NetworkTheory V3

The 13th Taiwan Nuclear Physics Summer School
2009 June 29 ~ July 4

National Chiao-Tung University
Network Theory Introduction

HC Lee
(Notes prepared with Dr. Rolf Sing-Guan Kong)
Computational Biology Laboratory
Graduate Institute of Systems Biology and Bioinformatics
National Central University
2009.06.29-07.01
Outline
Introduction
Network history
Types of network
Nomenclature
Properties of network
Networks in the real world
Model
Introduction
Network theory is an area of
applied mathematics and part of
graph theory. Network theory
concerns itself with the study of
graphs as a representation of
either symmetric relations or, more
generally, of asymmetric relations
between discrete objects.
A network is a set of items, which well call vertices
(nodes), which connections between them, called
edges.
Network history
Knigsberg Bridge Problem

The city of Knigberg
was built on the banks of
the Pregel River in what
was the Prussia
(1525-1947), and on two
islands that lie in
midstream. Seven
bridges connected the
land masses.
Does there exist any single path that crosses all seven
bridges exactly once each?
1736, Leonard Euler used graph theory to prove that its
impossibility of its existence. In the past three centuries,
graph theory has become the principal mathematical
language for describing the properties of networks.
Graph theory
By abstracting away the details of a problem, graph

theory is capable of describing the important
topological features with a clarity that would be
impossible were all the details retained.
Applications of graph theory

1950s, in response to a growing interest in
quantitative methods in sociology and
anthropology, the mathematical language of
graph theory was coopted by social scientists to
help understand data from ethnographic studies.
Much of the terminology of social network analysis
was borrowed directly from graph theory, to
address questions of status, influence,
cohesiveness, social roles, and identities in social
networks.
1950s, mathematicians began to think of graphs as
the medium through which various modes of
influence information and disease in particular
could propagate.
Types of network
Illustration
A set of vertices joined by edges is only the
simplest type of network; there are many ways in
which networks may be more complex than this.
For instance, there may be more than one
different type of vertex in a network, or more than
one different type of edge. And vertices or edges
may have a variety of properties, numerical or
otherwise, associated with them.
Edges can carry weights, or can be also directed.
Directed graphs can be either cyclic or acyclic.
Graphs may also evolve over time, with vertices or
edges appearing or disappearing, or values
defined on those vertices and edge changing.
Diagram
Nomenclature
Nomenclature
Vertex
Edge
Directed/
undirected
Degree
Component
Geodesic path
Diameter
Vertex: The fundamental unit

of a network, also called a
site (physics), a node
(computer science), or an
actor (sociology).
Edge: The line connecting
two vertices. Also called a
bond (physics), a link
(computer science), or a tie
(sociology).
Nomenclature
Vertex
Edge
Directed/
undirected
Degree
Component
Geodesic path
Diameter
Directed/undirected: An
edge is directed if it runs in
only direction (such as a oneway road between two
points), and undirected if it
runs in both directions.
Nomenclature
Vertex
Edge
Directed/
undirected
Degree
Component
Geodesic path
Diameter
Degree: The number of

edges connected to a
vertex. A directed graph has
both an in-degree and an
out-degree for each vertex,
which are the numbers of incoming and out-going edges
respectively.
Nomenclature
Vertex
Edge
Directed/
undirected
Degree
Component
Geodesic path
Diameter
Component: The component

to which a vertex belongs is
that set of vertices that can be
reached from it by paths
running along edges of the
graph. In a directed graph a
vertex has both an incomponent and outcomponent, which are the
sets of vertices from which the
vertex can be reached and
which can be reached from it.
Nomenclature
Vertex
Edge
Directed/
undirected
Degree
Component
Geodesic path
Diameter
Protein-protein interaction network

