Centrality in Modular Networks Zakariya Ghalmane, Mohammed El Hassouni, Chantal Cherifi, Hocine Cherifi
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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 -
Detecting Statistically Significant Communities
1 Detecting Statistically Significant Communities Zengyou He, Hao Liang, Zheng Chen, Can Zhao, Yan Liu Abstract—Community detection is a key data analysis problem across different fields. During the past decades, numerous algorithms have been proposed to address this issue. However, most work on community detection does not address the issue of statistical significance. Although some research efforts have been made towards mining statistically significant communities, deriving an analytical solution of p-value for one community under the configuration model is still a challenging mission that remains unsolved. The configuration model is a widely used random graph model in community detection, in which the degree of each node is preserved in the generated random networks. To partially fulfill this void, we present a tight upper bound on the p-value of a single community under the configuration model, which can be used for quantifying the statistical significance of each community analytically. Meanwhile, we present a local search method to detect statistically significant communities in an iterative manner. Experimental results demonstrate that our method is comparable with the competing methods on detecting statistically significant communities. Index Terms—Community Detection, Random Graphs, Configuration Model, Statistical Significance. F 1 INTRODUCTION ETWORKS are widely used for modeling the structure function that is able to always achieve the best performance N of complex systems in many fields, such as biology, in all possible scenarios. engineering, and social science. Within the networks, some However, most of these objective functions (metrics) do vertices with similar properties will form communities that not address the issue of statistical significance of commu- have more internal connections and less external links. -
Networks in Nature: Dynamics, Evolution, and Modularity
Networks in Nature: Dynamics, Evolution, and Modularity Sumeet Agarwal Merton College University of Oxford A thesis submitted for the degree of Doctor of Philosophy Hilary 2012 2 To my entire social network; for no man is an island Acknowledgements Primary thanks go to my supervisors, Nick Jones, Charlotte Deane, and Mason Porter, whose ideas and guidance have of course played a major role in shaping this thesis. I would also like to acknowledge the very useful sug- gestions of my examiners, Mark Fricker and Jukka-Pekka Onnela, which have helped improve this work. I am very grateful to all the members of the three Oxford groups I have had the fortune to be associated with: Sys- tems and Signals, Protein Informatics, and the Systems Biology Doctoral Training Centre. Their companionship has served greatly to educate and motivate me during the course of my time in Oxford. In particular, Anna Lewis and Ben Fulcher, both working on closely related D.Phil. projects, have been invaluable throughout, and have assisted and inspired my work in many different ways. Gabriel Villar and Samuel Johnson have been col- laborators and co-authors who have helped me to develop some of the ideas and methods used here. There are several other people who have gener- ously provided data, code, or information that has been directly useful for my work: Waqar Ali, Binh-Minh Bui-Xuan, Pao-Yang Chen, Dan Fenn, Katherine Huang, Patrick Kemmeren, Max Little, Aur´elienMazurie, Aziz Mithani, Peter Mucha, George Nicholson, Eli Owens, Stephen Reid, Nico- las Simonis, Dave Smith, Ian Taylor, Amanda Traud, and Jeffrey Wrana. -
Network Topologies Topologies
Network Topologies Topologies Logical Topologies A logical topology describes how the hosts access the medium and communicate on the network. The two most common types of logical topologies are broadcast and token passing. In a broadcast topology, a host broadcasts a message to all hosts on the same network segment. There is no order that hosts must follow to transmit data. Messages are sent on a First In, First Out (FIFO) basis. Token passing controls network access by passing an electronic token sequentially to each host. If a host wants to transmit data, the host adds the data and a destination address to the token, which is a specially-formatted frame. The token then travels to another host with the destination address. The destination host takes the data out of the frame. If a host has no data to send, the token is passed to another host. Physical Topologies A physical topology defines the way in which computers, printers, and other devices are connected to a network. The figure provides six physical topologies. Bus In a bus topology, each computer connects to a common cable. The cable connects one computer to the next, like a bus line going through a city. The cable has a small cap installed at the end called a terminator. The terminator prevents signals from bouncing back and causing network errors. Ring In a ring topology, hosts are connected in a physical ring or circle. Because the ring topology has no beginning or end, the cable is not terminated. A token travels around the ring stopping at each host. -
Modularity in Static and Dynamic Networks
Modularity in static and dynamic networks Sarah F. Muldoon University at Buffalo, SUNY OHBM – Brain Graphs Workshop June 25, 2017 Outline 1. Introduction: What is modularity? 2. Determining community structure (static networks) 3. Comparing community structure 4. Multilayer networks: Constructing multitask and temporal multilayer dynamic networks 5. Dynamic community structure 6. Useful references OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon Introduction: What is Modularity? OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon What is Modularity? Modularity (Community Structure) • A module (community) is a subset of vertices in a graph that have more connections to each other than to the rest of the network • Example social networks: groups of friends Modularity in the brain: • Structural networks: communities are groups of brain areas that are more highly connected to each other than the rest of the brain • Functional networks: communities are groups of brain areas with synchronous activity that is not synchronous with other brain activity OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon Findings: The Brain is Modular Structural networks: cortical thickness correlations sensorimotor/spatial strategic/executive mnemonic/emotion olfactocentric auditory/language visual processing Chen et al. (2008) Cereb Cortex OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon Findings: The Brain is Modular • Functional networks: resting state fMRI He et al. (2009) PLOS One OHBM 2017 – Brain Graphs Workshop – Sarah F. Muldoon Findings: The -
