We consider the problem of estimating a parameter associated to a Bayesian inverse problem. Treating the unknown initial condition as a nuisance parameter, typically one must resort to a numerical approximation of gradient of the log-likelihood and also adopt a discretization of the problem in space and/or time. We develop a new methodology to unbiasedly estimate the gradient of the log-likelihood with respect to the unknown parameter, i.e. the expectation of the estimate has no discretization bias. Such a property is not only useful for estimation in terms of the original stochastic model of interest, but can be used in stochastic gradient algorithms which benefit from unbiased estimates. Under appropriate assumptions, we prove that our estimator is not only unbiased but of finite variance. In addition, when implemented on a single processor, we show that the cost to achieve a given level of error is comparable to multilevel Monte Carlo methods, both practically and theoretically. However, the new algorithm provides the possibility for parallel computation on arbitrarily many processors without any loss of efficiency, asymptotically. In practice, this means any precision can be achieved in a fixed, finite constant time, provided that enough processors are available.
We consider the combined use of resampling and partial rejection control in sequential Monte Carlo methods, also known as particle filters. While the variance reducing properties of rejection control are known, there has not been (to the best of our knowledge) any work on unbiased estimation of the marginal likelihood (also known as the model evidence or the normalizing constant) in this type of particle filter. Being able to estimate the marginal likelihood without bias is highly relevant for model comparison, computation of interpretable and reliable confidence intervals, and in exact approx…
When an unbiased estimator of the likelihood is used within a Metropolis--Hastings chain, it is necessary to trade off the number of Monte Carlo samples used to construct this estimator against the asymptotic variances of averages computed under this chain. Many Monte Carlo samples will typically result in Metropolis--Hastings averages with lower asymptotic variances than the corresponding Metropolis--Hastings averages using fewer samples. However, the computing time required to construct the likelihood estimator increases with the number of Monte Carlo samples. Under the assumption that the d…
Estimating copulas with discrete marginal distributions is challenging, especially in high dimensions, because computing the likelihood contribution of each observation requires evaluating $2^{J}$ terms, with $J$ the number of discrete variables. Currently, data augmentation methods are used to carry out inference for discrete copula and, in practice, the computation becomes infeasible when $J$ is large. Our article proposes two new fast Bayesian approaches for estimating high dimensional copulas with discrete margins, or a combination of discrete and continuous margins. Both methods are based…
The variational auto-encoder (VAE) is a deep latent variable model that has two neural networks in an autoencoder-like architecture; one of them parameterizes the model's likelihood. Fitting its parameters via maximum likelihood (ML) is challenging since the computation of the marginal likelihood involves an intractable integral over the latent space; thus the VAE is trained instead by maximizing a variational lower bound. Here, we develop a ML training scheme for VAEs by introducing unbiased estimators of the log-likelihood gradient. We obtain the estimators by augmenting the latent space wit…
In this note we introduce an estimate for the marginal likelihood associated to hidden Markov models (HMMs) using sequential Monte Carlo (SMC) approximations of the generalized two-filter smoothing decomposition (Briers, 2010). This estimate is shown to be unbiased and a central limit theorem (CLT) is established. This latter CLT also allows one to prove a CLT associated to estimates of expectations w.r.t. a marginal of the joint smoothing distribution; these form some of the first theoretical results associated to the SMC approximation of the generalized two-filter smoothing decomposition. Th…
Stabilised weighted data subsampling for accelerated Bayesian inference in models with recursive likelihoods
University of Technology Sydney（悉尼科技大学）；University of New South Wales（新南威尔士大学）；Human Technology Institute, University of Technology Sydney（悉尼科技大学人类技术研究所）
Recent advances in Markov chain Monte Carlo (MCMC) extend the scope of Bayesian inference to models for which the likelihood function is intractable. Although these developments allow us to estimate model parameters, other basic problems such as estimating the marginal likelihood, a fundamental tool in Bayesian model selection, remain challenging. This is an important scientific limitation because testing psychological hypotheses with hierarchical models has proven difficult with current model selection methods. We propose an efficient method for estimating the marginal likelihood for models w…
Variational Bayes (VB) is a popular estimation method for Bayesian inference. However, most existing VB algorithms are restricted to cases where the likelihood is tractable, which precludes their use in many important situations. Tran et al. (2017) extend the scope of application of VB to cases where the likelihood is intractable but can be estimated unbiasedly, and name the method Variational Bayes with Intractable Likelihood (VBIL). This paper presents a version of VBIL, named Variational Bayes with Intractable Log-Likelihood (VBILL), that is useful for cases as Big Data and Big Panel Data m…
An empirical best linear unbiased prediction (EBLUP) estimator is utilized for efficient inference in small-area estimation. To measure its uncertainty, we need to estimate its mean squared error (MSE) since the true MSE cannot generally be derived in a closed form. The "naive MSE estimator", one of the estimators available for small-area inference, is unlikely to be chosen, since it does not achieve the desired asymptotic property, namely second-order unbiasedness, although it maintains strict positivity and tractability. Therefore, users tend to choose the second-order unbiased MSE estimator…
In this short note we provide an unbiased multilevel Monte Carlo estimator of the log marginal likelihood and discuss its application to variational Bayes.
