Visual Analytics for Multimodal Social Network Analysis: a Design Study with Social Scientists
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Simplified Computational Model for Generating Bio- Logical Networks
Simplified Computational Model for Generating Bio- logical Networks† Matthew H J Bailey,∗ David Ormrod Morley,∗ and Mark Wilson∗ A method to generate and simulate biological networks is discussed. An expanded Wooten- Winer-Weaire bond switching methods is proposed which allows for a distribution of node degrees in the network while conserving the mean average node degree. The networks are characterised in terms of their polygon structure and assortativities (a measure of local ordering). A wide range of experimental images are analysed and the underlying networks quantified in an analogous manner. Limitations in obtaining the network structure are discussed. A “network landscape” of the experimentally observed and simulated networks is constructed from the underlying metrics. The enhanced bond switching algorithm is able to generate networks spanning the full range of experimental observations. Two dimensional random networks are observed in a range of 17 contexts across considerably different length scales in nature: to be limited to avoid damaging the delicate networks . How- from nanometres, in the form of amorphous graphene; to me- ever, even when a high-quality image is obtained, there is further tres, in the form of the Giant’s causeway; to tens of kilometres, in difficulty in analysis. For example, each edge in a network is a the form of geopolitical borders 1–3. A framework for describing complex molecule made up of tens of thousands of atoms which these continuous random networks for chemical systems was first may not lie strictly in a single plane. In addition, the most inter- introduced by Zachariasen to describe silica-like glasses, and has esting dynamic behaviour often occurs over very long timescales proved to be extremely versatile in the years since 4, being used to – potentially decades. -
Biological Network Approaches and Applications in Rare Disease Studies
G C A T T A C G G C A T genes Review Biological Network Approaches and Applications in Rare Disease Studies Peng Zhang 1,* and Yuval Itan 2,3 1 St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA 2 The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; [email protected] 3 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA * Correspondence: [email protected]; Tel.: +1-646-830-6622 Received: 3 September 2019; Accepted: 10 October 2019; Published: 12 October 2019 Abstract: Network biology has the capability to integrate, represent, interpret, and model complex biological systems by collectively accommodating biological omics data, biological interactions and associations, graph theory, statistical measures, and visualizations. Biological networks have recently been shown to be very useful for studies that decipher biological mechanisms and disease etiologies and for studies that predict therapeutic responses, at both the molecular and system levels. In this review, we briefly summarize the general framework of biological network studies, including data resources, network construction methods, statistical measures, network topological properties, and visualization tools. We also introduce several recent biological network applications and methods for the studies of rare diseases. Keywords: biological network; bioinformatics; database; software; application; rare diseases 1. Introduction Network biology provides insights into complex biological systems and can reveal informative patterns within these systems through the integration of biological omics data (e.g., genome, transcriptome, proteome, and metabolome) and biological interactome data (e.g., protein-protein interactions and gene-gene associations). -
Evolution Leads to Emergence: an Analysis of Protein
bioRxiv preprint doi: https://doi.org/10.1101/2020.05.03.074419; this version posted May 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 2 3 Evolution leads to emergence: An analysis of protein interactomes 4 across the tree of life 5 6 7 8 Erik Hoel1*, Brennan Klein2,3, Anshuman Swain4, Ross Grebenow5, Michael Levin1 9 10 1 Allen Discovery Center at Tufts University, Medford, MA, USA 11 2 Network Science Institute, Northeastern University, Boston, MA, USA 12 3 Laboratory for the Modeling of Biological & Sociotechnical Systems, Northeastern University, 13 Boston, USA 14 4 Department of Biology, University of Maryland, College Park, MD, USA 15 5 Drexel University, Philadelphia, PA, USA 16 17 * Author for Correspondence: 18 200 Boston Ave., Suite 4600 19 Medford, MA 02155 20 e-mail: [email protected] 21 22 Running title: Evolution leads to higher scales 23 24 Keywords: emergence, information, networks, protein, interactomes, evolution 25 26 27 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.03.074419; this version posted May 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 2 28 Abstract 29 30 The internal workings of biological systems are notoriously difficult to understand. -
(2020) Small Worlds and Clustering in Spatial Networks