A network consisting of proteins known to be
involved in infertility (yellow nodes) and
interaction partners (grey nodes).
Adopted: http://www.cdsb.dk/about.php
Nomenclature
Vertex
Edge
Directed/
undirected
Degree
Component
Geodesic path
Diameter
Geodesic path: A geodesic

path is the shortest path
through the network from
one vertex to another.
Nomenclature
Vertex
Edge
Directed/
undirected
Degree
Component
Geodesic path
Diameter
Diameter: The diameter of a

network is the length (in
number of edges) of the
longest geodesic path
between any two vertices. A
few authors have also used
this term to mean the
average geodesic distance in
a graph, although strictly the
two quantities are quite
distinct.
Nomenclature
Vertex
Edge
Directed/
undirected
Degree
Component
Geodesic path
Diameter
Adopted:
http://igraph.sourceforge.net/screenshots2.html
Properties of network
Proper&esof
network
Stanley Milgram
(Aug.15,1933
A. Thesmallworldeect
Dec.20,1984) was
B. Transi7vityorclustering
a social
C. Degreedistribu7on
psychologist at
D. Networkresilience
Yale University,
E. MixingpaEerns
Harvard University
F. Degreecorrela7ons
and the City
G. Communitystructure
University of New
H. Networknaviga7on
York. While at Harvard, he
I. Othernetwork
conducted the small-world
proper7es
experiment (the source of the six
degrees of separation concept).
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Consider an undirected
network, and let us define l
to be the mean geodesic
distance between vertex
pairs in a network:
where dij is the geodesic

distance from vertex i to
vertex j.
Its problematic in
networks that have more
than one component.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
In multi-component networks,
there exist vertex pairs that
have no connecting path.
Conventionally one assigns
infinite geodesic distance to
such pairs, but then the value
of l also becomes infinite.
Infinite values of dij then

contribute nothing to sum.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
In many networks it is found

that if vertex A is connected
to vertex B and vertex B to
vertex C, then there is a
heightened probability that
vertex A will be also be
connected to vertex C. In
terms of network topology,
transitivity means the
presence of a heightened
number of triangles in the
network sets of three
vertices each of which is
connected to each of the
others.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
It can be quantified by
defining a clustering
coefficient C (0 to1) thus:
where a connected triple

means a single vertex with
edges running to an
unordered pair of others.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
C is the mean probability

that two vertices that are
network neighbors of the
same other vertex will
themselves be neighbors.
An alternative definition of
the clustering coefficient:
For vertices with degree 0 or

1, for which both numerator
and denominator are zero,
we put Ci = 0.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Then the clustering

coefficient for the whole
network is the average
Definition [3] is easier to

calculate analytically, but [4]
is easily calculated on a
computer and has found
wide use in numerical studies
and data analysis.
The clustering coefficient
measures the density of
triangles in a network.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Degree of a vertex in a
network is the number
connected to that vertex.
P(k) is the fraction of vertices
in the network that have
degree k.
A plot of P(k) for any given
network can be formed by
making a histogram of the
degrees of vertices. This
histogram is the degree
distribution for the network.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
In a random graph, each edge is

present or absent with equal
probability. Real-world networks are
mostly found to be very unlike the
random graph in their degree
distribution, and their distribution has
a long right tail of values.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Related to degree
distributions is the property of
resilience of networks to the
removal of their vertices. If
vertices are removed from a
network, the typical length
of these paths will increase,
and ultimately vertex pairs
will become disconnected
and communication
between them through the
network will become
impossible.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
There are also a variety of

different ways in which
vertices can be removed
and different networks show
varying degrees of resilience
to these also. For example,
one could remove vertices
at random from a network,
or once could target some
specific class of vertices,
such as those the highest
degrees.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Authors measured average vertexvertex distances as a function of

number of vertices removed, both
for random removal and for
progressive removal of the vertices
with the highest degrees.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
The distance was almost

