width in practice for a large class of graphs and problems.

[1]  Bengt Aspvall,et al.  Memory Requirements for Table Computations in Partial k-tree Algorithms , 1998, SWAT.

[2]  Liming Cai,et al.  Comparative Pathway Annotation with Protein-DNA Interaction and Operon Information via Graph Tree Decomposition , 2006, Pacific Symposium on Biocomputing.

[3]  Bengt Aspvall,et al.  Memory Requirements for Table Computations in Partial \sl k -Tree Algorithms , 2000, Algorithmica.

[4]  Martin Vatshelle,et al.  Graph classes with structured neighborhoods and algorithmic applications , 2011, Theor. Comput. Sci..

[5]  R. Fildes Journal of the Royal Statistical Society (B): Gary K. Grunwald, Adrian E. Raftery and Peter Guttorp, 1993, “Time series of continuous proportions”, 55, 103–116.☆ , 1993 .

[6]  Udi Rotics,et al.  On the Clique-Width of Perfect Graph Classes , 1999, WG.

[7]  Marko Vukolic,et al.  SOFSEM 2011: Theory and Practice of Computer Science - 37th Conference on Current Trends in Theory and Practice of Computer Science, Nový Smokovec, Slovakia, January 22-28, 2011. Proceedings , 2011, SOFSEM.

[8]  Liming Cai,et al.  Rapid ab initio prediction of RNA pseudoknots via graph tree decomposition , 2007, Journal of mathematical biology.

[9]  Jan Arne Telle,et al.  Boolean-width of graphs , 2009, Theor. Comput. Sci..

[10]  Arie M. C. A. Koster,et al.  Treewidth computations I. Upper bounds , 2010, Inf. Comput..

[11]  Paul D. Seymour,et al.  Approximating clique-width and branch-width , 2006, J. Comb. Theory, Ser. B.

[12]  David J. Spiegelhalter,et al.  Local computations with probabilities on graphical structures and their application to expert systems , 1990 .

[13]  Amos Fiat,et al.  Algorithms - ESA 2009 , 2009, Lecture Notes in Computer Science.

[14]  Gabriel Renault,et al.  On the Boolean-Width of a Graph: Structure and Applications , 2009, WG.

[15]  Russell L. Malmberg,et al.  Tree decomposition based fast search of RNA structures including pseudoknots in genomes , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

[16]  Peter Rossmanith,et al.  Dynamic Programming on Tree Decompositions Using Generalised Fast Subset Convolution , 2009, ESA.

[17]  Petr Hliněný,et al.  Finding branch-decomposition and rank-decomposition , 2008 .

[18]  Hans L. Bodlaender,et al.  A Local Search Algorithm for Branchwidth , 2011, SOFSEM.

[19]  Arie M. C. A. Koster,et al.  Branch and Tree Decomposition Techniques for Discrete Optimization , 2005 .

[20]  Hans L. Bodlaender A linear time algorithm for finding tree-decompositions of small treewidth , 1993, STOC '93.

[21]  Petr Hlinený,et al.  Finding Branch-Decompositions and Rank-Decompositions , 2007, SIAM J. Comput..

[22]  Hans L. Bodlaender,et al.  Treewidth: Characterizations, Applications, and Computations , 2006, WG.

[23]  Hubie Chen,et al.  Quantified Constraint Satisfaction and Bounded Treewidth , 2004, ECAI.

[24]  Arie M. C. A. Koster,et al.  Treewidth computations II. Lower bounds , 2011, Inf. Comput..

[25]  Martin Vatshelle,et al.  Graph Classes with Structured Neighborhoods and Algorithmic Applications , 2011, WG.

[26]  Vadim V. Lozin,et al.  On the linear structure and clique-width of bipartite permutation graphs , 2003, Ars Comb..

[27]  Georg Gottlob,et al.  A Comparison of Structural CSP Decomposition Methods , 1999, IJCAI.

[28]  Ki Hang Kim Boolean matrix theory and applications , 1982 .