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G. Caldarelli
CNR-INFM Centre SMC Dep. Physics University Sapienza Rome, Italy http://www.guidocaldarelli.com
INTRODUCTION
http://www.scale-freenetworks.com
INTRODUCTION
Free Resources on the web
R. Albert, A.-L. Barabasi STATISTICAL MECHANICS OF COMPLEX NETWORKS Review of Modern Physics 74, 47 (2002) http://arxiv.org/abs/cond-mat/0106096 M.E.J. Newman THE STRUCTURE AND FUNCTION OF COMPLEX NETWORKS, SIAM Review 45, 167-256 (2003) http://arxiv.org/abs/cond-mat/03030516 R. Diestel GRAPH THEORY, Springer-Verlag (2005) http://www.math.ubc.ca/~solymosi/443/GraphTheoryIII.pdf Networks Visualization and Analysis PAJEK, Springer-Verlag (2005) http://pajek.imfm.si/doku.php Bibliography I collected http://www.citeulike.org/user/gcalda/tag/book
INTRODUCTION
Dissemination on Networks
A.-L. Barabsi Linked, Perseus (2001)
D. Watts Six Degrees: the science of a Connected Age W.W. Norton (2004)
INTRODUCTION
Resources in your library
S.N. Dorogovtsev, J.F.F. Mendes Evolution of Networks, Oxford University Press (2003)
R.Pastor Satorras, M. Rubi, A. Diaz-Guilera Statistical Mechanics of Complex Networks Lecture Notes in Physics, Vol. 625 (2003)
R. Pastor Satorras, A. Vespignani Evolution and Structure of the Internet Cambridge University Press (2004)
INTRODUCTION
Resources in your library
G. Caldarelli, A. Vespignani (eds) Handbook of Graphs and Networks, Wiley (2003)
U Brandes T Erlebach, Network Analysis - Methodological Foundations, LNCS Tutorial 3418, Springer Verlag, (2005)
M.E.J Newman, A.-L. Barabsi, D. Watts The Structure and Dynamics of Networks, Princeton University Press (2006)
G. Caldarelli, A.Vespignani (eds) Large Scale Structure and Dynamics of Complex Networks, World Scientific Press (2007)
INTRODUCTION
Summary
1
1.1 1.2 1.3 1.4 1.5
2
2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.1.2 Basic Quantities (degree)
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.1 Definition and Adjacency Matrix
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.1.2 Basic Quantities (degree)
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1.1 1.2 1.3 1.4 1.5
ki =
aij
j =1,n
kiin =
out a k ij i = j =1,n
a
j =1,n
ji
kiw =
w a ij j =1,n
2
2.1 2.2 2.3 2.4 2.5 2.6 SIMPLE ORIENTED
WEIGHTED
GRAPH THEORY
1.1.2 Basic Quantities (degree)
1
1.1 1.2 1.3 1.4 1.5 One way to visualize the behaviour of the degree in a network (especially for large ones) is to check the behaviour of the degree frequency distribution P(k)
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.1.3 Basic Quantities (distance)
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1.1 1.2 1.3 1.4 1.5
dij = min akl k,l Pij 1 w dij = min akl dij = min w k,l Pij k,l Pij akl
2
2.1 2.2 2.3 2.4 2.5 2.6
WEIGHTED DISTANCE
SUM OF WEIGHTS
GRAPH THEORY
1.1.3 Basic Quantities (distance)
1
1.1 1.2 1.3 1.4 1.5 Similarly to the degree, one usually plots the histogram of the frequency density P(d) of distances d
2
2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.1.4 Basic Quantities (Clustering)
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.1.4 Basic Quantities (Clustering)
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.2 Trees
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.2 Trees
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1.1 1.2 1.3 1.4 1.5
Trees are particularly important, since they appear in Girvan-Newman Algorithm for communities Taxonomy of species Taxonomy of information
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.2 Trees
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
Trees can also be viewed as a way to filter information. In a stock exchange the prices of all stocks are correlated, but restricting only to a Minimum Spanning Tree is a way to visualize the stronger correlations In order to build a Minimum Spanning Tree 1) Compute the correlation between the N(n-1)/2 vertices 2) Define a distance out of correlation. 3) Rank the distances 4) Draw the vertices of the shortest distance 5) Run on the ranking, whenever you find a new (or two) vertex(-ices), draw it (them) if you do not close a cycle. 6) Stop whenever all the vertices have been drawn
Lectures on Complex Networks
GRAPH THEORY
1.2 Trees
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1.1 1.2 1.3 1.4 1.5 One way to visualize the behaviour of a tree (on top of the degree) is to check the behaviour of the basin size frequency distribution P(n).