entirely unaffected by
random vertex removal. On
the other hand, when
removal is targeted at the
highest degree vertices, it is
found to have devastating
effect.
The Internet is highly resilient
against the random failure of
vertices in the network, but
highly vulnerable to
deliberate attack on its
highest-degree vertices.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
In most kinds of networks

there are at least a few
different types of vertices,
and the probabilities of
connection between vertices
often depends on types. In
social networks this kind of
selective linking is called
assortative mixing or
homophily.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
A study of 1958 couples in the

city of San Francisco,
California. The study recorded
the race of study participants
in each couple. Participants
appear to draw their partners
preferentially from those of
their own race.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Assortative mixing can be

quantified by an
assortativity coefficient. Let
Eij be the number of edges in
a network that connect
vertices of types i and j, with i,
j = 1 N, and let E be the
matrix with elements Eij, then
[6]
where x means the sum of
all the elements of the matrix x.
The elements eij measure the
fraction of edges that fall
between vertices of types i and
j.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
One can ask about the

conditional probability P(j|i) that
my network neighbor is of type j
given that I am of type i, which is
given by P(j|i) = eij/jeij.
Another definition of assortative

mixing is
Its 1 for a perfectly assortative
network (every edge falls
between vertices of the same
type), and 0 for randomly mixed
networks.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Two shortcomings for Q:

(1) Q has two different values,
depending on the horizontal
axis, and its unclear which is
correct one for the network;
(2) the measure weights each
vertex type equally, regardless
of how many vertices there
are of each type, which can
give rise to misleading figures
for Q in cases where
community size is
heterogeneous, as it often is.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
An alternative assortatively
coefficient that remedies these
problems is:
This quantity is also 0 in a

randomly mixed network and
1 in a perfectly assortative
one. We find that r = 0.621 in
this example.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Do the high-degree vertices in a

network associate preferentially
with other high-degree vertices?
Or do they prefer to attach to
low-degree ones?
Calculation of the mean degree
of the network neighbors of a
vertex as a function of the
degree k of that vertex. That
gives a one-parameter curve
which increases with k if the
network is assortatively mixed.
And we call disassortativity if its
decrease with k.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Newman reduced the

measurement to a single
number by calculating the
Pearson correlation coefficient
of the degrees at either ends of
an edge. This gives a single
number that should be positive
for assortatively mixed networks
and negative for
disassortatively ones.
All social networks measured
appear to be assortative, but
other types of networks appear
to be disassortative.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Community structure means

groups of vertices that have a
high density of edges within
them, with a lower density of
edges between groups.
A visualization of the friendship
network of children in a US
school taken from a study by
Moody. The network appears
to have strong enough
community structure.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Moody colors the vertices according

to the races, it becomes clear that
one of the principal divisions in the
network is by individuals race, and
this is presumably what is driving the
formation of communities in this case.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
The traditional method for

extracting community
structure from a network is
cluster analysis, sometimes
also called hierarchical
clustering. In this method, one
assigns a connection
strength to vertex pairs in the
network of interest.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Clustering is possible
according to many different
definitions of the connection
strength. Reasonable choices
include various weighted
vertex-vertex distance
measures, the sizes of cut-sets,
and weighted path counts
between vertices.
Proper&esof
network
Tree of life
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Adopted: www.utexas.edu/.../features/story.php?
item=2757
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Stanley Milgrams famous smallworld experiment, in which

letters were passed from person
to person in an attempt to get
them to a desired target
individual, showed that there
exist short paths through social
networks between apparently
distant individuals.
The participants had no special
knowledge of the network
connecting them to the target
person. Nonetheless it proved
possible to get a message to a
distant target in only a small
number of steps.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
This is indicates that there is

something quite special
about the structure of the
network.
If it were possible to construct
artificial networks that were
easy to navigate in the same
way that social networks
appear to be, it has
suggested they could be
used to build efficient
database structures or better
peer-to-peer computer
networks.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
In some networks the size of

