6,720 research outputs found
Estimating Time-Varying Effective Connectivity in High-Dimensional fMRI Data Using Regime-Switching Factor Models
Recent studies on analyzing dynamic brain connectivity rely on sliding-window
analysis or time-varying coefficient models which are unable to capture both
smooth and abrupt changes simultaneously. Emerging evidence suggests
state-related changes in brain connectivity where dependence structure
alternates between a finite number of latent states or regimes. Another
challenge is inference of full-brain networks with large number of nodes. We
employ a Markov-switching dynamic factor model in which the state-driven
time-varying connectivity regimes of high-dimensional fMRI data are
characterized by lower-dimensional common latent factors, following a
regime-switching process. It enables a reliable, data-adaptive estimation of
change-points of connectivity regimes and the massive dependencies associated
with each regime. We consider the switching VAR to quantity the dynamic
effective connectivity. We propose a three-step estimation procedure: (1)
extracting the factors using principal component analysis (PCA) and (2)
identifying dynamic connectivity states using the factor-based switching vector
autoregressive (VAR) models in a state-space formulation using Kalman filter
and expectation-maximization (EM) algorithm, and (3) constructing the
high-dimensional connectivity metrics for each state based on subspace
estimates. Simulation results show that our proposed estimator outperforms the
K-means clustering of time-windowed coefficients, providing more accurate
estimation of regime dynamics and connectivity metrics in high-dimensional
settings. Applications to analyzing resting-state fMRI data identify dynamic
changes in brain states during rest, and reveal distinct directed connectivity
patterns and modular organization in resting-state networks across different
states.Comment: 21 page
Brain covariance selection: better individual functional connectivity models using population prior
Spontaneous brain activity, as observed in functional neuroimaging, has been
shown to display reproducible structure that expresses brain architecture and
carries markers of brain pathologies. An important view of modern neuroscience
is that such large-scale structure of coherent activity reflects modularity
properties of brain connectivity graphs. However, to date, there has been no
demonstration that the limited and noisy data available in spontaneous activity
observations could be used to learn full-brain probabilistic models that
generalize to new data. Learning such models entails two main challenges: i)
modeling full brain connectivity is a difficult estimation problem that faces
the curse of dimensionality and ii) variability between subjects, coupled with
the variability of functional signals between experimental runs, makes the use
of multiple datasets challenging. We describe subject-level brain functional
connectivity structure as a multivariate Gaussian process and introduce a new
strategy to estimate it from group data, by imposing a common structure on the
graphical model in the population. We show that individual models learned from
functional Magnetic Resonance Imaging (fMRI) data using this population prior
generalize better to unseen data than models based on alternative
regularization schemes. To our knowledge, this is the first report of a
cross-validated model of spontaneous brain activity. Finally, we use the
estimated graphical model to explore the large-scale characteristics of
functional architecture and show for the first time that known cognitive
networks appear as the integrated communities of functional connectivity graph.Comment: in Advances in Neural Information Processing Systems, Vancouver :
Canada (2010
Tensor Analysis and Fusion of Multimodal Brain Images
Current high-throughput data acquisition technologies probe dynamical systems
with different imaging modalities, generating massive data sets at different
spatial and temporal resolutions posing challenging problems in multimodal data
fusion. A case in point is the attempt to parse out the brain structures and
networks that underpin human cognitive processes by analysis of different
neuroimaging modalities (functional MRI, EEG, NIRS etc.). We emphasize that the
multimodal, multi-scale nature of neuroimaging data is well reflected by a
multi-way (tensor) structure where the underlying processes can be summarized
by a relatively small number of components or "atoms". We introduce
Markov-Penrose diagrams - an integration of Bayesian DAG and tensor network
notation in order to analyze these models. These diagrams not only clarify
matrix and tensor EEG and fMRI time/frequency analysis and inverse problems,
but also help understand multimodal fusion via Multiway Partial Least Squares
and Coupled Matrix-Tensor Factorization. We show here, for the first time, that
Granger causal analysis of brain networks is a tensor regression problem, thus
allowing the atomic decomposition of brain networks. Analysis of EEG and fMRI
recordings shows the potential of the methods and suggests their use in other
scientific domains.Comment: 23 pages, 15 figures, submitted to Proceedings of the IEE
Modeling Dynamic Functional Connectivity with Latent Factor Gaussian Processes
Dynamic functional connectivity, as measured by the time-varying covariance
of neurological signals, is believed to play an important role in many aspects
of cognition. While many methods have been proposed, reliably establishing the
presence and characteristics of brain connectivity is challenging due to the
high dimensionality and noisiness of neuroimaging data. We present a latent
factor Gaussian process model which addresses these challenges by learning a
parsimonious representation of connectivity dynamics. The proposed model
naturally allows for inference and visualization of time-varying connectivity.
As an illustration of the scientific utility of the model, application to a
data set of rat local field potential activity recorded during a complex
non-spatial memory task provides evidence of stimuli differentiation
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
- …