Symmetric Graph Drawing
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Networkx Tutorial
5.03.2020 tutorial NetworkX tutorial Source: https://github.com/networkx/notebooks (https://github.com/networkx/notebooks) Minor corrections: JS, 27.02.2019 Creating a graph Create an empty graph with no nodes and no edges. In [1]: import networkx as nx In [2]: G = nx.Graph() By definition, a Graph is a collection of nodes (vertices) along with identified pairs of nodes (called edges, links, etc). In NetworkX, nodes can be any hashable object e.g. a text string, an image, an XML object, another Graph, a customized node object, etc. (Note: Python's None object should not be used as a node as it determines whether optional function arguments have been assigned in many functions.) Nodes The graph G can be grown in several ways. NetworkX includes many graph generator functions and facilities to read and write graphs in many formats. To get started though we'll look at simple manipulations. You can add one node at a time, In [3]: G.add_node(1) add a list of nodes, In [4]: G.add_nodes_from([2, 3]) or add any nbunch of nodes. An nbunch is any iterable container of nodes that is not itself a node in the graph. (e.g. a list, set, graph, file, etc..) In [5]: H = nx.path_graph(10) file:///home/szwabin/Dropbox/Praca/Zajecia/Diffusion/Lectures/1_intro/networkx_tutorial/tutorial.html 1/18 5.03.2020 tutorial In [6]: G.add_nodes_from(H) Note that G now contains the nodes of H as nodes of G. In contrast, you could use the graph H as a node in G. -
Networkx: Network Analysis with Python
NetworkX: Network Analysis with Python Salvatore Scellato Full tutorial presented at the XXX SunBelt Conference “NetworkX introduction: Hacking social networks using the Python programming language” by Aric Hagberg & Drew Conway Outline 1. Introduction to NetworkX 2. Getting started with Python and NetworkX 3. Basic network analysis 4. Writing your own code 5. You are ready for your project! 1. Introduction to NetworkX. Introduction to NetworkX - network analysis Vast amounts of network data are being generated and collected • Sociology: web pages, mobile phones, social networks • Technology: Internet routers, vehicular flows, power grids How can we analyze this networks? Introduction to NetworkX - Python awesomeness Introduction to NetworkX “Python package for the creation, manipulation and study of the structure, dynamics and functions of complex networks.” • Data structures for representing many types of networks, or graphs • Nodes can be any (hashable) Python object, edges can contain arbitrary data • Flexibility ideal for representing networks found in many different fields • Easy to install on multiple platforms • Online up-to-date documentation • First public release in April 2005 Introduction to NetworkX - design requirements • Tool to study the structure and dynamics of social, biological, and infrastructure networks • Ease-of-use and rapid development in a collaborative, multidisciplinary environment • Easy to learn, easy to teach • Open-source tool base that can easily grow in a multidisciplinary environment with non-expert users -
Algebraic Graph Theory: Automorphism Groups and Cayley Graphs
Algebraic Graph Theory: Automorphism Groups and Cayley graphs Glenna Toomey April 2014 1 Introduction An algebraic approach to graph theory can be useful in numerous ways. There is a relatively natural intersection between the fields of algebra and graph theory, specifically between group theory and graphs. Perhaps the most natural connection between group theory and graph theory lies in finding the automorphism group of a given graph. However, by studying the opposite connection, that is, finding a graph of a given group, we can define an extremely important family of vertex-transitive graphs. This paper explores the structure of these graphs and the ways in which we can use groups to explore their properties. 2 Algebraic Graph Theory: The Basics First, let us determine some terminology and examine a few basic elements of graphs. A graph, Γ, is simply a nonempty set of vertices, which we will denote V (Γ), and a set of edges, E(Γ), which consists of two-element subsets of V (Γ). If fu; vg 2 E(Γ), then we say that u and v are adjacent vertices. It is often helpful to view these graphs pictorially, letting the vertices in V (Γ) be nodes and the edges in E(Γ) be lines connecting these nodes. A digraph, D is a nonempty set of vertices, V (D) together with a set of ordered pairs, E(D) of distinct elements from V (D). Thus, given two vertices, u, v, in a digraph, u may be adjacent to v, but v is not necessarily adjacent to u. This relation is represented by arcs instead of basic edges. -
How Symmetric Are Real-World Graphs? a Large-Scale Study
