arXiv subjects

Aliaksandr Hubin

Publications and source records attributed to Aliaksandr Hubin.

24 records · Page 2Linked to original sources

arXiv2020

A Bayesian binomial regression model with latent Gaussian processes for modelling DNA methylation

Epigenetic observations are represented by the total number of reads from a given pool of cells and the number of methylated reads, making it reasonable to model this data by a binomial distribution. There are numerous factors that can influence the probability of success in a particular region. Moreover, there is a strong spatial (alongside the genome) dependence of these probabilities. We incorporate dependence on the covariates and the spatial dependence of the methylation probability for observations from a pool of cells by means of a binomial regression model with a latent Gaussian field and a logit link function. We apply a Bayesian approach including prior specifications on model configurations. We run a mode jumping Markov chain Monte Carlo algorithm (MJMCMC) across different choices of covariates in order to obtain the joint posterior distribution of parameters and models. This also allows finding the best set of covariates to model methylation probability within the genomic region of interest and individual marginal inclusion probabilities of the covariates.

stat.AP↗

arXiv2019

An adaptive simulated annealing EM algorithm for inference on non-homogeneous hidden Markov models

Non-homogeneous hidden Markov models (NHHMM) are a subclass of dependent mixture models used for semi-supervised learning, where both transition probabilities between the latent states and mean parameter of the probability distribution of the responses (for a given state) depend on the set of $p$ covariates. A priori we do not know which (and how) covariates influence the transition probabilities and the mean parameters. This induces a complex combinatorial optimization problem for model selection with $4^p$ potential configurations. To address the problem, in this article we propose an adaptive (A) simulated annealing (SA) expectation maximization (EM) algorithm (ASA-EM) for joint optimization of models and their parameters with respect to a criterion of interest.

stat.ML↗

arXiv2019

Combining Model and Parameter Uncertainty in Bayesian Neural Networks

Bayesian neural networks (BNNs) have recently regained a significant amount of attention in the deep learning community due to the development of scalable approximate Bayesian inference techniques. There are several advantages of using Bayesian approach: Parameter and prediction uncertainty become easily available, facilitating rigid statistical analysis. Furthermore, prior knowledge can be incorporated. However so far there have been no scalable techniques capable of combining both model (structural) and parameter uncertainty. In this paper we introduce the concept of model uncertainty in BNNs and hence make inference in the joint space of models and parameters. Moreover, we suggest an adaptation of a scalable variational inference approach with reparametrization of marginal inclusion probabilities to incorporate the model space constraints. Finally, we show that incorporating model uncertainty via Bayesian model averaging and Bayesian model selection allows to drastically sparsify the structure of BNNs.

stat.ML↗

arXiv2018

Deep Bayesian regression models

Regression models are used for inference and prediction in a wide range of applications providing a powerful scientific tool for researchers and analysts from different fields. In many research fields the amount of available data as well as the number of potential explanatory variables is rapidly increasing. Variable selection and model averaging have become extremely important tools for improving inference and prediction. However, often linear models are not sufficient and the complex relationship between input variables and a response is better described by introducing non-linearities and complex functional interactions. Deep learning models have been extremely successful in terms of prediction although they are often difficult to specify and potentially suffer from overfitting. The aim of this paper is to bring the ideas of deep learning into a statistical framework which yields more parsimonious models and allows to quantify model uncertainty. To this end we introduce the class of deep Bayesian regression models (DBRM) consisting of a generalized linear model combined with a comprehensive non-linear feature space, where non-linear features are generated just like in deep learning but combined with variable selection in order to include only important features. DBRM can easily be extended to include latent Gaussian variables to model complex correlation structures between observations, which seems to be not easily possible with existing deep learning approaches. Two different algorithms based on MCMC are introduced to fit DBRM and to perform Bayesian inference. The predictive performance of these algorithms is compared with a large number of state of the art algorithms. Furthermore we illustrate how DBRM can be used for model inference in various applications.

stat.ME↗

arXiv2018

Mode jumping MCMC for Bayesian variable selection in GLMM

Generalized linear mixed models (GLMM) are used for inference and prediction in a wide range of different applications providing a powerful scientific tool. An increasing number of sources of data are becoming available, introducing a variety of candidate explanatory variables for these models. Selection of an optimal combination of variables is thus becoming crucial. In a Bayesian setting, the posterior distribution of the models, based on the observed data, can be viewed as a relevant measure for the model evidence. The number of possible models increases exponentially in the number of candidate variables. Moreover, the space of models has numerous local extrema in terms of posterior model probabilities. To resolve these issues a novel MCMC algorithm for the search through the model space via efficient mode jumping for GLMMs is introduced. The algorithm is based on that marginal likelihoods can be efficiently calculated within each model. It is recommended that either exact expressions or precise approximations of marginal likelihoods are applied. The suggested algorithm is applied to simulated data, the famous U.S. crime data, protein activity data and epigenetic data and is compared to several existing approaches.

stat.CO↗

arXiv2016

Estimating the marginal likelihood with Integrated nested Laplace approximation (INLA)

The marginal likelihood is a well established model selection criterion in Bayesian statistics. It also allows to efficiently calculate the marginal posterior model probabilities that can be used for Bayesian model averaging of quantities of interest. For many complex models, including latent modeling approaches, marginal likelihoods are however difficult to compute. One recent promising approach for approximating the marginal likelihood is Integrated Nested Laplace Approximation (INLA), design for models with latent Gaussian structures. In this study we compare the approximations obtained with INLA to some alternative approaches on a number of examples of different complexity. In particular we address a simple linear latent model, a Bayesian linear regression model, logistic Bayesian regression models with probit and logit links, and a Poisson longitudinal generalized linear mixed model.

stat.CO↗