Improving the Betweenness Centrality of a Node by Adding Links
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Approximating Network Centrality Measures Using Node Embedding and Machine Learning
Approximating Network Centrality Measures Using Node Embedding and Machine Learning Matheus R. F. Mendon¸ca,Andr´eM. S. Barreto, and Artur Ziviani ∗† Abstract Extracting information from real-world large networks is a key challenge nowadays. For instance, computing a node centrality may become unfeasible depending on the intended centrality due to its computational cost. One solution is to develop fast methods capable of approximating network centralities. Here, we propose an approach for efficiently approximating node centralities for large networks using Neural Networks and Graph Embedding techniques. Our proposed model, entitled Network Centrality Approximation using Graph Embedding (NCA-GE), uses the adjacency matrix of a graph and a set of features for each node (here, we use only the degree) as input and computes the approximate desired centrality rank for every node. NCA-GE has a time complexity of O(jEj), E being the set of edges of a graph, making it suitable for large networks. NCA-GE also trains pretty fast, requiring only a set of a thousand small synthetic scale-free graphs (ranging from 100 to 1000 nodes each), and it works well for different node centralities, network sizes, and topologies. Finally, we compare our approach to the state-of-the-art method that approximates centrality ranks using the degree and eigenvector centralities as input, where we show that the NCA-GE outperforms the former in a variety of scenarios. 1 Introduction Networks are present in several real-world applications spread among different disciplines, such as biology, mathematics, sociology, and computer science, just to name a few. Therefore, network analysis is a crucial tool for extracting relevant information. -
A Geometric Approach to Betweenness
A GEOMETRIC APPROACH TO BETWEENNESS y z BENNY CHOR AND MADHU SUDAN Abstract An input to the betweenness problem contains m constraints over n real variables p oints Each constraint consists of three p oints where one of the p oint is sp ecied to lie inside the interval dened by the other two The order of the other two p oints ie which one is the largest and which one is the smallest is not sp ecied This problem comes up in questions related to physical mapping in molecular biology In Opatrny showed that the problem of deciding whether the n p oints can b e totally ordered while satisfying the m b etweenness constraints is NPcomplete Furthermore the problem is MAX SNP complete and for every nding a total order that satises at least of the m constraints is NPhard even if all the constraints are satisable It is easy to nd an ordering of the p oints that satises of the m constraints eg by cho osing the ordering at random This pap er presents a p olynomial time algorithm that either determines that there is no feasible solution or nds a total order that satises at least of the m constraints The algorithm translates the problem into a set of quadratic inequalities and solves a semidenite relaxation of n them in R The n solution p oints are then pro jected on a random line through the origin The claimed p erformance guarantee is shown using simple geometric prop erties of the SDP solution Key words Approximation algorithm Semidenite programming NPcompleteness Compu tational biology AMS sub ject classications Q Q Intro duction An input -
Approximating Cumulative Pebbling Cost Is Unique Games Hard
Approximating Cumulative Pebbling Cost Is Unique Games Hard Jeremiah Blocki Department of Computer Science, Purdue University, West Lafayette, IN, USA https://www.cs.purdue.edu/homes/jblocki [email protected] Seunghoon Lee Department of Computer Science, Purdue University, West Lafayette, IN, USA https://www.cs.purdue.edu/homes/lee2856 [email protected] Samson Zhou School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA https://samsonzhou.github.io/ [email protected] Abstract P The cumulative pebbling complexity of a directed acyclic graph G is defined as cc(G) = minP i |Pi|, where the minimum is taken over all legal (parallel) black pebblings of G and |Pi| denotes the number of pebbles on the graph during round i. Intuitively, cc(G) captures the amortized Space-Time complexity of pebbling m copies of G in parallel. The cumulative pebbling complexity of a graph G is of particular interest in the field of cryptography as cc(G) is tightly related to the amortized Area-Time complexity of the Data-Independent Memory-Hard Function (iMHF) fG,H [7] defined using a constant indegree directed acyclic graph (DAG) G and a random oracle H(·). A secure iMHF should have amortized Space-Time complexity as high as possible, e.g., to deter brute-force password attacker who wants to find x such that fG,H (x) = h. Thus, to analyze the (in)security of a candidate iMHF fG,H , it is crucial to estimate the value cc(G) but currently, upper and lower bounds for leading iMHF candidates differ by several orders of magnitude. Blocki and Zhou recently showed that it is NP-Hard to compute cc(G), but their techniques do not even rule out an efficient (1 + ε)-approximation algorithm for any constant ε > 0. -
Contextual Experience Modifies Functional Connectome Indices of Topological Strength and Organization
