Complex Brain Networks Graph Theoretical Analysis of Structural and Functional Systems
Complex Brain Networks Graph Theoretical Analysis of Structural and Functional Systems
Complex Brain Networks Graph Theoretical Analysis of Structural and Functional Systems
Graph theory
A branch of mathematics that
deals with the formal
description and analysis of
graphs. A graph is defined
simply as a set of nodes
(vertices) linked by connections
(edges), and may be directed
or undirected. When describing
a real-world system, a graph
provides an abstract
representation of the systems
elements and their interactions.
*University of Cambridge,
Behavioural & Clinical
Neurosciences Institute,
Department of Psychiatry,
Addenbrookes Hospital,
Cambridge, CB2 2QQ, UK.
GlaxoSmithKline,
Clinical Unit Cambridge,
Addenbrookes Hospital,
Cambridge, CB2 2QQ, UK.
Department of Psychological
and Brain Sciences, Indiana
University, Bloomington,
Indiana 47405, USA.
Correspondence to E.B.
email: [email protected]
doi:10.1038/nrn2575
Published online
4 February 2009
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Box 1 | Structural and functional brain networks
Anatomical parcellation
Histological or
imaging data
Recording sites
Orbitofrontal
Temporal pole
Structural and functional brain networks can be explored using graph theory through the following four steps (see the figure):
Define the network nodes. These could be defined as electroencephalography or multielectrode-array electrodes, or as
Nature Reviews | Neuroscience
anatomically defined regions of histological, MRI or diffusion tensor imaging data.
Complex network
An informal description of a
network with certain
topological features, such as
high clustering,
small-worldness, the presence
of high-degree nodes or hubs,
assortativity, modularity or
hierarchy, that are not typical
of random graphs or regular
lattices. Most real-life networks
are complex by this definition,
and analysis of complex
networks therefore forms an
important methodological tool
for systems biology.
Adjacency matrix
An adjacency matrix indicates
the number of edges between
each pair of nodes in a graph.
For most brain networks, the
adjacency matrix is specified
as binary that is, each
element is either 1 (if there is
an edge between nodes) or 0
(if there is no edge). For
undirected graphs the
adjacency matrix is
symmetrical.
Estimate a continuous measure of association between nodes. This could be the spectral coherence or Granger causality
measures between two magnetoencephalography sensors, or the connection probability between two regions of an
individual diffusion tensor imaging data set, or the inter-regional correlations in cortical thickness or volume MRI
measurements estimated in groups of subjects.
Generate an association matrix by compiling all pairwise associations between nodes and (usually) apply a threshold to
each element of this matrix to produce a binary adjacency matrix or undirected graph.
Calculate the network parameters of interest in this graphical model of a brain network and compare them to the
equivalent parameters of a population of random networks.
Each step entails choices that can influence the final results and must be carefully informed by the experimental question.
At step 1, parcellation schemes can use prior anatomical criteria or be informed by the functional connectivity profiles of
different regions. Several such parcellation schemes may be available and can affect network measures147. In most magnetoencephalography and electroencephalography studies, network nodes are equivalent to individual electrodes or sensors,
but networks could also be based on reconstructed anatomical sources. However, some reconstruction algorithms will
determine the brain location of each source by minimizing the covariance between sensors, which has major effects on the
configuration of functional networks. At step 2, a range of different coupling metrics can be estimated, including measures
of both functional and effective connectivity. A crucial issue at step 3 is the choice of threshold used to generate an
adjacency matrix from the association matrix: different thresholds will generate graphs of different sparsity or connection
density, and so network properties are often explored over a range of plausible thresholds. Finally, at step 4 a large number of
network parameters can be quantified (BOX 2). These must be compared with the (null) distribution of equivalent parameters
estimated in random networks containing the same number of nodes and connections. Statistical testing of network
parameters may best be conducted by permutation- or resampling-based methods of non-parametric inference given the
lack of statistical theory concerning the distribution of most network metrics.