Particle Markov chain Monte Carlo (pMCMC) is now a popular method for performing Bayesian statistical inference on challenging state space models (SSMs) with unknown static parameters. It uses a particle filter (PF) at each iteration of an MCMC algorithm to unbiasedly estimate the likelihood for a given static parameter value. However, pMCMC can be computationally intensive when a large number of particles in the PF is required, such as when the data is highly informative, the model is misspecified and/or the time series is long. In this paper we exploit the ensemble Kalman filter (EnKF) devel…
We consider the problem of approximating the product of $n$ expectations with respect to a common probability distribution $μ$. Such products routinely arise in statistics as values of the likelihood in latent variable models. Motivated by pseudo-marginal Markov chain Monte Carlo schemes, we focus on unbiased estimators of such products. The standard approach is to sample $N$ particles from $μ$ and assign each particle to one of the expectations. This is wasteful and typically requires the number of particles to grow quadratically with the number of expectations. We propose an alternative esti…
We consider the efficient use of an approximation within Markov chain Monte Carlo (MCMC), with subsequent importance sampling (IS) correction of the Markov chain inexact output, leading to asymptotically exact inference. We detail convergence and central limit theorems for the resulting MCMC-IS estimators. We also consider the case where the approximate Markov chain is pseudo-marginal, requiring unbiased estimators for its approximate marginal target. Convergence results with asymptotic variance formulae are shown for this case, and for the case where the IS weights based on unbiased estimator…
In presence of nuisance parameters, profile likelihood inference is often unreliable and biased, particularly in small sample scenario. Over past decades several adjustments have been proposed to modify profile likelihood function in literature including a modified profile likelihood estimation technique introduced in Barndorff--Nielsen. In this study, adjustment of profile likelihood function of parameter of interest in presence of nuisance parameter is investigated. We particularly focuss to extend the Barndorff--Nielsen's technique on Inverse Gaussian distribution for estimating its dispers…
The pseudo-marginal (PM) approach is increasingly used for Bayesian inference in statistical models, where the likelihood is intractable but can be estimated unbiasedly. %Examples include random effect models, state-space models and data subsampling in big-data settings. Deligiannidis et al. (2016) show how the PM approach can be made much more efficient by correlating the underlying Monte Carlo (MC) random numbers used to form the estimate of the likelihood at the current and proposed values of the unknown parameters. Their approach greatly speeds up the standard PM algorithm, as it requires …
Synthetic likelihood is an attractive approach to likelihood-free inference when an approximately Gaussian summary statistic for the data, informative for inference about the parameters, is available. The synthetic likelihood method derives an approximate likelihood function from a plug-in normal density estimate for the summary statistic, with plug-in mean and covariance matrix obtained by Monte Carlo simulation from the model. In this article, we develop alternatives to Markov chain Monte Carlo implementations of Bayesian synthetic likelihoods with reduced computational overheads. Our approa…
In this article, we consider computing expectations w.r.t. probability measures which are subject to discretization error. Examples include partially observed diffusion processes or inverse problems, where one may have to discretize time and/or space, in order to practically work with the probability of interest. Given access only to these discretizations, we consider the construction of unbiased Monte Carlo estimators of expectations w.r.t. such target probability distributions. It is shown how to obtain such estimators using a novel adaptation of randomization schemes and Markov simulation m…
When conducting Bayesian inference, delayed acceptance (DA) Metropolis-Hastings (MH) algorithms and DA pseudo-marginal MH algorithms can be applied when it is computationally expensive to calculate the true posterior or an unbiased estimate thereof, but a computationally cheap approximation is available. A first accept-reject stage is applied, with the cheap approximation substituted for the true posterior in the MH acceptance ratio. Only for those proposals which pass through the first stage is the computationally expensive true posterior (or unbiased estimate thereof) evaluated, with a secon…
Variational Bayes (VB) is rapidly becoming a popular tool for Bayesian inference in statistical modeling. However, the existing VB algorithms are restricted to cases where the likelihood is tractable, which precludes the use of VB in many interesting situations such as in state space models and in approximate Bayesian computation (ABC), where application of VB methods was previously impossible. This paper extends the scope of application of VB to cases where the likelihood is intractable, but can be estimated unbiasedly. The proposed VB method therefore makes it possible to carry out Bayesian …
