lecture 3: describing network position and understanding assortative mixing © 2014 Aaron Clauset 003 052 002 001 Aaron Clauset @aaronclauset Assistant Professor of Computer Science University of Colorado Boulder External Faculty, Santa Fe Institute 051 Five Lectures on Networks Network Analysis and Modeling ! Instructor: Aaron Clauset ! http://santafe.edu/~aaronc/courses/5352/ 003 052 002 051 Full lectures notes online (~150 pages in PDF) 001 This graduate-level course will examine modern techniques for analyzing and modeling the structure and dynamics of complex networks. The focus will be on statistical algorithms and methods, and both lectures and assignments will emphasize model interpretability and understanding the processes that generate real data. Applications will be drawn from computational biology and computational social science. No biological or social science training is required. (Note: this is not a scientific computing course, but there will be plenty of computing for science.) Software Data sets R Python Matlab NetworkX [python] graph-tool [python, c++] GraphLab [python, c++] Mark Newman’s network data sets Stanford Network Analysis Project Carnegie Mellon CASOS data sets NCEAS food web data sets UCI NET data sets Pajek data sets Linkgroup’s list of network data sets Barabasi lab data sets Jake Hofman’s online network data sets Alex Arenas’s data sets 003 UCI-Net NodeXL Gephi Pajek Network Workbench Cytoscape yEd graph editor Graphviz 052 ! 002 Standalone editors 051 ! ! 001 ! 1. defining a network 2. describing a network 3. null models for networks 4. statistical inference describing networks position describing networks geometric position = centrality: measure of positional “importance” harmonic centrality closeness centrality betweenness centrality connectivity degree centrality eigenvector centrality PageRank Katz centrality many many more… Boldi & Vigna, arxiv:1308.2140 (2013) Borgatti, Social Networks 27, 55–71 (2005) describing networks position = centrality: harmonic, closeness centrality importance = being in “center” of the network harmonic ci = 1 n X 1 1 dij j6=i length of shortest path distance: dij = Boldi & Vigna, arxiv:1308.2140 (2013) Borgatti, Social Networks 27, 55–71 (2005) ⇢ `ij 1 if j reachable from i otherwise describing networks position = centrality: PageRank, Katz, eigenvector centrality importance = sum of importances* of nodes that point at you X Ij Ii = k j!i j or, the left eigenvector of Ax = Boldi & Vigna, arxiv:1308.2140 (2013) Borgatti, Social Networks 27, 55–71 (2005) x *modulo several technical details network position an example Giovanni de Medici network position 1993 Duomo Palazzo Medici Giovanni de Medici network position: closeness Bischeri Peruzzi Lamberteschi Strozzi Guadagni Castellani Ridolfi Tornabuoni nodes: Florence families edges: inter-family marriages ! Barbadori Albizzi Medici Acciaiuoli Salviati Pazzi Ginori which family is most central? network position: closeness B L Pe Str Gu C R T Alb B Medici Gi Ac Sal P Medici Guadagni Albizzi Strozzi Ridolfi Bischeri Tornabuoni Barbadori Peruzzi Castellani Salviati Acciaiuoli Ginori Lamberteschi Pazzi 9.5 7.92 7.83 7.67 7.25 7.2 7.17 7.08 6.87 6.87 6.58 5.92 5.33 5.28 4.77 network position actually, it’s complicated... network position an example Boston commuter rail 559 km of rail data FIG. 1: (a) Commuter rail network in the Boston area. The arrow marks the assumed root of (c) Minimum spanning tree. (d) The model of Eq. (3) applied to the same set of stations. Gastner & Newman, J. Stat. Mech. P01015 (2006) network position an example Boston commuter rail 559 km of rail 3272 km of rail data minimum travel time FIG. 1: (a) Commuter rail network in the Boston area. The arrow marks the assumed root of (c) Minimum spanning tree. (d) The model of Eq. (3) applied to the same set of stations. Gastner & Newman, J. Stat. Mech. P01015 (2006) network position an example Boston commuter rail 559 km of rail 3272 km of rail data minimum travel time 499 km of rail minimum weight tree FIG. 1: (a) Commuter rail network in the Boston area. The arrow marks the assumed root of (c) Minimum spanning tree. (d) The model of Eq. (3) applied to