Characterizations of Outerplanar Graphs
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Minimum Cycle Bases and Their Applications
Minimum Cycle Bases and Their Applications Franziska Berger1, Peter Gritzmann2, and Sven de Vries3 1 Department of Mathematics, Polytechnic Institute of NYU, Six MetroTech Center, Brooklyn NY 11201, USA [email protected] 2 Zentrum Mathematik, Technische Universit¨at M¨unchen, 80290 M¨unchen, Germany [email protected] 3 FB IV, Mathematik, Universit¨at Trier, 54286 Trier, Germany [email protected] Abstract. Minimum cycle bases of weighted undirected and directed graphs are bases of the cycle space of the (di)graphs with minimum weight. We survey the known polynomial-time algorithms for their con- struction, explain some of their properties and describe a few important applications. 1 Introduction Minimum cycle bases of undirected or directed multigraphs are bases of the cycle space of the graphs or digraphs with minimum length or weight. Their intrigu- ing combinatorial properties and their construction have interested researchers for several decades. Since minimum cycle bases have diverse applications (e.g., electric networks, theoretical chemistry and biology, as well as periodic event scheduling), they are also important for practitioners. After introducing the necessary notation and concepts in Subsections 1.1 and 1.2 and reviewing some fundamental properties of minimum cycle bases in Subsection 1.3, we explain the known algorithms for computing minimum cycle bases in Section 2. Finally, Section 3 is devoted to applications. 1.1 Definitions and Notation Let G =(V,E) be a directed multigraph with m edges and n vertices. Let + E = {e1,...,em},andletw : E → R be a positive weight function on E.A cycle C in G is a subgraph (actually ignoring orientation) of G in which every vertex has even degree (= in-degree + out-degree). -
K-Outerplanar Graphs, Planar Duality, and Low Stretch Spanning Trees
k-Outerplanar Graphs, Planar Duality, and Low Stretch Spanning Trees Yuval Emek∗ Abstract Low distortion probabilistic embedding of graphs into approximating trees is an extensively studied topic. Of particular interest is the case where the approximating trees are required to be (subgraph) spanning trees of the given graph (or multigraph), in which case, the focus is usually on the equivalent problem of finding a (single) tree with low average stretch. Among the classes of graphs that received special attention in this context are k-outerplanar graphs (for a fixed k): Chekuri, Gupta, Newman, Rabinovich, and Sinclair show that every k-outerplanar graph can be probabilistically embedded into approximating trees with constant distortion regardless of the size of the graph. The approximating trees in the technique of Chekuri et al. are not necessarily spanning trees, though. In this paper it is shown that every k-outerplanar multigraph admits a spanning tree with constant average stretch. This immediately translates to a constant bound on the distortion of probabilistically embedding k-outerplanar graphs into their spanning trees. Moreover, an efficient randomized algorithm is presented for constructing such a low average stretch spanning tree. This algorithm relies on some new insights regarding the connection between low average stretch spanning trees and planar duality. Keywords: planar graphs, outerplanarity, average stretch, planar dual. ∗Microsoft Israel R&D Center, Herzelia, Israel and School of Electrical Engineering, Tel Aviv University, Tel Aviv, Israel. E-mail: [email protected]. Supported in part by the Israel Science Foundation, grants 221/07 and 664/05. 1 Introduction The problem. -
1 Vertex Connectivity 2 Edge Connectivity 3 Biconnectivity