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.3 Vertex Correlation: Assortativity
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1.1 1.2 1.3 1.4 1.5 A way to check the Conditioned Probability P(k|k) that a vertex whose degree is k is connected with another vertex with degree k is given by the measure of the average degree of the neighbours.
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.3 Vertex Correlation: Assortativity
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1.1 1.2 1.3 1.4 1.5
Similarly, one can define a measure of the assortativity by starting from the correlation function for degrees of vertices i,j
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2.1 2.2 2.3 2.4 2.5 2.6
2 = k 2 P(k ) kP(k )
k
r=
GRAPH THEORY
1.3 Vertex Correlation: Assortativity
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1.1 1.2 1.3 1.4 1.5
2
2.1 2.2 2.3 2.4 2.5 2.6
M.E.J. Newman, Phys.Rev.Lett 89 208701 (2002)
GRAPH THEORY
1.4 Hierarchical Correlation of Graphs
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6 Many Complex Networks are originated or display a hierarchical form like the one described above (self-similar structure)
GRAPH THEORY
1.4 Hierarchical Correlation of Graphs
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
E.Ravasz, et al. Science 297 1551-1554 (2002) A. Clauset, C. Moore, M.E.J Newman Nature 453 98-101 (2008)
A typical case has been found in Metabolic Networks, where the various reaction can be assembled in different modules The key quantity is the assortativity
C (k ) k
GRAPH THEORY
1.5 The Properties of Complex Networks
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1.1 1.2 1.3 1.4 1.5 Scale Invariant Degree Distribution P(k) Distribution of distances P(l) peaked around small values Clustering (with respect to random connections) Assortativity
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2.1 2.2 2.3 2.4 2.5 2.6
GRAPH THEORY
1.5 The Properties of Complex Networks
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1.1 1.2 1.3 1.4 1.5 Scale Invariant Distribution P(k) Degree
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2.1 2.2 2.3 2.4 2.5 2.6 a) c)
Lectures on Complex Networks
WWW Physicists
b) d)
Actors Neuroscientists
GRAPH THEORY
1.5 The Properties of Complex Networks
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1.1 1.2 1.3 1.4 1.5 Distribution of distances p(l) peaked around small values
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2.1 2.2 2.3 2.4 2.5 2.6
A.Vazquez, R Pastor-Satorras, A.Vespignani Phys.Rev.E 65 066130 (2002)
GRAPH THEORY
1.5 The Properties of Complex Networks
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
M.E.J. Newman, M. Girvan, Phys.Rev.E 69 026113 (2004)
GRAPH THEORY
1.5 The Properties of Complex Networks
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
a, In assortative networks, well-connected nodes tend to join to other well-connected nodes, as in many social networks here illustrated by friendship links in a school in the United States6. b, In disassortative networks, by contrast, wellconnected nodes join to a much larger number of less-well-connected nodes. This is typical of biological networks; depicted here is the web of interactions between proteins in brewer's yeast, Saccharomyces cerevisiae7. Clauset and colleagues' hierarchical random graphs2 provide an easy way to categorize such networks.
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6 The presence of communities in a graph is one of the most important features. Communities are important for Amazon, to run their businesses For biologists to detect proteins with the same function For physicians to detect related diseases
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6 Motifs are the smallest version of communities, it is currently under debate if their presence is important or not in the area of Complex networks.
Mangan, S. and Alon, U. PNAS 100, 1198011985 (2003). Mazurie et al. Genome Biology 6 R35 (2005)
1
1.1 1.2 1.3 1.4 1.5
2
2.1 2.2 2.3 2.4 2.5 2.6 Some communites must be defined as made by vertices with similar properties (they could share no edge at all). More often the communities are made by vertices sharing many edges
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6 The concept of centrality is at the basis of the Newman-Girvan method for the analysis of communities.
b(i ) =
j ,l =1, N j l i
jl
(i )
jl
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1.1 1.2 1.3 1.4 1.5 Starting from a graph We iteratively Compute betweenness Cut the edges with the largest value of it
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2.1 2.2 2.3 2.4 2.5 2.6 For the graph above the result is given by the series of deletions E-F, E-I, B-D, A-D, C-F,C-L, D-H, G-L, D-I, B-E, A-B, H-I, F-L, C-G.
