Tractable classes of binary CSPs defined by excluded topological minors

The binary Constraint Satisfaction Problem (CSP) is to decide whether there exists an assignment to a set of variables which satisfies specified constraints between pairs of variables. A CSP instance can be presented as a labelled graph (called the microstructure) encoding both the forms of the constraints and where they are imposed. We consider subproblems defined by restricting the allowed form of the microstructure. One form of restriction that has previously been considered is to forbid certain specified substructures (patterns). This captures some tractable classes of the CSP, but does not capture the well-known property of acyclicity. In this paper we introduce the notion of a topological minor of a binary CSP instance. By forbidding certain patterns as topological minors we obtain a compact mechanism for expressing several novel tractable classes, including new generalisations of the class of acyclic instances

On Brambles, Grid-Like Minors, and Parameterized Intractability of Monadic Second-Order Logic

Brambles were introduced as the dual notion to treewidth, one of the most central concepts of the graph minor theory of Robertson and Seymour. Recently, Grohe and Marx showed that there are graphs G, in which every bramble of order larger than the square root of the treewidth is of exponential size in |G|. On the positive side, they show the existence of polynomial-sized brambles of the order of the square root of the treewidth, up to log factors. We provide the first polynomial time algorithm to construct a bramble in general graphs and achieve this bound, up to log-factors. We use this algorithm to construct grid-like minors, a replacement structure for grid-minors recently introduced by Reed and Wood, in polynomial time. Using the grid-like minors, we introduce the notion of a perfect bramble and an algorithm to find one in polynomial time. Perfect brambles are brambles with a particularly simple structure and they also provide us with a subgraph that has bounded degree and still large treewidth; we use them to obtain a meta-theorem on deciding certain parameterized subgraph-closed problems on general graphs in time singly exponential in the parameter. The second part of our work deals with providing a lower bound to Courcelle's famous theorem, stating that every graph property that can be expressed by a sentence in monadic second-order logic (MSO), can be decided by a linear time algorithm on classes of graphs of bounded treewidth. Using our results from the first part of our work we establish a strong lower bound for tractability of MSO on classes of colored graphs

Hitting forbidden minors: Approximation and Kernelization

We study a general class of problems called F-deletion problems. In an F-deletion problem, we are asked whether a subset of at most $k$ vertices can be deleted from a graph $G$ such that the resulting graph does not contain as a minor any graph from the family F of forbidden minors. We obtain a number of algorithmic results on the F-deletion problem when F contains a planar graph. We give (1) a linear vertex kernel on graphs excluding $t$-claw $K_{1,t}$, the star with $t$ leves, as an induced subgraph, where $t$ is a fixed integer. (2) an approximation algorithm achieving an approximation ratio of $O(\log^{3/2} OPT)$, where $OPT$ is the size of an optimal solution on general undirected graphs. Finally, we obtain polynomial kernels for the case when F contains graph $\theta_c$ as a minor for a fixed integer $c$. The graph $\theta_c$ consists of two vertices connected by $c$ parallel edges. Even though this may appear to be a very restricted class of problems it already encompasses well-studied problems such as {\sc Vertex Cover}, {\sc Feedback Vertex Set} and Diamond Hitting Set. The generic kernelization algorithm is based on a non-trivial application of protrusion techniques, previously used only for problems on topological graph classes

Finding detours is fixed-parameter tractable

We consider the following natural "above guarantee" parameterization of the classical Longest Path problem: For given vertices s and t of a graph G, and an integer k, the problem Longest Detour asks for an (s,t)-path in G that is at least k longer than a shortest (s,t)-path. Using insights into structural graph theory, we prove that Longest Detour is fixed-parameter tractable (FPT) on undirected graphs and actually even admits a single-exponential algorithm, that is, one of running time exp(O(k)) poly(n). This matches (up to the base of the exponential) the best algorithms for finding a path of length at least k. Furthermore, we study the related problem Exact Detour that asks whether a graph G contains an (s,t)-path that is exactly k longer than a shortest (s,t)-path. For this problem, we obtain a randomized algorithm with running time about 2.746^k, and a deterministic algorithm with running time about 6.745^k, showing that this problem is FPT as well. Our algorithms for Exact Detour apply to both undirected and directed graphs.Comment: Extended abstract appears at ICALP 201

Smooth Approximations and Relational Width Collapses

We prove that relational structures admitting specific polymorphisms (namely, canonical pseudo-WNU operations of all arities $n \geq 3$) have low relational width. This implies a collapse of the bounded width hierarchy for numerous classes of infinite-domain CSPs studied in the literature. Moreover, we obtain a characterization of bounded width for first-order reducts of unary structures and a characterization of MMSNP sentences that are equivalent to a Datalog program, answering a question posed by Bienvenu, ten Cate, Lutz, and Wolter. In particular, the bounded width hierarchy collapses in those cases as well

Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics

Hard graph problems are ubiquitous in Bioinformatics, inspiring the design of specialized Fixed-Parameter Tractable algorithms, many of which rely on a combination of tree-decomposition and dynamic programming. The time/space complexities of such approaches hinge critically on low values for the treewidth tw of the input graph. In order to extend their scope of applicability, we introduce the Tree-Diet problem, i.e. the removal of a minimal set of edges such that a given tree-decomposition can be slimmed down to a prescribed treewidth tw\u27. Our rationale is that the time gained thanks to a smaller treewidth in a parameterized algorithm compensates the extra post-processing needed to take deleted edges into account. Our core result is an FPT dynamic programming algorithm for Tree-Diet, using 2^{O(tw)}n time and space. We complement this result with parameterized complexity lower-bounds for stronger variants (e.g., NP-hardness when tw\u27 or tw-tw\u27 is constant). We propose a prototype implementation for our approach which we apply on difficult instances of selected RNA-based problems: RNA design, sequence-structure alignment, and search of pseudoknotted RNAs in genomes, revealing very encouraging results. This work paves the way for a wider adoption of tree-decomposition-based algorithms in Bioinformatics

When the decomposition meets the constraint satisfaction problem

This paper explores the joint use of decomposition methods and parallel computing for solving constraint satisfaction problems and introduces a framework called Parallel Decomposition for Constraint Satisfaction Problems (PD-CSP). The main idea is that the set of constraints are first clustered using a decomposition algorithm in which highly correlated constraints are grouped together. Next, parallel search of variables is performed on the produced clusters in a way that is friendly for parallel computing. In particular, for the first step, we propose the adaptation of two well-known clustering algorithms ( k -means and DBSCAN). For the second step, we develop a GPU-based approach to efficiently explore the clusters. The results from the extensive experimental evaluation show that the PD-CSP provides competitive results in terms of accuracy and runtime