This article addresses the problem of efficient Bayesian inference in dynamic systems using particle methods and makes a number of contributions. First, we develop a correlated pseudo-marginal (CPM) approach for Bayesian inference in state space (SS) models that is based on filtering the disturbances, rather than the states. This approach is useful when the state transition density is intractable or inefficient to compute, and also when the dimension of the disturbance is lower than the dimension of the state. Second, we propose a block pseudo-marginal (BPM) method that uses as the estimate of…
Performing numerical integration when the integrand itself cannot be evaluated point-wise is a challenging task that arises in statistical analysis, notably in Bayesian inference for models with intractable likelihood functions. Markov chain Monte Carlo (MCMC) algorithms have been proposed for this setting, such as the pseudo-marginal method for latent variable models and the exchange algorithm for a class of undirected graphical models. As with any MCMC algorithm, the resulting estimators are justified asymptotically in the limit of the number of iterations, but exhibit a bias for any fixed n…
In applications of Gaussian processes where quantification of uncertainty is a strict requirement, it is necessary to accurately characterize the posterior distribution over Gaussian process covariance parameters. Normally, this is done by means of standard Markov chain Monte Carlo (MCMC) algorithms. Motivated by the issues related to the complexity of calculating the marginal likelihood that can make MCMC algorithms inefficient, this paper develops an alternative inference framework based on Adaptive Multiple Importance Sampling (AMIS). This paper studies the application of AMIS in the case o…
We describe an "embarrassingly parallel" method for Bayesian phylogenetic inference, annealed Sequential Monte Carlo, based on recent advances in the Sequential Monte Carlo literature such as adaptive determination of annealing parameters. The algorithm provides an approximate posterior distribution over trees and evolutionary parameters as well as an unbiased estimator for the marginal likelihood. This unbiasedness property can be used for the purpose of testing the correctness of posterior simulation software. We evaluate the performance of phylogenetic annealed Sequential Monte Carlo by rev…
This paper concerns the use of the expectation-maximisation (EM) algorithm for inference in partially observed diffusion processes. In this context, a well known problem is that all except a few diffusion processes lack closed-form expressions of the transition densities. Thus, in order to estimate efficiently the EM intermediate quantity we construct, using novel techniques for unbiased estimation of diffusion transition densities, a random weight fixed-lag auxiliary particle smoother, which avoids the well known problem of particle trajectory degeneracy in the smoothing mode. The estimator i…
This paper focuses on variational inference with intractable likelihood functions that can be unbiasedly estimated. A flexible variational approximation based on Gaussian mixtures is developed, by adopting the mixture population Monte Carlo (MPMC) algorithm in \cite{cappe2008adaptive}. MPMC updates iteratively the parameters of mixture distributions with importance sampling computations, instead of the complicated gradient estimation of the optimization objective in usual variational Bayes. Noticing that MPMC uses a fixed number of mixture components, which is difficult to predict for real app…
This manuscript develops a general purpose inner-product norm for the Kendall \(τ\) and Spearman's \(ρ\), which operates as an unbiased MLE even in the presence of ties. We derive and prove the strict sub-Gaussianity of the Kemeny norm-space, thereby disproving conclusions developed by both \textcite{kendall1948} and \textcite{diaconis1977} as to the nature of the appropriate, finite sample, probability distribution and test statistics. A non-parametric MLE framework for all bivariate pairs is developed, thereby resolving an hypothesis of \textcite{olkin1994} concerning an exponential multivar…
We consider the problem of statistical inference for a class of partially-observed diffusion processes, with discretely-observed data and finite-dimensional parameters. We construct unbiased estimators of the score function, i.e. the gradient of the log-likelihood function with respect to parameters, with no time-discretization bias. These estimators can be straightforwardly employed within stochastic gradient methods to perform maximum likelihood estimation or Bayesian inference. As our proposed methodology only requires access to a time-discretization scheme such as the Euler-Maruyama method…
Posterior distributions often feature intractable normalizing constants, called marginal likelihoods or evidence, that are useful for model comparison via Bayes factors. This has motivated a number of methods for estimating ratios of normalizing constants in statistics. In computational physics the logarithm of these ratios correspond to free energy differences. Combining unbiased Markov chain Monte Carlo estimators with path sampling, also called thermodynamic integration, we propose new unbiased estimators of the logarithm of ratios of normalizing constants. As a by-product, we propose unbia…
