360 research outputs found
A Granger Causality Measure for Point Process Models of Ensemble Neural Spiking Activity
The ability to identify directional interactions that occur among multiple neurons in the brain is crucial to an understanding
of how groups of neurons cooperate in order to generate specific brain functions. However, an optimal method of assessing
these interactions has not been established. Granger causality has proven to be an effective method for the analysis of the
directional interactions between multiple sets of continuous-valued data, but cannot be applied to neural spike train
recordings due to their discrete nature. This paper proposes a point process framework that enables Granger causality to be
applied to point process data such as neural spike trains. The proposed framework uses the point process likelihood
function to relate a neuron’s spiking probability to possible covariates, such as its own spiking history and the concurrent
activity of simultaneously recorded neurons. Granger causality is assessed based on the relative reduction of the point
process likelihood of one neuron obtained excluding one of its covariates compared to the likelihood obtained using all of
its covariates. The method was tested on simulated data, and then applied to neural activity recorded from the primary
motor cortex (MI) of a Felis catus subject. The interactions present in the simulated data were predicted with a high degree
of accuracy, and when applied to the real neural data, the proposed method identified causal relationships between many
of the recorded neurons. This paper proposes a novel method that successfully applies Granger causality to point process
data, and has the potential to provide unique physiological insights when applied to neural spike trains.National Institutes of Health (U.S.) (Grant DP1-OD003646)National Institutes of Health (U.S.) (Grant R01-EB006385
Large-scale Spatiotemporal Spike Patterning Consistent with Wave Propagation in Motor Cortex
Aggregate signals in cortex are known to be spatiotemporally organized as propagating waves across the cortical surface, but it remains unclear whether the same is true for spiking activity in individual neurons. Furthermore, the functional interactions between cortical neurons are well documented but their spatial arrangement on the cortical surface has been largely ignored. Here we use a functional network analysis to demonstrate that a subset of motor cortical neurons in non-human primates spatially coordinate their spiking activity in a manner that closely matches wave propagation measured in the beta oscillatory band of the local field potential. We also demonstrate that sequential spiking of pairs of neuron contains task-relevant information that peaks when the neurons are spatially oriented along the wave axis. We hypothesize that the spatial anisotropy of spike patterning may reflect the underlying organization of motor cortex and may be a general property shared by other cortical areas
Transfer Entropy as a Log-likelihood Ratio
Transfer entropy, an information-theoretic measure of time-directed
information transfer between joint processes, has steadily gained popularity in
the analysis of complex stochastic dynamics in diverse fields, including the
neurosciences, ecology, climatology and econometrics. We show that for a broad
class of predictive models, the log-likelihood ratio test statistic for the
null hypothesis of zero transfer entropy is a consistent estimator for the
transfer entropy itself. For finite Markov chains, furthermore, no explicit
model is required. In the general case, an asymptotic chi-squared distribution
is established for the transfer entropy estimator. The result generalises the
equivalence in the Gaussian case of transfer entropy and Granger causality, a
statistical notion of causal influence based on prediction via vector
autoregression, and establishes a fundamental connection between directed
information transfer and causality in the Wiener-Granger sense
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
Model-free reconstruction of neuronal network connectivity from calcium imaging signals
A systematic assessment of global neural network connectivity through direct
electrophysiological assays has remained technically unfeasible even in
dissociated neuronal cultures. We introduce an improved algorithmic approach
based on Transfer Entropy to reconstruct approximations to network structural
connectivities from network activity monitored through calcium fluorescence
imaging. Based on information theory, our method requires no prior assumptions
on the statistics of neuronal firing and neuronal connections. The performance
of our algorithm is benchmarked on surrogate time-series of calcium
fluorescence generated by the simulated dynamics of a network with known
ground-truth topology. We find that the effective network topology revealed by
Transfer Entropy depends qualitatively on the time-dependent dynamic state of
the network (e.g., bursting or non-bursting). We thus demonstrate how
conditioning with respect to the global mean activity improves the performance
of our method. [...] Compared to other reconstruction strategies such as
cross-correlation or Granger Causality methods, our method based on improved
Transfer Entropy is remarkably more accurate. In particular, it provides a good
reconstruction of the network clustering coefficient, allowing to discriminate
between weakly or strongly clustered topologies, whereas on the other hand an
approach based on cross-correlations would invariantly detect artificially high
levels of clustering. Finally, we present the applicability of our method to
real recordings of in vitro cortical cultures. We demonstrate that these
networks are characterized by an elevated level of clustering compared to a
random graph (although not extreme) and by a markedly non-local connectivity.Comment: 54 pages, 8 figures (+9 supplementary figures), 1 table; submitted
for publicatio
Incremental Mutual Information: A New Method for Characterizing the Strength and Dynamics of Connections in Neuronal Circuits
Understanding the computations performed by neuronal circuits requires characterizing the strength and dynamics of the connections between individual neurons. This characterization is typically achieved by measuring the correlation in the activity of two neurons. We have developed a new measure for studying connectivity in neuronal circuits based on information theory, the incremental mutual information (IMI). By conditioning out the temporal dependencies in the responses of individual neurons before measuring the dependency between them, IMI improves on standard correlation-based measures in several important ways: 1) it has the potential to disambiguate statistical dependencies that reflect the connection between neurons from those caused by other sources (e. g. shared inputs or intrinsic cellular or network mechanisms) provided that the dependencies have appropriate timescales, 2) for the study of early sensory systems, it does not require responses to repeated trials of identical stimulation, and 3) it does not assume that the connection between neurons is linear. We describe the theory and implementation of IMI in detail and demonstrate its utility on experimental recordings from the primate visual system
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