Experimental Evaluation of a Branch and Bound Algorithm for Computing Pathwidth and Directed Pathwidth

International audiencePath-decompositions of graphs are an important ingredient of dynamic programming algorithms for solving efficiently many NP-hard problems. Therefore, computing the pathwidth and associated path-decomposition of graphs has both a theoretical and practical interest. In this paper, we design a Branch and Bound algorithm that computes the exact pathwidth of graphs and a corresponding path-decomposition. Our main contribution consists of several non-trivial techniques to reduce the size of the input graph (pre-processing) and to cut the exploration space during the search phase of the algorithm. We evaluate experimentally our algorithm by comparing it to existing algorithms of the literature. It appears from the simulations that our algorithm offers a significant gain with respect to previous work. In particular, it is able to compute the exact pathwidth of any graph with less than 60 nodes in a reasonable running-time (≤ 10 minutes on a standard laptop). Moreover, our algorithm achieves good performance when used as a heuristic (i.e., when returning best result found within bounded time-limit). Our algorithm is not restricted to undirected graphs since it actually computes the directed pathwidth which generalizes the notion of pathwidth to digraphs

Experimental Evaluation of a Branch and Bound Algorithm for computing Pathwidth

International audienceIt is well known that many NP-hard problems are tractable in the class of bounded pathwidth graphs. In particular, path-decompositions of graphs are an important ingredient of dynamic programming algorithms for solving such problems. Therefore, computing the pathwidth and associated path-decomposition of graphs has both a theoretical and practical interest. In this paper, we design a Branch and Bound algorithm that computes the exact pathwidth of graphs and a corresponding path-decomposition. Our main contribution consists of several non-trivial techniques to reduce the size of the input graph (pre-processing) and to cut the exploration space during the search phase of the algorithm. We evaluate experimentally our algorithm by comparing it to existing algorithms of the literature. It appears from the simulations that our algorithm offers a significative gain with respect to previous work. In particular, it is able to compute the exact pathwidth of any graph with less than 60 nodes in a reasonable running-time ( 10 min.). Moreover, our algorithm also achieves good performance when used as a heuristic (i.e., when returning best result found within bounded time-limit). Our algorithm is not restricted to undirected graphs since it actually computes the vertex-separation of digraphs (which coincides with the pathwidth in case of undirected graphs).Les décompositions en chemin de graphes sont très importants pour la conception d'algorithmes de programmation dynamique pour résoudre de nombreux problèmes NP-difficiles. Calculer la pathwidth et la décomposition en chemin correspondante sont donc d'un grand intérêt tant d'un point de vue théorique que pratique. Dans ce papier, nous proposons un algorithme de Branch and Bound qui calcule la pathwidth et une décomposition. Notre contribution principale réside dans les techniques que nous prouvons pour réduire la taille du graphe donné en entrée (prétraitement) et réduire la taille de l'espace d'exploration de la phase de recherche de l'algorithme. Nous évaluons expérimentalement notre algorithme en le comparant aux algorithmes proposés dans la littérature. Les simulations montrent que notre algorithme apporte un gain significatif par rapport aux algorithmes existants. Il est capable de calculer la valeur exacte de la pathwidth de tout graphe composé d'au plus 60 sommets en un temps raisonnable (moins de 10 minutes). De plus, notre algorithme montre de bonnes performances lorsqu'il est utilisé en heuristique (c'est-à-dire lorsqu'il retourne le meilleur résultat trouvé en un temps donné). Notre algorithme n'est pas spécifique au graphes non orientés car il permet de calculer la vertex-separation des digraphes (qui coïncide avec la pathwidth dans le cas des graphes non orientés)

A New Parametrization for Independent Set Reconfiguration and Applications to RNA Kinetics

International audienceIn this paper, we study the Independent Set (IS) reconfiguration problem in graphs. An IS reconfiguration is a scenario transforming an IS L into another IS R, inserting/removing vertices one step at a time while keeping the cardinalities of intermediate sets greater than a specified threshold. We focus on the bipartite variant where only start and end vertices are allowed in intermediate ISs. Our motivation is an application to the RNA energy barrier problem from bioinformatics, for which a natural parameter would be the difference between the initial IS size and the threshold. We first show the para-NP hardness of the problem with respect to this parameter. We then investigate a new parameter, the cardinality range, denoted by ρ which captures the maximum deviation of the reconfiguration scenario from optimal sets (formally, ρ is the maximum difference between the cardinalities of an intermediate IS and an optimal IS). We give two different routes to show that this problem is in XP for ρ: The first is a direct O(n 2)-space, O(n 2ρ+2.5)-time algorithm based on a separation lemma; The second builds on a parameterized equivalence with the directed pathwidth problem, leading to a O(n ρ+1)-space, O(n ρ+2)-time algorithm for the reconfiguration problem through an adaptation of a prior result by Tamaki [20]. This equivalence is an interesting result in its own right, connecting a reconfiguration problem (which is essentially a connectivity problem within a reconfiguration network) with a structural parameter for an auxiliary graph. We demonstrate the practicality of these algorithms, and the relevance of our introduced parameter, by considering the application of our algorithms on random small-degree instances for our problem. Moreover, we reformulate the computation of the energy barrier between two RNA secondary structures, a classic hard problem in computational biology, as an instance of bipartite reconfiguration. Our results on IS reconfiguration thus yield an XP algorithm in O(n ρ+2) for the energy barrier problem, improving upon a partial O(n 2ρ+2.5) algorithm for the problem