New York University（纽约大学）；Princeton University（普林斯顿大学）；University of Helsinki（赫尔辛基大学）；University of Geneva（日内瓦大学）
The fate of scientific hypotheses often relies on the ability of a computational model to explain the data, quantified in modern statistical approaches by the likelihood function. The log-likelihood is the key element for parameter estimation and model evaluation. However, the log-likelihood of complex models in fields such as computational biology and neuroscience is often intractable to compute analytically or numerically. In those cases, researchers can often only estimate the log-likelihood by comparing observed data with synthetic observations generated by model simulations. Standard tech…
In this work we consider Bayesian inference problems with intractable likelihood functions. We present a method to compute an approximate of the posterior with a limited number of model simulations. The method features an inverse Gaussian Process regression (IGPR), i.e., one from the output of a simulation model to the input of it. Within the method, we provide an adaptive algorithm with a tempering procedure to construct the approximations of the marginal posterior distributions. With examples we demonstrate that IGPR has a competitive performance compared to some commonly used algorithms, es…
Given n observations of a p-dimensional random vector, the covariance matrix and its inverse (precision matrix) are needed in a wide range of applications. Sample covariance (e.g. its eigenstructure) can misbehave when p is comparable to the sample size n. Regularization is often used to mitigate the problem. In this paper, we proposed an l1-norm penalized pseudo-likelihood estimate for the inverse covariance matrix. This estimate is sparse due to the l1-norm penalty, and we term this method SPLICE. Its regularization path can be computed via an algorithm based on the homotopy/LARS-Lasso algor…
In applications of Gaussian processes where quantification of uncertainty is of primary interest, it is necessary to accurately characterize the posterior distribution over covariance parameters. This paper proposes an adaptation of the Stochastic Gradient Langevin Dynamics algorithm to draw samples from the posterior distribution over covariance parameters with negligible bias and without the need to compute the marginal likelihood. In Gaussian process regression, this has the enormous advantage that stochastic gradients can be computed by solving linear systems only. A novel unbiased linear …
Many imaging problems require solving an inverse problem that is ill-conditioned or ill-posed. Imaging methods typically address this difficulty by regularising the estimation problem to make it well-posed. This often requires setting the value of the so-called regularisation parameters that control the amount of regularisation enforced. These parameters are notoriously difficult to set a priori, and can have a dramatic impact on the recovered estimates. In this work, we propose a general empirical Bayesian method for setting regularisation parameters in imaging problems that are convex w.r.t.…
In this article we consider the development of unbiased estimators of the Hessian, of the log-likelihood function with respect to parameters, for partially observed diffusion processes. These processes arise in numerous applications, where such diffusions require derivative information, either through the Jacobian or Hessian matrix. As time-discretizations of diffusions induce a bias, we provide an unbiased estimator of the Hessian. This is based on using Girsanov's Theorem and randomization schemes developed through Mcleish [2011] and Rhee & Glynn [2015]. We demonstrate our developed estimato…
In a Gaussian graphical model, the conditional independence between two variables are characterized by the corresponding zero entries in the inverse covariance matrix. Maximum likelihood method using the smoothly clipped absolute deviation (SCAD) penalty (Fan and Li, 2001) and the adaptive LASSO penalty (Zou, 2006) have been proposed in literature. In this article, we establish the result that using Bayesian information criterion (BIC) to select the tuning parameter in penalized likelihood estimation with both types of penalties can lead to consistent graphical model selection. We compare the …
In this paper we introduce five different algorithms based on method of moments, maximum likelihood and full Bayesian estimation for learning the parameters of the Inverse Gamma distribution. We also provide an expression for the KL divergence for Inverse Gamma distributions which allows us to quantify the estimation accuracy of each of the algorithms. All the presented algorithms are novel. The most relevant novelties include the first conjugate prior for the Inverse Gamma shape parameter which allows analytical Bayesian inference, and two very fast algorithms, a maximum likelihood and a Baye…