the same set of stations. Gastner & Newman, J. Stat. Mech. P01015 (2006) network position 559 km route factor n X 1 `i0 q= n i=1 di0 mean ratio of distance along edges `i0 to direct Euclidean distance di0 to root 0 3272 km q = 1.14 q =1 q = 1.61 FIG. 1: (a) Commuter rail network in the Boston area. The arrow marks the assumed root (c) Minimum spanning tree. (d) The model of Eq. (3) applied to the same set of stations. of the networks to two theoretical models that are each optimal by one of these two criteria. If one is interested solely in short, efficient paths to the root vertex then the optimal network is the “star graph,” in which every vertex is connected directly to the root by a single straight edge (see Fig. 1b). Conversely, if one is interested solely in minimizing total edge length, then the optimal network is the minimum spanning tree (MST) (see Fig. 1c). (Given a set of n vertices at specified points on a flat plane, the MST is the set of n − 1 edges joining them such that all vertices belong to a single component and the sum of the lengths of the edges is minimized [17].) To make the comparison with the star graph, we consider the distance from each non-root vertex to the root first along the edges of the network and second along a simple Euclidean straight line, and calculate the mean ratio of these two distances over all such vertices. Following Ref. [10], we refer to this quantity as the network’s route factor, and denote it q: q= Gastner & Newman, J. Stat. Mech. P01015 (2006) 499 km 1 n n i=1 li0 , di0 (1) where li0 is the distance along the edges of the network route network n actua sewer system 23 922 1.5 gas (WA) 226 1.1 gas (IL) 490 1.4 126 1.1 rail TABLE I: Number of vertices length for each of the netwo with the equivalent results fo spanning trees on the same factor for the star graph is al from the table.) with the optimal model, t the real networks ranging of the corresponding MSTs But now consider the r table, which give the route total edge lengths for the st these figures are for all ne optimal case and, more im the real-world networks to is optimal in terms of tota network position 559 km 3272 km 499 km a simple model embed n vertices in a plane until all vertices connected add edge (i, j) with minimum value for wij = dij + `j0 distance from i to j q = 1.61 of the networks to two theoretical models that are each optimal by one of these two criteria. If one is interested solely in short, efficient paths to the root vertex then the optimal network is the “star graph,” in which every vertex is connected directly to the root by a single straight edge (see Fig. 1b). Conversely, if one is interested solely in minimizing total edge length, then the optimal network is the minimum spanning tree (MST) (see Fig. 1c). (Given a set of n vertices at specified points on a flat plane, the MST is the set of n − 1 edges joining them such that all vertices belong to a single component and the sum of the lengths of the edges is minimized [17].) To make the comparison with the star graph, we consider the distance from each non-root vertex to the root first along the edges of the network* and second along a simple Euclidean straight line, and calculate the mean ratio of these two distances over all such vertices. Following Ref. [10], we refer to this quantity as the network’s route factor, and denote it q: minimum spanning tree prefer shorter paths to root q= Gastner & Newman, J. Stat. Mech. P01015 (2006) q =1 route length to root parameter =0 >0 q = 1.14 FIG. 1: (a) Commuter rail network in the Boston area. The arrow marks the assumed root (c) Minimum spanning tree. (d) The model of Eq. (3) applied to the same set of stations. 