S S symmetry Article How Symmetric Are Real-World Graphs? A Large-Scale Study Fabian Ball * and Andreas Geyer-Schulz Karlsruhe Institute of Technology, Institute of Information Systems and Marketing, Kaiserstr. 12, 76131 Karlsruhe, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-721-608-48404 Received: 22 December 2017; Accepted: 10 January 2018; Published: 16 January 2018 Abstract: The analysis of symmetry is a main principle in natural sciences, especially physics. For network sciences, for example, in social sciences, computer science and data science, only a few small-scale studies of the symmetry of complex real-world graphs exist. Graph symmetry is a topic rooted in mathematics and is not yet well-received and applied in practice. This article underlines the importance of analyzing symmetry by showing the existence of symmetry in real-world graphs. An analysis of over 1500 graph datasets from the meta-repository networkrepository.com is carried out and a normalized version of the “network redundancy” measure is presented. It quantifies graph symmetry in terms of the number of orbits of the symmetry group from zero (no symmetries) to one (completely symmetric), and improves the recognition of asymmetric graphs. Over 70% of the analyzed graphs contain symmetries (i.e., graph automorphisms), independent of size and modularity. Therefore, we conclude that real-world graphs are likely to contain symmetries. This contribution is the first larger-scale study of symmetry in graphs and it shows the necessity of handling symmetry in data analysis: The existence of symmetries in graphs is the cause of two problems in graph clustering we are aware of, namely, the existence of multiple equivalent solutions with the same value of the clustering criterion and, secondly, the inability of all standard partition-comparison measures of cluster analysis to identify automorphic partitions as equivalent. -
Graphprism: Compact Visualization of Network Structure
GraphPrism: Compact Visualization of Network Structure Sanjay Kairam, Diana MacLean, Manolis Savva, Jeffrey Heer Stanford University Computer Science Department {skairam, malcdi, msavva, jheer}@cs.stanford.edu GraphPrism Connectivity ABSTRACT nodeRadius 7.9 strokeWidth 1.12 charge -242 Visual methods for supporting the characterization, com- gravity 0.65 linkDistance 20 parison, and classification of large networks remain an open Transitivity updateGraph Close Controls challenge. Ideally, such techniques should surface useful 0 node(s) selected. structural features { such as effective diameter, small-world properties, and structural holes { not always apparent from Density either summary statistics or typical network visualizations. In this paper, we present GraphPrism, a technique for visu- Conductance ally summarizing arbitrarily large graphs through combina- tions of `facets', each corresponding to a single node- or edge- specific metric (e.g., transitivity). We describe a generalized Jaccard approach for constructing facets by calculating distributions of graph metrics over increasingly large local neighborhoods and representing these as a stacked multi-scale histogram. MeetMin Evaluation with paper prototypes shows that, with minimal training, static GraphPrism diagrams can aid network anal- ysis experts in performing basic analysis tasks with network Created by Sanjay Kairam. Visualization using D3. data. Finally, we contribute the design of an interactive sys- Figure 1: GraphPrism and node-link diagrams for tem using linked selection between GraphPrism overviews the largest component of a co-authorship graph. and node-link detail views. Using a case study of data from a co-authorship network, we illustrate how GraphPrism fa- compactly summarizing networks of arbitrary size. Graph- cilitates interactive exploration of network data. -
On the Group-Theoretic Properties of the Automorphism Groups of Various Graphs
ON THE GROUP-THEORETIC PROPERTIES OF THE AUTOMORPHISM GROUPS OF VARIOUS GRAPHS CHARLES HOMANS Abstract. In this paper we provide an introduction to the properties of one important connection between the theories of groups and graphs, that of the group formed by the automorphisms of a given graph. We provide examples of important results in graph theory that can be understood through group theory and vice versa, and conclude with a treatment of Frucht's theorem. Contents 1. Introduction 1 2. Fundamental Definitions, Concepts, and Theorems 2 3. Example 1: The Orbit-Stabilizer Theorem and its Application to Graph Automorphisms 4 4. Example 2: On the Automorphism Groups of the Platonic Solid Skeleton Graphs 4 5. Example 3: A Tight Bound on the Product of the Chromatic Number and Independence Number of Vertex-Transitive Graphs 6 6. Frucht's Theorem 7 7. Acknowledgements 9 8. References 9 1. Introduction Groups and graphs are two highly important kinds of structures studied in math- ematics. Interestingly, the theory of groups and the theory of graphs are deeply connected. In this paper, we examine one particular such connection: that which emerges from the observation that the automorphisms of any given graph form a group under composition. In section 2, we provide a framework for understanding the material discussed in the paper. In sections 3, 4, and 5, we demonstrate how important results in group theory illuminate some properties of automorphism groups, how the geo- metric properties of particular embeddings of graphs can be used to determine the structure of the automorphism groups of all embeddings of those graphs, and how the automorphism group can be used to determine fundamental truths about the structure of the graph. -