We consider the use of randomised forward models and log-likelihoods within the Bayesian approach to inverse problems. Such random approximations to the exact forward model or log-likelihood arise naturally when a computationally expensive model is approximated using a cheaper stochastic surrogate, as in Gaussian process emulation (kriging), or in the field of probabilistic numerical methods. We show that the Hellinger distance between the exact and approximate Bayesian posteriors is bounded by moments of the difference between the true and approximate log-likelihoods. Example applications of …
Identifying a low-dimensional informed parameter subspace offers a viable path to alleviating the dimensionality challenge in the sampled-based solution to large-scale Bayesian inverse problems. This paper introduces a novel gradient-based dimension reduction method in which the informed subspace does not depend on the data. This permits an online-offline computational strategy where the expensive low-dimensional structure of the problem is detected in an offline phase, meaning before observing the data. This strategy is particularly relevant for multiple inversion problems as the same informe…
Inverse probability weighting (IPW) is widely used in many areas when data are subject to unrepresentativeness, missingness, or selection bias. An inevitable challenge with the use of IPW is that the IPW estimator can be remarkably unstable if some probabilities are very close to zero. To overcome this problem, at least three remedies have been developed in the literature: stabilizing, thresholding, and trimming. However the final estimators are still IPW type estimators, and inevitably inherit certain weaknesses of the naive IPW estimator: they may still be unstable or biased. We propose a bi…
This paper is concerned with Bayesian inference when the likelihood is analytically intractable but can be unbiasedly estimated. We propose an annealed importance sampling procedure for estimating expectations with respect to the posterior. The proposed algorithm is useful in cases where finding a good proposal density is challenging, and when estimates of the marginal likelihood are required. The effect of likelihood estimation is investigated, and the results provide guidelines on how to set up the precision of the likelihood estimation in order to optimally implement the procedure. The meth…
For regular parametric problems, we show how median centering of the maximum likelihood estimate can be achieved by a simple modification of the score equation. For a scalar parameter of interest, the estimator is equivariant under interest respecting parameterizations and third-order median unbiased. With a vector parameter of interest, componentwise equivariance and third-order median centering are obtained. Like Firth's (1993, Biometrika) implicit method for bias reduction, the new method does not require finiteness of the maximum likelihood estimate and is effective in preventing infinite …
In the current paper, the estimation of the probability density function and the cumulative distribution function of the Topp-Leone distribution is considered. We derive the following estimators: maximum likelihood estimator, uniformly minimum variance unbiased estimator, percentile estimator, least squares estimator and weighted least squares estimator. A simulation study shows that the maximum likelihood estimator is more efficient than the others estimators.
We consider an empirical likelihood framework for inference for a statistical model based on an informative sampling design. Covariate information is incorporated both through the weights and the estimating equations. The estimator is based on conditional weights. We show that under usual conditions, with population size increasing unbounded, the estimates are strongly consistent, asymptotically unbiased and normally distributed. Our framework provides additional justification for inverse probability weighted score estimators in terms of conditional empirical likelihood. In doing so, it bridge…
Max Planck Institute for Intelligent Systems（马克斯·普朗克智能系统研究所）；Bosch Center for Artificial Intelligence（博世人工智能中心）
Likelihood-free (a.k.a. simulation-based) inference problems are inverse problems with expensive, or intractable, forward models. ODE inverse problems are commonly treated as likelihood-free, as their forward map has to be numerically approximated by an ODE solver. This, however, is not a fundamental constraint but just a lack of functionality in classic ODE solvers, which do not return a likelihood but a point estimate. To address this shortcoming, we employ Gaussian ODE filtering (a probabilistic numerical method for ODEs) to construct a local Gaussian approximation to the likelihood. This a…
Targeted maximum likelihood estimation is a general methodology combining flexible ensemble learning and semiparametric efficiency theory in a two-step procedure for estimation of causal parameters. Proposed targeted maximum likelihood procedures for survival and competing risks analysis have so far focused on events taken values in discrete time. We here present a targeted maximum likelihood estimation procedure for event times that take values in R+. We focuson the estimation of intervention-specific mean outcomes with stochastic interventions on a time-fixed treatment. For data-adaptive est…