Most graph theoretical network studies to date have used symmetrical measures of statistical association or functional
connectivity such as correlations, coherence and mutual information to construct undirected graphs. This approach
could be generalized to consider asymmetrical measures of causal association or effective connectivity such as Granger
causal148,149 or dynamic causal66 model coefficients to construct directed graphs. It is also possible to avoid the
thresholding step (step 3) by analysing weighted graphs that contain more information than the simpler unweighted and
undirected graphs that have been the focus of attention to date. Structural brain network image is reproduced from
ReF. 59. Functional brain network image is reproduced, with permission, from ReF. 70 (2006) Society for Neuroscience.
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and vulnerability topics that are likely to become
increasingly relevant in relation to neuroscience.
In this article, we describe and discuss the expanding
interface between systems neuroscience and the physics
of complex networks. We review the existing empirical
data on topological and dynamical properties of structural and functional brain networks, and ask what this
literature tells us about how structural networks shape
functional brain dynamics. Space limitations prevent us
from providing coverage of all animal models, in vitro
Motif
Path
Clustering
Connector hub
Community 2
Community 1
Provincial hub
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Box 3 | Random, scale-free and small-world networks
In random graphs each pair of nodes has an equal probability, p, of being connected152.
Large random graphs have Gaussian degree distributions (BOX 2). It is now known that
most graphs describing real-world networks significantly deviate from the simple
random-graph model.
Some networks (including the Internet and the World Wide Web) have degree
distributions in the form of a power law: that is, the probability that a node has degree k
is given as Prob(k) ~ k. In biological systems, the degree exponent often ranges
between 2 and 3, and the very gradual (heavy-tail) power law decay of the degree
distribution implies that the network lacks a characteristic scale hence such
networks are called scale-free networks. Barabsi and Albert90 demonstrated that
scale-free networks can originate from a process by which each node that is added to
the network as it grows connects preferentially to other nodes that already have high
degree. Scale-free networks are unlikely if the attachment of connections is subject to
physical constraints or associated with a cost15. Therefore, physically embedded
networks, in which nodes have limited capacity for making connections, often do not
have pure power law degree distributions but may instead demonstrate exponentially
truncated power law degree distributions, which are associated with a lower
probability of very high degree nodes.
Originally described in social networks153, the small-world property combines high
levels of local clustering among nodes of a network (to form families or cliques) and
short paths that globally link all nodes of the network. This means that all nodes of a
large system are linked through relatively few intermediate steps, despite the fact that
most nodes maintain only a few direct connections mostly within a clique of
neighbours. Small-world organization is intermediate between that of random
networks, the short overall path length of which is associated with a low level of local
clustering, and that of regular networks or lattices, the high-level of clustering of which
is accompanied by a long path length18. A convenient single-number summary of
small-worldness is thus the ratio of the clustering coefficient to the path length after
both metrics have been standardized by comparing their values to those in equivalent
random networks154. Evidence for small-world attributes has been reported in a wide
range of studies of genetic, signalling, communications, computational and neural
networks. These studies indicate that virtually all networks found in natural and
technological systems have non-random/non-regular or small-world architectures
and that the ways in which these networks deviate from randomness reflect their
specific functionality.
Connectivity
In the brain, connectivity can
be described as structural,
functional or effective.
Structural connectivity denotes
a network of anatomical links,
functional connectivity denotes
the symmetrical statistical
association or dependency
between elements of the
system, and effective
connectivity denotes directed
or causal relationships
between elements.
Microcircuit
A neuronal network composed
of specific cell types and
synaptic connections, often
arranged in a modular
architecture and capable of
generating functional outputs.
Connectome
The complete description of
the structural connections
between elements of a nervous
system.
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Box 4 | Origins of graph theory
Diffusion tensor imaging
(DTI). An MRI technique that
takes advantage of the
restricted diffusion of water
through myelinated nerve
fibres in the brain to map the
anatomical connectivity
between brain areas.
Cortical parcellation
A division of the continuous
cortical sheet into discrete
areas or regions; Brodmanns
division of the cortex into areas
defined by their
cytoarchitectonic criteria is the
most famous but not the only
parcellation scheme.