PHYSICAL REVIEW RESEARCH 2, 023040 (2020) Small worlds and clustering in spatial networks Marián Boguñá ,1,2,* Dmitri Krioukov,3,4,† Pedro Almagro ,1,2 and M. Ángeles Serrano1,2,5,‡ 1Departament de Física de la Matèria Condensada, Universitat de Barcelona, Martí i Franquès 1, E-08028 Barcelona, Spain 2Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, Barcelona, Spain 3Network Science Institute, Northeastern University, 177 Huntington avenue, Boston, Massachusetts 022115, USA 4Department of Physics, Department of Mathematics, Department of Electrical & Computer Engineering, Northeastern University, 110 Forsyth Street, 111 Dana Research Center, Boston, Massachusetts 02115, USA 5Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, E-08010 Barcelona, Spain (Received 20 August 2019; accepted 12 March 2020; published 14 April 2020) Networks with underlying metric spaces attract increasing research attention in network science, statistical physics, applied mathematics, computer science, sociology, and other fields. This attention is further amplified by the current surge of activity in graph embedding. In the vast realm of spatial network models, only a few repro- duce even the most basic properties of real-world networks. Here, we focus on three such properties—sparsity, small worldness, and clustering—and identify the general subclass of spatial homogeneous and heterogeneous network models that are sparse small worlds and that have nonzero clustering in the thermodynamic -
Denoising Large-Scale Biological Data Using Network Filters
Kavran and Clauset BMC Bioinformatics (2021) 22:157 https://doi.org/10.1186/s12859‑021‑04075‑x RESEARCH ARTICLE Open Access Denoising large‑scale biological data using network flters Andrew J. Kavran1,2 and Aaron Clauset2,3,4* *Correspondence: [email protected] Abstract 2 BioFrontiers Institute, Background: Large-scale biological data sets are often contaminated by noise, which University of Colorado, Boulder, CO, USA can impede accurate inferences about underlying processes. Such measurement Full list of author information noise can arise from endogenous biological factors like cell cycle and life history vari- is available at the end of the ation, and from exogenous technical factors like sample preparation and instrument article variation. Results: We describe a general method for automatically reducing noise in large- scale biological data sets. This method uses an interaction network to identify groups of correlated or anti-correlated measurements that can be combined or “fltered” to better recover an underlying biological signal. Similar to the process of denoising an image, a single network flter may be applied to an entire system, or the system may be frst decomposed into distinct modules and a diferent flter applied to each. Applied to synthetic data with known network structure and signal, network flters accurately reduce noise across a wide range of noise levels and structures. Applied to a machine learning task of predicting changes in human protein expression in healthy and cancer- ous tissues, network fltering prior to training increases accuracy up to 43% compared to using unfltered data. Conclusions: Network flters are a general way to denoise biological data and can account for both correlation and anti-correlation between diferent measurements. -
Modularity and Dynamics on Complex Networks
Modularity AND Dynamics ON CompleX Networks Cambridge Elements DOI: 10.xxxx/xxxxxxxx (do NOT change) First PUBLISHED online: MMM DD YYYY (do NOT change) Renaud Lambiotte University OF OxforD Michael T. Schaub RWTH Aachen University Abstract: CompleX NETWORKS ARE TYPICALLY NOT homogeneous, AS THEY TEND TO DISPLAY AN ARRAY OF STRUCTURES AT DIffERENT scales. A FEATURE THAT HAS ATTRACTED A LOT OF RESEARCH IS THEIR MODULAR ORganisation, i.e., NETWORKS MAY OFTEN BE CONSIDERED AS BEING COMPOSED OF CERTAIN BUILDING blocks, OR modules. IN THIS book, WE DISCUSS A NUMBER OF WAYS IN WHICH THIS IDEA OF MODULARITY CAN BE conceptualised, FOCUSING SPECIfiCALLY ON THE INTERPLAY BETWEEN MODULAR NETWORK STRUCTURE AND DYNAMICS TAKING PLACE ON A network. WE discuss, IN particular, HOW MODULAR STRUCTURE AND SYMMETRIES MAY IMPACT ON NETWORK DYNAMICS and, VICE versa, HOW OBSERVATIONS OF SUCH DYNAMICS MAY BE USED TO INFER THE MODULAR STRUCTURe. WE ALSO REVISIT SEVERAL OTHER NOTIONS OF MODULARITY THAT HAVE BEEN PROPOSED FOR COMPLEX NETWORKS AND SHOW HOW THESE CAN BE RELATED TO AND INTERPRETED FROM THE POINT OF VIEW OF DYNAMICAL PROCESSES ON networks. SeVERAL REFERENCES AND POINTERS FOR FURTHER DISCUSSION AND FUTURE WORK SHOULD INFORM PRACTITIONERS AND RESEARchers, AND MAY MOTIVATE FURTHER STUDIES IN THIS AREA AT THE CORE OF Network Science. KeYWORds: Network Science; modularity; dynamics; COMMUNITY detection; BLOCK models; NETWORK clustering; GRAPH PARTITIONS JEL CLASSIfications: A12, B34, C56, D78, E90 © Renaud Lambiotte, Michael T. Schaub, 2021 ISBNs: xxxxxxxxxxxxx(PB) -
Configuration Models As an Urn Problem