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
Guimer, R., Danon, L., Daz-Guilera, A., Giralt, F., and Arenas, A.. Physical Review E, 68, 065103 (2002).
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1.1 1.2 1.3 1.4 1.5
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2.1 2.2 2.3 2.4 2.5 2.6
2.5 Clustering detection modularity Several way have been proposed in order to check if a division is good or not. One of the quantities proposed is the modularity The starting point is to find a suitable division of the graph into g subgraphs. To detect whether the division is good or not, we define a g g matrix E whose entries eij give the fraction of edges that in the original graph connect subgraph i to subgraph j. We want the largest possible number of edges within a community and the lowest possible number of edges between different communities.
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1.1 1.2 1.3 1.4 1.5
fi =
j =1 , g
e ij
This gives the probability that in a random partition one random edge has one endvertices in i
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2.1 2.2 2.3 2.4 2.5 2.6
In order to define a null case (random partition) we can compare the diagonal elements of matrix E with the quantity f
Q =
i =1, g
e ii f i 2
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1.1 1.2 1.3 1.4 1.5
0 1 1 0 0 0 0 0 0 0
1 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 1 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
0 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0
0 0 1 1 1 0 1 1 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 1 0 0 1 1 1 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 1 0 1 1 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 1 1 0 1 0 1 1 0 0 0 0 0
0 0 0 0 0 0 0 1 1 1 0 1 1 0 0 0 0 0 0
0 0 0 0 0 0 0 1 1 0 1 0 1 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 1
0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1 1 0
0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1
0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1
0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 1 0
2
2.1 2.2 2.3 2.4 2.5 2.6
0 0 0 0 0 0 0 0 0
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1.1 1.2 1.3 1.4 1.5
Spectral analysis is based on the analysis of the following matrices The Adiacency Matrix A The Laplacian Matrix L= A - K The Normal(ized) Matrix N=K-1 A
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2.1 2.2 2.3 2.4 2.5 2.6
ki =
a
j =1, N
ij
1
1.1 1.2 1.3 1.4 1.5
Laplacian Matrix
a1 j a12 j=1,N a2 j a21 j =1, N L = ... ... an1 an2 ... a2n ... ... ... anj j =1, N ... a1n
2
2.1 2.2 2.3 2.4 2.5 2.6
1 2 ... n
If = L
'i =
2 a k = ij j i i i j =1, n
Normal Matrix
The elements of matrix N give the probability with which one field passes from a vertex i to the neighbours.
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1.1 1.2 1.3 1.4 1.5
Given this probabilistic explanation for the matrix N We have a series of results, for example One eigenvalue is equal to one and The eigenvector related is constant. Consider the case of disconnected subclusters: The matrix N is made of blocks and a general eigenvector will be given by the space product of blocks eigenvectors (the constant can be different!)
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2.1 2.2 2.3 2.4 2.5 2.6
Biological Networks
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6.1 6.2 6.3
Summary This third lecture wants to provide an overview of the applications in the following fields
6. Biological Networks
6.1 Protein Interaction Networks 6.2 Metabolic Networks 6.3 Gene Networks
7 8 9
9.1 9.2
10 11
Biological Networks
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6.1 6.2 6.3
6.1 Protein Interaction Network Protein interact in various ways during cell life.
7 8 9
9.1 9.2
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Uetz et al. Nature 403 623 (2000) H. Jeong et al. Nature, 411, 41 (2002) Giot et al. Science 302, 1727 (2003) Rual et al. Nature 437, 1173 (2005) Ramani et al. Molecular Biology 4, 180 (2008)
Biological Networks
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6.1 6.2 6.3
7 8 9
9.1 9.2
Multinetwork analysis of a carbon/light/nitrogenresponsive metabolic network. Most of the reactions are not reversible and the network is oriented.
