Curriculum Vitae Dmitri Krioukov
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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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 -
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. -
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Arxiv:2004.14879V1 [Physics.Soc-Ph] 30 Apr 2020
Effectiveness of dismantling strategies on moderated vs. unmoderated online social platforms Oriol Artime1, Valeria D'Andrea1, Riccardo Gallotti1, Pier Luigi Sacco2;3;4, Manlio De Domenico1 1CoMuNe Lab, Fondazione Bruno Kessler, Via Sommarive 18, 38123 Povo (TN), Italy. 2Fondazione Bruno Kessler, Via Santa Croce, 77, 38122 Trento, Italy. 3IULM University, Via Carlo Bo, 1, 20143 Milan, Italy. 4Berkman-Klein Center for Internet & Society, Harvard University, 23 Everett St # 2, Cambridge MA 02138 USA. May 1, 2020 Abstract Online social networks are the perfect test bed to better understand large-scale human behavior in interacting contexts. Although they are broadly used and studied, little is known about how their terms of service and posting rules affect the way users interact and information spreads. Acknowledging the relation between network connectivity and functionality, we compare the robustness of two different online social platforms, Twitter and Gab, with respect to dismantling strategies based on the recursive censor of users characterized by social prominence (degree) or intensity of inflammatory content (sentiment). We find that the moderated (Twitter) vs un-moderated (Gab) character of the network is not a discriminating factor for intervention effectiveness. We find, however, that more complex strategies based upon the combination of topological and content features may be effective for network dismantling. Our results provide useful indications to design better strategies for countervailing the production and dissemination of anti-social content in online social platforms. 1 Introduction Online social networks provide a rich laboratory for the analysis of large-scale social interaction and of their social effects [1, 2, 3, 4]. They facilitate the inclusive engagement of new actors by removing most barriers to participate in content-sharing platforms characteristic of the pre-digital era [5]. -
Visual Analytics for Multimodal Social Network Analysis: a Design Study with Social Scientists
Visual Analytics for Multimodal Social Network Analysis: A Design Study with Social Scientists Sohaib Ghani, Student member, IEEE, Bum chul Kwon, Student member, IEEE, Seungyoon Lee, Ji Soo Yi, Member, IEEE, and Niklas Elmqvist, Senior member, IEEE Fig. 1. Four design sketches for visualizing multimodal social networks, evolved through discussion between social network experts and visual analytics experts. Early designs (top two) focus on splitting node-link diagrams into separate spaces, whereas the latter (bottom left) use vertical bands while maintaining compatibility with node-link diagrams (bottom right). Abstract—Social network analysis (SNA) is becoming increasingly concerned not only with actors and their relations, but also with distinguishing between different types of such entities. For example, social scientists may want to investigate asymmetric relations in organizations with strict chains of command, or incorporate non-actors such as conferences and projects when analyzing co- authorship patterns. Multimodal social networks are those where actors and relations belong to different types, or modes, and multimodal social network analysis (mSNA) is accordingly SNA for such networks. In this paper, we present a design study that we conducted with several social scientist collaborators on how to support mSNA using visual analytics tools. Based on an open- ended, formative design process, we devised a visual representation called parallel node-link bands (PNLBs) that splits modes into separate bands and renders connections between adjacent ones, similar to the list view in Jigsaw. We then used the tool in a qualitative evaluation involving five social scientists whose feedback informed a second design phase that incorporated additional network metrics. -
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. -
Multiplex Network Regression: How Do Relations Drive Interactions? (Submitted for Publication: 10 July 2020)
G. Casiraghi: Multiplex Network Regression: How do relations drive interactions? (Submitted for publication: 10 July 2020) Multiplex Network Regression: How do relations drive interactions? Giona Casiraghi∗ Chair of Systems Design, ETH Zürich, Weinbergstrasse 56/58, 8092 Zürich, Switzerland. Abstract We introduce a statistical regression model to investigate the impact of dyadic relations on complex networks generated from observed repeated interactions. It is based on generalised hypergeometric ensembles (gHypEG), a class of statistical network ensembles developed re- cently to deal with multi-edge graph and count data. We represent different types of known relations between system elements by weighted graphs, separated in the different layers of a multiplex network. With our method, we can regress the influence of each relational layer, the explanatory variables, on the interaction counts, the dependent variables. Moreover, we can quantify the statistical significance of the relations as explanatory variables for the ob- served interactions. To demonstrate the power of our approach, we investigate an example based on empirical data. 1 Introduction In the study of real-world complex systems, we often deal with datasets of observed repeated interactions between individuals. These datasets are used to generate networks where system’s elements are represented by vertices and interactions by edges. We ask whether these interactions are random events or whether they are driven by existing relations between system’s elements. To answer this question, we propose a statistical model to regress relations, which we identify as covariate variables, on a network created from interactions, which we will refer to as our dependent variables. In general, a regression model explains dependent variables as a function of some covariates, accounting for random effects. -