1 Vertex Connectivity So far we've talked about connectivity for undirected graphs and weak and strong connec- tivity for directed graphs. For undirected graphs, we're going to now somewhat generalize the concept of connectedness in terms of network robustness. Essentially, given a graph, we may want to answer the question of how many vertices or edges must be removed in order to disconnect the graph; i.e., break it up into multiple components. Formally, for a connected graph G, a set of vertices S ⊆ V (G) is a separating set if subgraph G − S has more than one component or is only a single vertex. The set S is also called a vertex separator or a vertex cut. The connectivity of G, κ(G), is the minimum size of any S ⊆ V (G) such that G − S is disconnected or has a single vertex; such an S would be called a minimum separator. We say that G is k-connected if κ(G) ≥ k. 2 Edge Connectivity We have similar concepts for edges. For a connected graph G, a set of edges F ⊆ E(G) is a disconnecting set if G − F has more than one component. If G − F has two components, F is also called an edge cut. The edge-connectivity if G, κ0(G), is the minimum size of any F ⊆ E(G) such that G − F is disconnected; such an F would be called a minimum cut.A bond is a minimal non-empty edge cut; note that a bond is not necessarily a minimum cut. -
Simpler Sequential and Parallel Biconnectivity Augmentation
Simpler Sequential and Parallel Biconnectivity Augmentation Surabhi Jain and N.Sadagopan Department of Computer Science and Engineering, Indian Institute of Information Technology, Design and Manufacturing, Kancheepuram, Chennai, India. fsurabhijain,[email protected] Abstract. For a connected graph, a vertex separator is a set of vertices whose removal creates at least two components and a minimum vertex separator is a vertex separator of least cardinality. The vertex connectivity refers to the size of a minimum vertex separator. For a connected graph G with vertex connectivity k (k ≥ 1), the connectivity augmentation refers to a set S of edges whose augmentation to G increases its vertex connectivity by one. A minimum connectivity augmentation of G is the one in which S is minimum. In this paper, we focus our attention on connectivity augmentation of trees. Towards this end, we present a new sequential algorithm for biconnectivity augmentation in trees by simplifying the algorithm reported in [7]. The simplicity is achieved with the help of edge contraction tool. This tool helps us in getting a recursive subproblem preserving all connectivity information. Subsequently, we present a parallel algorithm to obtain a minimum connectivity augmentation set in trees. Our parallel algorithm essentially follows the overall structure of sequential algorithm. Our implementation is based on CREW PRAM model with O(∆) processors, where ∆ refers to the maximum degree of a tree. We also show that our parallel algorithm is optimal whose processor-time product is O(n) where n is the number of vertices of a tree, which is an improvement over the parallel algorithm reported in [3]. -
Lab05 - Matroid Exercises for Algorithms by Xiaofeng Gao, 2016 Spring Semester
Lab05 - Matroid Exercises for Algorithms by Xiaofeng Gao, 2016 Spring Semester Name: Student ID: Email: 1. Provide an example of (S; C) which is an independent system but not a matroid. Give an instance of S such that v(S) 6= u(S) (should be different from the example posted in class). 2. Matching matroid MC : Let G = (V; E) be an arbitrary undirected graph. C is the collection of all vertices set which can be covered by a matching in G. (a) Prove that MC = (V; C) is a matroid. (b) Given a graph G = (V; E) where each vertex vi has a weight w(vi), please give an algorithm to find the matching where the weight of all covered vertices is maximum. Prove the correctness and analyze the time complexity of your algorithm. Note: Given a graph G = (V; E), a matching M in G is a set of pairwise non-adjacent edges; that is, no two edges share a common vertex. A vertex is covered (or matched) if it is an endpoint of one of the edges in the matching. Otherwise the vertex is uncovered. 3. A Dyck path of length 2n is a path in the plane from (0; 0) to (2n; 0), with steps U = (1; 1) and D = (1; −1), that never passes below the x-axis. For example, P = UUDUDUUDDD is a Dyck path of length 10. Each Dyck path defines an up-step set: the subset of [2n] consisting of the integers i such that the i-th step of the path is U. -
