Configuration Models of Random Hypergraphs
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A Novel Neuronal Network Approach to Express Network Motifs
Introduction to NeuraBASE: A Novel Neuronal Network Approach to Express Network Motifs Robert Hercus Choong-Ming Chin Kim-Fong Ho Introduction Since the discovery by Alon et al. [1-3], network motifs are now at the forefront of unravelling complex networks, ranging from biological issues to managing the traffic on the Internet. Network motifs are used, in general, as a technique to detect recurring patterns featured in networks. This is based on the assumption that information flows in distinct networks and, hence, common causal associations between nodal networks can be surmised statistically. In essence, the motif discovery algorithm [1-4] begins with a list of variable-information of a particular network and, their connections to other network variables. An analysis is subsequently made on the most prevalent causal relationships in the network based on the frequency of occurrences. These are then compared with a randomised network with the same number of variables and directed edges. Finally, the algorithm lists out statistically significant patterns of associations that occur more frequently than they would at random. In the paper by Alon et al. [2], it was reported that most of the networks analysed demonstrate identical motifs, even though they belong to disparate network families. For example, the said literature discovered that gene regulation in genetics, neuronal connectivity network and electronic circuit systems share two identical network motifs, which involved less than four variables. This observation implies that some similarities exist in these three network architectures. Besides the MFinder tool [1], researchers have also developed other network motif discovery tools. However, MAVisto [6] was found to be as computationally costly with long run-time periods as the MFinder tool uses the same network search for the same subgraph sizes. -
Robustness and Assortativity for Diffusion-Like Processes in Scale
epl draft Robustness and Assortativity for Diffusion-like Processes in Scale- free Networks G. D’Agostino1, A. Scala2,3, V. Zlatic´4 and G. Caldarelli5,3 1 ENEA - CR ”Casaccia” - Via Anguillarese 301 00123, Roma - Italy 2 CNR-ISC and Department of Physics, University of Rome “Sapienza” P.le Aldo Moro 5 00185 Rome, Italy 3 London Institute of Mathematical Sciences, 22 South Audley St Mayfair London W1K 2NY, UK 4 Theoretical Physics Division, Rudjer Boˇskovi´cInstitute, P.O.Box 180, HR-10002 Zagreb, Croatia 5 IMT Lucca Institute for Advanced Studies, Piazza S. Ponziano 6, Lucca, 55100, Italy PACS 89.75.Hc – Networks and genealogical trees PACS 05.70.Ln – Nonequilibrium and irreversible thermodynamics PACS 87.23.Ge – Dynamics of social systems Abstract – By analysing the diffusive dynamics of epidemics and of distress in complex networks, we study the effect of the assortativity on the robustness of the networks. We first determine by spectral analysis the thresholds above which epidemics/failures can spread; we then calculate the slowest diffusional times. Our results shows that disassortative networks exhibit a higher epidemi- ological threshold and are therefore easier to immunize, while in assortative networks there is a longer time for intervention before epidemic/failure spreads. Moreover, we study by computer sim- ulations the sandpile cascade model, a diffusive model of distress propagation (financial contagion). We show that, while assortative networks are more prone to the propagation of epidemic/failures, degree-targeted immunization policies increases their resilience to systemic risk. Introduction. – The heterogeneity in the distribu- propagation of an epidemic [13–15]. -
Ollivier Ricci Curvature of Directed Hypergraphs Marzieh Eidi1* & Jürgen Jost1,2
www.nature.com/scientificreports OPEN Ollivier Ricci curvature of directed hypergraphs Marzieh Eidi1* & Jürgen Jost1,2 Many empirical networks incorporate higher order relations between elements and therefore are naturally modelled as, possibly directed and/or weighted, hypergraphs, rather than merely as graphs. In order to develop a systematic tool for the statistical analysis of such hypergraph, we propose a general defnition of Ricci curvature on directed hypergraphs and explore the consequences of that defnition. The defnition generalizes Ollivier’s defnition for graphs. It involves a carefully designed optimal transport problem between sets of vertices. While the defnition looks somewhat complex, in the end we shall be able to express our curvature in a very simple formula, κ = µ0 − µ2 − 2µ3 . This formula simply counts the fraction of vertices that have to be moved by distances 0, 2 or 3 in an optimal transport plan. We can then characterize various classes of hypergraphs by their curvature. Principles of network analysis. Network analysis constitutes one of the success stories in the study of complex systems3,6,11. For the mathematical analysis, a network is modelled as a (perhaps weighted and/or directed) graph. One can then look at certain graph theoretical properties of an empirical network, like its degree or motiv distribution, its assortativity or clustering coefcient, the spectrum of its Laplacian, and so on. One can also compare an empirical network with certain deterministic or random theoretical models. Successful as this analysis clearly is, we nevertheless see two important limitations. One is that many of the prominent concepts and quantities used in the analysis of empirical networks are node based, like the degree sequence. -