the largest component is an
important quantity, i.e., in a
communication network the
size of the largest component
represents the largest fraction
of the network within which
communication is possible
and hence is a measure of
the effectiveness of network.
The size of the largest
component is often equated
with the graph theoretical
concept of the giant
component.
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Adopted:
networkx.lanl.gov/.../giant_component.html
Proper&esof
network
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
The betweenness centrality of

a vertex i is the number of
geodesic paths between
other vertices that run through
i. And betweenness appears
to follow a power law for
many networks and propose a
classification of networks into
two kinds based on the
exponent of this power law.
Betweenness centrality can
also be viewed as a measure
of network resilience it tell us
how many geodesic paths will
get longer when a vertex is
removed from the network.
E. MixingpaEerns
H. Networknaviga7on
I. Othernetwork
proper7es
Milo et al. Network motifs: Simple building block of

complex networks. Science 298, 824-827 (2002).
Proper&esof
network
Networks in the real world

1.Social networks
2.Information networks
3.Technological networks
4.Biological networks
A social network is a set of

1.Socialnetworks
people or groups of people with
A. ThepaEernsof
some pattern of contacts or
friendships
interactions between them.
B. Businessrela7onships
Traditional social network studies
C. Intermarriages
often suffer from problems of
betweenfamilies
inaccuracy, subjectivity, and
D. PaEernsofsexual
contacts
small sample size. Data collection
E. Smallworldnetwork
is usually carried out be querying
F. Collabora7onnetwork
participants directly using
G. Communica7on
questionnaires or interviews. Such
recordsofcertain
methods are labor-intensive and
kinds
therefore limit the size of the
network that can be observed.
Watts and Strogatz, Collective

dynamics of small-world networks,
1.Socialnetworks
Nature, 393, 440-442 (1998).
A. ThepaEernsof
friendships
C. Intermarriages
betweenfamilies
D. PaEernsofsexual
contacts
G. Communica7on
recordsofcertain
kinds
Small-world networks:
Networks that are partly
disordered but not
random, are highly
clustered but have
small characteristic
path lengths, like
random graphs.
Watts and Strogatz, Nature, 393, 440-442 (1998)
Make random reconnections
Random
Ordered
Smallworld
L(0) > L(p) ~ L(1) ; C(0) >~ C(p) >> C(1)
Newman, M. E. J., Scientific

1.Socialnetworks
collaboration networks: I.
A. ThepaEernsof
Network construction and
friendships
fundamental results, Phys. Rev.
E 64, 016131 (2001);
C. Intermarriages
Newman, The structure of
betweenfamilies
scientific collaboration
D. PaEernsofsexual
contacts
networks. PNAS, 98, 404-409
(2001).
Newman, M. E. J., Scientific
G. Communica7on
collaboration networks: II.
recordsofcertain
Shortest paths, weighted
kinds
networks, and centrality, Phys.
Rev. E 64, 016132 (2001).
1.Socialnetworks
A. ThepaEernsof
friendships
C. Intermarriages
betweenfamilies
D. PaEernsofsexual
contacts
G. Communica7on
recordsofcertain
kinds
Power law for number of papers

versus authors
(Newman (I), Phys. Rev. E 64, 016131 (2001))
Connection is
co-authorship
~ -2.8 -3.4, C ~ 0.3 0.7
Inter-author distance is small-world
1.Socialnetworks
(Newman (II), Phys. Rev. E 64, 016132 (2001))
A. ThepaEernsof
friendships
C. Intermarriages
betweenfamilies
D. PaEernsofsexual
contacts
G. Communica7on
recordsofcertain
kinds
<l>author ~ <l>random grath
Adamic L. and Adar E., How to

search a social network, Social
1.Socialnetworks
Networks 27, 187-203 (2005).
A. ThepaEernsof
B.
C.
D.
E.
F.
G.
friendships
Businessrela7onships
Intermarriages
betweenfamilies
PaEernsofsexual
contacts
Smallworldnetwork
Collabora7onnetwork
Communica7on
recordsofcertain
kinds
How
to find short paths in a social

