Graph Bases and Diagram Commutativity
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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). -
Digraph Complexity Measures and Applications in Formal Language Theory
Digraph Complexity Measures and Applications in Formal Language Theory by Hermann Gruber Institut f¨urInformatik Justus-Liebig-Universit¨at Giessen Germany November 14, 2008 Introduction and Motivation Measuring Complexity for Digraphs Algorithmic Results on Cycle Rank Applications in Formal Language Theory Discussion Overview 1 Introduction and Motivation 2 Measuring Complexity for Digraphs 3 Algorithmic Results on Cycle Rank 4 Applications in Formal Language Theory 5 Discussion H. Gruber Digraph Complexity Measures and Applications Introduction and Motivation Measuring Complexity for Digraphs Algorithmic Results on Cycle Rank Applications in Formal Language Theory Discussion Outline 1 Introduction and Motivation 2 Measuring Complexity for Digraphs 3 Algorithmic Results on Cycle Rank 4 Applications in Formal Language Theory 5 Discussion H. Gruber Digraph Complexity Measures and Applications Introduction and Motivation Measuring Complexity for Digraphs Algorithmic Results on Cycle Rank Applications in Formal Language Theory Discussion Complexity Measures on Undirected Graphs Important topic in algorithmic graph theory: Structural complexity restrictions can speed up algorithms Main result: many hard problems solvable in linear time on graphs with bounded treewidth. depending on application, also other measures interesting H. Gruber Digraph Complexity Measures and Applications Introduction and Motivation Measuring Complexity for Digraphs Algorithmic Results on Cycle Rank Applications in Formal Language Theory Discussion What about Directed -
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. -
Algebraically Grid-Like Graphs Have Large Tree-Width
Algebraically grid-like graphs have large tree-width Daniel Weißauer Department of Mathematics University of Hamburg Abstract By the Grid Minor Theorem of Robertson and Seymour, every graph of sufficiently large tree-width contains a large grid as a minor. Tree-width may therefore be regarded as a measure of ’grid-likeness’ of a graph. The grid contains a long cycle on the perimeter, which is the F2-sum of the rectangles inside. Moreover, the grid distorts the metric of the cycle only by a factor of two. We prove that every graph that resembles the grid in this algebraic sense has large tree-width: Let k,p be integers, γ a real number and G a graph. Suppose that G contains a cycle of length at least 2γpk which is the F2-sum of cycles of length at most p and whose metric is distorted by a factor of at most γ. Then G has tree-width at least k. 1 Introduction For a positive integer n, the (n × n)-grid is the graph Gn whose vertices are all pairs (i, j) with 1 ≤ i, j ≤ n, where two points are adjacent when they are at Euclidean distance 1. The cycle Cn, which bounds the outer face in the natural drawing of Gn in the plane, has length 4(n−1) and is the F2-sum of the rectangles bounding the inner faces. This is by itself not a distinctive feature of graphs with large tree-width: The situation is similar for the n-wheel Wn, arXiv:1802.05158v1 [math.CO] 14 Feb 2018 the graph consisting of a cycle Dn of length n and a vertex x∈ / Dn which is adjacent to every vertex of Dn. -
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). -
Complexity and Geometry of Sampling Connected Graph Partitions
COMPLEXITY AND GEOMETRY OF SAMPLING CONNECTED GRAPH PARTITIONS LORENZO NAJT∗, DARYL DEFORDy, JUSTIN SOLOMONy Abstract. In this paper, we prove intractability results about sampling from the set of partitions of a planar graph into connected components. Our proofs are motivated by a technique introduced by Jerrum, Valiant, and Vazirani. Moreover, we use gadgets inspired by their technique to provide families of graphs where the “flip walk" Markov chain used in practice for this sampling task exhibits exponentially slow mixing. Supporting our theoretical results we present some empirical evidence demonstrating the slow mixing of the flip walk on grid graphs and on real data. Inspired by connections to the statistical physics of self-avoiding walks, we investigate the sensitivity of certain popular sampling algorithms to the graph topology. Finally, we discuss a few cases where the sampling problem is tractable. Applications to political redistricting have recently brought increased attention to this problem, and we articulate open questions about this application that are highlighted by our results. 1. Introduction. The problem of graph partitioning, or dividing the vertices of a graph into a small number of connected subgraphs that extremize an objective function, is a classical task in graph theory with application to network analytics, machine learning, computer vision, and other areas. Whereas this task is well-studied in computation and mathematics, a related problem remains relatively understudied: understanding how a given partition compares to other members of the set of possible partitions. In this case, the goal is not to generate a partition with favorable properties, but rather to compare a given partition to some set of alternatives. -