Networkx Reference Release 1.9.1
NetworkX Reference Release 1.9.1 Aric Hagberg, Dan Schult, Pieter Swart September 20, 2014 CONTENTS 1 Overview 1 1.1 Who uses NetworkX?..........................................1 1.2 Goals...................................................1 1.3 The Python programming language...................................1 1.4 Free software...............................................2 1.5 History..................................................2 2 Introduction 3 2.1 NetworkX Basics.............................................3 2.2 Nodes and Edges.............................................4 3 Graph types 9 3.1 Which graph class should I use?.....................................9 3.2 Basic graph types.............................................9 4 Algorithms 127 4.1 Approximation.............................................. 127 4.2 Assortativity............................................... 132 4.3 Bipartite................................................. 141 4.4 Blockmodeling.............................................. 161 4.5 Boundary................................................. 162 4.6 Centrality................................................. 163 4.7 Chordal.................................................. 184 4.8 Clique.................................................. 187 4.9 Clustering................................................ 190 4.10 Communities............................................... 193 4.11 Components............................................... 194 4.12 Connectivity.............................................. -
Multidimensional Network Analysis
Universita` degli Studi di Pisa Dipartimento di Informatica Dottorato di Ricerca in Informatica Ph.D. Thesis Multidimensional Network Analysis Michele Coscia Supervisor Supervisor Fosca Giannotti Dino Pedreschi May 9, 2012 Abstract This thesis is focused on the study of multidimensional networks. A multidimensional network is a network in which among the nodes there may be multiple different qualitative and quantitative relations. Traditionally, complex network analysis has focused on networks with only one kind of relation. Even with this constraint, monodimensional networks posed many analytic challenges, being representations of ubiquitous complex systems in nature. However, it is a matter of common experience that the constraint of considering only one single relation at a time limits the set of real world phenomena that can be represented with complex networks. When multiple different relations act at the same time, traditional complex network analysis cannot provide suitable an- alytic tools. To provide the suitable tools for this scenario is exactly the aim of this thesis: the creation and study of a Multidimensional Network Analysis, to extend the toolbox of complex network analysis and grasp the complexity of real world phenomena. The urgency and need for a multidimensional network analysis is here presented, along with an empirical proof of the ubiquity of this multifaceted reality in different complex networks, and some related works that in the last two years were proposed in this novel setting, yet to be systematically defined. Then, we tackle the foundations of the multidimensional setting at different levels, both by looking at the basic exten- sions of the known model and by developing novel algorithms and frameworks for well-understood and useful problems, such as community discovery (our main case study), temporal analysis, link prediction and more. -
Centrality in Modular Networks
Ghalmane et al. EPJ Data Science (2019)8:15 https://doi.org/10.1140/epjds/s13688-019-0195-7 REGULAR ARTICLE OpenAccess Centrality in modular networks Zakariya Ghalmane1,3, Mohammed El Hassouni1, Chantal Cherifi2 and Hocine Cherifi3* *Correspondence: hocine.cherifi@u-bourgogne.fr Abstract 3LE2I, UMR6306 CNRS, University of Burgundy, Dijon, France Identifying influential nodes in a network is a fundamental issue due to its wide Full list of author information is applications, such as accelerating information diffusion or halting virus spreading. available at the end of the article Many measures based on the network topology have emerged over the years to identify influential nodes such as Betweenness, Closeness, and Eigenvalue centrality. However, although most real-world networks are made of groups of tightly connected nodes which are sparsely connected with the rest of the network in a so-called modular structure, few measures exploit this property. Recent works have shown that it has a significant effect on the dynamics of networks. In a modular network, a node has two types of influence: a local influence (on the nodes of its community) through its intra-community links and a global influence (on the nodes in other communities) through its inter-community links. Depending on the strength of the community structure, these two components are more or less influential. Based on this idea, we propose to extend all the standard centrality measures defined for networks with no community structure to modular networks. The so-called “Modular centrality” is a two-dimensional vector. Its first component quantifies the local influence of a node in its community while the second component quantifies its global influence on the other communities of the network. -
Strongly Connected Components and Biconnected Components
