Given a graph, in the maximum clique problem one wants to find

vi Declaration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix List of Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii List of Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiv I Orthogonal Graph Drawing 1 1

This paper introduces a branch-and-bound algorithm for the maximum clique problem which applies existing clique finding and vertex coloring heuristics to determine lower and upper bounds for the size of a maximum clique. Computational results on a variety of graphs indicate the proposed procedure in most instances outperforms leading algorithms.

Many important problems arising in computational biochemistry and genomics have been formulated in terms of underlying combinatorial optimization models. In particular, a number have been formulated as clique-detection models. The proposed article includes an introduction to the underlying biochemistry and genomic aspects of the problems as well as to the graph-theoretic aspects of the solution approaches. Each subsequent section describes a particular type of problem, gives an example to show how the graph model can be derived, summarizes recent progress, and discusses challenges associated with solving the associated graph-theoretic models. Clique detection models include prescribing (a) a maximal clique, (b) a maximum clique, (c) a maximum weighted clique, or (d) all maximal cliques in a graph. The particular types of biochemistry and genomics problems that can be represented by a clique detection model include integration of genome mapping data, nonoverlapping local alignments, matching and comparing molecular structures, and protein docking.

. We consider the following map labelling problem: given distinct points p1 ; p2 ; : : : ; pn in the plane, nd a set of pairwise disjoint axisparallel squares Q1 ; Q2 ; : : : ; Qn where p i is a corner of Q i . This problem reduces to that of nding a maximum independent set in a graph. We present a branch and cut algorithm for nding maximum independent sets and apply it to independent set instances arising from map labelling. The algorithm uses a new technique for setting variables in the branch and bound tree that implicitly exploits the Euclidean nature of the independent set problems arising from map labelling. Computational experiments show that this technique contributes to controlling the size of the branch and bound tree. We also present a novel variant of the algorithm for generating violated odd-hole inequalities. Using our algorithm we can nd provably optimal solutions for map labelling instances with up to 950 cities within modest computing time, a considera...

We describe a new branch-and-bound algorithm for the exact solution of the maximum cardinality stable set problem. The bounding phase is based on a variation of the standard greedy algorithm for finding a colouring of a graph. Two different node-fixing heuristics are also described. Computational tests on random and structured graphs and very large graphs corresponding to `real-life' problems show that the algorithm is competitive with the fastest algorithms known so far. 1 Introduction We denote by G = (V; E) an undirected graph. V is the set of nodes and E the set of edges. A stable set is a subset of V such that no two nodes of the subset are pairwise adjacent. The cardinality of a maximum stable set of G will be denoted by ff(G). A clique is a subset of V with the property that all the nodes are pairwise adjacent. A clique covering is a set of disjoint cliques whose union is equal to V ; the cardinality of a minimum clique covering is denoted by `(G), and since at most one nod...

We compute approximate solutions to the maximum stable set problem and the minimum graph coloring problem using a positive semidefinite relaxation. The positive semidefinite programs are solved using an implementation of the dual scaling algorithm that takes advantage of the sparsity inherent in most graphs and the structure inherent in the problem formulation. From the solution to the relaxation, we apply a randomized algorithm to find approximate maximum stable sets and a modification of a popular heuristic to find graph colorings. We obtained high quality answers for graphs with over 1000 vertices and almost 7000 edges.

. Edge projection is a specialization of Lov'asz and Plummer's clique projection when restricted to edges. We discuss some properties of the edge projection which are then exploited to develop a new upper bound procedure for the Maximum Cardinality Stable Set Problem (MSS Problem). The upper bound computed by our heuristic, incorporated in a branch-and-bound scheme in conjunction with Balas and Yu branching rule, seems to be very effective for sparse graphs, which are typically hard instances of the MSS Problem. 1. Introduction We denote by G = (V; E) an undirected graph. V is the set of nodes and E the set of edges. A stable set is a subset of V such that no two nodes of the subset are pairwise adjacent. The cardinality of a maximum stable set of G will be denoted by ff(G). When G is the empty graph, ff(G) = 0. A clique is a subset of V with the property that all the nodes are pairwise adjacent. A clique partitioning of G is a family of cliques such that each node of G is contained ...

Finding the minimum column multiplicity for a bound set of variables is an important problem in Curtis decomposition. To investigate this problem, we compared two graph coloring programs: one exact, and another one based on heuristics which can give, however, provably exact results on some types of graphs. These programs were incorporated into the multi-valued decomposer MVGUD. We proved that the exact graph coloring is not necessary for high-quality functional decomposers. Thus we improved by orders of magnitude the speed of the column multiplicity problem, with very little or no sacrifice of decomposition quality. Comparison of our experimental results with competing decomposers shows that for nearly all benchmarks our solutions are best and time is usually not too high.

Traditionally, practical clique algorithms have been compared based on their performance on various random graphs. We propose a new testing methodology which permits testing to be completed in a fraction of the time required by previous methods. In addition, the range of testing can be extended to include problems that could not be attempted in the past because of being too time consuming. We accomplish this by applying the approach that makes dynamic programming a very effective algorithmic technique: we use tabulated estimates for the time required to solve subproblems rather than timing each exactly. Our computational experiments validate this approach. The next step is to use this workbench to develop fast new algorithms for the maximum clique problem. A mixed algorithm is an algorithm which applies different strategies for the subproblems that arise. Using the dynamic programming approach again for timing, we mechanize the process of developing table driven algorithms which apply ...