Assortativity and Mixing
Assortativity and Assortativity and Mixing General mixing between node categories Mixing Assortativity and Mixing Definition Definition I Assume types of nodes are countable, and are Complex Networks General mixing General mixing Assortativity by assigned numbers 1, 2, 3, . Assortativity by CSYS/MATH 303, Spring, 2011 degree degree I Consider networks with directed edges. Contagion Contagion References an edge connects a node of type µ References e = Pr Prof. Peter Dodds µν to a node of type ν Department of Mathematics & Statistics Center for Complex Systems aµ = Pr(an edge comes from a node of type µ) Vermont Advanced Computing Center University of Vermont bν = Pr(an edge leads to a node of type ν) ~ I Write E = [eµν], ~a = [aµ], and b = [bν]. I Requirements: X X X eµν = 1, eµν = aµ, and eµν = bν. µ ν ν µ Licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License. 1 of 26 4 of 26 Assortativity and Assortativity and Outline Mixing Notes: Mixing Definition Definition General mixing General mixing Assortativity by I Varying eµν allows us to move between the following: Assortativity by degree degree Definition Contagion 1. Perfectly assortative networks where nodes only Contagion References connect to like nodes, and the network breaks into References subnetworks. General mixing P Requires eµν = 0 if µ 6= ν and µ eµµ = 1. 2. Uncorrelated networks (as we have studied so far) Assortativity by degree For these we must have independence: eµν = aµbν . 3. Disassortative networks where nodes connect to nodes distinct from themselves. Contagion I Disassortative networks can be hard to build and may require constraints on the eµν. -
A Meta-Analysis of Boolean Network Models Reveals Design Principles of Gene Regulatory Networks
A meta-analysis of Boolean network models reveals design principles of gene regulatory networks Claus Kadelkaa,∗, Taras-Michael Butrieb,1, Evan Hiltonc,1, Jack Kinsetha,1, Haris Serdarevica,1 aDepartment of Mathematics, Iowa State University, Ames, Iowa 50011 bDepartment of Aerospace Engineering, Iowa State University, Ames, Iowa 50011 cDepartment of Computer Science, Iowa State University, Ames, Iowa 50011 Abstract Gene regulatory networks (GRNs) describe how a collection of genes governs the processes within a cell. Understanding how GRNs manage to consistently perform a particular function constitutes a key question in cell biology. GRNs are frequently modeled as Boolean networks, which are intuitive, simple to describe, and can yield qualitative results even when data is sparse. We generate an expandable database of published, expert-curated Boolean GRN models, and extracted the rules governing these networks. A meta-analysis of this diverse set of models enables us to identify fundamental design principles of GRNs. The biological term canalization reflects a cell's ability to maintain a stable phenotype despite ongoing environmental perturbations. Accordingly, Boolean canalizing functions are functions where the output is already determined if a specific variable takes on its canalizing input, regardless of all other inputs. We provide a detailed analysis of the prevalence of canalization and show that most rules describing the regulatory logic are highly canalizing. Independent from this, we also find that most rules exhibit a high level of redundancy. An analysis of the prevalence of small network motifs, e.g. feed-forward loops or feedback loops, in the wiring diagram of the identified models reveals several highly abundant types of motifs, as well as a surprisingly high overabundance of negative regulations in complex feedback loops. -
Adam Stier, Ties That Bind.Pdf
Ties That Bind: American Fiction and the Origins of Social Network Analysis DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Adam Charles Stier, M.A. Graduate Program in English The Ohio State University 2013 Dissertation Committee: Dr. David Herman, Advisor Dr. Brian McHale Dr. James Phelan Copyright by Adam Charles Stier 2013 Abstract Under the auspices of the digital humanities, scholars have recently raised the question of how current research on social networks might inform the study of fictional texts, even using computational methods to “quantify” the relationships among characters in a given work. However, by focusing on only the most recent developments in social network research, such criticism has so far neglected to consider how the historical development of social network analysis—a methodology that attempts to identify the rule-bound processes and structures underlying interpersonal relationships—converges with literary history. Innovated by sociologists and social psychologists of the late nineteenth and early twentieth centuries, including Georg Simmel (chapter 1), Charles Horton Cooley (chapter 2), Jacob Moreno (chapter 3), and theorists of the “small world” phenomenon (chapter 4), social network analysis emerged concurrently with the development of American literary modernism. Over the course of four chapters, Ties That Bind demonstrates that American modernist fiction coincided with a nascent “science” of social networks, such that we can discern striking parallels between emergent network-analytic procedures and the particular configurations by which American authors of this period structured (and more generally imagined) the social worlds of their stories. -
Multivariate Relations Aggregation Learning in Social Networks