Conguration Models as an Urn Problem: The Generalized Hypergeometric Ensemble of Random Graphs Giona Casiraghi ( [email protected] ) ETH Zurich Vahan Nanumyan ETH Zurich Research Article Keywords: fundamental issue of network data science, Monte-Carlo simulations, closed-form probability distribution Posted Date: March 5th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-254843/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Configuration models as an urn problem: the generalized hypergeometric ensemble of random graphs Giona Casiraghi1,* and Vahan Nanumyan1 1Chair of Systems Design, ETH Zurich,¨ Zurich,¨ 8092, Switzerland *[email protected] ABSTRACT A fundamental issue of network data science is the ability to discern observed features that can be expected at random from those beyond such expectations. Configuration models play a crucial role there, allowing us to compare observations against degree-corrected null-models. Nonetheless, existing formulations have limited large-scale data analysis applications either because they require expensive Monte-Carlo simulations or lack the required flexibility to model real-world systems. With the generalized hypergeometric ensemble, we address both problems. To achieve this, we map the configuration model to an urn problem, where edges are represented as balls in an appropriately constructed urn. Doing so, we obtain a random graph model reproducing and extending the properties of standard configuration models, with the critical advantage of a closed-form probability distribution. Introduction Essential features of complex systems are inferred by studying the deviations of empirical observations from suitable stochastic models. Network models, in particular, have become the state of the art for complex systems analysis, where systems’ constituents are represented as vertices, and their interactions are viewed as edges and modelled by means of edge probabilities in a random graph. -
Hyperbolic Graph Generator✩
Computer Physics Communications ( ) – Contents lists available at ScienceDirect Computer Physics Communications journal homepage: www.elsevier.com/locate/cpc Hyperbolic graph generatorI Rodrigo Aldecoa a,∗, Chiara Orsini b, Dmitri Krioukov a,c a Northeastern University, Department of Physics, Boston, MA, USA b Center for Applied Internet Data Analysis, University of California San Diego (CAIDA/UCSD), San Diego, CA, USA c Northeastern University, Department of Mathematics, Department of Electrical & Computer Engineering, Boston, MA, USA article info a b s t r a c t Article history: Networks representing many complex systems in nature and society share some common structural Received 23 March 2015 properties like heterogeneous degree distributions and strong clustering. Recent research on network Accepted 28 May 2015 geometry has shown that those real networks can be adequately modeled as random geometric graphs in Available online xxxx hyperbolic spaces. In this paper, we present a computer program to generate such graphs. Besides real- world-like networks, the program can generate random graphs from other well-known graph ensembles, Keywords: such as the soft configuration model, random geometric graphs on a circle, or Erdős–Rényi random Complex networks graphs. The simulations show a good match between the expected values of different network structural Network geometry Graph theory properties and the corresponding empirical values measured in generated graphs, confirming the accurate Hyperbolic graphs behavior of the program. Program summary Program title: Hyperbolic graph generator Catalogue identifier: AEXC_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEXC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. -
Introduction to Graph Theory
Introduction to Graph Theory Proteomes Interactomes and Biological Networks Department of Pharmacy and Emidio Capriotti Biotechnology (FaBiT) http://biofold.org/ University of Bologna Historical Perspective With the Seven Bridges of Königsberg problem, Euler in 1737 laid the foundations of the graph theory. Simon Kneebone – simonkneebone.com • Find path (Eulerian Path) that traverses all the Pregel’s bridges. • Find walk (Eulerian Circuit) that traverses all the Pregel’s bridges and has the same starting and ending point. Solution Describe the problem as a graph where the nodes represent the 4 locations and the edges correspond to the bridges Northern Bank Island 1 Island 2 Southern Bank Eulerian path exists only if zero or 2 nodes are connected by an odd number of bridges. Eulerian circuit exists only if zero nodes are connected by an odd number of bridges. Graph Definition A graph is a pair G=(V,E) consisting of two sets: • V is a set of elements called Nodes or Vertices. • E is a set of pairs (vi,vj) where vi∊V and vj∊V. The pairs E are links between two nodes and are called Edges A V = {A; B; C; D} B C E = {(A,B); (A,C); (B,C); (B,D); (C,D)} D Undirected Graph Undirected graph is a network where the relationship between nodes are symmetric. D V = {Group of People} A B C E E = {Pairs of Friends} F Directed Graph Directed graph is a network where the relationship between nodes are asymmetric. In this case the edges are directed lines. B C V = {Group of Animals} A D E E = {Pray/Predator Relationships} F G Signed Directed Graph Signed Directed graph is a network where the relationship between nodes are asymmetric and have positive or negative associated signs RecKinase RecCAMP_act RecCAMP_de Galpha_bnd Galpha_act_bnd + − C E − V = {Group of Genes} A B + E = {Activation/Inhibition Relationships} D Graph and Networks Graphs can be used to represent any observed network. -
An Integrative Approach to Modeling Biological Networks 1 Introduction