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.13.150060; this version posted June 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Contextual experience modifies functional connectome indices of topological strength and organization Marjory Pompilus1,2, Luis M. Colon-Perez4, Matteo M. Grudny1, **Marcelo Febo1,2,3 1 Department of Psychiatry, 2Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility, 3Evelyn F. and William L. McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, Florida; 4Center for the Neurobiology of Learning and Memory, Department of Neurobiology and Behavior, School of Medicine, University of California, Irvine, California Short title: Experience-dependent functional topology in rat brain **Corresponding author: Marcelo Febo, PhD P.O. Box 100256, Department of Psychiatry, College of Medicine, University of Florida, Gainesville, FL 32611 Email: [email protected]; Phone: +1 (352) 294 4911 Acknowledgments: Supported by National Institute on Drug Abuse grant R03 DA042971, R21 AG065819 and University of Florida College of Medicine Opportunity fund (DRPD-ROF2019) to MF. LMC-P was supported by a McKnight Brain Foundation postdoctoral fellowship and is supported by K25 DA047458 and a young investigator grant from the Brain and Behavior Research Foundation. The contents of this manuscript are solely the responsibility of the authors and do not necessarily represent the official views of the funding agencies. This work was performed in the McKnight Brain Institute at the National High Magnetic Field Laboratory’s AMRIS Facility, which is supported by National Science Foundation Cooperative Agreement No. -
Navigation of Brain Networks
Navigation of brain networks Caio Seguina,1, Martijn P. van den Heuvelb,c, and Andrew Zaleskya,d aMelbourne Neuropsychiatry Centre, The University of Melbourne and Melbourne Health, Melbourne, VIC 3010, Australia; bDutch Connectome Lab, Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands; cDepartment of Clinical Genetics, Amsterdam Neuroscience, VU University Medical Center, 1081 HV Amsterdam, The Netherlands; and dDepartment of Biomedical Engineering, Melbourne School of Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia Edited by Edward T. Bullmore, University of Cambridge, Cambridge, United Kingdom, and accepted by Editorial Board Member Michael S. Gazzaniga May 7, 2018 (received for review January 24, 2018) Understanding the mechanisms of neural communication in large- Navigation is a network communication strategy that routes scale brain networks remains a major goal in neuroscience. We information based on the distance between network nodes (23). investigated whether navigation is a parsimonious routing model Navigating a network is as simple as progressing to the next node for connectomics. Navigating a network involves progressing to that is closest in distance to a desired target. Navigation is not the next node that is closest in distance to a desired destina- guaranteed to successfully reach a target destination. Moreover, tion. We developed a measure to quantify navigation efficiency targets might be reached using long, inefficient paths. However, and found that connectomes in a range of mammalian species several real-world networks are known to be efficiently naviga- (human, mouse, and macaque) can be successfully navigated with ble, including biological, social, transportation, and technological near-optimal efficiency (>80% of optimal efficiency for typical systems (24–26). -
Communicability Betweenness in Complex Networks
Communicability Betweenness in Complex Networks Ernesto Estrada1,3*, Desmond J. Higham2 and Naomichi Hatano3 1 Institute of Complex Systems at Strathclyde, Department of Physics and Department of Mathematics, University of Strathclyde, Glasgow G1 1XH, UK 2Department of Mathematics, University of Strathclyde, Glasgow G1 1XH, UK 3Institute of Industrial Science, University of Tokyo, Komaba, Meguro, 153-8505, Japan PACS: 89.75.Fb; 89.75.Hc; 87.15.km; 02.10.Ox Keywords: centrality measures, protein-protein interactions, communicability, spectral graph theory, conserved proteins, linear response, Fréchet derivative * Corresponding author. E-mail: [email protected] 1 Abstract Betweenness measures provide quantitative tools to pick out fine details from the massive amount of interaction data that is available from large complex networks. They allow us to study the extent to which a node takes part when information is passed around the network. Nodes with high betweenness may be regarded as key players that have a highly active role. At one extreme, betweenness has been defined by considering information passing only through the shortest paths between pairs of nodes. At the other extreme, an alternative type of betweenness has been defined by considering all possible walks of any length. In this work, we propose a betweenness measure that lies between these two opposing viewpoints. We allow information to pass through all possible routes, but introduce a scaling so that longer walks carry less importance. This new definition shares a similar philosophy to that of communicability for pairs of nodes in a network, which was introduced by Estrada and Hatano (Phys. Rev. E 77 (2008) 036111). -
Node Centrality Measures Are a Poor Substitute for Causal Inference