1 n n i=1 li0 , di0 (1) where li0 is the distance along the edges of the network route network n actua sewer system 23 922 1.5 gas (WA) 226 1.1 gas (IL) 490 1.4 126 1.1 rail TABLE I: Number of vertices length for each of the netwo with the equivalent results fo spanning trees on the same factor for the star graph is al from the table.) with the optimal model, t the real networks ranging of the corresponding MSTs But now consider the r table, which give the route total edge lengths for the st these figures are for all ne optimal case and, more im the real-world networks to is optimal in terms of tota *this is exactly Prim’s algorithm for MSTs network position 559 km 3272 km 499 km a simple model embed n vertices in a plane until all vertices connected add edge (i, j) with minimum value for wij = dij + `2j0 511 km q = 1.11 = 0.4 Gastner & Newman, J. Stat. Mech. P01015 (2006) q = 1.14 q =1 q = 1.61 FIG. 1: (a) Commuter rail network in the Boston area. The arrow marks the assumed root (c) Minimum spanning tree. (d) The model of Eq. (3) applied to the same set of stations. of the networks to two theoretical models that are each optimal by one of these two criteria. If one is interested solely in short, efficient paths to the root vertex then the optimal network is the “star graph,” in which every verh`ithe root by a single straight tex is connected directly to edge (see Fig. 1b). Conversely, if one is interested solely in minimizing total edge length, then the optimal network is the minimum spanning tree (MST) (see Fig. 1c). (Given a set of n vertices at specified points on a flat plane, the MST is the set of n − 1 edges joining them such that all vertices belong to a single component and the sum of the lengths of the edges is minimized [17].) To make the comparison with the star graph, we consider the distance from each non-root vertex to the root first along the edges of the network and second along a simple Euclidean straight line, and calculate the mean ratio of these two distances over all such vertices. Following Ref. [10], we refer to this quantity as the network’s route factor, and denote it q: q= 1 n n i=1 li0 , di0 (1) where li0 is the distance along the edges of the network route parab network n actua = 0.4system 23 922 To sewer 1.5 gas (WA) 226 1.1 distri gas (IL) 490 1.4 126 1.1 rail sewer TABLE I: Number oftotal vertices length for each of the netwo work with the equivalent results fo spanning trees on the same called factor for the star graph is al some from the table.) decre ond, with the optimal model, t netwo the real networks ranging of the corresponding MSTs optim But now consider the r spatia table, which give the route total edge lengths for the str that these figures are for all ne posse optimal case and, more im the real-world networks to tal ed is optimal in terms of tota mecha network position most centralized vast wilderness of in-between most decentralized network position most centralized vast wilderness of in-between most decentralized network position most centralized vast wilderness of in-between most decentralized network position most centralized vast wilderness of in-between most decentralized network position positions: • geometric description of network structure • core vs. periphery • centrality = importance, influence B L Pe Str Gu C R T Alb B Medici Gi Ac Sal open questions: • position and dynamics • what does position predict? • when does position not matter? P FIG. 1: (a) Commuter rail network in the Boston area. The arrow marks the assumed root of t (c) Minimum spanning tree. (d) The model of Eq. (3) applied to the same set of stations. of the networks to two theoretical models that are each optimal by one of these two criteria. If one is interested solely in short, efficient paths to the root vertex then the optimal network is the “star graph,” in which every vertex is connected directly to the root by a single straight edge (see Fig. 1b). Conversely, if one is interested solely in minimizing total edge length, then the optimal network is the minimum spanning tree (MST) (see Fig. 1c). (Given a set of n vertices at specified points on a flat plane, the MST is the set of n − 1 edges joining them such that all vertices belong to a single component and the sum of the lengths of the edges is minimized [17].) To make the comparison with the star graph, we con- route fac network n actual M sewer system 23 922 1.59 gas (WA) 226 1.13 gas (IL) 490 1.48 126 1.14 rail TABLE I: Number of vertices n, length for each of the networks with the equivalent results for th spanning trees on the same ver factor for the star graph is alway from the table.) describing networks homophily and assortative mixing