Algorithmic Complexity Between Structure and Knowledge Nicolas Nisse
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Constrained Representations of Map Graphs and Half-Squares
Constrained Representations of Map Graphs and Half-Squares Hoang-Oanh Le Berlin, Germany [email protected] Van Bang Le Universität Rostock, Institut für Informatik, Rostock, Germany [email protected] Abstract The square of a graph H, denoted H2, is obtained from H by adding new edges between two distinct vertices whenever their distance in H is two. The half-squares of a bipartite graph B = (X, Y, EB ) are the subgraphs of B2 induced by the color classes X and Y , B2[X] and B2[Y ]. For a given graph 2 G = (V, EG), if G = B [V ] for some bipartite graph B = (V, W, EB ), then B is a representation of G and W is the set of points in B. If in addition B is planar, then G is also called a map graph and B is a witness of G [Chen, Grigni, Papadimitriou. Map graphs. J. ACM, 49 (2) (2002) 127-138]. While Chen, Grigni, Papadimitriou proved that any map graph G = (V, EG) has a witness with at most 3|V | − 6 points, we show that, given a map graph G and an integer k, deciding if G admits a witness with at most k points is NP-complete. As a by-product, we obtain NP-completeness of edge clique partition on planar graphs; until this present paper, the complexity status of edge clique partition for planar graphs was previously unknown. We also consider half-squares of tree-convex bipartite graphs and prove the following complexity 2 dichotomy: Given a graph G = (V, EG) and an integer k, deciding if G = B [V ] for some tree-convex bipartite graph B = (V, W, EB ) with |W | ≤ k points is NP-complete if G is non-chordal dually chordal and solvable in linear time otherwise. -
Lipics-WABI-2021-7.Pdf (2
Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics Bertrand Marchand # LIX CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France LIGM, CNRS, Univ Gustave Eiffel, F77454 Marne-la-vallée, France Yann Ponty1 # LIX CNRS UMR 7161, Ecole Polytechnique, Institut Polytechnique de Paris, Palaiseau, France Laurent Bulteau1 # LIGM, CNRS, Univ Gustave Eiffel, F77454 Marne-la-vallée, France Abstract 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′. 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 2O(tw)n time and space. We complement this result with parameterized complexity lower-bounds for stronger variants (e.g., NP-hardness when tw′ or tw−tw′ 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. -
Complexity and Exact Algorithms for Vertex Multicut in Interval and Bounded Treewidth Graphs 1
Complexity and Exact Algorithms for Vertex Multicut in Interval and Bounded Treewidth Graphs 1 Jiong Guo a,∗ Falk H¨uffner a Erhan Kenar b Rolf Niedermeier a Johannes Uhlmann a aInstitut f¨ur Informatik, Friedrich-Schiller-Universit¨at Jena, Ernst-Abbe-Platz 2, D-07743 Jena, Germany bWilhelm-Schickard-Institut f¨ur Informatik, Universit¨at T¨ubingen, Sand 13, D-72076 T¨ubingen, Germany Abstract Multicut is a fundamental network communication and connectivity problem. It is defined as: given an undirected graph and a collection of pairs of terminal vertices, find a minimum set of edges or vertices whose removal disconnects each pair. We mainly focus on the case of removing vertices, where we distinguish between allowing or disallowing the removal of terminal vertices. Complementing and refining previous results from the literature, we provide several NP-completeness and (fixed- parameter) tractability results for restricted classes of graphs such as trees, interval graphs, and graphs of bounded treewidth. Key words: Combinatorial optimization, Complexity theory, NP-completeness, Dynamic programming, Graph theory, Parameterized complexity 1 Introduction Motivation and previous results. Multicut in graphs is a fundamental network design problem. It models questions concerning the reliability and ∗ Corresponding author. Tel.: +49 3641 9 46325; fax: +49 3641 9 46002 E-mail address: [email protected]. 1 An extended abstract of this work appears in the proceedings of the 32nd Interna- tional Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2006) [19]. Now, in particular the proof of Theorem 5 has been much simplified. Preprint submitted to Elsevier Science 2 February 2007 robustness of computer and communication networks. -
A Width Parameter Useful for Chordal and Co-Comparability Graphs