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]. -
Section 2.6. Even Subgraphs
2.6. Even Subgraphs 1 Section 2.6. Even Subgraphs Note. Recall from Section 2.4, “Decompositions and Coverings,” that an even graph is a graph in which every vertex has even degree. In this section we consider the symmetric difference of even subgraphs of a given graph and we see how even subgraphs interact with edge cuts. We also define three vector spaces associated with a graph, the edge space, the cycle space, and the bond space. Definition. For a given graph G, an even subgraph of G is a spanning subgraph of G which is even. (Sometimes we may use the term “even subgraph of G” to indicate just the edge set of the subgraph.) Note. Theorem 2.10 and Proposition 2.13 of the previous section allow us to address the symmetric difference of two even subgraphs of a given graph, as follows. Corollary 2.16. The symmetric difference of two even subgraphs is an even subgraph. Note. Bondy and Murty comment that “. we show in Chapters 4 [“Trees”] and 21 [“Integer Flows and Coverings”], [that] the even subgraphs of a graph play an important structural role.” See page 64. In the context of even subgraphs, the term “cycle” may be used to mean the edge set of a cycle, and the term “disjoint cycles” may mean edge-disjoint cycles. With this convention, Veblen’s Theorem (Theorem 2.7), which states that a graph admits a cycle decomposition if and only if it is even, can be restated as follows. 2.6. Even Subgraphs 2 Theorem 2.17. -
List of NP-Complete Problems from Wikipedia, the Free Encyclopedia
List of NP -complete problems - Wikipedia, the free encyclopedia Page 1 of 17 List of NP-complete problems From Wikipedia, the free encyclopedia Here are some of the more commonly known problems that are NP -complete when expressed as decision problems. This list is in no way comprehensive (there are more than 3000 known NP-complete problems). Most of the problems in this list are taken from Garey and Johnson's seminal book Computers and Intractability: A Guide to the Theory of NP-Completeness , and are here presented in the same order and organization. Contents ■ 1 Graph theory ■ 1.1 Covering and partitioning ■ 1.2 Subgraphs and supergraphs ■ 1.3 Vertex ordering ■ 1.4 Iso- and other morphisms ■ 1.5 Miscellaneous ■ 2 Network design ■ 2.1 Spanning trees ■ 2.2 Cuts and connectivity ■ 2.3 Routing problems ■ 2.4 Flow problems ■ 2.5 Miscellaneous ■ 2.6 Graph Drawing ■ 3 Sets and partitions ■ 3.1 Covering, hitting, and splitting ■ 3.2 Weighted set problems ■ 3.3 Set partitions ■ 4 Storage and retrieval ■ 4.1 Data storage ■ 4.2 Compression and representation ■ 4.3 Database problems ■ 5 Sequencing and scheduling ■ 5.1 Sequencing on one processor ■ 5.2 Multiprocessor scheduling ■ 5.3 Shop scheduling ■ 5.4 Miscellaneous ■ 6 Mathematical programming ■ 7 Algebra and number theory ■ 7.1 Divisibility problems ■ 7.2 Solvability of equations ■ 7.3 Miscellaneous ■ 8 Games and puzzles ■ 9 Logic ■ 9.1 Propositional logic ■ 9.2 Miscellaneous ■ 10 Automata and language theory ■ 10.1 Automata theory http://en.wikipedia.org/wiki/List_of_NP-complete_problems 12/1/2011 List of NP -complete problems - Wikipedia, the free encyclopedia Page 2 of 17 ■ 10.2 Formal languages ■ 11 Computational geometry ■ 12 Program optimization ■ 12.1 Code generation ■ 12.2 Programs and schemes ■ 13 Miscellaneous ■ 14 See also ■ 15 Notes ■ 16 References Graph theory Covering and partitioning ■ Vertex cover [1][2] ■ Dominating set, a.k.a. -
Planarity and Duality of Finite and Infinite Graphs
JOURNAL OF COMBINATORIAL THEORY, Series B 29, 244-271 (1980) Planarity and Duality of Finite and Infinite Graphs CARSTEN THOMASSEN Matematisk Institut, Universitets Parken, 8000 Aarhus C, Denmark Communicated by the Editors Received September 17, 1979 We present a short proof of the following theorems simultaneously: Kuratowski’s theorem, Fary’s theorem, and the theorem of Tutte that every 3-connected planar graph has a convex representation. We stress the importance of Kuratowski’s theorem by showing how it implies a result of Tutte on planar representations with prescribed vertices on the same facial cycle as well as the planarity criteria of Whit- ney, MacLane, Tutte, and Fournier (in the case of Whitney’s theorem and MacLane’s theorem this has already been done by Tutte). In connection with Tutte’s planarity criterion in terms of non-separating cycles we give a short proof of the result of Tutte that the induced non-separating cycles in a 3-connected graph generate the cycle space. We consider each of the above-mentioned planarity criteria for infinite graphs. Specifically, we prove that Tutte’s condition in terms of overlap graphs is equivalent to Kuratowski’s condition, we characterize completely the infinite graphs satisfying MacLane’s condition and we prove that the 3- connected locally finite ones have convex representations. We investigate when an infinite graph has a dual graph and we settle this problem completely in the locally finite case. We show by examples that Tutte’s criterion involving non-separating cy- cles has no immediate extension to infinite graphs, but we present some analogues of that criterion for special classes of infinite graphs.