Journal of Integrative Bioinformatics, 7(3):120, 2010 http://journal.imbio.de An integrative approach to modeling biological networks Vesna Memisevˇ ic´ 1, Tijana Milenkovic´ 1, and Natasaˇ Prˇzulj2,∗ 1Department of Computer Science, University of California, Irvine, CA 92697-3435, USA 2Department of Computing, Imperial College London, London, SW7 2AZ, UK ∗Corresponding author (e-mail: [email protected]) Summary Networks are used to model real-world phenomena in various domains, including systems biology. Since proteins carry out biological processes by interacting with other proteins, it is expected that cellular functions are reflected in the structure of protein-protein inter- action (PPI) networks. Similarly, the topology of residue interaction graphs (RIGs) that model proteins’ 3-dimensional structure might provide insights into protein folding, sta- bility, and function. An important step towards understanding these networks is finding an adequate network model, since models can be exploited algorithmically as well as used for predicting missing data. Evaluating the fit of a model network to the data is a formidable challenge, since network comparisons are computationally infeasible and thus have to rely on heuristics, or “network properties.” We show that it is difficult to assess the reliability of the fit of a model using any network property alone. Thus, we present an integrative approach that feeds a variety of network properties into five machine learning classifiers to predict the best-fitting network model for PPI networks and RIGs. We confirm that ge- ometric random graphs (GEO) are the best-fitting model for RIGs. Since GEO networks model spatial relationships between objects and are thus expected to replicate well the un- derlying structure of spatially packed residues in a protein, the good fit of GEO to RIGs validates our approach. -
Communities and Homology in Protein-Protein Interactions
Communities and Homology in Protein-protein Interactions Anna Lewis Balliol College University of Oxford A thesis submitted for the degree of Doctor of Philosophy Michaelmas 2011 2 3 This thesis is dedicated to the inspirational Jen Weterings. Wishing her well in her ongoing recovery. Acknowledgements With thanks to Charlotte, Nick and Mason, for being the best supervisors a girl could ask for. With thanks to all those who have helped me with the work in this thesis. In particular Sumeet Agarwal, Rebecca Hamer, Gesine Reinert, James Wakefield, Simon Myers, Steve Kelly, Nicholas Lewis, members of the Oxford Protein Informatics Group and members of the Oxford/Imperial Systems and Signalling group. With thanks to all those who have made my DPhil years a wonderful experience, in particular my family, my Balliol family, and my DTC family. Abstract Knowledge of protein sequences has exploded, but knowledge of protein function is needed to make use of sequence information, and this lags behind. A protein’s function must be understood in context and part of this is the network of interactions between proteins. What are the relationships between protein function and the structure of the interaction network? In the first part of my thesis, I investigate the functional relevance of clusters, or communities, of proteins in the yeast protein interaction network. Communities are candidates for biological modules. The work I present is the first to systematically investigate this structure at multiple scales in such networks. I develop novel tests to assess whether communities are functionally homogeneous, and demonstrate that almost every protein is found in a functionally homogeneous community at some scale. -
Local Community Detection in Complex Networks Based on Maximum Cliques Extension
Hindawi Publishing Corporation Mathematical Problems in Engineering Volume 2014, Article ID 653670, 12 pages http://dx.doi.org/10.1155/2014/653670 Research Article Local Community Detection in Complex Networks Based on Maximum Cliques Extension Meng Fanrong, Zhu Mu, Zhou Yong, and Zhou Ranran School of Computer Science and Technology, China University of Mining and Technology, Xuzhou 221116, China Correspondence should be addressed to Zhu Mu; [email protected] Received 6 January 2014; Accepted 25 February 2014; Published 15 April 2014 Academic Editor: Guanghui Wen Copyright © 2014 Meng Fanrong et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Detecting local community structure in complex networks is an appealing problem that has attracted increasing attention in various domains. However, most of the current local community detection algorithms, on one hand, are influenced by the state of the source node and, on the other hand, cannot effectively identify the multiple communities linked with the overlapping nodes. We proposed a novel local community detection algorithm based on maximum clique extension called LCD-MC. The proposed method firstly finds the set of all the maximum cliques containing the source node and initializes them as the starting local communities; then, it extends each unclassified local community by greedy optimization until a certain objective is satisfied; finally, the expected local communities will be obtained until all maximum cliques are assigned into a community. An empirical evaluation using both synthetic and real datasets demonstrates that our algorithm has a superior performance to some of the state-of-the-art approaches.