like links with like assortative mixing ~vi ~vj vertex attributes Newman, Phys. Rev. E 67, 026126 (2003). homophily and assortative mixing like links with like ! assortativity coefficient r quantifies homophily three types: scalar attributes vertex degrees categorical variables assortative mixing ~vi ~vj homophily and assortative mixing like links with like ! scalar attributes: mean value across ties 1 XX µ= Aij vi 2m i j 1 X = ki v i 2m i Newman, Phys. Rev. E 67, 026126 (2003). assortative mixing ~vi homophily and assortative mixing like links with like ! scalar attributes: covariance across ties ~vj cov(vi , vj ) = 1 X µ= ki vi 2m i Newman, Phys. Rev. E 67, 026126 (2003). ! P ij Aij (vi P ij µ)(vj µ) Aij 1 X = Aij vi vj µ2 2m ij ✓ ◆ X 1 ki kj = Aij vi vj 2m ij 2m assortative mixing ~vi ~vj homophily and assortative mixing like links with like ! assortativity coefficient (scalar) cov(vi , vj ) r= var(vi , vj ) P ki kj /2m) vi vj ij (Aij = P ki kj /2m ij ki ij [this is just a Pearson correlation across edges] 1r1 Newman, Phys. Rev. E 67, 026126 (2003). assortative mixing 40 ~vi ~vj age of wife [years] su su 30 w th un no m Pe 20 10 10 20 30 40 50 age of husband [years] r = 0.574 strongly assortative 200 150 number (top) scatter plot of ages of 1141 married couples at time of marriage [1995 US National Survey of Family Growth] 100 50 (bottom) histogram of age differences (M-F) for same data 0 -5 0 5 10 15 20 25 age difference [years] Newman, Phys. Rev. E 67, 026126 (2003). FIG. 1: Top: scatter plot of the ages of 1141 married couples at time of marriage, from the 1995 US National Survey of w tr − an fe da in do ex It w rit ra de pl pa assortative mixing ki Newman, Phys. Rev. E 67, 026126 (2003). kj homophily and assortative mixing like links with like ! degree: just another scalar * * the assortativity coefficient formula simplifies somewhat in this case. see the Ref in the left corner for more details assortative mixing network ⎧ physics coauthorship ⎪ ⎪ biology coauthorship ⎪ ⎪ ⎪ ⎪ ⎨ mathematics coauthorship film actor collaborations social ⎪ ⎪ company directors ⎪ ⎪ ⎪ ⎪ ⎩ student relationships email address books ⎧ power grid ⎪ ⎨ Internet technological ⎪ ⎩ World-Wide Web software dependencies ⎧ protein interactions ⎪ ⎪ ⎨ metabolic network neural network biological ⎪ ⎪ ⎩ marine food web freshwater food web ki type undirected undirected undirected undirected undirected undirected directed undirected undirected directed directed undirected undirected directed directed directed size n 52 909 1 520 251 253 339 449 913 7 673 573 16 881 4 941 10 697 269 504 3 162 2 115 765 307 134 92 degree assortativity r 0.363 0.127 0.120 0.208 0.276 −0.029 0.092 −0.003 −0.189 −0.067 −0.016 −0.156 −0.240 −0.226 −0.263 −0.326 kj error σr 0.002 0.0004 0.002 0.0002 0.004 0.037 0.004 0.013 0.002 0.0002 0.020 0.010 0.007 0.016 0.037 0.031 ref. a a b c d e f g h i j k l m n o TABLE II: Size n, degree assortativity coefficient r, and expected error σr on the assortativity, for a number o technological, and biological networks, both directed and undirected. Social networks: coauthorship networks of (a) p and biologists [43] and (b) mathematicians [44], in which authors are connected if they have coauthored one or more in learned journals; (c) collaborations of film actors in which actors are connected if they have appeared together in more movies [5, (2003). 7]; (d) directors of Fortune 1000 companies for 1999, in which two directors are connected if they si Newman, Phys. Rev. E 67, 026126 assortative mixing homophily and assortative mixing like links with like ! categorical variables: let eij be fraction of edges connecting vertices of type i to vertices of type j matrix sum X eij = 1 ij marginals X j Newman, Phys. Rev. E 67, 026126 (2003). eij = ai X i eij = bj assortative mixing homophily and assortative mixing like links with like ! categorical variables: assortativity coefficient * P P i eii P i a i bi r= 1 i a i bi Tr e ||e2 || = 1 ||e2 || Newman, Phys. Rev. E 67, 026126 (2003). * this equation is equivalent to the popular modularity measure Q used to score the strength of community structure assortative mixing men 1992 study of heterosexual partnerships