Label switching is a well-known and fundamental problem in Bayesian estimation of mixture or hidden Markov models. In case that the prior distribution of the model parameters is the same for all states, then both the likelihood and posterior distribution are invariant to permutations of the parameters. This property makes Markov chain Monte Carlo (MCMC) samples simulated from the posterior distribution non-identifiable. In this paper, the \pkg{label.switching} package is introduced. It contains one probabilistic and seven deterministic relabelling algorithms in order to post-process a given MCMC sample, provided by the user. Each method returns a set of permutations that can be used to reorder the MCMC output. Then, any parametric function of interest can be inferred using the reordered MCMC sample. A set of user-defined permutations is also accepted, allowing the researcher to benchmark new relabelling methods against the available ones
The R package MfUSampler provides Monte Carlo Markov Chain machinery for generating samples from multivariate probability distributions using univariate sampling algorithms such as Slice Sampler and Adaptive Rejection Sampler. The sampler function performs a full cycle of univariate sampling steps, one coordinate at a time. In each step, the latest sample values obtained for other coordinates are used to form the conditional distributions. The concept is an extension of Gibbs sampling where each step involves, not an independent sample from the conditional distribution, but a Markov transition…
We present an R package bssm for Bayesian non-linear/non-Gaussian state space modelling. Unlike the existing packages, bssm allows for easy-to-use approximate inference based on Gaussian approximations such as the Laplace approximation and the extended Kalman filter. The package accommodates also discretely observed latent diffusion processes. The inference is based on fully automatic, adaptive Markov chain Monte Carlo (MCMC) on the hyperparameters, with optional importance sampling post-correction to eliminate any approximation bias. The package implements also a direct pseudo-marginal MCMC a…
Joint models for longitudinal and time-to-event data constitute an attractive modeling framework that has received a lot of interest in the recent years. This paper presents the capabilities of the R package JMbayes for fitting these models under a Bayesian approach using Markon chain Monte Carlo algorithms. JMbayes can fit a wide range of joint models, including among others joint models for continuous and categorical longitudinal responses, and provides several options for modeling the association structure between the two outcomes. In addition, this package can be used to derive dynamic pre…
Uncertainty Quantification through Markov Chain Monte Carlo (MCMC) can be prohibitively expensive for target probability densities with expensive likelihood functions, for instance when the evaluation it involves solving a Partial Differential Equation (PDE), as is the case in a wide range of engineering applications. Multilevel Delayed Acceptance (MLDA) with an Adaptive Error Model (AEM) is a novel approach, which alleviates this problem by exploiting a hierarchy of models, with increasing complexity and cost, and correcting the inexpensive models on-the-fly. The method has been integrated wi…
In \textit{computer-based testing} it has become standard to collect response accuracy (RA) and response times (RTs) for each test item. IRT models are used to measure a latent variable (e.g., ability, intelligence) using the RA observations. The information in the RTs can help to improve routine operations in (educational) testing, and provide information about speed of working. In modern applications, the joint models are needed to integrate RT information in a test analysis. The R-package LNIRT supports fitting joint models through a user-friendly setup which only requires specifying RA, RT…
Handling multimodality that commonly arises from complicated statistical models remains a challenge. Current Markov chain Monte Carlo (MCMC) methodology tackling this subject is based on an ensemble of chains targeting a product of power-tempered distributions. Despite the theoretical validity of such methods, practical implementations typically suffer from bad mixing and slow convergence due to the high-computation cost involved. In this work we study novel extensions of the t-walk algorithm, an existing MCMC method that is inexpensive and invariant to affine transformations of the state spac…
Reversible jump MCMC (RJ-MCMC) sampling techniques, which allow to jointly tackle model selection and parameter estimation problems in a coherent Bayesian framework, have become increasingly popular in the signal processing literature since the seminal paper of Andrieu and Doucet (IEEE Trans. Signal Process., 47(10), 1999). Crucial to the implementation of any RJ-MCMC sampler is the computation of the so-called Metropolis-Hastings-Green (MHG) ratio, which determines the acceptance probability for the proposed moves. It turns out that the expression of the MHG ratio that was given in the paper …
