16,607 research outputs found
Disentangling causal webs in the brain using functional Magnetic Resonance Imaging: A review of current approaches
In the past two decades, functional Magnetic Resonance Imaging has been used
to relate neuronal network activity to cognitive processing and behaviour.
Recently this approach has been augmented by algorithms that allow us to infer
causal links between component populations of neuronal networks. Multiple
inference procedures have been proposed to approach this research question but
so far, each method has limitations when it comes to establishing whole-brain
connectivity patterns. In this work, we discuss eight ways to infer causality
in fMRI research: Bayesian Nets, Dynamical Causal Modelling, Granger Causality,
Likelihood Ratios, LiNGAM, Patel's Tau, Structural Equation Modelling, and
Transfer Entropy. We finish with formulating some recommendations for the
future directions in this area
Editorial Comment on the Special Issue of "Information in Dynamical Systems and Complex Systems"
This special issue collects contributions from the participants of the
"Information in Dynamical Systems and Complex Systems" workshop, which cover a
wide range of important problems and new approaches that lie in the
intersection of information theory and dynamical systems. The contributions
include theoretical characterization and understanding of the different types
of information flow and causality in general stochastic processes, inference
and identification of coupling structure and parameters of system dynamics,
rigorous coarse-grain modeling of network dynamical systems, and exact
statistical testing of fundamental information-theoretic quantities such as the
mutual information. The collective efforts reported herein reflect a modern
perspective of the intimate connection between dynamical systems and
information flow, leading to the promise of better understanding and modeling
of natural complex systems and better/optimal design of engineering systems
Maximum Entropy Vector Kernels for MIMO system identification
Recent contributions have framed linear system identification as a
nonparametric regularized inverse problem. Relying on -type
regularization which accounts for the stability and smoothness of the impulse
response to be estimated, these approaches have been shown to be competitive
w.r.t classical parametric methods. In this paper, adopting Maximum Entropy
arguments, we derive a new penalty deriving from a vector-valued
kernel; to do so we exploit the structure of the Hankel matrix, thus
controlling at the same time complexity, measured by the McMillan degree,
stability and smoothness of the identified models. As a special case we recover
the nuclear norm penalty on the squared block Hankel matrix. In contrast with
previous literature on reweighted nuclear norm penalties, our kernel is
described by a small number of hyper-parameters, which are iteratively updated
through marginal likelihood maximization; constraining the structure of the
kernel acts as a (hyper)regularizer which helps controlling the effective
degrees of freedom of our estimator. To optimize the marginal likelihood we
adapt a Scaled Gradient Projection (SGP) algorithm which is proved to be
significantly computationally cheaper than other first and second order
off-the-shelf optimization methods. The paper also contains an extensive
comparison with many state-of-the-art methods on several Monte-Carlo studies,
which confirms the effectiveness of our procedure
On directed information theory and Granger causality graphs
Directed information theory deals with communication channels with feedback.
When applied to networks, a natural extension based on causal conditioning is
needed. We show here that measures built from directed information theory in
networks can be used to assess Granger causality graphs of stochastic
processes. We show that directed information theory includes measures such as
the transfer entropy, and that it is the adequate information theoretic
framework needed for neuroscience applications, such as connectivity inference
problems.Comment: accepted for publications, Journal of Computational Neuroscienc
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
Supervised estimation of Granger-based causality between time series
Brain effective connectivity aims to detect causal interactions between distinct brain units and it is typically studied through the analysis of direct measurements of the neural activity, e.g., magneto/electroencephalography (M/EEG) signals. The literature on methods for causal inference is vast. It includes model-based methods in which a generative model of the data is assumed and model-free methods that directly infer causality from the probability distribution of the underlying stochastic process. Here, we firstly focus on the model-based methods developed from the Granger criterion of causality, which assumes the autoregressive model of the data. Secondly, we introduce a new perspective, that looks at the problem in a way that is typical of the machine learning literature. Then, we formulate the problem of causality detection as a supervised learning task, by proposing a classification-based approach. A classifier is trained to identify causal interactions between time series for the chosen model and by means of a proposed feature space. In this paper, we are interested in comparing this classification-based approach with the standard Geweke measure of causality in the time domain, through simulation study. Thus, we customized our approach to the case of a MAR model and designed a feature space which contains causality measures based on the idea of precedence and predictability in time. Two variations of the supervised method are proposed and compared to a standard Granger causal analysis method. The results of the simulations show that the supervised method outperforms the standard approach, in particular it is more robust to noise. As evidence of the efficacy of the proposed method, we report the details of our submission to the causality detection competition of Biomag2014, where the proposed method reached the 2nd place. Moreover, as empirical application, we applied the supervised approach on a dataset of neural recordings of rats obtaining an important reduction in the false positive rate
Pedestrian Attribute Recognition: A Survey
Recognizing pedestrian attributes is an important task in computer vision
community due to it plays an important role in video surveillance. Many
algorithms has been proposed to handle this task. The goal of this paper is to
review existing works using traditional methods or based on deep learning
networks. Firstly, we introduce the background of pedestrian attributes
recognition (PAR, for short), including the fundamental concepts of pedestrian
attributes and corresponding challenges. Secondly, we introduce existing
benchmarks, including popular datasets and evaluation criterion. Thirdly, we
analyse the concept of multi-task learning and multi-label learning, and also
explain the relations between these two learning algorithms and pedestrian
attribute recognition. We also review some popular network architectures which
have widely applied in the deep learning community. Fourthly, we analyse
popular solutions for this task, such as attributes group, part-based,
\emph{etc}. Fifthly, we shown some applications which takes pedestrian
attributes into consideration and achieve better performance. Finally, we
summarized this paper and give several possible research directions for
pedestrian attributes recognition. The project page of this paper can be found
from the following website:
\url{https://sites.google.com/view/ahu-pedestrianattributes/}.Comment: Check our project page for High Resolution version of this survey:
https://sites.google.com/view/ahu-pedestrianattributes
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