Graph and String Parameters: Connections Between Pathwidth, Cutwidth and the Locality Number

We investigate the locality number, a recently introduced structural parameter for strings (with applications in pattern matching with variables), and its connection to two important graph-parameters, cutwidth and pathwidth. These connections allow us to show that computing the locality number is NP-hard but fixed-parameter tractable (when the locality number or the alphabet size is treated as a parameter), and can be approximated with ratio O(sqrt{log{opt}} log n). As a by-product, we also relate cutwidth via the locality number to pathwidth, which is of independent interest, since it improves the best currently known approximation algorithm for cutwidth. In addition to these main results, we also consider the possibility of greedy-based approximation algorithms for the locality number

Fixed-Parameter Algorithms for Rectilinear Steiner tree and Rectilinear Traveling Salesman Problem in the plane

Given a set $P$ of $n$ points with their pairwise distances, the traveling salesman problem (TSP) asks for a shortest tour that visits each point exactly once. A TSP instance is rectilinear when the points lie in the plane and the distance considered between two points is the $l_1$ distance. In this paper, a fixed-parameter algorithm for the Rectilinear TSP is presented and relies on techniques for solving TSP on bounded-treewidth graphs. It proves that the problem can be solved in $O\left(nh7^h\right)$ where $h \leq n$ denotes the number of horizontal lines containing the points of $P$. The same technique can be directly applied to the problem of finding a shortest rectilinear Steiner tree that interconnects the points of $P$ providing a $O\left(nh5^h\right)$ time complexity. Both bounds improve over the best time bounds known for these problems.Comment: 24 pages, 13 figures, 6 table

Order-Related Problems Parameterized by Width

In the main body of this thesis, we study two different order theoretic problems. The first problem, called Completion of an Ordering, asks to extend a given finite partial order to a complete linear order while respecting some weight constraints. The second problem is an order reconfiguration problem under width constraints. While the Completion of an Ordering problem is NP-complete, we show that it lies in FPT when parameterized by the interval width of ρ. This ordering problem can be used to model several ordering problems stemming from diverse application areas, such as graph drawing, computational social choice, and computer memory management. Each application yields a special partial order ρ. We also relate the interval width of ρ to parameterizations for these problems that have been studied earlier in the context of these applications, sometimes improving on parameterized algorithms that have been developed for these parameterizations before. This approach also gives some practical sub-exponential time algorithms for ordering problems. In our second main result, we combine our parameterized approach with the paradigm of solution diversity. The idea of solution diversity is that instead of aiming at the development of algorithms that output a single optimal solution, the goal is to investigate algorithms that output a small set of sufficiently good solutions that are sufficiently diverse from one another. In this way, the user has the opportunity to choose the solution that is most appropriate to the context at hand. It also displays the richness of the solution space. There, we show that the considered diversity version of the Completion of an Ordering problem is fixed-parameter tractable with respect to natural paramaters that capture the notion of diversity and the notion of sufficiently good solutions. We apply this algorithm in the study of the Kemeny Rank Aggregation class of problems, a well-studied class of problems lying in the intersection of order theory and social choice theory. Up to this point, we have been looking at problems where the goal is to find an optimal solution or a diverse set of good solutions. In the last part, we shift our focus from finding solutions to studying the solution space of a problem. There we consider the following order reconfiguration problem: Given a graph G together with linear orders τ and τ ′ of the vertices of G, can one transform τ into τ ′ by a sequence of swaps of adjacent elements in such a way that at each time step the resulting linear order has cutwidth (pathwidth) at most w? We show that this problem always has an affirmative answer when the input linear orders τ and τ ′ have cutwidth (pathwidth) at most w/2. Using this result, we establish a connection between two apparently unrelated problems: the reachability problem for two-letter string rewriting systems and the graph isomorphism problem for graphs of bounded cutwidth. This opens an avenue for the study of the famous graph isomorphism problem using techniques from term rewriting theory. In addition to the main part of this work, we present results on two unrelated problems, namely on the Steiner Tree problem and on the Intersection Non-emptiness problem from automata theory.Doktorgradsavhandlin