in San Francisco* (bipartite network) black hispanic white other bi black 0.258 0.012 0.013 0.005 0.289 women hispanic white 0.016 0.035 0.157 0.058 0.023 0.306 0.007 0.024 0.204 0.423 other 0.013 0.019 0.035 0.016 0.084 ai 0.323 0.247 0.377 0.053 TABLE I: The mixing matrix eij and the values of ai and bi for sexual partnerships the study of Catania et al. [23]. r =in0.621 After Morris [24]. strongly assortative A. Mea To quantify we define an a r= where e is the means the sum formula gives r since eij = ai perfect assorta is perfectly dis vertices of diffe value effect on network structure and behavior. The outline of the paper is as follows. In Section II we study the effects of assortative mixing by discrete characteristics such as language or race. In Section III we study *Catania mixing Newman, Phys. Rev. E 67, 026126 (2003). et al., Am. J. Public Health 82, 284-287 (1992). Northeast Midwest South West Canada assortative mixing 4388 Computer Science faculty vertices are PhD granting institutions in North America edge (u, v) means PhD at u and now faculty at v labels are US census regions + Canada Northeast Midwest South West Canada bi Northeast 0.119 0.031 0.025 0.049 0.006 0.229 Midwest 0.053 0.067 0.027 0.033 0.005 0.185 South 0.074 0.061 0.083 0.043 0.005 0.267 r = 0.264 moderately assortative West 0.055 0.026 0.024 0.073 0.005 0.184 Canada 0.022 0.011 0.006 0.011 0.085 0.135 ai 0.322 0.196 0.166 0.209 0.107 assortative mixing ~vi ~vj homophily and assortative mixing like links with like ! • random graphs tend to be disassortative r 0 because the mixing is uniform • social networks (apparently) highly assortative, in every way (attribute, degree, category) • extremal values r ⇡ { 1, 1} suggest underlying mechanism on that variable Newman, Phys. Rev. E 67, 026126 (2003). describing networks community structure describing networks Y APN QKD 13 NY TYK DDP DPN YKD KET KHY assortative community structure (edges inside the groups) KLK 0 sitio nt 600 7 8 Y 9 ons D community structure: a group of vertices that connect to other groups in similar ways community structure “internal” edges Y APN QKD 13 NY TYK DDP DPN YKD KET KHY assortative community structure (edges inside the groups) KLK 0 sitio nt 600 7 8 Y 9 ons D “bridge” edges community structure: a group of vertices that connect to other groups in similar ways DAP NY 13 PNY DDP YQK t 600 7 D ble NY 8 s 9 ion reg s C D es cor tors ica ind ion reg aria yv ghl ed ent nm alig lign rt a t to nt s me lign te a c toraslcula C community structure community structure: a group of vertices that connect to other groups in similar ways mixing matrix community structure assortative disassortative ordered core-periphery edges within groups edges between groups linear group hierarchy dense core, sparse periphery community structure ! • enormous interest, especially since 2000 • dozens of algorithms for extracting various large-scale patterns assortative disassortative ordered core-periphery • hundreds of papers published • spanning Physics, Computer Science, Statistics, Biology, Sociology, and more • this was one of the first: PNAS 2002 5700+ citations on Google Scholar network communities 1983 most new job opportunities from “weak ties” • within-community links = strong • bridge links = weak network communities 1983 most new job opportunities from “weak ties” • within-community links = strong • bridge links = weak why? information propagates quickly within a community, but slowly between communities network communities 2004 1494 blogs 759 liberal 735 conservative liberal conservative network communities 2004 amazon.com co-purchasing network network communities 2004 amazon.com co-purchasing network find partition that maximizes assortativity r on those groups n = 409,687 items m = 2,464,630 edges network communities clustered network purchases = interests interests = clustered network communities political books on amazon (2004) ©2004 Valdis Krebs network communities • community = vertices with same pattern of intercommunity connections • network macro-structure • finding them like “network clustering” • allow us to coarse grain system structure [decompose heterogeneous structure into