Graph Simplification and Interaction
Graph Clarity, Simplification, & Interaction http://i.imgur.com/cW19IBR.jpg https://www.reddit.com/r/CableManagement/ Today • Today’s Reading: Lombardi Graphs – Bezier Curves • Today’s Reading: Clustering/Hierarchical edge Bundling – Definition of Betweenness Centrality • Emergency Management Graph Visualization – Sean Kim’s masters project • Reading for Tuesday & Homework 3 • Graph Interaction Brainstorming Exercise "Lombardi drawings of graphs", Duncan, Eppstein, Goodrich, Kobourov, Nollenberg, Graph Drawing 2010 • Circular arcs • Perfect angular resolution (edges for equal angles at vertices) • Arcs only intersect 2 vertices (at endpoints) • (not required to be crossing free) • Vertices may be constrained to lie on circle or concentric circles • People are more patient with aesthetically pleasing graphs (will spend longer studying to learn/draw conclusions) • What about relaxing the circular arc requirement and allowing Bezier arcs? • How does it scale to larger data? • Long curved arcs can be much harder to follow • Circular layout of nodes is often very good! • Would like more pseudocode Cubic Bézier Curve • 4 control points • Curve passes through first & last control point • Curve is tangent at P0 to (P1-P0) and at P3 to (P3-P2) http://www.e-cartouche.ch/content_reg/carto http://www.webreference.com/dla uche/graphics/en/html/Curves_learningObject b/9902/bezier.html 2.html “Force-directed Lombardi-style graph drawing”, Chernobelskiy et al., Graph Drawing 2011. • Relaxation of the Lombardi Graph requirements • “straight-line segments -
Constraint Graph Drawing
Constrained Graph Drawing Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften vorgelegt von Barbara Pampel, geb. Schlieper an der Universit¨at Konstanz Mathematisch-Naturwissenschaftliche Sektion Fachbereich Informatik und Informationswissenschaft Tag der mundlichen¨ Prufung:¨ 14. Juli 2011 1. Referent: Prof. Dr. Ulrik Brandes 2. Referent: Prof. Dr. Michael Kaufmann II Teile dieser Arbeit basieren auf Ver¨offentlichungen, die aus der Zusammenar- beit mit anderen Wissenschaftlerinnen und Wissenschaftlern entstanden sind. Zu allen diesen Inhalten wurden wesentliche Beitr¨age geleistet. Kapitel 3 (Bachmaier, Brandes, and Schlieper, 2005; Brandes and Schlieper, 2009) Kapitel 4 (Brandes and Pampel, 2009) Kapitel 6 (Brandes, Cornelsen, Pampel, and Sallaberry, 2010b) Zusammenfassung Netzwerke werden in den unterschiedlichsten Forschungsgebieten zur Repr¨asenta- tion relationaler Daten genutzt. Durch geeignete mathematische Methoden kann man diese Netzwerke als Graphen darstellen. Ein Graph ist ein Gebilde aus Kno- ten und Kanten, welche die Knoten verbinden. Hierbei k¨onnen sowohl die Kan- ten als auch die Knoten weitere Informationen beinhalten. Diese Informationen k¨onnen den einzelnen Elementen zugeordnet sein, sich aber auch aus Anordnung und Verteilung der Elemente ergeben. Mit Algorithmen (strukturierten Reihen von Arbeitsanweisungen) aus dem Gebiet des Graphenzeichnens kann man die unterschiedlichsten Informationen aus verschiedenen Forschungsbereichen visualisieren. Graphische Darstellungen k¨onnen das -
Construction of Strongly Regular Graphs Having an Automorphism Group of Composite Order
Volume 15, Number 1, Pages 22{41 ISSN 1715-0868 CONSTRUCTION OF STRONGLY REGULAR GRAPHS HAVING AN AUTOMORPHISM GROUP OF COMPOSITE ORDER DEAN CRNKOVIC´ AND MARIJA MAKSIMOVIC´ Abstract. In this paper we outline a method for constructing strongly regular graphs from orbit matrices admitting an automorphism group of composite order. In 2011, C. Lam and M. Behbahani introduced the concept of orbit matrices of strongly regular graphs and developed an algorithm for the construction of orbit matrices of strongly regu- lar graphs with a presumed automorphism group of prime order, and construction of corresponding strongly regular graphs. The method of constructing strongly regular graphs developed and employed in this paper is a generalization of that developed by C. Lam and M. Behba- hani. Using this method we classify SRGs with parameters (49,18,7,6) having an automorphism group of order six. Eleven of the SRGs with parameters (49,18,7,6) constructed in that way are new. We obtain an additional 385 new SRGs(49,18,7,6) by switching. Comparing the con- structed graphs with previously known SRGs with these parameters, we conclude that up to isomorphism there are at least 727 SRGs with parameters (49,18,7,6). Further, we show that there are no SRGs with parameters (99,14,1,2) having an automorphism group of order six or nine, i.e. we rule out automorphism groups isomorphic to Z6, S3, Z9, or E9. 1. Introduction One of the main problems in the theory of strongly regular graphs (SRGs) is constructing and classifying SRGs with given parameters. -
