14,756 research outputs found
The generalized shrinkage estimator for the analysis of functional connectivity of brain signals
We develop a new statistical method for estimating functional connectivity
between neurophysiological signals represented by a multivariate time series.
We use partial coherence as the measure of functional connectivity. Partial
coherence identifies the frequency bands that drive the direct linear
association between any pair of channels. To estimate partial coherence, one
would first need an estimate of the spectral density matrix of the multivariate
time series. Parametric estimators of the spectral density matrix provide good
frequency resolution but could be sensitive when the parametric model is
misspecified. Smoothing-based nonparametric estimators are robust to model
misspecification and are consistent but may have poor frequency resolution. In
this work, we develop the generalized shrinkage estimator, which is a weighted
average of a parametric estimator and a nonparametric estimator. The optimal
weights are frequency-specific and derived under the quadratic risk criterion
so that the estimator, either the parametric estimator or the nonparametric
estimator, that performs better at a particular frequency receives heavier
weight. We validate the proposed estimator in a simulation study and apply it
on electroencephalogram recordings from a visual-motor experiment.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS396 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Graph analysis of functional brain networks: practical issues in translational neuroscience
The brain can be regarded as a network: a connected system where nodes, or
units, represent different specialized regions and links, or connections,
represent communication pathways. From a functional perspective communication
is coded by temporal dependence between the activities of different brain
areas. In the last decade, the abstract representation of the brain as a graph
has allowed to visualize functional brain networks and describe their
non-trivial topological properties in a compact and objective way. Nowadays,
the use of graph analysis in translational neuroscience has become essential to
quantify brain dysfunctions in terms of aberrant reconfiguration of functional
brain networks. Despite its evident impact, graph analysis of functional brain
networks is not a simple toolbox that can be blindly applied to brain signals.
On the one hand, it requires a know-how of all the methodological steps of the
processing pipeline that manipulates the input brain signals and extract the
functional network properties. On the other hand, a knowledge of the neural
phenomenon under study is required to perform physiological-relevant analysis.
The aim of this review is to provide practical indications to make sense of
brain network analysis and contrast counterproductive attitudes
The MVGC multivariate Granger causality toolbox: a new approach to Granger-causal inference
Background: Wiener-Granger causality (“G-causality”) is a statistical notion of causality applicable to time series data, whereby cause precedes, and helps predict, effect. It is defined in both time and frequency domains, and allows for the conditioning out of common causal influences. Originally developed in the context of econometric theory, it has since achieved broad application in the neurosciences and beyond. Prediction in the G-causality formalism is based on VAR (Vector AutoRegressive) modelling.
New Method: The MVGC Matlab c Toolbox approach to G-causal inference is based on multiple equivalent representations of a VAR model by (i) regression parameters, (ii) the autocovariance sequence and (iii) the cross-power spectral density of the underlying process. It features a variety of algorithms for moving between these representations, enabling selection of the most suitable algorithms with regard to computational efficiency and numerical accuracy.
Results: In this paper we explain the theoretical basis, computational strategy and application to empirical G-causal inference of the MVGC Toolbox. We also show via numerical simulations the advantages of our Toolbox over previous methods in terms of computational accuracy and statistical inference.
Comparison with Existing Method(s): The standard method of computing G-causality involves estimation of parameters for both a full and a nested (reduced) VAR model. The MVGC approach, by contrast, avoids explicit estimation of the reduced model, thus eliminating a source of estimation error and improving statistical power, and in addition facilitates fast and accurate estimation of the computationally awkward case of conditional G-causality in the frequency domain.
Conclusions: The MVGC Toolbox implements a flexible, powerful and efficient approach to G-causal inference.
Keywords: Granger causality, vector autoregressive modelling, time series analysi
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
Bits from Biology for Computational Intelligence
Computational intelligence is broadly defined as biologically-inspired
computing. Usually, inspiration is drawn from neural systems. This article
shows how to analyze neural systems using information theory to obtain
constraints that help identify the algorithms run by such systems and the
information they represent. Algorithms and representations identified
information-theoretically may then guide the design of biologically inspired
computing systems (BICS). The material covered includes the necessary
introduction to information theory and the estimation of information theoretic
quantities from neural data. We then show how to analyze the information
encoded in a system about its environment, and also discuss recent
methodological developments on the question of how much information each agent
carries about the environment either uniquely, or redundantly or
synergistically together with others. Last, we introduce the framework of local
information dynamics, where information processing is decomposed into component
processes of information storage, transfer, and modification -- locally in
space and time. We close by discussing example applications of these measures
to neural data and other complex systems
Seizure-onset mapping based on time-variant multivariate functional connectivity analysis of high-dimensional intracranial EEG : a Kalman filter approach
The visual interpretation of intracranial EEG (iEEG) is the standard method used in complex epilepsy surgery cases to map the regions of seizure onset targeted for resection. Still, visual iEEG analysis is labor-intensive and biased due to interpreter dependency. Multivariate parametric functional connectivity measures using adaptive autoregressive (AR) modeling of the iEEG signals based on the Kalman filter algorithm have been used successfully to localize the electrographic seizure onsets. Due to their high computational cost, these methods have been applied to a limited number of iEEG time-series (< 60). The aim of this study was to test two Kalman filter implementations, a well-known multivariate adaptive AR model (Arnold et al. 1998) and a simplified, computationally efficient derivation of it, for their potential application to connectivity analysis of high-dimensional (up to 192 channels) iEEG data. When used on simulated seizures together with a multivariate connectivity estimator, the partial directed coherence, the two AR models were compared for their ability to reconstitute the designed seizure signal connections from noisy data. Next, focal seizures from iEEG recordings (73-113 channels) in three patients rendered seizure-free after surgery were mapped with the outdegree, a graph-theory index of outward directed connectivity. Simulation results indicated high levels of mapping accuracy for the two models in the presence of low-to-moderate noise cross-correlation. Accordingly, both AR models correctly mapped the real seizure onset to the resection volume. This study supports the possibility of conducting fully data-driven multivariate connectivity estimations on high-dimensional iEEG datasets using the Kalman filter approach
High-Dimensional Dependency Structure Learning for Physical Processes
In this paper, we consider the use of structure learning methods for
probabilistic graphical models to identify statistical dependencies in
high-dimensional physical processes. Such processes are often synthetically
characterized using PDEs (partial differential equations) and are observed in a
variety of natural phenomena, including geoscience data capturing atmospheric
and hydrological phenomena. Classical structure learning approaches such as the
PC algorithm and variants are challenging to apply due to their high
computational and sample requirements. Modern approaches, often based on sparse
regression and variants, do come with finite sample guarantees, but are usually
highly sensitive to the choice of hyper-parameters, e.g., parameter
for sparsity inducing constraint or regularization. In this paper, we present
ACLIME-ADMM, an efficient two-step algorithm for adaptive structure learning,
which estimates an edge specific parameter in the first step,
and uses these parameters to learn the structure in the second step. Both steps
of our algorithm use (inexact) ADMM to solve suitable linear programs, and all
iterations can be done in closed form in an efficient block parallel manner. We
compare ACLIME-ADMM with baselines on both synthetic data simulated by partial
differential equations (PDEs) that model advection-diffusion processes, and
real data (50 years) of daily global geopotential heights to study information
flow in the atmosphere. ACLIME-ADMM is shown to be efficient, stable, and
competitive, usually better than the baselines especially on difficult
problems. On real data, ACLIME-ADMM recovers the underlying structure of global
atmospheric circulation, including switches in wind directions at the equator
and tropics entirely from the data.Comment: 21 pages, 8 figures, International Conference on Data Mining 201
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