1,524 research outputs found
Information-geometric Markov Chain Monte Carlo methods using Diffusions
Recent work incorporating geometric ideas in Markov chain Monte Carlo is
reviewed in order to highlight these advances and their possible application in
a range of domains beyond Statistics. A full exposition of Markov chains and
their use in Monte Carlo simulation for Statistical inference and molecular
dynamics is provided, with particular emphasis on methods based on Langevin
diffusions. After this geometric concepts in Markov chain Monte Carlo are
introduced. A full derivation of the Langevin diffusion on a Riemannian
manifold is given, together with a discussion of appropriate Riemannian metric
choice for different problems. A survey of applications is provided, and some
open questions are discussed.Comment: 22 pages, 2 figure
The coefficient of determination R2 and intra-class correlation coefficient from generalized linear mixed-effects models revisited and expanded
The coefficient of determinationR2quantifies the proportion of varianceexplained by a statistical model and is an important summary statisticof biological interest. However, estimatingR2for generalized linear mixedmodels (GLMMs) remains challenging. We have previously introduced a ver-sion ofR2that we calledR2GLMMfor Poisson and binomial GLMMs, but notfor other distributional families. Similarly, we earlier discussed how to estimateintra-class correlation coefficients (ICCs) using Poisson and binomial GLMMs.Inthis paper, we generalize our methodsto allothernon-Gaussian distributions,in particular to negative binomial and gamma distributions that are commonlyused formodellingbiological data. Whileexpanding ourapproach,we highlighttwo useful concepts for biologists, Jensen’s inequality and the delta method,both of which help us in understanding the properties of GLMMs. Jensen’sinequality has important implications for biologically meaningful interpretationof GLMMs, whereas the delta method allows a general derivation of varianceassociated with non-Gaussian distributions. We also discuss some special con-siderations for binomial GLMMs with binary or proportion data. We illustratethe implementation of our extension by worked examples from the field of ecol-ogy and evolution in theRenvironment. However, our method can be usedacross disciplines and regardless of statistical environments
Kinetic energy choice in Hamiltonian/hybrid Monte Carlo
We consider how different choices of kinetic energy in Hamiltonian Monte
Carlo affect algorithm performance. To this end, we introduce two quantities
which can be easily evaluated, the composite gradient and the implicit noise.
Results are established on integrator stability and geometric convergence, and
we show that choices of kinetic energy that result in heavy-tailed momentum
distributions can exhibit an undesirable negligible moves property, which we
define. A general efficiency-robustness trade off is outlined, and
implementations which rely on approximate gradients are also discussed. Two
numerical studies illustrate our theoretical findings, showing that the
standard choice which results in a Gaussian momentum distribution is not always
optimal in terms of either robustness or efficiency.Comment: 15 pages (+7 page supplement, included here as an appendix), 2
figures (+1 in supplement
Rose Effect and the Euro: The Magic is Gone
This paper presents an updated meta-analysis of the effect of currency unions on trade, focusing on the Euro area. Using meta-regression methods such as funnel asymmetry test, evidence for strong publication bias is found. The estimated underlying effect for non-Euro studies reaches about 50%. However, the Euro's trade promoting effect corrected for publication bias is insignificant. The Rose effect literature shows signs of the economics research cycle: reported t-statistic is a quadratic function of publication year. Explanatory meta-regression (robust fixed effects and random effects) suggests that some authors produce predictable results. Interestingly, proxies for authors' IT skills were also found significant.Rose effect; Trade; Currency union; Euro; Meta-analysis; Publication bias
Bounding stationary averages of polynomial diffusions via semidefinite programming
We introduce an algorithm based on semidefinite programming that yields
increasing (resp. decreasing) sequences of lower (resp. upper) bounds on
polynomial stationary averages of diffusions with polynomial drift vector and
diffusion coefficients. The bounds are obtained by optimising an objective,
determined by the stationary average of interest, over the set of real vectors
defined by certain linear equalities and semidefinite inequalities which are