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M.L. Gifford et al. Plant Physioloogy on-line Essay 12.2 H. Jeong et al. Nature 407 651 (2000). D. Segr et al. PNAS 99 15112 (2002). R. Gumer et al. Nature 433, 895 (2005)
INTRODUCTION
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6.1 6.2 6.3
6.3 Gene Regulatory Networks A particular class of reactions in which there is the expression of a gene is at the basis of GRN.
7 8 9
9.1 9.2
10 11
J. Hasty et al. Nat. Rev. Gen., 2, 268 (2001). T.I. Lee et al. Science 298, 799 (2002)
Geophysical Networks
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6.1 6.2 6.3
Trees and Basin distributions The case of river networks presents a scale invariance in the basin size distributions
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9.1 9.2
10 11
Dodds, P.S. and Rothman, D.H. Physical Review E, 63, 016115, 016116, 016117 (2000). Rodrguez-Iturbe, I. and Rinaldo, A. Fractal River Basins: Chance and Self-Organization. Cambridge University Press, Cambridge (1996).
Ecological Networks
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6.1 6.2 6.3
Food Webs data Most of the activity on ecological networks is related to the statistical properties of food webs
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9.1 9.2
10 11
PEaCE LAB http://www.foodwebs.org R.J. Williams N.D. Martinez Nature 404 180 (2000)
Ecological Networks
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6.1 6.2 6.3
7 8 9
9.1 9.2
10 11
J.M. Montoya, R.V. Sol, Journal of Theoretical Biology 214 405 (2002) D.B. Stouffer et al. Ecology, 86, 13011311 (2005).
Technological Networks
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6.1 6.2 6.3
9.1 Internet Traditionally the analysis of the Internet structure is made by means of traceroutes. That is to say, by exploring all the paths from a given point to all the possible destinations.
7 8 9
9.1 9.2
10 11
Technological Networks
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6.1 6.2 6.3
9.1 Internet
7 8 9
9.1 9.2
10 11
A. Vazquez, R. Pastor-Satorras and A. Vespignani PRE 65 066130 (2002) R. Pastor-Satorras and A. Vespignani Evolution and Structure of Internet: A Statistical Physics Approach. Cambridge University Press (2004)
Technological Networks
6
6.1 6.2 6.3
9.2 World Wide Web WWW is probably the largest network available of the order of billions of elements. Different centrality properties arise in such structure.
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9.1 9.2
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A. Broder et al. Computer Network, 33, 309 (2000). D. Donato et al. Journal of Phys A, 41, 224017 (2008).
Social Networks
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6.1 6.2 6.3
Wikipedia
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9.1 9.2
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Social Networks
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6.1 6.2 6.3
Wikipedia The degree shows fat tails that can be approximated by a power-law function of the kind P(k) ~ k- Where the exponent is the same both for in-degree and out-degree.
7 8 9
9.1 9.2
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indegree(empty) and outdegree(filled) Occurrency distributions for the Wikgraph in English (o) and Portuguese ().
V. Zlatic et al. Physical Review E, 74, 016115 (2006). A. Capocci et al. Physical Review E, 74, 036116 (2006).
Financial Networks
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6.1 6.2 6.3
7 8 9
9.1 9.2
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Correlation based minimal spanning trees of real data from daily stock returns of 1071 stocks for the 12-year period 1987-1998 (3030 trading days). The node colour is based on Standard Industrial Classification system. The correspondence is: red for mining cyan for construction yellow for manufacturing green for transportation,, light blue for public electric,gas and sanitary services administration magenta wholesale trade black for retail trade purple for finance and insurance orange for service industries
046130 (2003).
Financial Networks
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6.1 6.2 6.3
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9.1 9.2
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Garlaschelli et al. Physica A, 350 491 (2005).
Financial Networks
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6.1 6.2 6.3
Trading Webs
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9.1 9.2
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M. Angeles Serrano, M. Boguna Phys Rev. E 68 015101 (2003) D. Garlaschelli et al. Physica A, 350 491 (2005). C.A. Hidalgo, et al. Science 317 482 (2007)
Financial Networks
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6.1 6.2 6.3
Banks Credit Network Banks exchange money overnightly, in order to meet the customer needs of liquidity as well as ECB requirements
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9.1 9.2
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The network shows a rather peculiar architecture The banks form a disassortative network where large banks interact mostly with small ones.
G. De Masi et al. PRE, 98 208701 (2007)