network using only local information?
Simulate network experiments with
network of email contacts and online
student social networking websites.
Finds local information strategy works
well when underlying organizational
hierarchy is known, but not so well
otherwise.
1.Socialnetworks
A. ThepaEernsof
friendships
C. Intermarriages
betweenfamilies
D. PaEernsofsexual
contacts
G. Communica7on
recordsofcertain
kinds
Adamic and Adar. Social Networks 27, 187-203 (2005).
Adamic and Adar, Social Networks 27, 187-203 (2005).
1.Socialnetworks
A. ThepaEernsof
friendships
C. Intermarriages
betweenfamilies
D. PaEernsofsexual
contacts
G. Communica7on
recordsofcertain
kinds
E-mail communication (grey lines) clings to

organizational chart (black lines)
Local information search strategy works well

when underlying organizational hierarchy is
known, but not so well otherwise.
2.Informa&on
networks
A. Cita7onsbetween
academicpapers
B. WorldWideWeb
C. Cita7onsbetweenUS
patents
D. Peertopeernetworks
E. Networkofword
classesinthesaurus
F. Preferencenetwork
Information networks also

sometimes called
knowledge networks.
2.Informa&on
networks
A. Cita7onsbetween
academicpapers
B. WorldWideWeb
patents
E. Networkofword
classesinthesaurus
Redner, S., How popular is your

paper? An empirical study of
the citation distribution, Eur.
Phys. J. B 4, 131-134 (1998).
Citation distribution from 783,000 papers
N(x) ~ x- , ~ 3
2.Informa&on
networks
A. Cita7onsbetween
academicpapers
B. WorldWideWeb
patents
E. Networkofword
classesinthesaurus
A. Albert and A.-L. Barabasi,

Statistical mechanics of complex
network, Rev. Mod. Phys. 74, 47-97
(2002).
Connections
in WWW are
hyperlinks; in
Internet are
physical wires.
2.Informa&on
networks
Albert & Barabasi Rev. Mod. Phys. 74,

47-97 (2002).
A. Cita7onsbetween
academicpapers
B. WorldWideWeb
patents
E. Networkofword
classesinthesaurus
Degree distribution of 326,000 (square) and 200
million (circle) samples.
P(k)=k-,out~ 2.4-2.7, in~ 1.9-2.1
General characteristics of some real networks

(Albert & Barabasi Rev. Mod. Phys. 74, 47-97 (2002))
l ~ lrand ,
C >> Crand
General characteristics of some real scale-free networks

(Albert & Barabasi Rev. Mod. Phys. 74, 47-97 (2002))
~ 2-3,
l ~ lrand ,
2.Informa&on
networks
A. Cita7onsbetween
academicpapers
B. WorldWideWeb
patents
E. Wordnetwork
Cancho and Sole, The small

world of human language,
The Royal Society B268,
2261-2265 (2001).
2.Informa&on
networks
Cancho and Sole,
A. Cita7onsbetween
academicpapers
B. WorldWideWeb
patents
E. Wordnetwork
C>>Crandom , d~drandom, ~ -2.7 (small world)
3.Technological
networks
A. Distribu7onofsome
commodity/resource
B. Airlineroutes
C. Roads
D. Railway
E. Pedestriantrac
F. River
G. Telephone
H. Deliverynetworks
I. Electroniccircuits
J. Internet
Third class of networks is

technological networks, manmade networks designed
typically for distribution of
some commodity or resource.
3.Technological
networks
commodity/resource
B. Airtransporta7on
network
C. Roads
D. Railway
E. Pedestriantrac
F. River
G. Telephone
H. Deliverynetworks
J. Internet
Guimera, The worldwide air transportation

network: Anomalous centrality, community
structure, and cities' global roles, PNAS 31,
7794-7799 (2005).
Betweenness of
node i: number of
shortest paths that
passes through i.
3.Technological
networks
commodity/resource
B. Airtransporta7on
network
C. Roads
D. Railway
E. Pedestriantrac
F. River
G. Telephone
H. Deliverynetworks
J. Internet
Guimera, PNAS 31, 7794-7799 (2005)

