A Graph Theory Package for Maple, Part II: Graph Coloring, Graph Drawing, Support Tools, and Networks
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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 -
Network Monitoring & Management Using Cacti
Network Monitoring & Management Using Cacti Network Startup Resource Center www.nsrc.org These materials are licensed under the Creative Commons Attribution-NonCommercial 4.0 International license (http://creativecommons.org/licenses/by-nc/4.0/) Introduction Network Monitoring Tools Availability Reliability Performance Cact monitors the performance and usage of devices. Introduction Cacti: Uses RRDtool, PHP and stores data in MySQL. It supports the use of SNMP and graphics with RRDtool. “Cacti is a complete frontend to RRDTool, it stores all of the necessary information to create graphs and populate them with data in a MySQL database. The frontend is completely PHP driven. Along with being able to maintain Graphs, Data Sources, and Round Robin Archives in a database, cacti handles the data gathering. There is also SNMP support for those used to creating traffic graphs with MRTG.” Introduction • A tool to monitor, store and present network and system/server statistics • Designed around RRDTool with a special emphasis on the graphical interface • Almost all of Cacti's functionality can be configured via the Web. • You can find Cacti here: http://www.cacti.net/ Getting RRDtool • Round Robin Database for time series data storage • Command line based • From the author of MRTG • Made to be faster and more flexible • Includes CGI and Graphing tools, plus APIs • Solves the Historical Trends and Simple Interface problems as well as storage issues Find RRDtool here:http://oss.oetiker.ch/rrdtool/ RRDtool Database Format General Description 1. Cacti is written as a group of PHP scripts. 2. The key script is “poller.php”, which runs every 5 minutes (by default). -
Munin Documentation Release 2.0.44
Munin Documentation Release 2.0.44 Stig Sandbeck Mathisen <[email protected]> Dec 20, 2018 Contents 1 Munin installation 3 1.1 Prerequisites.............................................3 1.2 Installing Munin...........................................4 1.3 Initial configuration.........................................7 1.4 Getting help.............................................8 1.5 Upgrading Munin from 1.x to 2.x..................................8 2 The Munin master 9 2.1 Role..................................................9 2.2 Components.............................................9 2.3 Configuration.............................................9 2.4 Other documentation.........................................9 3 The Munin node 13 3.1 Role.................................................. 13 3.2 Configuration............................................. 13 3.3 Other documentation......................................... 13 4 The Munin plugin 15 4.1 Role.................................................. 15 4.2 Other documentation......................................... 15 5 Documenting Munin 21 5.1 Nomenclature............................................ 21 6 Reference 25 6.1 Man pages.............................................. 25 6.2 Other reference material....................................... 40 7 Examples 43 7.1 Apache virtualhost configuration.................................. 43 7.2 lighttpd configuration........................................ 44 7.3 nginx configuration.......................................... 45 7.4 Graph aggregation -
Automatic Placement of Authorization Hooks in the Linux Security Modules Framework
Automatic Placement of Authorization Hooks in the Linux Security Modules Framework Vinod Ganapathy [email protected] University of Wisconsin, Madison Joint work with Trent Jaeger Somesh Jha [email protected] [email protected] Pennsylvania State University University of Wisconsin, Madison Context of this talk Authorization policies and their enforcement Three concepts: Subjects (e.g., users, processes) Objects (e.g., system resources) Security-sensitive operations on objects. Authorization policy: A set of triples: (Subject, Object, Operation) Key question: How to ensure that the authorization policy is enforced? CCS 2005 Automatic Placement of Authorization Hooks in the Linux Security Modules Framework 2 Enforcing authorization policies Reference monitor consults the policy. Application queries monitor at appropriate locations. Can I perform operation OP? Reference Monitor Application to Policy be secured Yes/No (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) CCS 2005 Automatic Placement of Authorization Hooks in the Linux Security Modules Framework 3 Linux security modules framework Framework for authorization policy enforcement. Uses a reference monitor-based architecture. Integrated into Linux-2.6 Linux Kernel Reference Monitor Policy (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) CCS 2005 Automatic Placement of Authorization Hooks in the Linux Security Modules Framework 4 Linux security modules framework Reference monitor calls (hooks) placed appropriately in the Linux kernel. Each hook is an authorization query. Linux Kernel Reference Monitor Policy (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) (subj.,obj.,oper.) Hooks CCS 2005 Automatic Placement of Authorization Hooks in the Linux Security Modules Framework 5 Linux security modules framework Authorization query of the form: (subj., obj., oper.)? Kernel performs operation only if query succeeds. -
Masked Graph Modeling for Molecule Generation ✉ Omar Mahmood 1, Elman Mansimov2, Richard Bonneau 3 & Kyunghyun Cho 2
