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65
Implementing approximate Bayesian inference for latent Gaussian models using integrated nested Laplace approximations: A manual for the inlaprogram
, 2008
"... Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalised) linear models, (generalised) additive models, smoothingspline models, statespace models, semiparametric regression, spatial and spatiotemp ..."
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Cited by 91 (17 self)
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Structured additive regression models are perhaps the most commonly used class of models in statistical applications. It includes, among others, (generalised) linear models, (generalised) additive models, smoothingspline models, statespace models, semiparametric regression, spatial and spatiotemporal models, logGaussian Coxprocesses, geostatistical and geoadditive models. In this paper we consider approximate Bayesian inference in a popular subset of structured additive regression models, latent Gaussian models, where the latent field is Gaussian, controlled by a few hyperparameters and with nonGaussian response variables. The posterior marginals are not available in closed form due to the nonGaussian response variables. For such models, Markov chain Monte Carlo methods can be implemented, but they are not without problems, both in terms of convergence and computational time. In some practical applications, the extent of these problems is such that Markov chain Monte Carlo is simply not an appropriate tool for routine analysis. We show that, by using an integrated nested Laplace approximation and its simplified version, we can directly compute very accurate approximations to the posterior marginals. The main benefit of these approximations
Bayesian inference for nonlinear multivariate diffusion models observed with error
 Computational Statistics and Data Analysis
, 2008
"... Diffusion processes governed by stochastic differential equations (SDEs) are a well established tool for modelling continuous time data from a wide range of areas. Consequently, techniques have been developed to estimate diffusion parameters from partial and discrete observations. Likelihood based i ..."
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Cited by 37 (7 self)
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Diffusion processes governed by stochastic differential equations (SDEs) are a well established tool for modelling continuous time data from a wide range of areas. Consequently, techniques have been developed to estimate diffusion parameters from partial and discrete observations. Likelihood based inference can be problematic as closed form transition densities are rarely available. One widely used solution involves the introduction of latent data points between every pair of observations to allow an EulerMaruyama approximation of the true transition densities to become accurate. In recent literature, Markov chain Monte Carlo (MCMC) methods have been used to sample the posterior distribution of latent data and model parameters; however, naive schemes suffer from a mixing problem that worsens with the degree of augmentation. In this paper, we explore an MCMC scheme whose performance is not adversely affected by the number of latent values. We illustrate the methodology by estimating parameters governing an autoregulatory gene network, using partial and discrete data that is subject to measurement error.
Variational inference for diffusion processes
 In
, 2008
"... Diffusion processes are a family of continuoustime continuousstate stochastic processes that are in general only partially observed. The joint estimation of the forcing parameters and the system noise (volatility) in these dynamical systems is a crucial, but nontrivial task, especially when the s ..."
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Cited by 20 (4 self)
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Diffusion processes are a family of continuoustime continuousstate stochastic processes that are in general only partially observed. The joint estimation of the forcing parameters and the system noise (volatility) in these dynamical systems is a crucial, but nontrivial task, especially when the system is nonlinear and multimodal. We propose a variational treatment of diffusion processes, which allows us to compute type II maximum likelihood estimates of the parameters by simple gradient techniques and which is computationally less demanding than most MCMC approaches. We also show how a cheap estimate of the posterior over the parameters can be constructed based on the variational free energy. 1
Computational Methods for Complex Stochastic Systems: A Review of Some Alternatives to MCMC
"... We consider analysis of complex stochastic models based upon partial information. MCMC and reversible jump MCMC are often the methods of choice for such problems, but in some situations they can be difficult to implement; and suffer from problems such as poor mixing, and the difficulty of diagnosing ..."
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Cited by 15 (2 self)
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We consider analysis of complex stochastic models based upon partial information. MCMC and reversible jump MCMC are often the methods of choice for such problems, but in some situations they can be difficult to implement; and suffer from problems such as poor mixing, and the difficulty of diagnosing convergence. Here we review three alternatives to MCMC methods: importance sampling, the forwardbackward algorithm, and sequential Monte Carlo (SMC). We discuss how to design good proposal densities for importance sampling, show some of the range of models for which the forwardbackward algorithm can be applied, and show how resampling ideas from SMC can be used to improve the efficiency of the other two methods. We demonstrate these methods on a range of examples, including estimating the transition density of a diffusion and of a discretestate continuoustime Markov chain; inferring structure in population genetics; and segmenting genetic divergence data.
Time series analysis via mechanistic models. In review; prepublished at arxiv.org/abs/0802.0021
, 2008
"... The purpose of time series analysis via mechanistic models is to reconcile the known or hypothesized structure of a dynamical system with observations collected over time. We develop a framework for constructing nonlinear mechanistic models and carrying out inference. Our framework permits the consi ..."