Statistical analyses proceed by an iterative process of model fitting and checking. The R-INLA package facilitates this iteration by fitting many Bayesian models much faster than alternative MCMC approaches. As the interpretation of results and model objects from Bayesian analyses can be complex, the R package INLAutils provides users with easily accessible, clear and customisable graphical summaries of model outputs from R- INLA. Furthermore, it offers a function for performing and visualizing the results of a spatial leave-one-out cross-validation (SLOOCV) approach that can be applied to com…
There is a tension between robustness and efficiency when designing Markov chain Monte Carlo (MCMC) sampling algorithms. Here we focus on robustness with respect to tuning parameters, showing that more sophisticated algorithms tend to be more sensitive to the choice of step-size parameter and less robust to heterogeneity of the distribution of interest. We characterise this phenomenon by studying the behaviour of spectral gaps as an increasingly poor step-size is chosen for the algorithm. Motivated by these considerations, we propose a novel and simple gradient-based MCMC algorithm, inspired b…
Particle MCMC involves using a particle filter within an MCMC algorithm. For inference of a model which involves an unobserved stochastic process, the standard implementation uses the particle filter to propose new values for the stochastic process, and MCMC moves to propose new values for the parameters. We show how particle MCMC can be generalised beyond this. Our key idea is to introduce new latent variables. We then use the MCMC moves to update the latent variables, and the particle filter to propose new values for the parameters and stochastic process given the latent variables. A generic…
In this article, we describe a {\tt R} package for sampling from an empirical likelihood-based posterior using a Hamiltonian Monte Carlo method. Empirical likelihood-based methodologies have been used in Bayesian modeling of many problems of interest in recent times. This semiparametric procedure can easily combine the flexibility of a non-parametric distribution estimator together with the interpretability of a parametric model. The model is specified by estimating equations-based constraints. Drawing an inference from a Bayesian empirical likelihood (BayesEL) posterior is challenging. The li…
The RRUM is a model that is frequently seen in language assessment studies. The objective of this research is to advance an MCMC algorithm for the Bayesian RRUM. The algorithm starts with estimating correlated attributes. Using a saturated model and a binary decimal conversion, the algorithm transforms possible attribute patterns to a Multinomial distribution. Along with the likelihood of an attribute pattern, a Dirichlet distribution is used as the prior to sample from the posterior. The Dirichlet distribution is constructed using Gamma distributions. Correlated attributes of examinees are ge…
Target tracking faces the challenge in coping with large volumes of data which requires efficient methods for real time applications. The complexity considered in this paper is when there is a large number of measurements which are required to be processed at each time step. Sequential Markov chain Monte Carlo (MCMC) has been shown to be a promising approach to target tracking in complex environments, especially when dealing with clutter. However, a large number of measurements usually results in large processing requirements. This paper goes beyond the current state-of-the-art and presents a …
We propose approaches for testing implementations of Markov Chain Monte Carlo methods as well as of general Monte Carlo methods. Based on statistical hypothesis tests, these approaches can be used in a unit testing framework to, for example, check if individual steps in a Gibbs sampler or a reversible jump MCMC have the desired invariant distribution. Two exact tests for assessing whether a given Markov chain has a specified invariant distribution are discussed. These and other tests of Monte Carlo methods can be embedded into a sequential method that allows low expected effort if the simulati…
GNM: The MCMC Jagger. A rocking awesome sampler. This python package is an affine invariant Markov chain Monte Carlo (MCMC) sampler based on the dynamic Gauss-Newton-Metropolis (GNM) algorithm. The GNM algorithm is specialized in sampling highly non-linear posterior probability distribution functions of the form $e^{-||f(x)||^2/2}$, and the package is an implementation of this algorithm. On top of the back-off strategy in the original GNM algorithm, there is the dynamic hyper-parameter optimization feature added to the algorithm and included in the package to help increase performance of the b…
Traditional Markov chain Monte Carlo (MCMC) sampling of hidden Markov models (HMMs) involves latent states underlying an imperfect observation process, and generates posterior samples for top-level parameters concurrently with nuisance latent variables. When potentially many HMMs are embedded within a hierarchical model, this can result in prohibitively long MCMC runtimes. We study combinations of existing methods, which are shown to vastly improve computational efficiency for these hierarchical models while maintaining the modeling flexibility provided by embedded HMMs. The methods include di…