Highcentralitydoesnotnecessarilyimplylargebetweenness
bogus
3.Technological
networks
commodity/resource
B. Airtransporta7on
network
C. Roads
D. Railway
E. Pedestriantrac
F. River
G. Telephone
H. Deliverynetworks
J. Internet
Balthrop, et al. Technological

networks and the spread of
computer viruses, Science 304,
527-529 (2004).
(Right) IP and Admin. networks are from a large

corporation. (Left) Address books and e-mail traffic
data are from a large university. Throttling is the
best strategy for slowing virus and worm spread.
4.Biological
networks
A. Metabolicpathways
B. Sta7s7calproper7esof
metabolicnetworks
C. Proteininterac7on
D. Gene7cregulatory
networks
E. Diseasenetwork
F. Cellcycle
G. Bloodvesselsandthe
equivalentvascular
networkinplants
Giot, L., et al., A protein interaction map of

Drosophila melanogaster, Science 302,
1727-1736 (2003).
Top 3000 interactions among 3522 proteins in fruit fly
Transcriptional regulation of gene (cartoon)

Biological functions
DNA upstream of a gene
controlled by
transcription factors
(TFs, a type of proteins)
acting as switches
Machine (ribosome) that
transcribes gene
aaaaaaaa
Activator: activating TF
Suppressor: suppressing TF
TF binding sites
aaaaaaaa
Coding of gene
4.Biological
networks
metabolicnetworks
D. Gene7cregulatory
networks
E. Diseasenetwork
F. Cellcycle
equivalentvascular
networkinplants
Tong Ihn Lee, et al., Transcription regulatory

networks in Saccharomyces cerevisiae,
Science 298, 799-804 (2002).
Yeast.Muchlarger
numberofpromoter
regionsharedby
manyregulators
Random
system
Eukaryo7ccellularfunc7onsarehighlyconnectedthrough
networks transcrip7onalregulatorsthatregulateother
transcrip7onalregulators.
4.Biological
networks
Tong Ihn Lee, et al., Science 298, 799-804

(2002).
metabolicnetworks
D. Gene7cregulatory
networks
E. Diseasenetwork
F. Cellcycle
equivalentvascular
networkinplants
aaaaaaaaaaaaaaaaaaaaaaa
4.Biological
networks
metabolicnetworks
D. Gene7cregulatory
networks
E. Diseasenetwork
F. Cellcycle
equivalentvascular
networkinplants
K. Goh et al., The human disease

network, PNAS 104, 8685-8690
(2007).
Conclusion
Proteins/genes contributing
to common disease tend to
interact with each other
Study offers network-based
explanation for complex
disorders: a phenotype
correlating with malfunction
of a particular functional
module
Use map of diseasome to construct networks
Nodes: diseases, connection: shared gene
Nodes: genes; connection: shared disease
4.Biological
networks
metabolicnetworks
D. Gene7cregulatory
networks
E. Diseasenetwork
F. Cellcycle
equivalentvascular
networkinplants
Class Exercise
Li FT, et al., The yeast cell-cycle
network is robustly designed, PNAS
101, 4781-4786 (2003).
Simplified regulatory network of yeast
cycle (down from> 400 genes)
Li FT, et al., PNAS 101, 4781-4786 (2003).
Network of cycle paths
Each (green)
node is a
configuration:
{Si|i= 1 to 11}.
Genes have
two states:
Si = 1, active
Si = 0, inactive
Li FT, et al., PNAS 101, 4781-4786 (2003).