Neuronographic
measurements
Recordings of epileptiform
electrical activity at specific
sites in the cortex following
topical application of a
pro-convulsive drug to a distant
cortical site; rapid propagation
of electrical activity from
stimulation to recording sites
implies that the sites are
anatomically connected.
Functional MRI
(fMRI). The detection of
changes in regional brain
activity through their effects on
blood flow and blood
oxygenation (which, in turn,
affect magnetic susceptibility
and tissue contrast in magnetic
resonance images).
Electroencephalography
(eeG). A technique used to
measure neural activity by
monitoring electrical signals
from the brain, usually through
scalp electrodes. eeG has good
temporal resolution but
relatively poor spatial
resolution.
Magnetoencephalography
(MeG). A method of measuring
brain activity by detecting
minute perturbations in the
extracranial magnetic field that
are generated by the electrical
activity of neuronal
populations.
Graph theory is rooted in the physical world155. In 1736, Euler showed that it was impossible to traverse the city of
Knigsbergs seven bridges across the river Pregel exactly once and return to the starting point. To prove this conjecture,
Euler represented the problem as a graph, and his original publication156 is generally taken to be the origin of a new
branch of mathematics called graph theory. In the middle of the nineteenth century, the analysis of electrical circuits and
the exploration of chemical isomers led to the discovery of additional graph theoretic concepts149. Today, graph theory
pervades many areas of science.
Significant progress in graph theory has come from the study of social networks157. One prominent experiment153
tracked paths of acquaintanceship across a large social network and found that even very large networks could be
traversed, on average, in a small number of steps. Although this small-world phenomenon quickly captured the public
imagination, its origins remained obscure until its association with specific types of connectivity was demonstrated
(BOX 3). The dual discoveries of small-world18 and scale-free90 networks launched the modern era of graph theory, which
now extends into biology and neuroscience. Neural systems have long been described as sets of discrete elements linked
by connections. Nonetheless, graph theory has essentially only been applied to neuroscience in the past 10 years.
study derived structural connection patterns from crosscorrelations in cortical thickness or volume across
individual brains, which might indirectly indicate the
presence of corticocortical pathways51,52. Graph analysis
revealed small-world attributes and the existence of local
communities of brain regions. a more detailed analysis53
of the modularity or community structure of connection
data sets derived from cortical thickness correlations
revealed significant overlap between anatomical network
modules and functional systems in the cortex.
Human brain structural networks have also been
mapped using diffusion imaging and tractography. a map
of 7090 cortical and basal brain grey matter areas was
constructed using diffusion tensor imaging (DTI) and analysed using methods from graph theory 54,55. The network
exhibited high clustering and short path length, and contained motif classes similar to those identified from tracttracing data48. Several areas, including the precuneus, the
insula, the superior parietal cortex and the superior frontal
cortex, were found to have high betweenness centrality
and thus to constitute putative hubs. another study that
mapped connections between 78 cortical regions using
DTI also identified several hub regions, including the
precuneus and the superior frontal gyrus56.
Due to limitations in the model that is used to infer
fibre bundle orientation, DTI has difficulty detecting
crossing fibre bundles. Diffusion spectrum imaging can overcome this limitation by reconstructing multiple diffusion
directions in each voxel57 and was used to build cortical
connection matrices between 5004,000 homogeneously
distributed regions of interest 58. again, network analyses
revealed the small-world architecture of the cortical network. a more extensive analysis of 998 region-of-interest
networks obtained from 5 participants 59 identified
structural modules interconnected by highly central hub
regions. When considering multiple network measures
(including node degree, connection strength and centrality), a particular set of brain regions located predominantly in the posterior medial cortex, including portions
of the posterior cingulate and the precuneus, was highly
and densely interconnected, forming a structural core59.
although they differ in terms of their experimental methodology and cortical parcellation, most of these
studies reveal highly clustered large-scale cortical
networks, with most pathways existing between areas
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between multiple regions can be used to generate a
directed graph, which can then be topologically described
using graph theory. However, the functional network
studies reviewed below have all been based on undirected graphs, derived from simpler measures of functional connectivity or symmetrical statistical association
between brain regions. The key point is that, in principle,
graph theory could be applied to an association matrix of
either functional or effective connectivity measures, to
generate either undirected or directed graphs, respectively, although all neuroscientific studies to date have in
fact been based on measures of functional connectivity.
