30,320 research outputs found
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
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
Efficient transfer entropy analysis of non-stationary neural time series
Information theory allows us to investigate information processing in neural
systems in terms of information transfer, storage and modification. Especially
the measure of information transfer, transfer entropy, has seen a dramatic
surge of interest in neuroscience. Estimating transfer entropy from two
processes requires the observation of multiple realizations of these processes
to estimate associated probability density functions. To obtain these
observations, available estimators assume stationarity of processes to allow
pooling of observations over time. This assumption however, is a major obstacle
to the application of these estimators in neuroscience as observed processes
are often non-stationary. As a solution, Gomez-Herrero and colleagues
theoretically showed that the stationarity assumption may be avoided by
estimating transfer entropy from an ensemble of realizations. Such an ensemble
is often readily available in neuroscience experiments in the form of
experimental trials. Thus, in this work we combine the ensemble method with a
recently proposed transfer entropy estimator to make transfer entropy
estimation applicable to non-stationary time series. We present an efficient
implementation of the approach that deals with the increased computational
demand of the ensemble method's practical application. In particular, we use a
massively parallel implementation for a graphics processing unit to handle the
computationally most heavy aspects of the ensemble method. We test the
performance and robustness of our implementation on data from simulated
stochastic processes and demonstrate the method's applicability to
magnetoencephalographic data. While we mainly evaluate the proposed method for
neuroscientific data, we expect it to be applicable in a variety of fields that
are concerned with the analysis of information transfer in complex biological,
social, and artificial systems.Comment: 27 pages, 7 figures, submitted to PLOS ON
Electroencephalography (EEG)-Derived Markers to Measure Components of Attention Processing
Although extensively studied for decades,
attention system remains an interesting challenge in
neuroscience field. The Attention Network Task (ANT)
has been developed to provide a measure of the
efficiency for the three attention components identified
in the Posner’s theoretical model: alerting, orienting and
executive control. Here we propose a study on 15 healthy
subjects who performed the ANT. We combined
advanced methods for connectivity estimation on
electroencephalographic (EEG) signals and graph theory
with the aim to identify neuro-physiological indices
describing the most important features of the three
networks correlated with behavioral performances. Our
results provided a set of band-specific connectivity
indices able to follow the behavioral task performances
among subjects for each attention component as defined
in the ANT paradigm. Extracted EEG-based indices
could be employed in future clinical applications to
support the behavioral assessment or to evaluate the
influence of specific attention deficits on Brain Computer
Interface (BCI) performance and/or the effects of BCI
training in cognitive rehabilitation applications
Conditional Reliability in Uncertain Graphs
Network reliability is a well-studied problem that requires to measure the
probability that a target node is reachable from a source node in a
probabilistic (or uncertain) graph, i.e., a graph where every edge is assigned
a probability of existence. Many approaches and problem variants have been
considered in the literature, all assuming that edge-existence probabilities
are fixed. Nevertheless, in real-world graphs, edge probabilities typically
depend on external conditions. In metabolic networks a protein can be converted
into another protein with some probability depending on the presence of certain
enzymes. In social influence networks the probability that a tweet of some user
will be re-tweeted by her followers depends on whether the tweet contains
specific hashtags. In transportation networks the probability that a network
segment will work properly or not might depend on external conditions such as
weather or time of the day. In this paper we overcome this limitation and focus
on conditional reliability, that is assessing reliability when edge-existence
probabilities depend on a set of conditions. In particular, we study the
problem of determining the k conditions that maximize the reliability between
two nodes. We deeply characterize our problem and show that, even employing
polynomial-time reliability-estimation methods, it is NP-hard, does not admit
any PTAS, and the underlying objective function is non-submodular. We then
devise a practical method that targets both accuracy and efficiency. We also
study natural generalizations of the problem with multiple source and target
nodes. An extensive empirical evaluation on several large, real-life graphs
demonstrates effectiveness and scalability of the proposed methods.Comment: 14 pages, 13 figure
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