Fixed-points of cell-cycle network
Thirteen configurations of temporal evolution of a pathway to the largest fixed-point
Models
1. Help us to understanding the
construction of networks
2. Predict the behaviors of networks.
Three classical models
The small-world model
References
PDFcopiesofthefollowingpaperscanbeobtainedatthewebsite
hEp://sansan.phy.ncu.edu.tw/~hclee/ref/nucl_school09/papers.html
A. Albert and A.-L. Barabasi, Statistical mechanics of complex network, Rev. Mod.
Phys. 74, 47-97 (2002)

-Watts and Strogatz, Collective dynamics of "small-world" networks, Nature, 393,
440-442 (1998).
-Newman, M. E. J., Scientific collaboration networks: I & II. Network construction and
fundamental results, Phys. Rev. E 64, 016131-2 (2001).
-Cancho and Sole, The small world of human language, The Royal Society B268,
2261-2265 (2001).
-Guimera et al., The worldwide air transportation network: Anomalous centrality,
community structure, and cities' global roles, PNAS 31, 7794-7799 (2005).
-Balthrop, et al. Technological networks and the spread of computer viruses, Science
304, 527-529 (2004).
-Tong Ihn Lee, et al., Transcription regulatory networks in Saccharomyces cerevisiae,
Science 298, 799-804 (2002).
-K. Goh et al., The human disease network, PNAS 104, 8685-8690 (2007).
-Sporns, et al., Organization, development and function of complex brain networks,
TRENDS in Cognitive Sciences 8(9), 418-425 (2004).
-Li FT, et al., The yeast cell-cycle network is robustly designed, PNAS 101, 4781-4786
(2003).
-Giot, L., et al., A protein interaction map of Drosophila melanogaster, Science 302,
1727-1736 (2003).
Thank for your attention

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The 13th Taiwan Nuclear Physics Summer School

2009 June 29 ~ July 4

Network Theory Introduction

Knigsberg Bridge Problem

By abstracting away the details of a problem, graph

Applications of graph theory

Vertex: The fundamental unit

Degree: The number of

Component: The component

Protein-protein interaction network

Geodesic path: A geodesic

Diameter: The diameter of a

where dij is the geodesic

Infinite values of dij then

In many networks it is found

where a connected triple

C is the mean probability

For vertices with degree 0 or

Then the clustering

Definition [3] is easier to

In a random graph, each edge is

There are also a variety of

Authors measured average vertexvertex distances as a function of

The distance was almost

In most kinds of networks

A study of 1958 couples in the

Assortative mixing can be

One can ask about the

Another definition of assortative

Two shortcomings for Q:

This quantity is also 0 in a

Do the high-degree vertices in a

Newman reduced the

Community structure means

Moody colors the vertices according

The traditional method for

Stanley Milgrams famous smallworld experiment, in which

This is indicates that there is

In some networks the size of

The betweenness centrality of

Milo et al. Network motifs: Simple building block of

Networks in the real world

A social network is a set of

Watts and Strogatz, Collective

Watts and Strogatz, Nature, 393, 440-442 (1998)

Watts and Strogatz, Nature, 393, 440-442 (1998)

Make random reconnections

Watts and Strogatz, Nature, 393, 440-442 (1998)

L(0) > L(p) ~ L(1) ; C(0) >~ C(p) >> C(1)

Newman, M. E. J., Scientific

Power law for number of papers

~ -2.8 -3.4, C ~ 0.3 0.7

Inter-author distance is small-world

(Newman (II), Phys. Rev. E 64, 016132 (2001))

<l>author ~ <l>random grath

Adamic L. and Adar E., How to

to find short paths in a social

Adamic and Adar. Social Networks 27, 187-203 (2005).

Adamic and Adar, Social Networks 27, 187-203 (2005).

E-mail communication (grey lines) clings to

Local information search strategy works well

Information networks also

Redner, S., How popular is your