homogeneous blocks] • constrains network synchronization, information flows, diffusion, influence network communities • community = vertices with same pattern of intercommunity connections • network macro-structure • finding them like “network clustering” • allow us to coarse grain system structure [decompose heterogeneous structure into homogeneous blocks] • constrains network synchronization, information flows, diffusion, influence open questions: • what processes generate communities? • what impact on dynamics? network function? describing networks motifs o Arqueolo´gico is found in four of the six own caves (22) [see review in (23)]. It is o found on the coast of Peru in sites that e associated with ephemeral streams (24). e southern limit in Chile and northwest gentina has yet to be explored. describing networks References and Notes T. Dillehay, Science 245, 1436 (1989). D. J. Meltzer et al., Am. Antiq. 62, 659 (1997). T. F. Lynch, C. M. Stevenson, Quat. Res. 37, 117 (1992). D. H. Sandweiss et al., Science 281, 1830 (1998). L. Nu ´n˜ez, M. Grosjean, I. Cartajena, in Interhemispheric Climate Linkages, V. Markgraf, Ed. (Academic Press, San Diego, CA 2001), pp. 105–117. M. A. Geyh, M. Grosjean, L. Nu ´n˜ez, U. Schotterer, Quat. Res. 52, 143 (1999). J. L. Betancourt, C. Latorre, J. A. Rech, J. Quade, K. Rylander, Science 289, 1542 (2000). M. Grosjean et al., Global Planet. Change 28, 35 (2001). C. Latorre, J. L. Betancourt, K. A. Rylander, J. Quade, Geol. Soc. Am. Bull. 114, 349 (2002). Charcoal in layers containing triangular points has been 14C dated at Tuina-1, Tuina-5, Tambillo-1, San Lorenzo-1, and Tuyajto-1 between 13,000 and 9000 cal yr B.P. (table S1 and fig. S1). P. A. Baker et al., Science 291, 640 (2001). G. O. Seltzer, S. Cross, P. Baker, R. Dunbar, S. Fritz, Geology 26, 167 (1998). L. G. Thompson et al., Science 282, 1858 (1998). M. Grosjean, Science 292, 2391 (2001). E. P. Tonni, written communication. M. T. Alberdi, written communication. J. Fernandez et al., Geoarchaeology 6, 251 (1991). The histogram of middens is processed from (9). M. Grosjean, L. Nu ´n˜ez, I. Cartajena, B. Messerli, Quat. Res. 48, 239 (1997). The term Silencio Arqueolo ´gico describes the midHolocene collapse of human population at those archaeological sites of the Atacama Desert that are vulnerable to multicentennial or millennial-scale drought. The term Silencio Archaeolo ´gico does not conflict with the presence of humans at sites that are not susceptible to climate change, such as in spring and river oases that drain large (Pleistocene) aquifers or at sites where wetlands were created during the arid middle Holocene, such as(2002). Tulan-67, Tulan-68, Milo et al., Science 298, 824-827 networks of Escherichia coli and Saccharomyces cerevisiae or from those found in the World Wide Web. Similar motifs were found in networks that perform information processing, even though they describe elements as different as biomolecules within a cell and synaptic connections between neurons in Caenorhabditis elegans. Motifs may thus define universal classes of networks. This approach may uncover the basic building blocks of most networks. Many of the complex networks that occur in nature have been shown to share global statistical features (1–10). These include the “small world” property (1–9) of short paths between any two nodes and highly clustered connections. In addition, in many natural networks, there are a few nodes with many more connections than the average node has. In these types of networks, termed “scale-free networks” (4, 6), the fraction of nodes having k edges, p(k), decays as a power law p(k) ϳ k–␥ (where ␥ is often between 2 and 3). To go beyond these global features would require an understanding of the basic structural elements particular to each class of networks (9). To do this, we developed an algorithm for detecting network motifs: recurring, significant patterns of interconnections. A detailed application to a gene regulation network has been presented (11). Related methods were used to test hypotheses on social networks (12, 13). Here we generalize this approach to virtually any type of connectivity graph and find the striking