Blast Domination for Mycielski's Graph of Graphs
International Journal of Engineering and Advanced Technology (IJEAT) ISSN: 2249 – 8958, Volume-8, Issue-6S3, September 2019 Blast Domination for Mycielski’s Graph of Graphs K. Ameenal Bibi, P.Rajakumari AbstractThe hub of this article is a search on the behavior of is the minimum cardinality of a distance-2 dominating set in the Blast domination and Blast distance-2 domination for 퐺. Mycielski’s graph of some particular graphs and zero divisor graphs. Definition 2.3[7] A non-empty subset 퐷 of 푉 of a connected graph 퐺 is Key Words:Blast domination number, Blast distance-2 called a Blast dominating set, if 퐷 is aconnected dominating domination number, Mycielski’sgraph. set and the induced sub graph < 푉 − 퐷 >is triple connected. The minimum cardinality taken over all such Blast I. INTRODUCTION dominating sets is called the Blast domination number of The concept of triple connected graphs was introduced by 퐺and is denoted by tc . Paulraj Joseph et.al [9]. A graph is said to be triple c (G) connected if any three vertices lie on a path in G. In [6] the Definition2.4 authors introduced triple connected domination number of a graph. A subset D of V of a nontrivial graph G is said to A non-empty subset 퐷 of vertices in a graph 퐺 is a blast betriple connected dominating set, if D is a dominating set distance-2 dominating set if every vertex in 푉 − 퐷 is within and <D> is triple connected. The minimum cardinality taken distance-2 of atleast one vertex in 퐷. -
BIOINFORMATICS Doi:10.1093/Bioinformatics/Btt213
Vol. 29 ISMB/ECCB 2013, pages i352–i360 BIOINFORMATICS doi:10.1093/bioinformatics/btt213 Haplotype assembly in polyploid genomes and identical by descent shared tracts Derek Aguiar and Sorin Istrail* Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA ABSTRACT Standard genome sequencing workflows produce contiguous Motivation: Genome-wide haplotype reconstruction from sequence DNA segments of an unknown chromosomal origin. De novo data, or haplotype assembly, is at the center of major challenges in assemblies for genomes with two sets of chromosomes (diploid) molecular biology and life sciences. For complex eukaryotic organ- or more (polyploid) produce consensus sequences in which the isms like humans, the genome is vast and the population samples are relative haplotype phase between variants is undetermined. The growing so rapidly that algorithms processing high-throughput set of sequencing reads can be mapped to the phase-ambiguous sequencing data must scale favorably in terms of both accuracy and reference genome and the diploid chromosome origin can be computational efficiency. Furthermore, current models and methodol- determined but, without knowledge of the haplotype sequences, ogies for haplotype assembly (i) do not consider individuals sharing reads cannot be mapped to the particular haploid chromosome haplotypes jointly, which reduces the size and accuracy of assembled sequence. As a result, reference-based genome assembly algo- haplotypes, and (ii) are unable to model genomes having more than rithms also produce unphased assemblies. However, sequence two sets of homologous chromosomes (polyploidy). Polyploid organ- reads are derived from a single haploid fragment and thus pro- isms are increasingly becoming the target of many research groups vide valuable phase information when they contain two or more variants. -
Characterizations of Restricted Pairs of Planar Graphs Allowing Simultaneous Embedding with Fixed Edges