Node Centrality Measures are a poor substitute for Causal Inference Fabian Dablander and Max Hinne Department of Psychological Methods, University of Amsterdam Abstract Network models have become a valuable tool in making sense of a diverse range of social, biological, and information systems. These models marry graph and probability theory to visualize, understand, and interpret variables and their relations as nodes and edges in a graph. Many applications of network models rely on undirected graphs in which the absence of an edge between two nodes encodes conditional independence between the corresponding variables. To gauge the importance of nodes in such a network, various node centrality measures have become widely used, especially in psychology and neuroscience. It is intuitive to interpret nodes with high centrality measures as being important in a causal sense. Here, using the causal framework based on directed acyclic graphs (DAGs), we show that the relation between causal influence and node centrality measures is not straightforward. In particular, the correlation between causal influence and several node centrality measures is weak, except for eigenvector centrality. Our results provide a cautionary tale: if the underlying real-world system can be modeled as a DAG, but researchers interpret nodes with high centrality as causally important, then this may result in sub-optimal interventions. 1 Introduction In the last two decades, network analysis has become increasingly popular across many disciplines dealing with a diverse range of social, biological, and information systems. From a network per- spective, variables and their interactions are considered nodes and edges in a graph. Throughout this paper, we illustrate the network paradigm with two areas where it has been applied exten- sively: psychology and neuroscience. -
Virtual Identification of Essential Proteins Within the Protein Interaction Network of Yeast
Virtual Identification of Essential Proteins Within the Protein Interaction Network of Yeast Ernesto Estrada Complex Systems Research Group, X-Ray Unit, RIAIDT, University of Santiago de Compostela, Edificio CACTUS, Campus Sur, Santiago de Compostela 15782, Spain. Tel. +34 981 563 100 Ext. 16262 Fax: +34 981 547 077 E-mail: estrada66ahoo.com Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has been observed to be correlated with its indispensability. Essential proteins generally have more interactions than the non-essential ones. We show here that the lethality associated with removal of a protein from the yeast proteome correlates with different centrality measures of the nodes in the PIN, such as the closeness of a protein to many other proteins, or the number of pairs of proteins which need a specific protein as an intermediary in their communications, or the participation of a protein in different protein clusters in the PIN. These measures are significantly better than random selection in identifying essential proteins in a PIN. Centrality measures based on graph spectral properties of the network, in particular the subgraph centrality, show the best performance in identifying essential proteins in the yeast PIN. Subgraph centrality gives important structural information about the role of individual proteins and permits the selection of possible targets for rational drug discovery through the identification of essential proteins in the PIN. 1 1 Introduction A recent explosion of research papers related to the structure of complex networks has led to important results related to the topological properties of biological networks [1]. -
Variations on an Ordering Theme with Constraints
Variations on an Ordering Theme with Constraints Walter Guttmann and Markus Maucher Fakult¨at fur¨ Informatik, Universit¨at Ulm, 89069 Ulm, Germany [email protected] · [email protected] Abstract. We investigate the problem of finding a total order of a finite set that satisfies various local ordering constraints. Depending on the admitted constraints, we provide an efficient algorithm or prove NP-completeness. We discuss several generalisations and systematically classify the problems. Key words: total ordering, NP-completeness, computational complex- ity, betweenness, cyclic ordering, topological sorting 1 Introduction An instance of the betweenness problem is given by a finite set A and a collection C of triples from A, with the task to decide if there is a total order < of A such that for each (a; b; c) 2 C, either a < b < c or c < b < a [1, problem MS1]. The betweenness problem is NP-complete [2]. Applications arise, for example, in the design of circuits and in computational biology [2, 3]. Similarly, the cyclic ordering problem asks for a total order < of A such that for each (a; b; c) 2 C, either a < b < c or b < c < a or c < a < b [1, prob- lem MS2]. The cyclic ordering problem, too, is NP-complete [4]. Applications arise, for example, in qualitative spatial reasoning [5]. On the other hand, if a < b < c or a < c < b is allowed, the problem can be solved with linear time complexity by topological sorting [6, Sect. 2.2.3]. Yet another choice, namely c < a or c < b, is needed to model an object- relational mapping problem described in Sect. -
Comparing the Speed and Accuracy of Approaches to Betweenness Centrality Approximation