A width parameter useful for chordal and co-comparability graphs Dong Yeap Kang1, O-joung Kwon2, Torstein J. F. Strømme3, and Jan Arne Telle3 ? 1 Department of Mathematical Sciences, KAIST, Daejeon, South Korea 2 Institute of Software Technology and Theoretical Computer Science, TU Berlin, Germany 3 Department of Informatics, University of Bergen, Norway [email protected], [email protected], [email protected], [email protected] Abstract. In 2013 Belmonte and Vatshelle used mim-width, a graph parameter bounded on interval graphs and permutation graphs that strictly generalizes clique-width, to explain existing algorithms for many domination-type problems, also known as (σ; ρ)- problems or LC-VSVP problems, on many special graph classes. In this paper, we focus on chordal graphs and co-comparability graphs, that strictly contain interval graphs and permutation graphs respectively. First, we show that mim-width is unbounded on these classes, thereby settling an open problem from 2012. Then, we introduce two graphs Kt Kt and Kt St to restrict these graph classes, obtained from the disjoint union of two cliques of size t, and one clique of size t and one independent set of size t respec- tively, by adding a perfect matching. We prove that (Kt St)-free chordal graphs have mim-width at most t − 1, and (Kt Kt)-free co-comparability graphs have mim-width at most t − 1. From this, we obtain several algorithmic consequences, for instance, while Dominating Set is NP-complete on chordal graphs, like all LC-VSVP problems it can be solved in time O(nt) on chordal graphs where t is the maximum among induced sub- graphs Kt St in the given graph. -
Graceful Labeling of Graphs
GRACEFUL LABELING OF GRAPHS Rodrigo Ming Zhou Dissertação de Mestrado apresentada ao Programa de Pós-graduação em Engenharia de Sistemas e Computação, COPPE, da Universidade Federal do Rio de Janeiro, como parte dos requisitos necessários à obtenção do título de Mestre em Engenharia de Sistemas e Computação. Orientadores: Celina Miraglia Herrera de Figueiredo Vinícius Gusmão Pereira de Sá Rio de Janeiro Dezembro de 2016 GRACEFUL LABELING OF GRAPHS Rodrigo Ming Zhou DISSERTAÇÃO SUBMETIDA AO CORPO DOCENTE DO INSTITUTO ALBERTO LUIZ COIMBRA DE PÓS-GRADUAÇÃO E PESQUISA DE ENGENHARIA (COPPE) DA UNIVERSIDADE FEDERAL DO RIO DE JANEIRO COMO PARTE DOS REQUISITOS NECESSÁRIOS PARA A OBTENÇÃO DO GRAU DE MESTRE EM CIÊNCIAS EM ENGENHARIA DE SISTEMAS E COMPUTAÇÃO. Examinada por: Prof. Celina Miraglia Herrera de Figueiredo, D.Sc. Prof. Vinícius Gusmão Pereira de Sá, D.Sc. Prof. Rosiane de Freitas Rodrigues, D.Sc. Prof. Raphael Carlos Santos Machado, D.Sc. RIO DE JANEIRO, RJ – BRASIL DEZEMBRO DE 2016 Zhou, Rodrigo Ming Graceful Labeling of Graphs/Rodrigo Ming Zhou. – Rio de Janeiro: UFRJ/COPPE, 2016. IX, 40 p.: il.; 29; 7cm. Orientadores: Celina Miraglia Herrera de Figueiredo Vinícius Gusmão Pereira de Sá Dissertação (mestrado) – UFRJ/COPPE/Programa de Engenharia de Sistemas e Computação, 2016. Bibliography: p. 38 – 40. 1. graceful labeling. 2. computational proofs. 3. graphs. I. de Figueiredo, Celina Miraglia Herrera et al. II. Universidade Federal do Rio de Janeiro, COPPE, Programa de Engenharia de Sistemas e Computação. III. Título. iii Resumo da Dissertação apresentada à COPPE/UFRJ como parte dos requisitos necessários para a obtenção do grau de Mestre em Ciências (M.Sc.) GRACEFUL LABELING OF GRAPHS Rodrigo Ming Zhou Dezembro/2016 Orientadores: Celina Miraglia Herrera de Figueiredo Vinícius Gusmão Pereira de Sá Programa: Engenharia de Sistemas e Computação Em 1966, A. -
Improved Lower Bounds for Graph Embedding Problems
Improved Lower Bounds for Graph Embedding Problems Hans L. Bodlaender1;2? and Tom C. van der Zanden1 1 Department of Computer Science, Utrecht University, Utrecht, The Netherlands fH.L.Bodlaender,[email protected] 2 Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands Abstract. In this paper, we give new, tight subexponential lower bounds for a number of graph embedding problems. We introduce two related combinatorial problems, which we call String Crafting and Orthog- onal Vector Crafting, and show that these cannot be solved in time 2o(jsj= log jsj), unless the Exponential Time Hypothesis fails. These results are used to obtain simplified hardness results for several graph embedding problems, on more restricted graph classes than previ- ously known: assuming the Exponential Time Hypothesis, there do not exist algorithms that run in 2o(n= log n) time for Subgraph Isomorphism on graphs of pathwidth 1, Induced Subgraph Isomorphism on graphs of pathwidth 1, Graph Minor on graphs of pathwidth 1, Induced Graph Minor on graphs of pathwidth 1, Intervalizing 5-Colored Graphs on trees, and finding a tree or path decomposition with width at most c with a minimum number of bags, for any fixed c ≥ 16. 2Θ(n= log n) appears to be the \correct" running time for many pack- ing and embedding problems on restricted graph classes, and we think String Crafting and Orthogonal Vector Crafting form a useful framework for establishing lower bounds of this form. 1 Introduction Many NP-complete graph problems admit faster algorithms when restricted to planar graphs. -