Characterizations of Restricted Pairs of Planar Graphs Allowing Simultaneous Embedding with Fixed Edges J. Joseph Fowler1, Michael J¨unger2, Stephen Kobourov1, and Michael Schulz2 1 University of Arizona, USA {jfowler,kobourov}@cs.arizona.edu ⋆ 2 University of Cologne, Germany {mjuenger,schulz}@informatik.uni-koeln.de ⋆⋆ Abstract. A set of planar graphs share a simultaneous embedding if they can be drawn on the same vertex set V in the Euclidean plane without crossings between edges of the same graph. Fixed edges are common edges between graphs that share the same simple curve in the simultaneous drawing. Determining in polynomial time which pairs of graphs share a simultaneous embedding with fixed edges (SEFE) has been open. We give a necessary and sufficient condition for when a pair of graphs whose union is homeomorphic to K5 or K3,3 can have an SEFE. This allows us to determine which (outer)planar graphs always an SEFE with any other (outer)planar graphs. In both cases, we provide efficient al- gorithms to compute the simultaneous drawings. Finally, we provide an linear-time decision algorithm for deciding whether a pair of biconnected outerplanar graphs has an SEFE. 1 Introduction In many practical applications including the visualization of large graphs and very-large-scale integration (VLSI) of circuits on the same chip, edge crossings are undesirable. A single vertex set can be used with multiple edge sets that each correspond to different edge colors or circuit layers. While the pairwise union of all edge sets may be nonplanar, a planar drawing of each layer may be possible, as crossings between edges of distinct edge sets are permitted. -
Determination and Testing the Domination Numbers of Tadpole Graph, Book Graph and Stacked Book Graph Using MATLAB Ayhan A
College of Basic Education Researchers Journal Vol. 10, No. 1 Determination and Testing the Domination Numbers of Tadpole Graph, Book Graph and Stacked Book Graph Using MATLAB Ayhan A. khalil Omar A.Khalil Technical College of Mosul -Foundation of Technical Education Received: 11/4/2010 ; Accepted: 24/6/2010 Abstract: A set is said to be dominating set of G if for every there exists a vertex such that . The minimum cardinality of vertices among dominating set of G is called the domination number of G denoted by . We investigate the domination number of Tadpole graph, Book graph and Stacked Book graph. Also we test our theoretical results in computer by introducing a matlab procedure to find the domination number , dominating set S and draw this graph that illustrates the vertices of domination this graphs. It is proved that: . Keywords: Dominating set, Domination number, Tadpole graph, Book graph, stacked graph. إﯾﺟﺎد واﺧﺗﺑﺎر اﻟﻌدد اﻟﻣﮭﯾﻣن(اﻟﻣﺳﯾطر)Domination number ﻟﻠﺑﯾﺎﻧﺎت ﺗﺎدﺑول (Tadpole graph)، ﺑﯾﺎن ﺑوك (Book graph) وﺑﯾﺎن ﺳﺗﺎﻛﯾت ﺑوك (Stacked Book graph) ﺑﺎﺳﺗﻌﻣﺎل اﻟﻣﺎﺗﻼب أﯾﮭﺎن اﺣﻣد ﺧﻠﯾل ﻋﻣر اﺣﻣد ﺧﻠﯾل اﻟﻛﻠﯾﺔ اﻟﺗﻘﻧﯾﺔ-ﻣوﺻل- ھﯾﺋﺔ اﻟﺗﻌﻠﯾم اﻟﺗﻘﻧﻲ ﻣﻠﺧص اﻟﺑﺣث : ﯾﻘﺎل ﻷﯾﺔ ﻣﺟﻣوﻋﺔ ﺟزﺋﯾﺔ S ﻣن ﻣﺟﻣوﻋﺔ اﻟرؤوس V ﻓﻲ ﺑﯾﺎن G ﺑﺄﻧﻬﺎ ﻣﺟﻣوﻋﺔ ﻣﻬﯾﻣﻧﺔ Dominating set إذا ﻛﺎن ﻟﻛل أرس v ﻓﻲ اﻟﻣﺟﻣوﻋﺔ V-S ﯾوﺟد أرس u ﻓﻲS ﺑﺣﯾث uv ﺿﻣن 491 Ayhan A. & Omar A. ﺣﺎﻓﺎت اﻟﺑﯾﺎن،. وﯾﻌرف اﻟﻌدد اﻟﻣﻬﯾﻣن Domination number ﺑﺄﻧﻪ أﺻﻐر ﻣﺟﻣوﻋﺔ أﺳﺎﺳﯾﺔ ﻣﻬﯾﻣﻧﺔ Domination. ﻓﻲ ﻫذا اﻟﺑﺣث ﺳوف ﻧدرس اﻟﻌدد اﻟﻣﻬﯾﻣن Domination number ﻟﺑﯾﺎن ﺗﺎدﺑول (Tadpole graph) ، ﺑﯾﺎن ﺑوك (Book graph) وﺑﯾﺎن ﺳﺗﺎﻛﯾت ﺑوك ( Stacked Book graph). -
Minor-Closed Graph Classes with Bounded Layered Pathwidth
Minor-Closed Graph Classes with Bounded Layered Pathwidth Vida Dujmovi´c z David Eppstein y Gwena¨elJoret x Pat Morin ∗ David R. Wood { 19th October 2018; revised 4th June 2020 Abstract We prove that a minor-closed class of graphs has bounded layered pathwidth if and only if some apex-forest is not in the class. This generalises a theorem of Robertson and Seymour, which says that a minor-closed class of graphs has bounded pathwidth if and only if some forest is not in the class. 1 Introduction Pathwidth and treewidth are graph parameters that respectively measure how similar a given graph is to a path or a tree. These parameters are of fundamental importance in structural graph theory, especially in Roberston and Seymour's graph minors series. They also have numerous applications in algorithmic graph theory. Indeed, many NP-complete problems are solvable in polynomial time on graphs of bounded treewidth [23]. Recently, Dujmovi´c,Morin, and Wood [19] introduced the notion of layered treewidth. Loosely speaking, a graph has bounded layered treewidth if it has a tree decomposition and a layering such that each bag of the tree decomposition contains a bounded number of vertices in each layer (defined formally below). This definition is interesting since several natural graph classes, such as planar graphs, that have unbounded treewidth have bounded layered treewidth. Bannister, Devanny, Dujmovi´c,Eppstein, and Wood [1] introduced layered pathwidth, which is analogous to layered treewidth where the tree decomposition is arXiv:1810.08314v2 [math.CO] 4 Jun 2020 required to be a path decomposition. -