Multivariate Relations Aggregation Learning in Social Networks Jin Xu1, Shuo Yu1, Ke Sun1, Jing Ren1, Ivan Lee2, Shirui Pan3, Feng Xia4 1 School of Software, Dalian University of Technology, Dalian, China 2 School of IT and Mathematical Sciences, University of South Australia, Adelaide, Australia 3 Faculty of Information Technology, Monash University, Melbourne, Australia 4 School of Science, Engineering and Information Technology, Federation University Australia, Ballarat, Australia [email protected],[email protected],[email protected],[email protected] [email protected],[email protected],[email protected] ABSTRACT 1 INTRODUCTION Multivariate relations are general in various types of networks, such We are living in a world full of relations. It is of great significance as biological networks, social networks, transportation networks, to explore existing social relationships as well as predict poten- and academic networks. Due to the principle of ternary closures tial relationships. These abundant relations generally exist among and the trend of group formation, the multivariate relationships in multiple entities; thus, these relations are also called multivariate social networks are complex and rich. Therefore, in graph learn- relations. Multivariate relations are the most fundamental rela- ing tasks of social networks, the identification and utilization of tions, containing interpersonal relations, public relations, logical multivariate relationship information are more important. Existing relations, social relations, etc [3, 37]. Multivariate relations are of graph learning methods are based on the neighborhood informa- more complicated structures comparing with binary relations. Such tion diffusion mechanism, which often leads to partial omission or higher-order structures contain more information to express inner even lack of multivariate relationship information, and ultimately relations among multiple entities. -
Extraction and Analysis of Facebook Friendship Relations
Chapter 12 Extraction and Analysis of Facebook Friendship Relations Salvatore Catanese, Pasquale De Meo, Emilio Ferrara, Giacomo Fiumara, and Alessandro Provetti Abstract Online social networks (OSNs) are a unique web and social phenomenon, affecting tastes and behaviors of their users and helping them to maintain/create friendships. It is interesting to analyze the growth and evolution of online social networks both from the point of view of marketing and offer of new services and from a scientific viewpoint, since their structure and evolution may share similarities with real-life social networks. In social sciences, several techniques for analyzing (off-line) social networks have been developed, to evaluate quantitative properties (e.g., defining metrics and measures of structural characteristics of the networks) or qualitative aspects (e.g., studying the attachment model for the network evolution, the binary trust relationships, and the link prediction problem). However, OSN analysis poses novel challenges both to computer and Social scientists. We present our long-term research effort in analyzing Facebook, the largest and arguably most successful OSN today: it gathers more than 500 million users. Access to data about Facebook users and their friendship relations is restricted; thus, we acquired the necessary information directly from the front end of the website, in order to reconstruct a subgraph representing anonymous interconnections among a significant subset of users. We describe our ad hoc, privacy-compliant crawler for Facebook data extraction. To minimize bias, we adopt two different graph mining techniques: breadth-first-search (BFS) and rejection sampling. To analyze the structural properties of samples consisting of millions of nodes, we developed a S.Catanese•P.DeMeo•G.Fiumara Department of Physics, Informatics Section. -
The Perceived Assortativity of Social Networks: Methodological Problems and Solutions
The perceived assortativity of social networks: Methodological problems and solutions David N. Fisher1, Matthew J. Silk2 and Daniel W. Franks3 Abstract Networks describe a range of social, biological and technical phenomena. An important property of a network is its degree correlation or assortativity, describing how nodes in the network associate based on their number of connections. Social networks are typically thought to be distinct from other networks in being assortative (possessing positive degree correlations); well-connected individuals associate with other well-connected individuals, and poorly-connected individuals associate with each other. We review the evidence for this in the literature and find that, while social networks are more assortative than non-social networks, only when they are built using group-based methods do they tend to be positively assortative. Non-social networks tend to be disassortative. We go on to show that connecting individuals due to shared membership of a group, a commonly used method, biases towards assortativity unless a large enough number of censuses of the network are taken. We present a number of solutions to overcoming this bias by drawing on advances in sociological and biological fields. Adoption of these methods across all fields can greatly enhance our understanding of social networks and networks in general. 1 1. Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada. Email: [email protected] (primary corresponding author) 2. Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, TR10 9FE, UK Email: [email protected] 3. Department of Biology & Department of Computer Science, University of York, York, YO10 5DD, UK Email: [email protected] Keywords: Assortativity; Degree assortativity; Degree correlation; Null models; Social networks Introduction Network theory is a useful tool that can help us explain a range of social, biological and technical phenomena (Pastor-Satorras et al 2001; Girvan and Newman 2002; Krause et al 2007). -