ARTICLE https://doi.org/10.1038/s41467-021-23415-2 OPEN Masked graph modeling for molecule generation ✉ Omar Mahmood 1, Elman Mansimov2, Richard Bonneau 3 & Kyunghyun Cho 2 De novo, in-silico design of molecules is a challenging problem with applications in drug discovery and material design. We introduce a masked graph model, which learns a dis- tribution over graphs by capturing conditional distributions over unobserved nodes (atoms) and edges (bonds) given observed ones. We train and then sample from our model by iteratively masking and replacing different parts of initialized graphs. We evaluate our 1234567890():,; approach on the QM9 and ChEMBL datasets using the GuacaMol distribution-learning benchmark. We find that validity, KL-divergence and Fréchet ChemNet Distance scores are anti-correlated with novelty, and that we can trade off between these metrics more effec- tively than existing models. On distributional metrics, our model outperforms previously proposed graph-based approaches and is competitive with SMILES-based approaches. Finally, we show our model generates molecules with desired values of specified properties while maintaining physiochemical similarity to the training distribution. 1 Center for Data Science, New York University, New York, NY, USA. 2 Department of Computer Science, Courant Institute of Mathematical Sciences, New ✉ York, NY, USA. 3 Center for Genomics and Systems Biology, New York University, New York, NY, USA. email: [email protected] NATURE COMMUNICATIONS | (2021) 12:3156 | https://doi.org/10.1038/s41467-021-23415-2 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-021-23415-2 he design of de novo molecules in-silico with desired prop- enable more informative comparisons between models that use Terties is an essential part of drug discovery and materials different molecular representations. -
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. -
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 -
Chapter 18 Spectral Graph Drawing
Chapter 18 Spectral Graph Drawing 18.1 Graph Drawing and Energy Minimization Let G =(V,E)besomeundirectedgraph.Itisoftende- sirable to draw a graph, usually in the plane but possibly in 3D, and it turns out that the graph Laplacian can be used to design surprisingly good methods. n Say V = m.Theideaistoassignapoint⇢(vi)inR to the vertex| | v V ,foreveryv V ,andtodrawaline i 2 i 2 segment between the points ⇢(vi)and⇢(vj). Thus, a graph drawing is a function ⇢: V Rn. ! 821 822 CHAPTER 18. SPECTRAL GRAPH DRAWING We define the matrix of a graph drawing ⇢ (in Rn) as a m n matrix R whose ith row consists of the row vector ⇥ n ⇢(vi)correspondingtothepointrepresentingvi in R . Typically, we want n<m;infactn should be much smaller than m. Arepresentationisbalanced i↵the sum of the entries of every column is zero, that is, 1>R =0. If a representation is not balanced, it can be made bal- anced by a suitable translation. We may also assume that the columns of R are linearly independent, since any basis of the column space also determines the drawing. Thus, from now on, we may assume that n m. 18.1. GRAPH DRAWING AND ENERGY MINIMIZATION 823 Remark: Agraphdrawing⇢: V Rn is not required to be injective, which may result in! degenerate drawings where distinct vertices are drawn as the same point. For this reason, we prefer not to use the terminology graph embedding,whichisoftenusedintheliterature. This is because in di↵erential geometry, an embedding always refers to an injective map. The term graph immersion would be more appropriate. -
Operational Semantics with Hierarchical Abstract Syntax Graphs*
Operational Semantics with Hierarchical Abstract Syntax Graphs* Dan R. Ghica Huawei Research, Edinburgh University of Birmingham, UK This is a motivating tutorial introduction to a semantic analysis of programming languages using a graphical language as the representation of terms, and graph rewriting as a representation of reduc- tion rules. We show how the graphical language automatically incorporates desirable features, such as a-equivalence and how it can describe pure computation, imperative store, and control features in a uniform framework. The graph semantics combines some of the best features of structural oper- ational semantics and abstract machines, while offering powerful new methods for reasoning about contextual equivalence. All technical details are available in an extended technical report by Muroya and the author [11] and in Muroya’s doctoral dissertation [21]. 1 Hierarchical abstract syntax graphs Before proceeding with the business of analysing and transforming the source code of a program, a com- piler first parses the input text into a sequence of atoms, the lexemes, and then assembles them into a tree, the Abstract Syntax Tree (AST), which corresponds to its grammatical structure. The reason for preferring the AST to raw text or a sequence of lexemes is quite obvious. The structure of the AST incor- porates most of the information needed for the following stage of compilation, in particular identifying operations as nodes in the tree and operands as their branches. This makes the AST algorithmically well suited for its purpose. Conversely, the AST excludes irrelevant lexemes, such as separators (white-space, commas, semicolons) and aggregators (brackets, braces), by making them implicit in the tree-like struc- ture. -
A Property Graph Is a Directed Edge-Labeled, Attributed Multigraph
- In IT Security for 10+ years - consulting and research - My first talk at a Data-conference :) - PhD thesis: “Pattern-based Vulnerability Discovery” on using unsupervised machine learning and graph databases for vulnerability discovery - Chief scientist at ShiftLeft Inc. - Modern development processes are optimized for fast feature delivery - Cloud services: multiple deployments a day - Each deployment is a security-related decision - Enforce code-level security policies automatically! Example: enforce a policy for propagation of sensitive data: “Environment variables must not be written to the logger” public void init() { String user = env.getProperty(“sfdc.uname”); String pwd = env.getProperty(“sfdc.pwd”); ... if (!validLogin(user, pwd)) { ... log.error("Invalid username/password: {}/{}", user, pwd); } } Jackson - Critical code execution vulnerabilities. A program is vulnerable if 1. a vulnerable version of jackson-databind is used 2. attacker controlled input is deserialized in a call to “readValue” 3. “Default typing” is enabled globally via a call to “enableDefaultTyping” Jackson Jackson Detecting this particular vulnerability types requires modeling program dependencies, syntax, data flow and method invocations. > cpg.dependency.name(".*jackson-databind.*").version("2.8..*") .and{ cpg.call.name(“.*enableDefaultTyping.*”) } .and{ cpg.method.name(“.*readValue.*”).parameter.index(1).reachableBy( cpg.parameter.evalType(".*HttpServletRequest.*")) }.location Code Property Graph cpg.method.name(“sink”).parameter .reachableBy(cpg.method.name(“source”))