Search results for "Statistics - Computation"
showing 10 items of 41 documents
Unbiased Inference for Discretely Observed Hidden Markov Model Diffusions
2021
We develop a Bayesian inference method for diffusions observed discretely and with noise, which is free of discretisation bias. Unlike existing unbiased inference methods, our method does not rely on exact simulation techniques. Instead, our method uses standard time-discretised approximations of diffusions, such as the Euler--Maruyama scheme. Our approach is based on particle marginal Metropolis--Hastings, a particle filter, randomised multilevel Monte Carlo, and importance sampling type correction of approximate Markov chain Monte Carlo. The resulting estimator leads to inference without a bias from the time-discretisation as the number of Markov chain iterations increases. We give conver…
Local inhomogeneous weighted summary statistics for marked point processes
2023
We introduce a family of local inhomogeneous mark-weighted summary statistics, of order two and higher, for general marked point processes. Depending on how the involved weight function is specified, these summary statistics capture different kinds of local dependence structures. We first derive some basic properties and show how these new statistical tools can be used to construct most existing summary statistics for (marked) point processes. We then propose a local test of random labelling. This procedure allows us to identify points, and consequently regions, where the random labelling assumption does not hold, e.g.~when the (functional) marks are spatially dependent. Through a simulatio…
Estimation of causal effects with small data in the presence of trapdoor variables
2021
We consider the problem of estimating causal effects of interventions from observational data when well-known back-door and front-door adjustments are not applicable. We show that when an identifiable causal effect is subject to an implicit functional constraint that is not deducible from conditional independence relations, the estimator of the causal effect can exhibit bias in small samples. This bias is related to variables that we call trapdoor variables. We use simulated data to study different strategies to account for trapdoor variables and suggest how the related trapdoor bias might be minimized. The importance of trapdoor variables in causal effect estimation is illustrated with rea…
Grapham: Graphical models with adaptive random walk Metropolis algorithms
2008
Recently developed adaptive Markov chain Monte Carlo (MCMC) methods have been applied successfully to many problems in Bayesian statistics. Grapham is a new open source implementation covering several such methods, with emphasis on graphical models for directed acyclic graphs. The implemented algorithms include the seminal Adaptive Metropolis algorithm adjusting the proposal covariance according to the history of the chain and a Metropolis algorithm adjusting the proposal scale based on the observed acceptance probability. Different variants of the algorithms allow one, for example, to use these two algorithms together, employ delayed rejection and adjust several parameters of the algorithm…
Mixture Hidden Markov Models for Sequence Data: The seqHMM Package in R
2019
Sequence analysis is being more and more widely used for the analysis of social sequences and other multivariate categorical time series data. However, it is often complex to describe, visualize, and compare large sequence data, especially when there are multiple parallel sequences per subject. Hidden (latent) Markov models (HMMs) are able to detect underlying latent structures and they can be used in various longitudinal settings: to account for measurement error, to detect unobservable states, or to compress information across several types of observations. Extending to mixture hidden Markov models (MHMMs) allows clustering data into homogeneous subsets, with or without external covariate…
Imputation Procedures in Surveys Using Nonparametric and Machine Learning Methods: An Empirical Comparison
2020
Abstract Nonparametric and machine learning methods are flexible methods for obtaining accurate predictions. Nowadays, data sets with a large number of predictors and complex structures are fairly common. In the presence of item nonresponse, nonparametric and machine learning procedures may thus provide a useful alternative to traditional imputation procedures for deriving a set of imputed values used next for the estimation of study parameters defined as solution of population estimating equation. In this paper, we conduct an extensive empirical investigation that compares a number of imputation procedures in terms of bias and efficiency in a wide variety of settings, including high-dimens…
KFAS : Exponential Family State Space Models in R
2017
State space modelling is an efficient and flexible method for statistical inference of a broad class of time series and other data. This paper describes an R package KFAS for state space modelling with the observations from an exponential family, namely Gaussian, Poisson, binomial, negative binomial and gamma distributions. After introducing the basic theory behind Gaussian and non-Gaussian state space models, an illustrative example of Poisson time series forecasting is provided. Finally, a comparison to alternative R packages suitable for non-Gaussian time series modelling is presented.
Efficient Bayesian generalized linear models with time-varying coefficients : The walker package in R
2020
The R package walker extends standard Bayesian general linear models to the case where the effects of the explanatory variables can vary in time. This allows, for example, to model the effects of interventions such as changes in tax policy which gradually increases their effect over time. The Markov chain Monte Carlo algorithms powering the Bayesian inference are based on Hamiltonian Monte Carlo provided by Stan software, using a state space representation of the model to marginalise over the regression coefficients for efficient low-dimensional sampling.
Fast Estimation of Diffusion Tensors under Rician noise by the EM algorithm
2016
Diffusion tensor imaging (DTI) is widely used to characterize, in vivo, the white matter of the central nerve system (CNS). This biological tissue contains much anatomic, structural and orientational information of fibers in human brain. Spectral data from the displacement distribution of water molecules located in the brain tissue are collected by a magnetic resonance scanner and acquired in the Fourier domain. After the Fourier inversion, the noise distribution is Gaussian in both real and imaginary parts and, as a consequence, the recorded magnitude data are corrupted by Rician noise. Statistical estimation of diffusion leads a non-linear regression problem. In this paper, we present a f…
A penalized approach to the bivariate logistic regression model for the association between ordinal responses
2014
Bivariate ordered logistic models (BOLMs) are appealing to jointly model the marginal distribution of two ordered responses and their association, given a set of covariates. When the number of categories of the responses increases, the number of global odds ratios (or their re-parametrizations) to be estimated also increases and estimating the association structure becomes crucial for this type of data. In fact, such data could be too "rich" to be fully modelled with an ordinary BOLM while, sometimes, the well-known Dale's model could be too parsimonious to provide a good fit. In addition, when the cross-tabulation of the responses contains some zeros, for a number of model configurations, …