scholarly journals Bayesian estimation of spatial filters with Moran's eigenvectors and hierarchical shrinkage priors

2020 ◽  
Author(s):  
Connor Donegan ◽  
Yongwan Chun ◽  
Amy E. Hughes

This paper proposes a Bayesian method for spatial regression using eigenvector spatial filtering (ESF) and Piironen and Vehtari's (2017) regularized horseshoe (RHS) prior. ESF models are most often estimated using variable selection procedures such as stepwise selection, but in the absence of a Bayesian model averaging procedure variable selection methods cannot properly account for parameter uncertainty. Hierarchical shrinkage priors such as the RHS address the foregoing concern in a computationally efficient manner by encoding prior information about spatial filters into an adaptive prior distribution which shrinks posterior estimates towards zero in the absence of a strong signal while only minimally regularizing coefficients of important eigenvectors. This paper presents results from a large simulation study which compares the performance of the proposed Bayesian model (RHS-ESF) to alternative spatial models under a variety of spatial autocorrelation scenarios. The RHS-ESF model performance matched that of the SAR model from which the data was generated. The study highlights that reliable uncertainty estimates require greater attention to spatial autocorrelation in covariates than is typically given. A demonstration analysis of 2016 U.S. Presidential election results further evidences robustness of results to hyper-prior specifications as well as the advantages of estimating spatial models using the Stan probabilistic programming language.

Nutrients ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 1098
Author(s):  
Ewelina Łukaszyk ◽  
Katarzyna Bień-Barkowska ◽  
Barbara Bień

Identifying factors that affect mortality requires a robust statistical approach. This study’s objective is to assess an optimal set of variables that are independently associated with the mortality risk of 433 older comorbid adults that have been discharged from the geriatric ward. We used both the stepwise backward variable selection and the iterative Bayesian model averaging (BMA) approaches to the Cox proportional hazards models. Potential predictors of the mortality rate were based on a broad range of clinical data; functional and laboratory tests, including geriatric nutritional risk index (GNRI); lymphocyte count; vitamin D, and the age-weighted Charlson comorbidity index. The results of the multivariable analysis identified seven explanatory variables that are independently associated with the length of survival. The mortality rate was higher in males than in females; it increased with the comorbidity level and C-reactive proteins plasma level but was negatively affected by a person’s mobility, GNRI and lymphocyte count, as well as the vitamin D plasma level.


Author(s):  
Oliver M. Crook ◽  
Laurent Gatto ◽  
Paul D. W. Kirk

Abstract The Dirichlet Process (DP) mixture model has become a popular choice for model-based clustering, largely because it allows the number of clusters to be inferred. The sequential updating and greedy search (SUGS) algorithm (Wang & Dunson, 2011) was proposed as a fast method for performing approximate Bayesian inference in DP mixture models, by posing clustering as a Bayesian model selection (BMS) problem and avoiding the use of computationally costly Markov chain Monte Carlo methods. Here we consider how this approach may be extended to permit variable selection for clustering, and also demonstrate the benefits of Bayesian model averaging (BMA) in place of BMS. Through an array of simulation examples and well-studied examples from cancer transcriptomics, we show that our method performs competitively with the current state-of-the-art, while also offering computational benefits. We apply our approach to reverse-phase protein array (RPPA) data from The Cancer Genome Atlas (TCGA) in order to perform a pan-cancer proteomic characterisation of 5157 tumour samples. We have implemented our approach, together with the original SUGS algorithm, in an open-source R package named sugsvarsel, which accelerates analysis by performing intensive computations in C++ and provides automated parallel processing. The R package is freely available from: https://github.com/ococrook/sugsvarsel


2001 ◽  
Vol 20 (21) ◽  
pp. 3215-3230 ◽  
Author(s):  
Valerie Viallefont ◽  
Adrian E. Raftery ◽  
Sylvia Richardson

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Zihang Lu ◽  
Wendy Lou

Abstract In many clinical studies, researchers are interested in parsimonious models that simultaneously achieve consistent variable selection and optimal prediction. The resulting parsimonious models will facilitate meaningful biological interpretation and scientific findings. Variable selection via Bayesian inference has been receiving significant advancement in recent years. Despite its increasing popularity, there is limited practical guidance for implementing these Bayesian approaches and evaluating their comparative performance in clinical datasets. In this paper, we review several commonly used Bayesian approaches to variable selection, with emphasis on application and implementation through R software. These approaches can be roughly categorized into four classes: namely the Bayesian model selection, spike-and-slab priors, shrinkage priors, and the hybrid of both. To evaluate their variable selection performance under various scenarios, we compare these four classes of approaches using real and simulated datasets. These results provide practical guidance to researchers who are interested in applying Bayesian approaches for the purpose of variable selection.


Author(s):  
Lorenzo Bencivelli ◽  
Massimiliano Giuseppe Marcellino ◽  
Gianluca Moretti

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