satisfied by the moments of any stationary measure of the diffusion. We
exemplify the use of the approach through several applications: a Bayesian
inference problem; the computation of Lyapunov exponents of linear ordinary
differential equations perturbed by multiplicative white noise; and a
reliability problem from structural mechanics. Additionally, we prove that the
bounds converge to the infimum and supremum of the set of stationary averages
for certain SDEs associated with the computation of the Lyapunov exponents, and
we provide numerical evidence of convergence in more general settings
Age Differences in Intra-Individual Variability in Simple and Choice Reaction Time: Systematic Review and Meta-Analysis
Intra-individual variability in reaction time (RT IIV) is considered to be an index of central nervous system functioning. Such variability is elevated in neurodegenerative diseases or following traumatic brain injury. It has also been suggested to increase with age in healthy ageing.To investigate and quantify age differences in RT IIV in healthy ageing; to examine the effect of different tasks and procedures; to compare raw and mean-adjusted measures of RT IIV.Four electronic databases: PsycINFO, Medline, Web of Science and EMBASE, and hand searching of reference lists of relevant studies.English language journal articles, books or book chapters, containing quantitative empirical data on simple and/or choice RT IIV. Samples had to include younger (under 60 years) and older (60 years and above) human adults.Studies were evaluated in terms of sample representativeness and data treatment. Relevant data were extracted, using a specially-designed form, from the published report or obtained directly from the study authors. Age-group differences in raw and RT-mean-adjusted measures of simple and choice RT IIV were quantified using random effects meta-analyses.Older adults (60+ years) had greater RT IIV than younger (20-39) and middle-aged (40-59) adults. Age effects were larger in choice RT tasks than in simple RT tasks. For all measures of RT IIV, effect sizes were larger for the comparisons between older and younger adults than between older and middle-aged adults, indicating that the age-related increases in RT IIV are not limited to old age. Effect sizes were also larger for raw than for RT-mean-adjusted RT IIV measures.RT IIV is greater among older adults. Some (but not all) of the age-related increases in RT IIV are accounted for by the increased RT means
INLA or MCMC? A Tutorial and Comparative Evaluation for Spatial Prediction in log-Gaussian Cox Processes
We investigate two options for performing Bayesian inference on spatial
log-Gaussian Cox processes assuming a spatially continuous latent field: Markov
chain Monte Carlo (MCMC) and the integrated nested Laplace approximation
(INLA). We first describe the device of approximating a spatially continuous
Gaussian field by a Gaussian Markov random field on a discrete lattice, and
present a simulation study showing that, with careful choice of parameter
values, small neighbourhood sizes can give excellent approximations. We then
introduce the spatial log-Gaussian Cox process and describe MCMC and INLA
methods for spatial prediction within this model class. We report the results
of a simulation study in which we compare MALA and the technique of
approximating the continuous latent field by a discrete one, followed by
approximate Bayesian inference via INLA over a selection of 18 simulated
scenarios. The results question the notion that the latter technique is both
significantly faster and more robust than MCMC in this setting; 100,000
iterations of the MALA algorithm running in 20 minutes on a desktop PC
delivered greater predictive accuracy than the default \verb=INLA= strategy,
which ran in 4 minutes and gave comparative performance to the full Laplace
approximation which ran in 39 minutes.Comment: This replaces the previous version of the report. The new version
includes results from an additional simulation study, and corrects an error
in the implementation of the INLA-based method
Precise large deviations for dependent regularly varying sequences
We study a precise large deviation principle for a stationary regularly
varying sequence of random variables. This principle extends the classical
results of A.V. Nagaev (1969) and S.V. Nagaev (1979) for iid regularly varying
sequences. The proof uses an idea of Jakubowski (1993,1997) in the context of
centra limit theorems with infinite variance stable limits. We illustrate the
principle for \sv\ models, functions of a Markov chain satisfying a polynomial
drift condition and solutions of linear and non-linear stochastic recurrence
equations
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