Strongly Connected Components and Biconnected Components Daniel Wisdom 27 January 2017 1 2 3 4 5 6 7 8 Figure 1: A directed graph. Credit: Crash Course Coding Companion. 1 Strongly Connected Components A strongly connected component (SCC) is a set of vertices where every vertex can reach every other vertex. In an undirected graph the SCCs are just the groups of connected vertices. We can find them using a simple DFS. This works because, in an undirected graph, u can reach v if and only if v can reach u. This is not true in a directed graph, which makes finding the SCCs harder. More on that later. 2 Kernel graph We can travel between any two nodes in the same strongly connected component. So what if we replaced each strongly connected component with a single node? This would give us what we call the kernel graph, which describes the edges between strongly connected components. Note that the kernel graph is a directed acyclic graph because any cycles would constitute an SCC, so the cycle would be compressed into a kernel. 3 1,2,5,6 4,7 8 Figure 2: Kernel graph of the above directed graph. 3 Tarjan's SCC Algorithm In a DFS traversal of the graph every SCC will be a subtree of the DFS tree. This subtree is not necessarily proper, meaning that it may be missing some branches which are their own SCCs. This means that if we can identify every node that is the root of its SCC in the DFS, we can enumerate all the SCCs. -
A Network Approach to Define Modularity of Components In
A Network Approach to Define Modularity of Components Manuel E. Sosa1 Technology and Operations Management Area, in Complex Products INSEAD, 77305 Fontainebleau, France Modularity has been defined at the product and system levels. However, little effort has e-mail: [email protected] gone into defining and quantifying modularity at the component level. We consider com- plex products as a network of components that share technical interfaces (or connections) Steven D. Eppinger in order to function as a whole and define component modularity based on the lack of Sloan School of Management, connectivity among them. Building upon previous work in graph theory and social net- Massachusetts Institute of Technology, work analysis, we define three measures of component modularity based on the notion of Cambridge, Massachusetts 02139 centrality. Our measures consider how components share direct interfaces with adjacent components, how design interfaces may propagate to nonadjacent components in the Craig M. Rowles product, and how components may act as bridges among other components through their Pratt & Whitney Aircraft, interfaces. We calculate and interpret all three measures of component modularity by East Hartford, Connecticut 06108 studying the product architecture of a large commercial aircraft engine. We illustrate the use of these measures to test the impact of modularity on component redesign. Our results show that the relationship between component modularity and component redesign de- pends on the type of interfaces connecting product components. We also discuss direc- tions for future work. ͓DOI: 10.1115/1.2771182͔ 1 Introduction The need to measure modularity has been highlighted implicitly by Saleh ͓12͔ in his recent invitation “to contribute to the growing Previous research on product architecture has defined modular- field of flexibility in system design” ͑p. -
Topological Optimisation of Artificial Neural Networks for Financial Asset
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by LSE Theses Online The London School of Economics and Political Science Topological Optimisation of Artificial Neural Networks for Financial Asset Forecasting Shiye (Shane) He A thesis submitted to the Department of Management of the London School of Economics for the degree of Doctor of Philosophy. April 2015, London 1 Declaration I certify that the thesis I have presented for examination for the MPhil/PhD degree of the London School of Economics and Political Science is solely my own work other than where I have clearly indicated that it is the work of others (in which case the extent of any work carried out jointly by me and any other person is clearly identified in it). The copyright of this thesis rests with the author. Quotation from it is permitted, provided that full acknowledgement is made. This thesis may not be reproduced without the prior written consent of the author. I warrant that this authorization does not, to the best of my belief, infringe the rights of any third party. 2 Abstract The classical Artificial Neural Network (ANN) has a complete feed-forward topology, which is useful in some contexts but is not suited to applications where both the inputs and targets have very low signal-to-noise ratios, e.g. financial forecasting problems. This is because this topology implies a very large number of parameters (i.e. the model contains too many degrees of freedom) that leads to over fitting of both signals and noise. -
Task-Dependent Evolution of Modularity in Neural Networks1
Task-dependent evolution of modularity in neural networks1 Michael Husk¨ en, Christian Igel, and Marc Toussaint Institut fur¨ Neuroinformatik, Ruhr-Universit¨at Bochum, 44780 Bochum, Germany Telephone: +49 234 32 25558, Fax: +49 234 32 14209 fhuesken,igel,[email protected] Connection Science Vol 14, No 3, 2002, p. 219-229 Abstract. There exist many ideas and assumptions about the development and meaning of modu- larity in biological and technical neural systems. We empirically study the evolution of connectionist models in the context of modular problems. For this purpose, we define quantitative measures for the degree of modularity and monitor them during evolutionary processes under different constraints. It turns out that the modularity of the problem is reflected by the architecture of adapted systems, although learning can counterbalance some imperfection of the architecture. The demand for fast learning systems increases the selective pressure towards modularity. 1 Introduction The performance of biological as well as technical neural systems crucially depends on their ar- chitectures. In case of a feed-forward neural network (NN), architecture may be defined as the underlying graph constituting the number of neurons and the way these neurons are connected. Particularly one property of architectures, modularity, has raised a lot of interest among researchers dealing with biological and technical aspects of neural computation. It appears to be obvious to emphasise modularity in neural systems because the vertebrate brain is highly modular both in an anatomical and in a functional sense. It is important to stress that there are different concepts of modules. `When a neuroscientist uses the word \module", s/he is usually referring to the fact that brains are structured, with cells, columns, layers, and regions which divide up the labour of information processing in various ways' 1This paper is a revised and extended version of the GECCO 2001 Late-Breaking Paper by Husk¨ en, Igel, & Toussaint (2001).