43,143 research outputs found
Markov models for fMRI correlation structure: is brain functional connectivity small world, or decomposable into networks?
Correlations in the signal observed via functional Magnetic Resonance Imaging
(fMRI), are expected to reveal the interactions in the underlying neural
populations through hemodynamic response. In particular, they highlight
distributed set of mutually correlated regions that correspond to brain
networks related to different cognitive functions. Yet graph-theoretical
studies of neural connections give a different picture: that of a highly
integrated system with small-world properties: local clustering but with short
pathways across the complete structure. We examine the conditional independence
properties of the fMRI signal, i.e. its Markov structure, to find realistic
assumptions on the connectivity structure that are required to explain the
observed functional connectivity. In particular we seek a decomposition of the
Markov structure into segregated functional networks using decomposable graphs:
a set of strongly-connected and partially overlapping cliques. We introduce a
new method to efficiently extract such cliques on a large, strongly-connected
graph. We compare methods learning different graph structures from functional
connectivity by testing the goodness of fit of the model they learn on new
data. We find that summarizing the structure as strongly-connected networks can
give a good description only for very large and overlapping networks. These
results highlight that Markov models are good tools to identify the structure
of brain connectivity from fMRI signals, but for this purpose they must reflect
the small-world properties of the underlying neural systems
Generalized Network Psychometrics: Combining Network and Latent Variable Models
We introduce the network model as a formal psychometric model,
conceptualizing the covariance between psychometric indicators as resulting
from pairwise interactions between observable variables in a network structure.
This contrasts with standard psychometric models, in which the covariance
between test items arises from the influence of one or more common latent
variables. Here, we present two generalizations of the network model that
encompass latent variable structures, establishing network modeling as parts of
the more general framework of Structural Equation Modeling (SEM). In the first
generalization, we model the covariance structure of latent variables as a
network. We term this framework Latent Network Modeling (LNM) and show that,
with LNM, a unique structure of conditional independence relationships between
latent variables can be obtained in an explorative manner. In the second
generalization, the residual variance-covariance structure of indicators is
modeled as a network. We term this generalization Residual Network Modeling
(RNM) and show that, within this framework, identifiable models can be obtained
in which local independence is structurally violated. These generalizations
allow for a general modeling framework that can be used to fit, and compare,
SEM models, network models, and the RNM and LNM generalizations. This
methodology has been implemented in the free-to-use software package lvnet,
which contains confirmatory model testing as well as two exploratory search
algorithms: stepwise search algorithms for low-dimensional datasets and
penalized maximum likelihood estimation for larger datasets. We show in
simulation studies that these search algorithms performs adequately in
identifying the structure of the relevant residual or latent networks. We
further demonstrate the utility of these generalizations in an empirical
example on a personality inventory dataset.Comment: Published in Psychometrik
Learning Large-Scale Bayesian Networks with the sparsebn Package
Learning graphical models from data is an important problem with wide
applications, ranging from genomics to the social sciences. Nowadays datasets
often have upwards of thousands---sometimes tens or hundreds of thousands---of
variables and far fewer samples. To meet this challenge, we have developed a
new R package called sparsebn for learning the structure of large, sparse
graphical models with a focus on Bayesian networks. While there are many
existing software packages for this task, this package focuses on the unique
setting of learning large networks from high-dimensional data, possibly with
interventions. As such, the methods provided place a premium on scalability and
consistency in a high-dimensional setting. Furthermore, in the presence of
interventions, the methods implemented here achieve the goal of learning a
causal network from data. Additionally, the sparsebn package is fully
compatible with existing software packages for network analysis.Comment: To appear in the Journal of Statistical Software, 39 pages, 7 figure
Latent space models for multidimensional network data
Network data are any relational data recorded among a group of individuals, the nodes. When multiple relations are recorded among the same set of nodes, a more complex object arises, which we refer to as “multidimensional network”, or
“multiplex”, where different relations corresponding to different networks. In the past, statistical analysis of networks has mainly focused on single-relation network data, referring to a single relation of interest. Only in recent years statistical
models specifically tailored for multiplex data begun to be developed. In this context, only a few works have been introduced in the literature with the aim at extending the latent space modeling framework to multiplex data. Such framework postulates
that nodes may be characterized by latent positions in a p-dimensional Euclidean space and that the presence/absence of an edge between any two nodes depends on such positions. When considering multidimensional network data, latent space
models can help capture the associations between the nodes and summarize the observed structure in the different networks composing a multiplex. This dissertation discusses some latent space models for multidimensional network
data, to account for different features that observed multiplex data may present. A first proposal allows to jointly represent the different networks into a single latent space, so that average similarities between the nodes may be captured as
proximities in such space. A second work introduces a class of latent space models with node-specific effects, in order to deal with different degrees of heterogeneity within and between networks in multiplex data, corresponding to different types
of node-specific behaviours. A third work addresses the issue of clustering of the nodes in the latent space, a frequently observed feature in many real world network and multidimensional network data. Here, clusters of nodes in the latent space
correspond to communities of nodes in the multiplex. The proposed models are illustrated both via simulation studies and real world applications, to study their perfomances and abilities
Estimating mutual information and multi--information in large networks
We address the practical problems of estimating the information relations
that characterize large networks. Building on methods developed for analysis of
the neural code, we show that reliable estimates of mutual information can be
obtained with manageable computational effort. The same methods allow
estimation of higher order, multi--information terms. These ideas are
illustrated by analyses of gene expression, financial markets, and consumer
preferences. In each case, information theoretic measures correlate with
independent, intuitive measures of the underlying structures in the system
- …