This paper describes the R package EpiILMCT, which allows users to study the spread of infectious disease using continuous time individual level models (ILMs). The package provides tools for simulation from continuous time ILMs that are based on either spatial demographic, contact network, or a combination of both of them, and for the graphical summarization of epidemics. Model fitting is carried out within a Bayesian Markov Chain Monte Carlo (MCMC) framework. The continuous time ILMs can be implemented within either susceptible-infected-removed (SIR) or susceptible-infected-notified-removed (…
nimble is an R package for constructing algorithms and conducting inference on hierarchical models. The nimble package provides a unique combination of flexible model specification and the ability to program model-generic algorithms. Specifically, the package allows users to code models in the BUGS language, and it allows users to write algorithms that can be applied to any appropriate model. In this paper, we introduce nimble's capabilities for state-space model analysis using sequential Monte Carlo (SMC) techniques. We first provide an overview of state-space models and commonly-used SMC alg…
The Integrated Nested Laplace Approximation (INLA) has established itself as a widely used method for approximate inference on Bayesian hierarchical models which can be represented as a latent Gaussian model (LGM). INLA is based on producing an accurate approximation to the posterior marginal distributions of the parameters in the model and some other quantities of interest by using repeated approximations to intermediate distributions and integrals that appear in the computation of the posterior marginals. INLA focuses on models whose latent effects are a Gaussian Markov random field (GMRF). …
This work extends the Integrated Nested Laplace Approximation (INLA) method to latent models outside the scope of latent Gaussian models, where independent components of the latent field can have a near-Gaussian distribution. The proposed methodology is an essential component of a bigger project that aim to extend the R package INLA (R-INLA) in order to allow the user to add flexibility and challenge the Gaussian assumptions of some of the model components in a straightforward and intuitive way. Our approach is applied to two examples and the results are compared with that obtained by Markov C…
emcee is a Python library implementing a class of affine-invariant ensemble samplers for Markov chain Monte Carlo (MCMC). This package has been widely applied to probabilistic modeling problems in astrophysics where it was originally published, with some applications in other fields. When it was first released in 2012, the interface implemented in emcee was fundamentally different from the MCMC libraries that were popular at the time, such as PyMC, because it was specifically designed to work with "black box" models instead of structured graphical models. This has been a popular interface for …
This paper describes and illustrates functionality of the spNNGP R package. The package provides a suite of spatial regression models for Gaussian and non-Gaussian point-referenced outcomes that are spatially indexed. The package implements several Markov chain Monte Carlo (MCMC) and MCMC-free Nearest Neighbor Gaussian Process (NNGP) models for inference about large spatial data. Non-Gaussian outcomes are modeled using a NNGP Polya-Gamma latent variable. OpenMP parallelization options are provided to take advantage of multiprocessor systems. Package features are illustrated using simulated and…
This paper introduces the R package sgmcmc; which can be used for Bayesian inference on problems with large datasets using stochastic gradient Markov chain Monte Carlo (SGMCMC). Traditional Markov chain Monte Carlo (MCMC) methods, such as Metropolis-Hastings, are known to run prohibitively slowly as the dataset size increases. SGMCMC solves this issue by only using a subset of data at each iteration. SGMCMC requires calculating gradients of the log likelihood and log priors, which can be time consuming and error prone to perform by hand. The sgmcmc package calculates these gradients itself usi…
Hamiltonian Monte Carlo (HMC) is a premier Markov Chain Monte Carlo (MCMC) algorithm for continuous target distributions. Its full potential can only be unleashed when its problem-dependent hyperparameters are tuned well. The adaptation of one such hyperparameter, trajectory length ($τ$), has been closely examined by many research programs with the No-U-Turn Sampler (NUTS) coming out as the preferred method in 2011. A decade later, the evolving hardware profile has lead to the proliferation of personal and cloud based SIMD hardware in the form of Graphics and Tensor Processing Units (GPUs, TPU…