Tree-Breadth of Graphs with Variants and Applications
Tree-Breadth of Graphs with Variants and Applications A dissertation submitted to Kent State University in partial fulfilment of the requirements for the degree of Doctor of Philosophy by Arne Leitert August 2017 Dissertation written by Arne Leitert Diplom, University of Rostock, 2012 Ph.D., Kent State University, 2017 Approved by Dr. Feodor F. Dragan , Chair, Doctoral Dissertation Committee Dr. Ruoming Jin , Members, Doctoral Dissertation Committee Dr. Ye Zhao , Dr. Artem Zvavitch , Dr. Lothar Reichel Accepted by Dr. Javed Khan , Chair, Department of Computer Science Dr. James L. Blank , Dean, College of Arts and Sciences Contents Contents iii List of Figures vi List of Tables vii 1 Introduction 1 1.1 Existing and Recent Results . .2 1.2 Outline . .3 2 Preliminaries 4 2.1 General Definitions . .4 2.2 Tree-Decompositions . .6 2.3 Layering Partitions . .7 2.4 Special Graph Classes . .8 3 Computing Decompositions with Small Breadth 12 3.1 Approximation Algorithms . 12 3.1.1 Layering Based Approaches . 13 3.1.2 Neighbourhood Based Approaches . 15 3.2 Strong Tree-Breadth . 20 3.2.1 NP-Completeness . 20 3.2.2 Polynomial Time Cases . 26 3.3 Computing Decompositions for Special Graph Classes . 31 iii 4 Connected r-Domination 38 4.1 Using a Layering Partition . 39 4.2 Using a Tree-Decomposition . 49 4.2.1 Preprocessing . 50 4.2.2 r-Domination . 53 4.2.3 Connected r-Domination . 55 4.3 Implications for the p-Center Problem . 63 5 Bandwidth and Line-Distortion 65 5.1 Existing Results . 66 5.2 k-Dominating Pairs . -
Durham Research Online
Durham Research Online Deposited in DRO: 08 November 2010 Version of attached le: Published Version Peer-review status of attached le: Peer-reviewed Citation for published item: Carvalho, C. and Dalmau, V. and Krokhin, A. (2008) 'Caterpillar duality for constraint satisfaction problems.', in Twenty-third Annual IEEE Symposium on Logic in Computer Science, 24-27 June 2008, Pittsburgh, PA ; proceedings. Los Alamitos, CA: IEEE, 307 -316 . Further information on publisher's website: http://dx.doi.org/10.1109/LICS.2008.19 Publisher's copyright statement: c 2008 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE. Additional information: Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full DRO policy for further details. Durham University Library, Stockton Road, Durham DH1 3LY, United Kingdom Tel : +44 (0)191 334 3042 | Fax : +44 (0)191 334 2971 https://dro.dur.ac.uk 23rd Annual IEEE Symposium on Logic in Computer Science Caterpillar duality for constraint satisfaction problems Catarina Carvalho V´ıctor Dalmau Andrei Krokhin Durham University University Pompeu Fabra Durham University Durham, DH1 3LE, UK Barcelona, 08003 Spain Durham, DH1 3LE, UK [email protected] [email protected] [email protected] Abstract programming language Datalog and its fragments are ar- guably some of the most important tools for solving CSPs. -
The Line Graph of a Tree and Its Edge Ideal
THE LINE GRAPH OF A TREE AND ITS EDGE IDEAL ANDA OLTEANU Abstract. We describe all the trees with the property that the corresponding edge ideal of their line graph has a linear resolution. As a consequence, we give a complete characterization of those trees T for which the line graph L(T ) is co- chordal. We compute also the second Betti number of the edge ideal of L(T ) and we determine the number of cycles in L(T ). As a consequence, we obtain also the first Zagreb index of a graph. For edge ideals of line graphs of caterpillar graphs we determine the Krull dimension, the Castelnuovo-Mumford regularity, and the projective dimension under some additional assumption on the degrees of the cutpoints. Introduction Firstly used under this name by Harary and Norman in [15], line graphs have been intensively studied in combinatorics. Recall that, for a finite simple graph G, its line graph, denoted by L(G), is the graph with the vertex set given by the edges of G and two vertices in L(G) are joined by an edge if the corresponding edges are adjacent in G. There are several characterizations of graphs which are lines of some graphs. For instance, Beineken characterized the line graphs in terms of the forbidden induced subgraphs [3]. Moreover, combinatorial properties of line graphs have been studied: Akiyama solved seven graph equations which involved line graphs, powers of graphs and the complementary of a graph [1] and Milaniˇc,Oversberg and Schaudt gave a characterization of those line graphs which are squares of graphs [23]. -
