Open Problems in Parameterized and Exact Computation - IWPEC 2006

In September 2006, the Second International Workshop on Parameterized and Exact Computation was held in Zürich, Switzerland, as part of ALGO 2006. At the end of IWPEC 2006, a problem session was held. (Most of) the problems mentioned at this problem session, and some other problems, contributed by the participants of IWPEC 2006 are listed here

07281 Abstracts Collection -- Structure Theory and FPT Algorithmics for Graphs, Digraphs and Hypergraphs

From 8th to 13th July 2007, the Dagstuhl Seminar ``Structure Theory and FPT Algorithmics for Graphs, Digraphs and Hypergraphs\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Although taxonomy is often used informally to evaluate the results of phylogenetic inference and find the root of phylogenetic trees, algorithmic methods to do so are lacking. In this paper we formalize these procedures and develop algorithms to solve the relevant problems. In particular, we introduce a new algorithm that solves a "subcoloring" problem for expressing the difference between the taxonomy and phylogeny at a given rank. This algorithm improves upon the current best algorithm in terms of asymptotic complexity for the parameter regime of interest; we also describe a branch-and-bound algorithm that saves orders of magnitude in computation on real data sets. We also develop a formalism and an algorithm for rooting phylogenetic trees according to a taxonomy. All of these algorithms are implemented in freely-available software.Comment: Version submitted to Algorithms for Molecular Biology. A number of fixes from previous versio

Upper and lower bounds for finding connected motifs in vertex-colored graphs

International audienceWe study the problem of finding occurrences of motifs in vertex-colored graphs, where a motif is a multiset of colors, and an occurrence of a motif is a subset of connected vertices whose multiset of colors equals the motif. This problem is a natural graph-theoretic pattern matching variant where we are not interested in the actual structure of the occurrence of the pattern, we only require it to preserve the very basic topological requirement of connectedness. We give two positive results and three negative results that together give an extensive picture of tractable and intractable instances of the problem

On Reconfiguration Problems: Structure and Tractability

Given an n-vertex graph G and two vertices s and t in G, determining whether there exists a path and computing the length of the shortest path between s and t are two of the most fundamental graph problems. In the classical battle of P versus NP or ``easy'' versus ``hard'', both of these problems are on the easy side. That is, they can be solved in poly(n) time, where poly is any polynomial function. But what if our input consisted of a 2^n-vertex graph? Of course, we can no longer assume G to be part of the input, as reading the input alone requires more than poly(n) time. Instead, we are given an oracle encoded using poly(n) bits and that can, in constant or poly(n) time, answer queries of the form ``is u a vertex in G'' or ``is there an edge between u and v?''. Given such an oracle and two vertices of the 2^n-vertex graph, can we still determine if there is a path or compute the length of the shortest path between s and t in poly(n) time? A slightly different, but equally insightful, formulation of the question above is as follows. Given a set S of n objects, consider the graph R(S) which contains one vertex for each set in the power set of S, 2^S, and two vertices are adjacent in R(S) whenever the size of their symmetric difference is equal to one. Clearly, this graph contains 2^n vertices and can be easily encoded in poly(n) bits using the oracle described above. It is not hard to see that there exists a path between any two vertices of R(S). Moreover, computing the length of a shortest path can be accomplished in constant time; it is equal to the size of the symmetric difference of the two underlying sets. If the vertex set of R(S) were instead restricted to a subset of 2^S, both of our problems can become NP-complete or even PSPACE-complete. Therefore, another interesting question is whether we can determine what types of ``restriction'' on the vertex set of R(S) induce such variations in the complexity of the two problems. These two seemingly artificial questions are in fact quite natural and appear in many practical and theoretical problems. In particular, these are exactly the types of questions asked under the reconfiguration framework, the main subject of this thesis. Under the reconfiguration framework, instead of finding a feasible solution to some instance I of a search problem Q, we are interested in structural and algorithmic questions related to the solution space of Q. Naturally, given some adjacency relation A defined over feasible solutions of Q, size of the symmetric difference being one such relation, the solution space can be represented using a graph R_Q(I). R_Q(I) contains one vertex for each feasible solution of Q on instance I and two vertices share an edge whenever their corresponding solutions are adjacent under A. An edge in R_Q(I) corresponds to a reconfiguration step, a walk in R_Q(I) is a sequence of such steps, a reconfiguration sequence, and R_Q(I) is a reconfiguration graph. Studying problems related to reconfiguration graphs has received considerable attention in recent literature, the most popular problem being to determine whether there exists a reconfiguration sequence between two given feasible solutions; for most NP-complete problems, this problem has been shown to be PSPACE-complete. The purpose of our work is to embark on a systematic investigation of the tractability and structural properties of such problems under both classical and parameterized complexity assumptions. Parameterized complexity is another framework which has become an essential tool for researchers in computational complexity during the last two decades or so and one of its main goals is to provide a better explanation of why some hard problems (in a classical sense) can be in fact much easier than others. Hence, we are interested in what separates the tractable instances from the intractable ones and the fixed-parameter tractable instances from the fixed-parameter intractable ones. It is clear from the generic definition of reconfiguration problems that several factors affect their complexity status. Our work aims at providing a finer classification of the complexity of reconfiguration problems with respect to some of these factors, including the definition of the adjacency relation A, structural properties of the input instance I, structural properties of the reconfiguration graph, and the length of a reconfiguration sequence. As most of these factors can be numerically quantified, we believe that the investigation of reconfiguration problems under both parameterized and classical complexity assumptions will help us further understand the boundaries between tractability and intractability. We consider reconfiguration problems related to Satisfiability, Coloring, Dominating Set, Vertex Cover, Independent Set, Feedback Vertex Set, and Odd Cycle Transversal, and provide lower bounds, polynomial-time algorithms, and fixed-parameter tractable algorithms. In doing so, we answer some of the questions left open in recent work and push the known boundaries between tractable and intractable even closer. As a byproduct of our initiating work on parameterized reconfiguration problems, we present a generic adaptation of parameterized complexity techniques which we believe can be used as a starting point for studying almost any such problem