Multielectrode array
(MeA). A technique for
simultaneously measuring the
electrical activity of local
neuronal populations or single
neurons, usually in tissue slices
or cell cultures in vitro.
Association matrix
A matrix that represents the
strength of the association
between each pair of nodes in
a graph. Association between
nodes can be quantified by
many continuously variable
metrics, such as correlation or
mutual information. either
functional or effective
connectivity measures can be
used to construct an
association matrix.
Blood oxygen
level-dependent (BOLD)
signals
Changes in magnetic
susceptibility and MRI tissue
contrast that are indirectly
indicative of underlying
changes in spontaneous or
experimentally controlled brain
activation.
Default-mode network
A set of brain regions, including
medial frontal and posterior
cingulate areas of the cortex,
that are consistently
deactivated during the
performance of diverse
cognitive tasks.
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dynamic properties of brain functional networks were
conserved across frequencies81. This timescale invariance of wavelet correlations and the brain functional
network parameters derived from them is a theoretically
predictable corollary of the long-range autocorrelations
of neurophysiological time series8284.
Metastable dynamics
Transitions between marginally
stable network states; these
transitions can occur
spontaneously or as a result of
weak external perturbations.
Resting state
A cognitive state in which a
subject is quietly awake and
alert but does not engage in or
attend to a specific cognitive
or behavioural task.
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Structural brain network
Anatomical
tract tracing
Simulated BOLD
time series
Mutual information
Cross-correlation
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Cellular functional network
Module 1
Hub node
Module 2
PIP
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CITd
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LIP
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V4
V3
PITv
TF
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AITv
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V1
TH
FST
V4t
Whole-brain structural network
PITd
CITv
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a Healthy volunteers
Frontal
Temporal
Parietal
Occipital
High clustering
Low clustering
44'
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20
36'
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Assortativity
A measure of the tendency for
nodes to be connected to
other nodes of the same or
similar degree.
Endophenotype
A quantifiable biological
marker of the genetic risk for a
neuropsychiatric disorder.
patient groups as well as to the differences in imaging and analytic methods. Some of these differences
may perhaps be resolved by studies combining network
measurements on structural and functional neuroimaging data acquired on the same patients. It also seems
likely that evidence for network abnormalities in other
neuropsychiatric disorders and conditions (such as epilepsy 125127, attention-deficit hyperactivity disorder 128 or
spinal cord injury 129) will accumulate as the disorders
are increasingly investigated from this perspective.
Understanding the pathogenesis and treatment of brain
disorders from a network perspective. many psychiatric
disorders are highly heritable and are likely to represent the clinical outcome of aberrations in the formation of large-scale networks in utero or during early
postnatal life. measures of network topology may be
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Dopaminergic drugs can modulate measures of functional
connectivity in animal and human fmRI140,141 and meG
recordings142, suggesting that drug effects might be quantifiable in terms of altered functional network topology.
This has been confirmed directly in a study which demonstrated that a dopamine D2 receptor antagonist impaired
the economical small-world properties of human brain
fmRI networks75. Future work might include efforts
using graph theoretical measures to quantify how therapeutically effective treatments remediate topologically
sub-optimal network configurations in patients.
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Acknowledgements
FURTHER INFORMATION
Ed Bullmores homepage: http://www.neuroscience.cam.
ac.uk/directory/profile.php?edbullmore
Olaf Sporns homepage: http://www.indiana.edu/~cortex
Brain Connectivity Toolbox: http://www.brainconnectivity-toolbox.net/
BrainwaveR Toolbox: http://www.nitrc.org/projects/
brainwaver/
All liNks Are Active iN tHe oNliNe PDf
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