Variations Ofy-Dominating Functions on Graphs
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Discrete Mathematics 308 (2008) 4185–4204 www.elsevier.com/locate/disc Variations of Y-dominating functions on graphsଁ Chuan-Min Lee, Maw-Shang Chang∗ Department of Computer Science and Information Engineering, National Chung Cheng University, Ming-Hsiung, Chiayi 621, Taiwan, ROC Received 8 May 2006; received in revised form 28 July 2007; accepted 3 August 2007 Available online 1 October 2007 Abstract Let Y be a subset of real numbers. A Y-dominating function of a graph G = (V, E) is a function f : V → Y such that f (u)1 for all vertices v ∈ V , where N [v]={v}∪{u|(u, v) ∈ E}. Let f(S)= f (u) for any subset S of V and let u∈NG[v] G u∈S f(V)be the weight of f. The Y-domination problem is to find a Y-dominating function of minimum weight for a graph G = (V, E). In this paper, we study the variations of Y-domination such as {k}-domination, k-tuple domination, signed domination, and minus domination for some classes of graphs. We give formulas to compute the {k}-domination, k-tuple domination, signed domination, and minus domination numbers of paths, cycles, n-fans, n-wheels, n-pans, and n-suns. Besides, we present a unified approach to these four problems on strongly chordal graphs. Notice that trees, block graphs, interval graphs, and directed path graphs are subclasses of strongly chordal graphs. This paper also gives complexity results for the problems on doubly chordal graphs, dually chordal graphs, bipartite planar graphs, chordal bipartite graphs, and planar graphs. -
A Joint Study of Chordal and Dually Chordal Graphs
Universidad Nacional de La Plata Facultad de Ciencias Exactas Departamento de Matemática A joint study of chordal and dually chordal graphs Pablo De Caria PhD. Thesis Advisor: Dr. Marisa Gutierrez April, 2012 Celebrating the month of the 35th anniversary of my parents’ first meeting In memory of aunt Sara II Thanks… To my parents Francisco and Norma, for their support and company and because, as father and mother, they never stop surprising me in a favourable way. To my sisters Laura and Mariana and my niece Ariadna, for all the time we shared and surely are to share together, and for being part of a family that I really cherish. To Hernan and Paula, for their company, which helped me to get the energy to lead a better life. I look forward to sharing more adventures with you. To María, for the many years of friendship, her permanent interest in my activities and her advice. To Marisa, for making graphs known to me and letting me work on them with a level of freedom that made me feel very comfortable over all these years. I would also like to thank her for her words in the right moments and her guidance on several administrative issues. To Juraj, for accepting to come and be a member of the jury and for his willingness, which was by no means limited to the evaluation of this thesis. To Liliana and Oscar, the other two jurors, for their commitment to improving this work. To Silvia, my official camerawoman at the symposiums, for being a very good mate. -
Distance Approximating Trees for Chordal and Dually Chordal Graphs*
Journal of Algorithms 30, 166]184Ž. 1999 Article ID jagm.1998.0962, available online at http:rrwww.idealibrary.com on Distance Approximating Trees for Chordal and Dually Chordal Graphs* Andreas BrandstadtÈ Uni¨ersitatÈÈ Rostock, Fachbereich Informatik, Lehrstuhl fur Theoretische Informatik, D-18051 Rostock, Germany E-mail: [email protected] Victor Chepoi* Laboratoire de Biomathematiques,ÂÂ Uni¨ersite d'Aix Marseille II, F-13385 Marseille Cedex 5, France E-mail: [email protected] and Feodor Dragan Uni¨ersitatÈÈ Rostock, Fachbereich Informatik, Lehrstuhl fur Theoretische Informatik, D-18051 Rostock, Germany E-mail: [email protected] Received April 23, 1997; revised March 10, 1998 In this paper we show that, for each chordal graph G, there is a tree T such that T is a spanning tree of the square G2 of G and, for every two vertices, the distance between them in T is not larger than the distance in G plus 2. Moreover, we prove that, if G is a strongly chordal graph or even a dually chordal graph, then there exists a spanning tree T of G that is an additive 3-spanner as well as a multiplica- tive 4-spanner of G. In all cases the tree T can be computed in linear time. Q 1999 Academic Press 1. INTRODUCTION Many combinatorial and algorithmic problems concern the distance dG on the vertices of a possibly weighted graph G s Ž.V, E . Approximating * The second and third authors were supported by VW, Project no. Ir69041; the third author was also supported by DFG.