Social Network Analysis: Homophily
Social Network Analysis: homophily Donglei Du ([email protected]) Faculty of Business Administration, University of New Brunswick, NB Canada Fredericton E3B 9Y2 Donglei Du (UNB) Social Network Analysis 1 / 41 Table of contents 1 Homophily the Schelling model 2 Test of Homophily 3 Mechanisms Underlying Homophily: Selection and Social Influence 4 Affiliation Networks and link formation Affiliation Networks Three types of link formation in social affiliation Network 5 Empirical evidence Triadic closure: Empirical evidence Focal Closure: empirical evidence Membership closure: empirical evidence (Backstrom et al., 2006; Crandall et al., 2008) Quantifying the Interplay Between Selection and Social Influence: empirical evidence—a case study 6 Appendix A: Assortative mixing in general Quantify assortative mixing Donglei Du (UNB) Social Network Analysis 2 / 41 Homophily: introduction The material is adopted from Chapter 4 of (Easley and Kleinberg, 2010). "love of the same"; "birds of a feather flock together" At the aggregate level, links in a social network tend to connect people who are similar to one another in dimensions like Immutable characteristics: racial and ethnic groups; ages; etc. Mutable characteristics: places living, occupations, levels of affluence, and interests, beliefs, and opinions; etc. A.k.a., assortative mixing Donglei Du (UNB) Social Network Analysis 4 / 41 Homophily at action: racial segregation Figure: Credit: (Easley and Kleinberg, 2010) Donglei Du (UNB) Social Network Analysis 5 / 41 Homophily at action: racial segregation Credit: (Easley and Kleinberg, 2010) Figure: Credit: (Easley and Kleinberg, 2010) Donglei Du (UNB) Social Network Analysis 6 / 41 Homophily: the Schelling model Thomas Crombie Schelling (born 14 April 1921): An American economist, and Professor of foreign affairs, national security, nuclear strategy, and arms control at the School of Public Policy at University of Maryland, College Park. -
Motif Aware Node Representation Learning for Heterogeneous Networks
motif2vec: Motif Aware Node Representation Learning for Heterogeneous Networks Manoj Reddy Dareddy* Mahashweta Das Hao Yang University of California, Los Angeles Visa Research Visa Research Los Angeles, CA, USA Palo Alto, CA, USA Palo Alto, CA, USA [email protected] [email protected] [email protected] Abstract—Recent years have witnessed a surge of interest in is originally sequential in nature [35], product review graph machine learning on graphs and networks with applications constructed from reviews written by users for stores [34], ranging from vehicular network design to IoT traffic manage- credit card fraud network constructed from fraudulent and non- ment to social network recommendations. Supervised machine learning tasks in networks such as node classification and link fraudulent transaction activity data [33], etc. prediction require us to perform feature engineering that is Supervised machine learning tasks over nodes and links known and agreed to be the key to success in applied machine in networks1 such as node classification and link prediction learning. Research efforts dedicated to representation learning, require us to perform feature engineering that is known and especially representation learning using deep learning, has shown agreed to be the key to success in applied machine learning. us ways to automatically learn relevant features from vast amounts of potentially noisy, raw data. However, most of the However, feature engineering is challenging and tedious since methods are not adequate to handle heterogeneous information -
GAMARALLAGE-THESIS-2020.Pdf
c 2020 Anuththari Gamarallage NETWORK MOTIF PREDICTION USING GENERATIVE MODELS FOR GRAPHS BY ANUTHTHARI GAMARALLAGE THESIS Submitted in partial fulfillment of the requirements for the degree of Master of Science in Electrical and Computer Engineering in the Graduate College of the University of Illinois at Urbana-Champaign, 2020 Urbana, Illinois Adviser: Professor Olgica Milenkovic ABSTRACT Graphs are commonly used to represent pairwise interactions between dif- ferent entities in networks. Generative graph models create new graphs that mimic the properties of already existing graphs. Generative models are suc- cessful at retaining the pairwise interactions of the underlying networks but often fail to capture higher-order connectivity patterns between more than two entities. A network motif is one such pattern observed in various real- world networks. Different types of graphs contain different network motifs, an example of which are triangles that often arise in social and biological net- works. Motifs model important functional properties of the graph. Hence, it is vital to capture these higher-order structures to simulate real-world net- works accurately. This thesis introduces a motif-targeted graph generative model based on a generative adversarial network (GAN) architecture that generalizes and outperforms the current benchmark approach, NetGAN, at motif prediction. This model and its extension to hypergraphs are tested on real-world social and biological network data, and they are shown to be better at both capturing the underlying motif statistics in the networks as well as predicting missing motifs in incomplete networks. ii ACKNOWLEDGMENTS The work was supported by the NSF Center for Science of Information under grant number 0939370.