Random Simplicial Complexes: Models and Phenomena
Random Simplicial Complexes: Models and Phenomena Omer Bobrowski and Dmitri Krioukov Abstract We review a collection of models of random simplicial complexes to- gether with some of the most exciting phenomena related to them. We do not attempt to cover all existing models, but try to focus on those for which many important results have been recently established rigorously in mathematics, especially in the context of algebraic topology. In ap- plication to real-world systems, the reviewed models are typically used as null models, so that we take a statistical stance, emphasizing, where applicable, the entropic properties of the reviewed models. We also re- view a collection of phenomena and features observed in these models, and split the presented results into two classes: phase transitions and distributional limits. We conclude with an outline of interesting future research directions. 1 Introduction Simplicial complexes serve as a powerful tool in algebraic topology, a field of mathematics fathered by Poincar´eat the end of the 19th century. This tool was built|or discovered, depending on one's philosophical view|by topologists in order to study topology. Much more recently, over the past decade or so, this tool was also discovered by network and data scientists who study complex real- world systems in which interactions are not necessarily diadic. The complexity of interactions in these systems is amplified by their stochasticity, making them difficult or impossible to predict, and suggesting that these intricate systems should be modeled by random objects. In other words, the combination of stochasticity and high-order interactions in real-world complex systems suggests arXiv:2105.12914v1 [math.PR] 27 May 2021 that models of random simplicial complexes may be useful models of these systems. -
Random Hyperbolic Graphs in D + 1 Dimensions
Random hyperbolic graphs in d + 1 dimensions Maksim Kitsak,1, 2, 3 Rodrigo Aldecoa,2, 3 Konstantin Zuev,4 and Dmitri Krioukov5, 3 1Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2628 CD, Delft, Netherlands 2Department of Physics, Northeastern University, 110 Forsyth Street, 111 Dana Research Center, Boston, MA 02115, USA. 3Network Science Institute, Northeastern University, 177 Huntington avenue, Boston, MA, 022115 4Department of Computing and Mathematical Sciences, California Institute of Technology, 1200 E. California Blvd. Pasadena, CA, 91125, USA 5Department of Physics, Department of Mathematics, Department of Electrical&Computer Engineering, Northeastern University, 110 Forsyth Street, 111 Dana Research Center, Boston, MA 02115, USA. (Dated: October 23, 2020) We generalize random hyperbolic graphs to arbitrary dimensionality. We find the rescaling of network parameters that allows to reduce random hyperbolic graphs of arbitrary dimensionality to a single mathematical framework. Our results indicate that RHGs exhibit similar topological properties, regardless of the dimensionality of their latent hyperbolic spaces. I. INTRODUCTION The spherical coordinate system on the hyperboloid (r; θ1; :::; θd) is defined by Random hyperbolic graphs (RHGs) have been intro- 1 duced as latent space models, where nodes correspond to x0 = cosh ζr; 2 ζ points in the 2-dimensional hyperboloid H and connec- 1 tions between the nodes are established with distance- x = sinh ζr cos θ ; dependent probabilities [1,2]. RHGs have been shown 1 ζ 1 to accurately model structural properties of real net- 1 x = sinh ζr sin θ cos θ ; (3) works including sparsity, self-similarity, scale-free de- 2 ζ 1 2 gree distribution, strong clustering, the small-world prop- :: erty, and community structure [2{6]. -
Network Science Introduction
1 ALBERT-LÁSZLÓ BARABÁSI NETWORK SCIENCE INTRODUCTION ACKNOWLEDGEMENTS MÁRTON PÓSFAI PHILIPP HOEVEL GABRIELE MUSELLA SARAH MORRISON MAURO MARTINO AMAL HUSSEINI ROBERTA SINATRA INDEX Vulnerability Due to Interconnectivity 1 Networks at the Heart of Complex Systems 2 Two Forces Helped the Emergence of Network Science 3 The Characteristics of Network Science 4 Societal Impact 5 Scientific Impact 6 Summary 7 Homework 8 Bibliography 9 Figure 1.0 (front cover) Mark Lombardi: Global International Airway and Indian Spring State Bank Mark Lombardi (1951 – 2000) was an Amer- ican artist who documented “the uses and abuses of power.” His work was preceded by careful research, resulting in thousands of in- dex cards, whose number began to overwhelm his ability to deal with them. Hence Lombardi began assembling them into hand-drawn dia- grams, intended to focus his work. Eventually these diagrams became a form of art on their own [1]. The image shows one such drawing, created between 1977 and 1983 in colored pen- cil and graphite on paper. This work is licensed under a Creative Commons: CC BY-NC-SA 2.0. PDF V26, 03.09.2014 SECTION 1.1 VULNERABILITY DUE TO INTERCONNECTIVITY At a first glance the two satellite images of Figure 1.1 are indistinguish- (a) able, showing lights shining brightly in highly populated areas and dark spaces that mark vast uninhabited forests and oceans. Yet, upon closer in- spection we notice differences: Toronto, Detroit, Cleveland, Columbus and Long Island, bright and shining in (a), have have gone dark in (b). This is not a doctored shot from the next Armageddon movie but represents a real im- age of the US Northeast on August 14, 2003, before and after the blackout that left without power an estimated 45 million people in eight US states and another 10 million in Ontario.