TETRAVALENT SYMMETRIC GRAPHS of ORDER 9P
J. Korean Math. Soc. 49 (2012), No. 6, pp. 1111–1121 http://dx.doi.org/10.4134/JKMS.2012.49.6.1111 TETRAVALENT SYMMETRIC GRAPHS OF ORDER 9p Song-Tao Guo and Yan-Quan Feng Abstract. A graph is symmetric if its automorphism group acts transi- tively on the set of arcs of the graph. In this paper, we classify tetravalent symmetric graphs of order 9p for each prime p. 1. Introduction Let G be a permutation group on a set Ω and α ∈ Ω. Denote by Gα the stabilizer of α in G, that is, the subgroup of G fixing the point α. We say that G is semiregular on Ω if Gα = 1 for every α ∈ Ω and regular if G is transitive and semiregular. Throughout this paper, we consider undirected finite connected graphs without loops or multiple edges. For a graph X we use V (X), E(X) and Aut(X) to denote its vertex set, edge set, and automorphism group, respectively. For u , v ∈ V (X), denote by {u , v} the edge incident to u and v in X. A graph X is said to be vertex-transitive if Aut(X) acts transitively on V (X). An s-arc in a graph is an ordered (s + 1)-tuple (v0, v1,...,vs−1, vs) of vertices of the graph X such that vi−1 is adjacent to vi for 1 ≤ i ≤ s, and vi−1 = vi+1 for 1 ≤ i ≤ s − 1. In particular, a 1-arc is called an arc for short and a 0-arc is a vertex. -
Graph Automorphism Groups
Graph Automorphism Groups Robert A. Beeler, Ph.D. East Tennessee State University February 23, 2018 Robert A. Beeler, Ph.D. (East Tennessee State University)Graph Automorphism Groups February 23, 2018 1 / 1 What is a graph? A graph G =(V , E) is a set of vertices, V , together with as set of edges, E. For our purposes, each edge will be an unordered pair of distinct vertices. a e b d c V (G)= {a, b, c, d, e} E(G)= {ab, ae, bc, be, cd, de} Robert A. Beeler, Ph.D. (East Tennessee State University)Graph Automorphism Groups February 23, 2018 2 / 1 Graph Automorphisms A graph automorphism is simply an isomorphism from a graph to itself. In other words, an automorphism on a graph G is a bijection φ : V (G) → V (G) such that uv ∈ E(G) if and only if φ(u)φ(v) ∈ E(G). Note that graph automorphisms preserve adjacency. In layman terms, a graph automorphism is a symmetry of the graph. Robert A. Beeler, Ph.D. (East Tennessee State University)Graph Automorphism Groups February 23, 2018 3 / 1 An Example Consider the following graph: a d b c Robert A. Beeler, Ph.D. (East Tennessee State University)Graph Automorphism Groups February 23, 2018 4 / 1 An Example (Part 2) One automorphism simply maps every vertex to itself. This is the identity automorphism. a a d b d b c 7→ c e =(a)(b)(c)(d) Robert A. Beeler, Ph.D. (East Tennessee State University)Graph Automorphism Groups February 23, 2018 5 / 1 An Example (Part 3) One automorphism switches vertices a and c. -
Cores of Vertex-Transitive Graphs
Cores of Vertex-Transitive Graphs Ricky Rotheram Submitted in total fulfilment of the requirements of the degree of Master of Philosophy October 2013 Department of Mathematics and Statistics The University of Melbourne Parkville, VIC 3010, Australia Produced on archival quality paper Abstract The core of a graph Γ is the smallest graph Γ∗ for which there exist graph homomor- phisms Γ ! Γ∗ and Γ∗ ! Γ. Thus cores are fundamental to our understanding of general graph homomorphisms. It is known that for a vertex-transitive graph Γ, Γ∗ is vertex-transitive, and that jV (Γ∗)j divides jV (Γ)j. The purpose of this thesis is to determine the cores of various families of vertex-transitive and symmetric graphs. We focus primarily on finding the cores of imprimitive symmetric graphs of order pq, where p < q are primes. We choose to investigate these graphs because their cores must be symmetric graphs with jV (Γ∗)j = p or q. These graphs have been completely classified, and are split into three broad families, namely the circulants, the incidence graphs and the Maruˇsiˇc-Scapellato graphs. We use this classification to determine the cores of all imprimitive symmetric graphs of order pq, using differ- ent approaches for the circulants, the incidence graphs and the Maruˇsiˇc-Scapellato graphs. Circulant graphs are examples of Cayley graphs of abelian groups. Thus, we generalise the approach used to determine the cores of the symmetric circulants of order pq, and apply it to other Cayley graphs of abelian groups. Doing this, we show that if Γ is a Cayley graph of an abelian group, then Aut(Γ∗) contains a transitive subgroup generated by semiregular automorphisms, and either Γ∗ is an odd cycle or girth(Γ∗) ≤ 4.