Cycle Interpolation Properties of 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). -
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. -
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. -
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. -
Dominating Cycles in Halin Graphs*
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Discrete Mathematics 86 (1990) 215-224 215 North-Holland DOMINATING CYCLES IN HALIN GRAPHS* Mirosiawa SKOWRONSKA Institute of Mathematics, Copernicus University, Chopina 12/18, 87-100 Torun’, Poland Maciej M. SYStO Institute of Computer Science, University of Wroclaw, Przesmyckiego 20, 51-151 Wroclaw, Poland Received 2 December 1988 A cycle in a graph is dominating if every vertex lies at distance at most one from the cycle and a cycle is D-cycle if every edge is incident with a vertex of the cycle. In this paper, first we provide recursive formulae for finding a shortest dominating cycle in a Hahn graph; minor modifications can give formulae for finding a shortest D-cycle. Then, dominating cycles and D-cycles in a Halin graph H are characterized in terms of the cycle graph, the intersection graph of the faces of H. 1. Preliminaries The various domination problems have been extensively studied. Among them is the problem whether a graph has a dominating cycle. All graphs in this paper have no loops and multiple edges. A dominating cycle in a graph G = (V(G), E(G)) is a subgraph C of G which is a cycle and every vertex of V(G) \ V(C) is adjacent to a vertex of C. There are graphs which have no dominating cycles, and moreover, determining whether a graph has a dominating cycle on at most 1 vertices is NP-complete even in the class of planar graphs [7], chordal, bipartite and split graphs [3]. -
On Pancyclism in Hamiltonian Graphs
CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector Discrete Mathematics 251 (2002) 119–127 www.elsevier.com/locate/disc On pancyclism in hamiltonian graphs Mekkia Kouidera, Antoni Marczykb; ∗ aL.R.I, Universiteà de Paris-Sud, Bat.ˆ 490, 91405 Orsay, France bFaculty of Applied Mathematics, AGH, Al. Mickiewicza 30, 30-059 Krakow,à Poland Received 11 May 1999; revised 5 November 1999; accepted 3 June 2001 Abstract We investigate the set of cycle lengths occurring in a hamiltonian graph with at least one or two vertices of large degree. We prove that in every case this set contains all the integers between 3 and some t, where t depends on the order of the graph and the degrees of vertices. c 2002 Elsevier Science B.V. All rights reserved. MSC: 05C38; 05C45 Keywords: Hamiltonian graphs; Pancyclic graphs; Cycles 1. Introduction Throughout this paper, we consider only ÿnite, undirected and simple graphs. For a graph G we denote by V = V (G) its vertex set, by E = E(G) its set of edges. By Cp we mean a p-cycle of G, i.e., a cycle of length p. The vertices of a graph G of order n will be denoted by integers 0; 1; 2;:::;n− 1 and considered modulo n.We write EG(k)=E(k) for the set of edges that are incident to a vertex k. For a subgraph H of G and a vertex k of G; dH (k) denotes the number of all edges (k; j)ofE(k) with j ∈ V (H), i.e., if k ∈ V (H) then dH (k) is the degree of k in the subgraph of G induced by the set V (H). -
On the Pancyclicity of 1-Tough Graphs 1
Discrete Mathematics Letters Discrete Math. Lett. 5 (2021) 1–4 www.dmlett.com DOI: 10.47443/dml.2020.0046 Research Article On the pancyclicity of 1-tough graphs Rao Li∗ Department of Mathematical Sciences, University of South Carolina Aiken, Aiken, SC 29801, USA (Received: 14 August 2020. Received in revised form: 5 October 2020. Accepted: 13 November 2020. Published online: 23 November 2020.) c 2020 the author. This is an open access article under the CC BY (International 4.0) license (www.creativecommons.org/licenses/by/4.0/) Abstract Let G be a graph of order n ≥ 6r−2, size e, and minimum degree δ ≥ r, where r is an integer greater than 1. The main result obtained in this note is that if G is 1-tough with the degree sequence (d1; d2; ··· ; dn) and if e ≥ ((n−r)(n−r−1)+r(2r−1))=2, then G is pancyclic, Hamiltonian bipartite, or Hamiltonian such that d1 = d2 = ··· = dk = k, dk+1 = dk+2 = ··· = dn−k+1 = n − k − 1, and dn−k+2 = dn−k+3 = ··· = dn = n − 1, where k < n=2. This result implies that the following conjecture of Hoa, posed in 2002, is true under the conditions n ≥ 40 and δ ≥ 7: every path-tough graph on n vertices and with at least ((n − 6)(n − 7) + 34)=2 edges is Hamiltonian. Using the main result of this note, additional sufficient conditions for 1-tough graphs to be pancyclic are also obtained. Keywords: pancyclic graph; 1-tough graph; Hamiltonian graph. 2020 Mathematics Subject Classification: 05C45. -
A Neighborhood and Degree Condition for Pancyclicity and Vertex Pancyclicity
