Setting Parameters by Example

We introduce a class of "inverse parametric optimization" problems, in which one is given both a parametric optimization problem and a desired optimal solution; the task is to determine parameter values that lead to the given solution. We describe algorithms for solving such problems for minimum spanning trees, shortest paths, and other "optimal subgraph" problems, and discuss applications in multicast routing, vehicle path planning, resource allocation, and board game programming.Comment: 13 pages, 3 figures. To be presented at 40th IEEE Symp. Foundations of Computer Science (FOCS '99

Sampling decomposable graphs using a Markov chain on junction trees

Full Bayesian computational inference for model determination in undirected graphical models is currently restricted to decomposable graphs, except for problems of very small scale. In this paper we develop new, more efficient methodology for such inference, by making two contributions to the computational geometry of decomposable graphs. The first of these provides sufficient conditions under which it is possible to completely connect two disconnected complete subsets of vertices, or perform the reverse procedure, yet maintain decomposability of the graph. The second is a new Markov chain Monte Carlo sampler for arbitrary positive distributions on decomposable graphs, taking a junction tree representing the graph as its state variable. The resulting methodology is illustrated with numerical experiments on three specific models.Comment: 22 pages, 7 figures, 1 table. V2 as V1 except that Fig 1 was corrected. V3 has significant edits, dropping some figures and including additional examples and a discussion of the non-decomposable case. V4 is further edited following review, and includes additional reference

Clearing Contamination in Large Networks

In this work, we study the problem of clearing contamination spreading through a large network where we model the problem as a graph searching game. The problem can be summarized as constructing a search strategy that will leave the graph clear of any contamination at the end of the searching process in as few steps as possible. We show that this problem is NP-hard even on directed acyclic graphs and provide an efficient approximation algorithm. We experimentally observe the performance of our approximation algorithm in relation to the lower bound on several large online networks including Slashdot, Epinions and Twitter. The experiments reveal that in most cases our algorithm performs near optimally

Maximum common subgraph isomorphism algorithms for the matching of chemical structures

The maximum common subgraph (MCS) problem has become increasingly important in those aspects of chemoinformatics that involve the matching of 2D or 3D chemical structures. This paper provides a classification and a review of the many MCS algorithms, both exact and approximate, that have been described in the literature, and makes recommendations regarding their applicability to typical chemoinformatics tasks

Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

Efficient Algorithms for Node Disjoint Subgraph Homeomorphism Determination

Recently, great efforts have been dedicated to researches on the management of large scale graph based data such as WWW, social networks, biological networks. In the study of graph based data management, node disjoint subgraph homeomorphism relation between graphs is more suitable than (sub)graph isomorphism in many cases, especially in those cases that node skipping and node mismatching are allowed. However, no efficient node disjoint subgraph homeomorphism determination (ndSHD) algorithms have been available. In this paper, we propose two computationally efficient ndSHD algorithms based on state spaces searching with backtracking, which employ many heuristics to prune the search spaces. Experimental results on synthetic data sets show that the proposed algorithms are efficient, require relative little time in most of the testing cases, can scale to large or dense graphs, and can accommodate to more complex fuzzy matching cases.Comment: 15 pages, 11 figures, submitted to DASFAA 200

Orientation-Constrained Rectangular Layouts

We construct partitions of rectangles into smaller rectangles from an input consisting of a planar dual graph of the layout together with restrictions on the orientations of edges and junctions of the layout. Such an orientation-constrained layout, if it exists, may be constructed in polynomial time, and all orientation-constrained layouts may be listed in polynomial time per layout.Comment: To appear at Algorithms and Data Structures Symposium, Banff, Canada, August 2009. 12 pages, 5 figure

On almost hypohamiltonian graphs

A graph $G$ is almost hypohamiltonian (a.h.) if $G$ is non-hamiltonian, there exists a vertex $w$ in $G$ such that $G - w$ is non-hamiltonian, and $G - v$ is hamiltonian for every vertex $v \ne w$ in $G$. The second author asked in [J. Graph Theory 79 (2015) 63--81] for all orders for which a.h. graphs exist. Here we solve this problem. To this end, we present a specialised algorithm which generates complete sets of a.h. graphs for various orders. Furthermore, we show that the smallest cubic a.h. graphs have order 26. We provide a lower bound for the order of the smallest planar a.h. graph and improve the upper bound for the order of the smallest planar a.h. graph containing a cubic vertex. We also determine the smallest planar a.h. graphs of girth 5, both in the general and cubic case. Finally, we extend a result of Steffen on snarks and improve two bounds on longest paths and longest cycles in polyhedral graphs due to Jooyandeh, McKay, {\"O}sterg{\aa}rd, Pettersson, and the second author.Comment: 18 pages. arXiv admin note: text overlap with arXiv:1602.0717