The use of heuristics to assess the convergence and compress the output of Markov chain Monte Carlo can be sub-optimal in terms of the empirical approximations that are produced. Typically a number of the initial states are attributed to "burn in" and removed, whilst the remainder of the chain is "thinned" if compression is also required. In this paper we consider the problem of retrospectively selecting a subset of states, of fixed cardinality, from the sample path such that the approximation provided by their empirical distribution is close to optimal. A novel method is proposed, based on gr…
The R package BiDAG implements Markov chain Monte Carlo (MCMC) methods for structure learning and sampling of Bayesian networks. The package includes tools to search for a maximum a posteriori (MAP) graph and to sample graphs from the posterior distribution given the data. A new hybrid approach to structure learning enables inference in large graphs. In the first step, we define a reduced search space by means of the PC algorithm or based on prior knowledge. In the second step, an iterative order MCMC scheme proceeds to optimize within the restricted search space and estimate the MAP graph. Sa…
The R package sns implements Stochastic Newton Sampler (SNS), a Metropolis-Hastings Monte Carlo Markov Chain algorithm where the proposal density function is a multivariate Gaussian based on a local, second-order Taylor series expansion of log-density. The mean of the proposal function is the full Newton step in Newton-Raphson optimization algorithm. Taking advantage of the local, multivariate geometry captured in log-density Hessian allows SNS to be more efficient than univariate samplers, approaching independent sampling as the density function increasingly resembles a multivariate Gaussian.…
Estimating Transition Rates in Two-State Non-Homogeneous Markov Jump Processes with Intermittent Observations: A Pseudo-Marginal McMC Approach via Honest Times
In this article, we introduce the R package EpiILM, which provides tools for simulation from, and inference for, discrete-time individual-level models of infectious disease transmission proposed by Deardon et al. (2010). The inference is set in a Bayesian framework and is carried out via Metropolis-Hastings Markov chain Monte Carlo (MCMC). For its fast implementation, key functions are coded in Fortran. Both spatial and contact network models are implemented in the package and can be set in either susceptible-infected (SI) or susceptible-infected-removed (SIR) compartmental frameworks. The use…
Practitioners of Markov chain Monte Carlo (MCMC) may hesitate to use random walk Metropolis-Hastings algorithms, especially variable-at-a-time algorithms with many parameters, because these algorithms require users to select values of tuning parameters (step sizes). These algorithms perform poorly if the step sizes are set to be too low or too high. We show in this paper that it is not difficult for an algorithm to tune these step sizes automatically to obtain a desired acceptance probability, since the logit of the acceptance probability is very nearly linear in the log of the step size, with…
Variational autoencoder (VAE) is a very popular and well-investigated generative model in neural learning research. To leverage VAE in practical tasks dealing with a massive dataset of large dimensions, it is required to deal with the difficulty of building low variance evidence lower bounds (ELBO). Markov Chain Monte Carlo (MCMC) is an effective approach to tighten the ELBO for approximating the posterior distribution and Hamiltonian Variational Autoencoder (HVAE) is an effective MCMC inspired approach for constructing a low-variance ELBO that is amenable to the reparameterization trick. The …
We introduce Pathogen.jl for simulation and inference of transmission network individual level models (TN-ILMs) of infectious disease spread in continuous time. TN-ILMs can be used to jointly infer transmission networks, event times, and model parameters within a Bayesian framework via Markov chain Monte Carlo (MCMC). We detail our specific strategies for conducting MCMC for TN-ILMs, and our implementation of these strategies in the Julia package, Pathogen.jl, which leverages key features of the Julia language. We provide an example using Pathogen.jl to simulate an epidemic following a suscept…
INRIA Lille — Nord Europe（法国国家信息与自动化研究所里尔-北欧中心）；Univ. Lille（里尔大学）；CNRS（法国国家科学研究中心）；Centrale Lille（里尔中央理工学院）；CRIStAL（里尔信号与自动化信息研究中心）
Determinantal point processes (DPPs) are distributions over sets of items that model diversity using kernels. Their applications in machine learning include summary extraction and recommendation systems. Yet, the cost of sampling from a DPP is prohibitive in large-scale applications, which has triggered an effort towards efficient approximate samplers. We build a novel MCMC sampler that combines ideas from combinatorial geometry, linear programming, and Monte Carlo methods to sample from DPPs with a fixed sample cardinality, also called projection DPPs. Our sampler leverages the ability of the…
