10,182 research outputs found
Global sensitivity analysis for stochastic simulators based on generalized lambda surrogate models
Global sensitivity analysis aims at quantifying the impact of input
variability onto the variation of the response of a computational model. It has
been widely applied to deterministic simulators, for which a set of input
parameters has a unique corresponding output value. Stochastic simulators,
however, have intrinsic randomness due to their use of (pseudo)random numbers,
so they give different results when run twice with the same input parameters
but non-common random numbers. Due to this random nature, conventional Sobol'
indices, used in global sensitivity analysis, can be extended to stochastic
simulators in different ways. In this paper, we discuss three possible
extensions and focus on those that depend only on the statistical dependence
between input and output. This choice ignores the detailed data generating
process involving the internal randomness, and can thus be applied to a wider
class of problems. We propose to use the generalized lambda model to emulate
the response distribution of stochastic simulators. Such a surrogate can be
constructed without the need for replications. The proposed method is applied
to three examples including two case studies in finance and epidemiology. The
results confirm the convergence of the approach for estimating the sensitivity
indices even with the presence of strong heteroskedasticity and small
signal-to-noise ratio
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
Categorical Inputs, Sensitivity Analysis, Optimization and Importance Tempering with tgp Version 2, an R Package for Treed Gaussian Process Models
This document describes the new features in version 2.x of the tgp package for R, implementing treed Gaussian process (GP) models. The topics covered include methods for dealing with categorical inputs and excluding inputs from the tree or GP part of the model; fully Bayesian sensitivity analysis for inputs/covariates; sequential optimization of black-box functions; and a new Monte Carlo method for inference in multi-modal posterior distributions that combines simulated tempering and importance sampling. These additions extend the functionality of tgp across all models in the hierarchy: from Bayesian linear models, to classification and regression trees (CART), to treed Gaussian processes with jumps to the limiting linear model. It is assumed that the reader is familiar with the baseline functionality of the package, outlined in the first vignette (Gramacy 2007).
Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package
We introduce the \texttt{pyunicorn} (Pythonic unified complex network and
recurrence analysis toolbox) open source software package for applying and
combining modern methods of data analysis and modeling from complex network
theory and nonlinear time series analysis. \texttt{pyunicorn} is a fully
object-oriented and easily parallelizable package written in the language
Python. It allows for the construction of functional networks such as climate
networks in climatology or functional brain networks in neuroscience
representing the structure of statistical interrelationships in large data sets
of time series and, subsequently, investigating this structure using advanced
methods of complex network theory such as measures and models for spatial
networks, networks of interacting networks, node-weighted statistics or network
surrogates. Additionally, \texttt{pyunicorn} provides insights into the
nonlinear dynamics of complex systems as recorded in uni- and multivariate time
series from a non-traditional perspective by means of recurrence quantification
analysis (RQA), recurrence networks, visibility graphs and construction of
surrogate time series. The range of possible applications of the library is
outlined, drawing on several examples mainly from the field of climatology.Comment: 28 pages, 17 figure
Coordinate Transformation and Polynomial Chaos for the Bayesian Inference of a Gaussian Process with Parametrized Prior Covariance Function
This paper addresses model dimensionality reduction for Bayesian inference
based on prior Gaussian fields with uncertainty in the covariance function
hyper-parameters. The dimensionality reduction is traditionally achieved using
the Karhunen-\Loeve expansion of a prior Gaussian process assuming covariance
function with fixed hyper-parameters, despite the fact that these are uncertain
in nature. The posterior distribution of the Karhunen-Lo\`{e}ve coordinates is
then inferred using available observations. The resulting inferred field is
therefore dependent on the assumed hyper-parameters. Here, we seek to
efficiently estimate both the field and covariance hyper-parameters using
Bayesian inference. To this end, a generalized Karhunen-Lo\`{e}ve expansion is
derived using a coordinate transformation to account for the dependence with
respect to the covariance hyper-parameters. Polynomial Chaos expansions are
employed for the acceleration of the Bayesian inference using similar
coordinate transformations, enabling us to avoid expanding explicitly the
solution dependence on the uncertain hyper-parameters. We demonstrate the
feasibility of the proposed method on a transient diffusion equation by
inferring spatially-varying log-diffusivity fields from noisy data. The
inferred profiles were found closer to the true profiles when including the
hyper-parameters' uncertainty in the inference formulation.Comment: 34 pages, 17 figure
Dynamic fluctuations coincide with periods of high and low modularity in resting-state functional brain networks
We investigate the relationship of resting-state fMRI functional connectivity
estimated over long periods of time with time-varying functional connectivity
estimated over shorter time intervals. We show that using Pearson's correlation
to estimate functional connectivity implies that the range of fluctuations of
functional connections over short time scales is subject to statistical
constraints imposed by their connectivity strength over longer scales. We
present a method for estimating time-varying functional connectivity that is
designed to mitigate this issue and allows us to identify episodes where
functional connections are unexpectedly strong or weak. We apply this method to
data recorded from participants, and show that the number of
unexpectedly strong/weak connections fluctuates over time, and that these
variations coincide with intermittent periods of high and low modularity in
time-varying functional connectivity. We also find that during periods of
relative quiescence regions associated with default mode network tend to join
communities with attentional, control, and primary sensory systems. In
contrast, during periods where many connections are unexpectedly strong/weak,
default mode regions dissociate and form distinct modules. Finally, we go on to
show that, while all functional connections can at times manifest stronger
(more positively correlated) or weaker (more negatively correlated) than
expected, a small number of connections, mostly within the visual and
somatomotor networks, do so a disproportional number of times. Our statistical
approach allows the detection of functional connections that fluctuate more or
less than expected based on their long-time averages and may be of use in
future studies characterizing the spatio-temporal patterns of time-varying
functional connectivityComment: 47 Pages, 8 Figures, 4 Supplementary Figure
Risk Aversion in Finite Markov Decision Processes Using Total Cost Criteria and Average Value at Risk
In this paper we present an algorithm to compute risk averse policies in
Markov Decision Processes (MDP) when the total cost criterion is used together
with the average value at risk (AVaR) metric. Risk averse policies are needed
when large deviations from the expected behavior may have detrimental effects,
and conventional MDP algorithms usually ignore this aspect. We provide
conditions for the structure of the underlying MDP ensuring that approximations
for the exact problem can be derived and solved efficiently. Our findings are
novel inasmuch as average value at risk has not previously been considered in
association with the total cost criterion. Our method is demonstrated in a
rapid deployment scenario, whereby a robot is tasked with the objective of
reaching a target location within a temporal deadline where increased speed is
associated with increased probability of failure. We demonstrate that the
proposed algorithm not only produces a risk averse policy reducing the
probability of exceeding the expected temporal deadline, but also provides the
statistical distribution of costs, thus offering a valuable analysis tool
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