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Cited by 13 (5 self)
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The purpose of time series analysis via mechanistic models is to reconcile the known or hypothesized structure of a dynamical system with observations collected over time. We develop a framework for constructing nonlinear mechanistic models and carrying out inference. Our framework permits the consideration of implicit dynamic models, meaning statistical models for stochastic dynamical systems which are specified by a simulation algorithm to generate sample paths. Inference procedures that operate on implicit models are said to have the plugandplay property. Our work builds on recently developed plugandplay inference methodology for partially observed Markov models. We introduce a class of implicitly specified Markov chains with stochastic transition rates, and we demonstrate its applicability to open problems in statistical inference for biological systems. As one example, these models are shown to give a fresh perspective on measles transmission dynamics. As a second example, we present a mechanistic analysis of cholera incidence data, involving interaction between two competing strains of the pathogen Vibrio cholerae. 1. Introduction. A
Statistical Aspects of the fractional stochastic calculus
 ANN. STAT
, 2007
"... We apply the techniques of stochastic integration with respect to the fractional Brownian motion and the theory of regularity and supremum estimation for stochastic processes to study the maximum likelihood estimator (MLE) for the drift parameter of stochastic processes satisfying stochastic equati ..."
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Cited by 11 (5 self)
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We apply the techniques of stochastic integration with respect to the fractional Brownian motion and the theory of regularity and supremum estimation for stochastic processes to study the maximum likelihood estimator (MLE) for the drift parameter of stochastic processes satisfying stochastic equations driven by fractional Brownian motion with any level of Holderregularity (any Hurst parameter). We prove existence and strong consistency of the MLE for linear and nonlinear equations. We also prove that a version of the MLE using only discrete observations is still a strongly consistent estimator.
A General Framework for the Parametrization of Hierarchical Models
 Statistical Science
, 2007
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Monte Carlo maximum likelihood estimation for discretely observed diffusion porcesses
 The Annals of Statistics
, 2009
"... This paper introduces a Monte Carlo method for maximum likelihood inference in the context of discretely observed diffusion processes. The method gives unbiased and a.s. continuous estimators of the likelihood function for a family of diffusion models and its performance in numerical examples is com ..."
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Cited by 10 (1 self)
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This paper introduces a Monte Carlo method for maximum likelihood inference in the context of discretely observed diffusion processes. The method gives unbiased and a.s. continuous estimators of the likelihood function for a family of diffusion models and its performance in numerical examples is computationally efficient. It uses a recently developed technique for the exact simulation of diffusions, and involves no discretization error. We show that, under regularity conditions, the Monte Carlo MLE converges a.s. to the true MLE. For datasize n → ∞, we show that the number of Monte Carlo iterations should be tuned as O(n 1/2) and we demonstrate the consistency properties of the Monte Carlo MLE as an estimator of the true parameter value. 1. Introduction. We introduce a Monte Carlo
Exact retrospective Monte Carlo computation of arithmetic average Asian options, in "Monte Carlo methods and Applications", vol. 13, n o 2
"... Taking advantage of the recent litterature on exact simulation algorithms (Beskos, Papaspiliopoulos and Roberts [1]) and unbiased estimation of the expectation of certain fonctional integrals (Wagner [27], Beskos et al. [2] and Fearnhead et al. [6]), we apply an exact simulation based technique for ..."
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Cited by 6 (0 self)
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Taking advantage of the recent litterature on exact simulation algorithms (Beskos, Papaspiliopoulos and Roberts [1]) and unbiased estimation of the expectation of certain fonctional integrals (Wagner [27], Beskos et al. [2] and Fearnhead et al. [6]), we apply an exact simulation based technique for pricing continuous arithmetic average Asian options in the Black & Scholes framework. Unlike existing Monte Carlo methods, we are no longer prone to the discretization bias resulting from the approximation of continuous time processes through discrete sampling. Numerical results of simulation studies are presented and variance reduction problems are considered.
The Gaussian Process Density Sampler
"... We present the Gaussian Process Density Sampler (GPDS), an exchangeable generative model for use in nonparametric Bayesian density estimation. Samples drawn from the GPDS are consistent with exact, independent samples from a fixed density function that is a transformation of a function drawn from a ..."
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Cited by 6 (3 self)
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We present the Gaussian Process Density Sampler (GPDS), an exchangeable generative model for use in nonparametric Bayesian density estimation. Samples drawn from the GPDS are consistent with exact, independent samples from a fixed density function that is a transformation of a function drawn from a Gaussian process prior. Our formulation allows us to infer an unknown density from data using Markov chain Monte Carlo, which gives samples from the posterior distribution over density functions and from the predictive distribution on data space. We can also infer the hyperparameters of the Gaussian process. We compare this density modeling technique to several existing techniques on a toy problem and a skullreconstruction task. 1