AUSTRALASIAN JOURNAL OF COMBINATORICS Volume 40 (2008), Pages 15–25 A neighborhood and degree condition for pancyclicity and vertex pancyclicity Ryota Matsubara Masao Tsugaki Department of Mathematical Information Science Tokyo University of Science 1-3 Kagurazaka, Shinjuku-ku, Tokyo 162-8601 Japan [email protected] [email protected] Tomoki Yamashita Department of Mathematics School of Dentistry, Asahi University 1851 Hozumi, Gifu 501–0296 Japan [email protected] Abstract Let G be a 2-connected graph of order n. For any u ∈ V (G) and l ∈ {m, m + 1,...,n}, if G has a cycle of length l, then G is called [m, n]- pancyclic, and if G has a cycle of length l which contains u, then G is called [m, n]-vertex pancyclic. Let δ(G) be a minimum degree of G and let NG(x) be the neighborhood of a vertex x in G. In [Australas. J. Combin. 12 (1995), 81–91] Liu, Lou and Zhao proved that if |NG(u) ∪ NG(v)| + δ(G) ≥ n+1 for any nonadjacent vertices u, v of G, then G is [3, n]-vertex pancyclic. In this paper, we prove if n ≥ 6 and |NG(u)∪NG(v)|+dG(w) ≥ n for every triple independent vertices u,v,w of G, then (i) G is [3, n]- pancyclic or isomorphic to the complete bipartite graph Kn/2,n/2, and (ii) G is [5, n]-vertex pancyclic or isomorphic to the complete bipartite graph Kn/2,n/2. 1 Introduction In this paper, we consider only finite graphs without loops or multiple edges. -
Exam DM840 Cheminformatics (2016)
Exam DM840 Cheminformatics (2016) Time and Place Time: Thursday, June 2nd, 2016, starting 10:30. Place: The exam takes place in U-XXX (to be decided) Even though the expected total examination time per student is about 27 minutes (see below), it is not possible to calculate the exact examination time from the placement on the list, since students earlier on the list may not show up. Thus, students are expected to show up plenty early. In principle, all students who are taking the exam on a particular date are supposed to show up when the examination starts, i.e., at the time the rst student is scheduled. This is partly because of the way external examiners are paid, which is by the number of students who show up for examination. For this particular exam, we do not expect many no-shows, so showing up one hour before the estimated time of the exam should be safe. Procedure The exam is in English. When it is your turn for examination, you will draw a question. Note that you have no preparation time. The list of questions can be found below. Then the actual exam takes place. The whole exam (without the censor and the examiner agreeing on a grade) lasts approximately 25-30 minutes. You should start by presenting material related to the question you drew. Aim for a reasonable high pace and focus on the most interesting material related to the question. You are not supposed to use note material, textbooks, transparencies, computer, etc. You are allowed to bring keywords for each question, such that you can remember what you want to present during your presentation. -
Vertex Pancyclic Graphs
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Discrete Applied Mathematics 120 (2002) 219–237 Vertex pancyclic graphs Bert Randeratha; ∗,Ingo Schiermeyer b,Meike Tewes b,Lutz Volkmann c aInstitut fur Informatik, Universitat zu Koln, Pohligstrasse 1 50969 Koln, Germany bFakultat fur Mathematik und Informatik, TU Bergakademie Freiberg, 09596 Freiberg, Germany cLehrstuhl II fur Mathematik, RWTH Aachen, 52056 Aachen, Germany Received 17 September 1999; received in revised form 31 July 2000; accepted 21 July 2001 Abstract Let G be a graph of order n. A graph G is called pancyclic if it contains a cycle of length k for every 3 6 k 6 n,and it is called vertex pancyclic if every vertex is contained in a cycle of length k for every 3 6 k 6 n. In this paper,we shall present di0erent su1cient conditions for graphs to be vertex pancyclic. ? 2002 Elsevier Science B.V. All rights reserved. 1. Terminology We consider ÿnite,undirected,and simple graphs G with the vertex set V (G) and the edge set E(G). The order of a graph G is denoted by n and the size by m, respectively. The complete graph of order n is denoted by Kn,and the complete bipartite graph with the partite sets A and B with |A| = p and |B| = q is denoted by Kp;q. A graph G is k-connected if G − S is connected for every subset S ⊆ V (G) with |S| 6 k − 1. A vertex v of a connected graph G is called a cut vertex if G − v is disconnected. -
Cheminformatics for Genome-Scale Metabolic Reconstructions
CHEMINFORMATICS FOR GENOME-SCALE METABOLIC RECONSTRUCTIONS John W. May European Molecular Biology Laboratory European Bioinformatics Institute University of Cambridge Homerton College A thesis submitted for the degree of Doctor of Philosophy June 2014 Declaration This thesis is the result of my own work and includes nothing which is the outcome of work done in collaboration except where specifically indicated in the text. This dissertation is not substantially the same as any I have submitted for a degree, diploma or other qualification at any other university, and no part has already been, or is currently being submitted for any degree, diploma or other qualification. This dissertation does not exceed the specified length limit of 60,000 words as defined by the Biology Degree Committee. This dissertation has been typeset using LATEX in 11 pt Palatino, one and half spaced, according to the specifications defined by the Board of Graduate Studies and the Biology Degree Committee. June 2014 John W. May to Róisín Acknowledgements This work was carried out in the Cheminformatics and Metabolism Group at the European Bioinformatics Institute (EMBL-EBI). The project was fund- ed by Unilever, the Biotechnology and Biological Sciences Research Coun- cil [BB/I532153/1], and the European Molecular Biology Laboratory. I would like to thank my supervisor, Christoph Steinbeck for his guidance and providing intellectual freedom. I am also thankful to each member of my thesis advisory committee: Gordon James, Julio Saez-Rodriguez, Kiran Patil, and Gos Micklem who gave their time, advice, and guidance. I am thankful to all members of the Cheminformatics and Metabolism Group.