The R package stochvol provides a fully Bayesian implementation of heteroskedasticity modeling within the framework of stochastic volatility. It utilizes Markov chain Monte Carlo (MCMC) samplers to conduct inference by obtaining draws from the posterior distribution of parameters and latent variables which can then be used for predicting future volatilities. The package can straightforwardly be employed as a stand-alone tool; moreover, it allows for easy incorporation into other MCMC samplers. The main focus of this paper is to show the functionality of stochvol. In addition, it provides a bri…
Advances in digital sensors, digital data storage and communications have resulted in systems being capable of accumulating large collections of data. In the light of dealing with the challenges that massive data present, this work proposes solutions to inference and filtering problems within the Bayesian framework. Two novel Bayesian inference algorithms are developed for non-linear and non-Gaussian state space models, able to deal with large volumes of data (or observations). These are sequential Markov chain Monte Carlo (MCMC) approaches relying on two key ideas: 1) subsample the massive da…
Markov chain Monte Carlo (MCMC) is the predominant tool used in Bayesian parameter estimation for hierarchical models. When the model expands due to an increasing number of hierarchical levels, number of groups at a particular level, or number of observations in each group, a fully Bayesian analysis via MCMC can easily become computationally demanding, even intractable. We illustrate how the steps in an MCMC for hierarchical models are predominantly one of two types: conditionally independent draws or low-dimensional draws based on summary statistics of parameters at higher levels of the hiera…
Quantifying the uncertainty in model parameters and output is a critical component in model-driven decision support systems for groundwater management. This paper presents a novel algorithmic approach which fuses Markov Chain Monte Carlo (MCMC) and Machine Learning methods to accelerate uncertainty quantification for groundwater flow models. We formulate the governing mathematical model as a Bayesian inverse problem, considering model parameters as a random process with an underlying probability distribution. MCMC allows us to sample from this distribution, but it comes with some limitations: …
This paper addresses the problem of summarizing the posterior distributions that typically arise, in a Bayesian framework, when dealing with signal decomposition problems with unknown number of components. Such posterior distributions are defined over union of subspaces of differing dimensionality and can be sampled from using modern Monte Carlo techniques, for instance the increasingly popular RJ-MCMC method. No generic approach is available, however, to summarize the resulting variable-dimensional samples and extract from them component-specific parameters. We propose a novel approach to thi…
We present dynesty, a public, open-source, Python package to estimate Bayesian posteriors and evidences (marginal likelihoods) using Dynamic Nested Sampling. By adaptively allocating samples based on posterior structure, Dynamic Nested Sampling has the benefits of Markov Chain Monte Carlo algorithms that focus exclusively on posterior estimation while retaining Nested Sampling's ability to estimate evidences and sample from complex, multi-modal distributions. We provide an overview of Nested Sampling, its extension to Dynamic Nested Sampling, the algorithmic challenges involved, and the variou…
Time-varying parameter (TVP) models are widely used in time series analysis to flexibly deal with processes which gradually change over time. However, the risk of overfitting in TVP models is well known. This issue can be dealt with using appropriate global-local shrinkage priors, which pull time-varying parameters towards static ones. In this paper, we introduce the R package shrinkTVP (Knaus, Bitto-Nemling, Cadonna, and Frühwirth-Schnatter 2019), which provides a fully Bayesian implementation of shrinkage priors for TVP models, taking advantage of recent developments in the literature, in pa…
A well known identifiability issue in factor analytic models is the invariance with respect to orthogonal transformations. This problem burdens the inference under a Bayesian setup, where Markov chain Monte Carlo (MCMC) methods are used to generate samples from the posterior distribution. We introduce a post-processing scheme in order to deal with rotation, sign and permutation invariance of the MCMC sample. The exact version of the contributed algorithm requires to solve $2^q$ assignment problems per (retained) MCMC iteration, where $q$ denotes the number of factors of the fitted model. For l…
This is a vignette for the R package eggCounts version 2.0. The package implements a suite of Bayesian hierarchical models dealing with faecal egg count reductions. The models are designed for a variety of practical situations, including individual treatment efficacy, zero inflation, small sample size (less than 10) and potential outliers. The functions are intuitive to use and their output are easy to interpret, such that users are protected from being exposed to complex Bayesian hierarchical modelling tasks. In addition, the package includes plotting functions to display data and results in …