Matta et al. Comput Soc Netw (2019) 6:2 https://doi.org/10.1186/s40649-019-0062-5 RESEARCH Open Access Comparing the speed and accuracy of approaches to betweenness centrality approximation John Matta1* , Gunes Ercal1 and Koushik Sinha2 *Correspondence: [email protected] Abstract 1 Southern Illinois University Background: Many algorithms require doing a large number of betweenness central- Edwardsville, Edwardsville, IL, USA ity calculations quickly, and accommodating this need is an active open research area. Full list of author information There are many diferent ideas and approaches to speeding up these calculations, and is available at the end of the it is difcult to know which approach will work best in practical situations. article Methods: The current study attempts to judge performance of betweenness central- ity approximation algorithms by running them under conditions that practitioners are likely to experience. For several approaches to approximation, we run two tests, clustering and immunization, on identical hardware, along with a process to determine appropriate parameters. This allows an across-the-board comparison of techniques based on the dimensions of speed and accuracy of results. Results: Overall, the speed of betweenness centrality can be reduced several orders of magnitude by using approximation algorithms. We fnd that the speeds of individual algorithms can vary widely based on input parameters. The fastest algorithms utilize parallelism, either in the form of multi-core processing or GPUs. Interestingly, getting fast results does not require an expensive GPU. Conclusions: The methodology presented here can guide the selection of a between- ness centrality approximation algorithm depending on a practitioner’s needs and can also be used to compare new methods to existing ones. -
Social Networking Analysis
Social Networking Analysis Kevin Curran and Niamh Curran Abstract A social network indicates relationships between people or organisations and how they are connected through social familiarities. The concept of social net- work provides a powerful model for social structure, and that a number of important formal methods of social network analysis can be perceived. Social network analysis can be used in studies of kinship structure, social mobility, science citations, con- tacts among members of nonstandard groups, corporate power, international trade exploitation, class structure and many other areas. A social network structure is made up of nodes and ties. There may be few or many nodes in the networks or one or more different types of relations between the nodes. Building a useful understanding of a social network is to sketch a pattern of social relationships, kinships, community structure, interlocking dictatorships and so forth for analysis. 1 Introduction Communication is and has always been vital to the growth and the development of human society. An individual’s attitudes opinions and behaviours can only be characterised in a group or community [5]. Social networking is not an exact science, it can be described as a means of discovering the method in which problems are solved, how individuals achieve goals and how businesses and operations are run. In network theory, social networks are discussed in terms of node and ties (see Fig. 1). Nodes are individual actors and ties are relationships within networks. The social capital of individual nodes/actors can be measured through social network diagrams, as can measures of determination of the usefulness of the network to the actors individually [4]. -
Measures of Centrality
Measures of centrality Measures of centrality Background Centrality Complex Networks measures Degree centrality CSYS/MATH 303, Spring, 2011 Closeness centrality Betweenness Eigenvalue centrality Hubs and Authorities Prof. Peter Dodds References Department of Mathematics & Statistics Center for Complex Systems Vermont Advanced Computing Center University of Vermont Licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License. 1 of 28 Measures of Outline centrality Background Centrality measures Degree centrality Closeness centrality Background Betweenness Eigenvalue centrality Hubs and Authorities References Centrality measures Degree centrality Closeness centrality Betweenness Eigenvalue centrality Hubs and Authorities References 2 of 28 Measures of How big is my node? centrality Background Centrality measures I Basic question: how ‘important’ are specific nodes Degree centrality Closeness centrality and edges in a network? Betweenness Eigenvalue centrality I An important node or edge might: Hubs and Authorities 1. handle a relatively large amount of the network’s References traffic (e.g., cars, information); 2. bridge two or more distinct groups (e.g., liason, interpreter); 3. be a source of important ideas, knowledge, or judgments (e.g., supreme court decisions, an employee who ‘knows where everything is’). I So how do we quantify such a slippery concept as importance? I We generate ad hoc, reasonable measures, and examine their utility... 3 of 28 Measures of Centrality centrality Background Centrality measures Degree centrality I One possible reflection of importance is centrality. Closeness centrality Betweenness I Presumption is that nodes or edges that are (in some Eigenvalue centrality Hubs and Authorities sense) in the middle of a network are important for References the network’s function.