Short Cycles
Short Cycles Minimum Cycle Bases of Graphs from Chemistry and Biochemistry Dissertation zur Erlangung des akademischen Grades Doctor rerum naturalium an der Fakultat¨ fur¨ Naturwissenschaften und Mathematik der Universitat¨ Wien Vorgelegt von Petra Manuela Gleiss im September 2001 An dieser Stelle m¨ochte ich mich herzlich bei all jenen bedanken, die zum Entstehen der vorliegenden Arbeit beigetragen haben. Allen voran Peter Stadler, der mich durch seine wissenschaftliche Leitung, sein ub¨ er- w¨altigendes Wissen und seine Geduld unterstutzte,¨ sowie Josef Leydold, ohne den ich so manch tieferen Einblick in die Mathematik nicht gewonnen h¨atte. Ivo Hofacker, dermich oftmals aus den unendlichen Weiten des \Computer Universums" rettete. Meinem Bruder Jurgen¨ Gleiss, fur¨ die Einfuhrung¨ und Hilfstellungen bei meinen Kampf mit C++. Daniela Dorigoni, die die Daten der atmosph¨arischen Netzwerke in den Computer eingeben hat. Allen Kolleginnen und Kollegen vom Institut, fur¨ die Hilfsbereitschaft. Meine Eltern Erika und Franz Gleiss, die mir durch ihre Unterstutzung¨ ein Studium erm¨oglichten. Meiner Oma Maria Fischer, fur¨ den immerw¨ahrenden Glauben an mich. Meinen Schwiegereltern Irmtraud und Gun¨ ther Scharner, fur¨ die oftmalige Betreuung meiner Kinder. Zum Schluss Roland Scharner, Florian und Sarah Gleiss, meinen drei Liebsten, die mich immer wieder aufbauten und in die reale Welt zuruc¨ kfuhrten.¨ Ich wurde teilweise vom osterreic¨ hischem Fonds zur F¨orderung der Wissenschaftlichen Forschung, Proj.No. P14094-MAT finanziell unterstuzt.¨ Zusammenfassung In der Biochemie werden Kreis-Basen nicht nur bei der Betrachtung kleiner einfacher organischer Molekule,¨ sondern auch bei Struktur Untersuchungen hoch komplexer Biomolekule,¨ sowie zur Veranschaulichung chemische Reaktionsnetzwerke herange- zogen. Die kleinste kanonische Menge von Kreisen zur Beschreibung der zyklischen Struk- tur eines ungerichteten Graphen ist die Menge der relevanten Kreis (Vereingungs- menge aller minimaler Kreis-Basen). -
A Cycle-Based Formulation for the Distance Geometry Problem
A cycle-based formulation for the Distance Geometry Problem Leo Liberti, Gabriele Iommazzo, Carlile Lavor, and Nelson Maculan Abstract The distance geometry problem consists in finding a realization of a weighed graph in a Euclidean space of given dimension, where the edges are realized as straight segments of length equal to the edge weight. We propose and test a new mathematical programming formulation based on the incidence between cycles and edges in the given graph. 1 Introduction The Distance Geometry Problem (DGP), also known as the realization problem in geometric rigidity, belongs to a more general class of metric completion and embedding problems. DGP. Given a positive integer K and a simple undirected graph G = ¹V; Eº with an edge K weight function d : E ! R≥0, establish whether there exists a realization x : V ! R of the vertices such that Eq. (1) below is satisfied: fi; jg 2 E kxi − xj k = dij; (1) 8 K where xi 2 R for each i 2 V and dij is the weight on edge fi; jg 2 E. L. Liberti LIX CNRS Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France, e-mail: [email protected] G. Iommazzo LIX Ecole Polytechnique, France and DI Università di Pisa, Italy, e-mail: giommazz@lix. polytechnique.fr C. Lavor IMECC, University of Campinas, Brazil, e-mail: [email protected] N. Maculan COPPE, Federal University of Rio de Janeiro (UFRJ), Brazil, e-mail: [email protected] 1 2 L. Liberti et al. In its most general form, the DGP might be parametrized over any norm.