99,148 research outputs found
Different approaches to community detection
A precise definition of what constitutes a community in networks has remained
elusive. Consequently, network scientists have compared community detection
algorithms on benchmark networks with a particular form of community structure
and classified them based on the mathematical techniques they employ. However,
this comparison can be misleading because apparent similarities in their
mathematical machinery can disguise different reasons for why we would want to
employ community detection in the first place. Here we provide a focused review
of these different motivations that underpin community detection. This
problem-driven classification is useful in applied network science, where it is
important to select an appropriate algorithm for the given purpose. Moreover,
highlighting the different approaches to community detection also delineates
the many lines of research and points out open directions and avenues for
future research.Comment: 14 pages, 2 figures. Written as a chapter for forthcoming Advances in
network clustering and blockmodeling, and based on an extended version of The
many facets of community detection in complex networks, Appl. Netw. Sci. 2: 4
(2017) by the same author
Statistical Network Analysis for Functional MRI: Summary Networks and Group Comparisons
Comparing weighted networks in neuroscience is hard, because the topological
properties of a given network are necessarily dependent on the number of edges
of that network. This problem arises in the analysis of both weighted and
unweighted networks. The term density is often used in this context, in order
to refer to the mean edge weight of a weighted network, or to the number of
edges in an unweighted one. Comparing families of networks is therefore
statistically difficult because differences in topology are necessarily
associated with differences in density. In this review paper, we consider this
problem from two different perspectives, which include (i) the construction of
summary networks, such as how to compute and visualize the mean network from a
sample of network-valued data points; and (ii) how to test for topological
differences, when two families of networks also exhibit significant differences
in density. In the first instance, we show that the issue of summarizing a
family of networks can be conducted by adopting a mass-univariate approach,
which produces a statistical parametric network (SPN). In the second part of
this review, we then highlight the inherent problems associated with the
comparison of topological functions of families of networks that differ in
density. In particular, we show that a wide range of topological summaries,
such as global efficiency and network modularity are highly sensitive to
differences in density. Moreover, these problems are not restricted to
unweighted metrics, as we demonstrate that the same issues remain present when
considering the weighted versions of these metrics. We conclude by encouraging
caution, when reporting such statistical comparisons, and by emphasizing the
importance of constructing summary networks.Comment: 16 pages, 5 figure
Modeling Information Propagation with Survival Theory
Networks provide a skeleton for the spread of contagions, like, information,
ideas, behaviors and diseases. Many times networks over which contagions
diffuse are unobserved and need to be inferred. Here we apply survival theory
to develop general additive and multiplicative risk models under which the
network inference problems can be solved efficiently by exploiting their
convexity. Our additive risk model generalizes several existing network
inference models. We show all these models are particular cases of our more
general model. Our multiplicative model allows for modeling scenarios in which
a node can either increase or decrease the risk of activation of another node,
in contrast with previous approaches, which consider only positive risk
increments. We evaluate the performance of our network inference algorithms on
large synthetic and real cascade datasets, and show that our models are able to
predict the length and duration of cascades in real data.Comment: To appear at ICML '1
Structure Learning in Coupled Dynamical Systems and Dynamic Causal Modelling
Identifying a coupled dynamical system out of many plausible candidates, each
of which could serve as the underlying generator of some observed measurements,
is a profoundly ill posed problem that commonly arises when modelling real
world phenomena. In this review, we detail a set of statistical procedures for
inferring the structure of nonlinear coupled dynamical systems (structure
learning), which has proved useful in neuroscience research. A key focus here
is the comparison of competing models of (ie, hypotheses about) network
architectures and implicit coupling functions in terms of their Bayesian model
evidence. These methods are collectively referred to as dynamical casual
modelling (DCM). We focus on a relatively new approach that is proving
remarkably useful; namely, Bayesian model reduction (BMR), which enables rapid
evaluation and comparison of models that differ in their network architecture.
We illustrate the usefulness of these techniques through modelling
neurovascular coupling (cellular pathways linking neuronal and vascular
systems), whose function is an active focus of research in neurobiology and the
imaging of coupled neuronal systems
Computational strategies for dissecting the high-dimensional complexity of adaptive immune repertoires
The adaptive immune system recognizes antigens via an immense array of
antigen-binding antibodies and T-cell receptors, the immune repertoire. The
interrogation of immune repertoires is of high relevance for understanding the
adaptive immune response in disease and infection (e.g., autoimmunity, cancer,
HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the
quantitative and molecular-level profiling of immune repertoires thereby
revealing the high-dimensional complexity of the immune receptor sequence
landscape. Several methods for the computational and statistical analysis of
large-scale AIRR-seq data have been developed to resolve immune repertoire
complexity in order to understand the dynamics of adaptive immunity. Here, we
review the current research on (i) diversity, (ii) clustering and network,
(iii) phylogenetic and (iv) machine learning methods applied to dissect,
quantify and compare the architecture, evolution, and specificity of immune
repertoires. We summarize outstanding questions in computational immunology and
propose future directions for systems immunology towards coupling AIRR-seq with
the computational discovery of immunotherapeutics, vaccines, and
immunodiagnostics.Comment: 27 pages, 2 figure
HypTrails: A Bayesian Approach for Comparing Hypotheses About Human Trails on the Web
When users interact with the Web today, they leave sequential digital trails
on a massive scale. Examples of such human trails include Web navigation,
sequences of online restaurant reviews, or online music play lists.
Understanding the factors that drive the production of these trails can be
useful for e.g., improving underlying network structures, predicting user
clicks or enhancing recommendations. In this work, we present a general
approach called HypTrails for comparing a set of hypotheses about human trails
on the Web, where hypotheses represent beliefs about transitions between
states. Our approach utilizes Markov chain models with Bayesian inference. The
main idea is to incorporate hypotheses as informative Dirichlet priors and to
leverage the sensitivity of Bayes factors on the prior for comparing hypotheses
with each other. For eliciting Dirichlet priors from hypotheses, we present an
adaption of the so-called (trial) roulette method. We demonstrate the general
mechanics and applicability of HypTrails by performing experiments with (i)
synthetic trails for which we control the mechanisms that have produced them
and (ii) empirical trails stemming from different domains including website
navigation, business reviews and online music played. Our work expands the
repertoire of methods available for studying human trails on the Web.Comment: Published in the proceedings of WWW'1
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