Balanced Connected Subgraph Problem in Geometric Intersection Graphs

We study the Balanced Connected Subgraph(shortly, BCS) problem on geometric intersection graphs such as interval, circular-arc, permutation, unit-disk, outer-string graphs, etc. Given a vertex-colored graph $G=(V,E)$, where each vertex in $V$ is colored with either ``red'' or ``blue'', the BCS problem seeks a maximum cardinality induced connected subgraph $H$ of $G$ such that $H$ is color-balanced, i.e., $H$ contains an equal number of red and blue vertices. We study the computational complexity landscape of the BCS problem while considering geometric intersection graphs. On one hand, we prove that the BCS problem is NP-hard on the unit disk, outer-string, complete grid, and unit square graphs. On the other hand, we design polynomial-time algorithms for the BCS problem on interval, circular-arc and permutation graphs. In particular, we give algorithm for the Steiner Tree problem on both the interval graphs and circular arc graphs, that is used as a subroutine for solving BCS problem on same graph classes. Finally, we present a FPT algorithm for the BCS problem on general graphs.Comment: 17 pages, 3 figure

On the complexity of some colorful problems parameterized by treewidth

In this paper,we study the complexity of several coloring problems on graphs, parameterizedby the treewidth of the graph.1. The List Coloring problem takes as input a graph G, togetherwith an assignment to each vertex v of a set of colors Cv. The problem is to determinewhether it is possible to choose a color for vertex v from the set of permitted colors Cv, for each vertex, so that the obtained coloring of G is proper. We show that this problem is W[1]-hard, parameterized by the treewidth of G. The closely related Precoloring Extension problem is also shown to be W[1]-hard, parameterized by treewidth.2. An equitable coloring of a graph G is a proper coloring of the verticeswhere the numbers of vertices having any two distinct colors differs by at most one.We show that the problem is hard forW[1], parameterized by the treewidth plus the number of colors.We also show that a list-based variation, List Equitable Coloring is W[1]-hard for forests, parameterizedby the number of colors on the lists.3. The list chromatic number χl(G) of a graph G is defined to be the smallest positive integer r, such that for every assignment to the vertices v of G, of a list Lv of colors, where each list has length at least r, there is a choice of one color fromeach vertex list Lv yielding a proper coloring of G. We show that the problem of determining whether χl(G) ≤ r, the ListChromatic Number problem, is solvable in linear time on graphs of constant treewidth