appearance of motifs: small subgraphs (of interest), which we then count Departments of Physics of Complex Systems and compare counts against null Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel 76100. Cold Spring Harbor Labmodel (random graph model) oratory, Cold Spring Harbor, NY 11724, USA. 1 2 *To whom correspondence should be addressed. Email: [email protected] Fig. 1. (A) Examples of interactions represented by directed edges between nodes in some of the networks used for the present study. These networks go from the scale of biomolecules (transcription factor protein X binds regulatory DNA regions of a gene to regulate the production rate of protein Y), through cells (neuron X is synaptically connected to neuron Y), to organisms (X describing networks motifs: small subgraphs (of interest), which we then count compare counts against null model (random graph model) • efficient counting is tricky (combinatorics + graph isomorphism) • choice of null model key (see Lecture 2) • lots of work in this area, mainly in molecular biology and neuroscience • see Sporns and Kotter, PLoS Biol. 2, e369 (2004) Matias et al., REVSTAT 4, 31-51 (2006) Wong et al., Brief. in Bioinfo. 13, 202-215 (2011) 003 052 002 051 001 end of lecture 3 selected references • The structure and function of complex networks. M. E. J. • • • • • • • • • • • Newman, SIAM Review 45, 167–256 (2003). The Structure and Dynamics of Networks. M. E. J. Newman, A.-L. Barabási, and D. J. Watts, Princeton University Press (2006). Hierarchical structure and the prediction of missing links in networks. A. Clauset, C. Moore, and M. E. J. Newman, Nature 453, 98–101 (2008). Modularity and community structure in networks. M. E. J. Newman, Proc. Natl. Acad. Sci. USA 103, 8577–8582 (2006). Why social networks are different from other types of networks. M. E. J. Newman and J. Park, Phys. Rev. E 68, 036122 (2003) Random graphs with arbitrary degree distributions and their applications. M. E. J. Newman, S. H. Strogatz, and D. J. Watts, Phys. Rev. E 64, 026118 (2001). Comparing community structure identification. L. Danon, A. Diaz-Guilera, J. Duch and A. Arenas. J. Stat. Mech. P09008 (2005). Characterization of Complex Networks: A Survey of measurements. L. daF. Costa, F. A. Rodrigues, G. Travieso and P. R. VillasBoas. arxiv:cond-mat/050585 (2005). Evolution in Networks. S.N. Dorogovtsev and J. F. F. Mendes. Adv. Phys. 51, 1079 (2002). Revisting “scale-free” networks. E. F. Keller. BioEssays 27, 1060-1068 (2005). Currency metabolites and network representations of metabolism. P. Holme and M. Huss. arxiv:0806.2763 (2008). Functional cartography of complex metabolic networks. R. Guimera and L. A. N. Amaral. Nature 433, 895 (2005). • Graphs over Time: Densification Laws, Shrinking Diameters • • • • • • • • • and Possible Explanations. J. Leskovec, J. Kleinberg and C. Faloutsos. Proc. 11th ACM SIGKDD Intl. Conf. on Knowledge Discovery and Data Mining 2005. The Structure of the Web. J. Kleinberg and S. Lawrence. Science 294, 1849 (2001). Navigation in a Small World. J. Kleinberg. Nature 406 (2000), 845. Towards a Theory of Scale-Free Graphs: Definitions, Properties and Implications. L. Li, D. Alderson, J. Doyle, and W. Willinger. Internet Mathematics 2(4), 2006. A First-Principles Approach to Understanding the Internet’s Router-Level Topology. L. Li, D. Alderson, W. Willinger, and J. Doyle. ACM SIGCOMM 2004. Inferring network mechanisms: The Drosophila melanogaster protein interaction network. M. Middendorf, E. Ziv and C. H. Wiggins. Proc. Natl. Acad. Sci. USA 102, 3192 (2005). Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology. S. Ciliberti, O. C. Martin and A. Wagner. PLoS Comp. Bio. 3, e15 (2007). Simple rules yield complex food webs. R. J. Williams and N. D. Martinez. Nature 404, 180 (2000). A network analysis of committees in the U.S. House of Representatives. M. A. Porter, P. J. Mucha, M. E. J. Newman and C. M. Warmbrand. Proc. Natl. Acad. Sci. USA 102, 7057 (2005). On the Robustness of Centrality Measures under Conditions of Imperfect Data. S. P. Borgatti, K. M. Carley and D. Krackhardt. Social Networks 28, 124 (2006).
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