Joint Bayesian Estimation of Voxel Activation and Inter-regional Connectivity in fMRI Experiments.

Brain activation and connectivity analyses in task-based functional magnetic resonance imaging (fMRI) experiments with multiple subjects are currently at the forefront of data-driven neuroscience. In such experiments, interest often lies in understanding activation of brain voxels due to external stimuli and strong association or connectivity between the measurements on a set of pre-specified groups of brain voxels, also known as regions of interest (ROI). This article proposes a joint Bayesian additive mixed modeling framework that simultaneously assesses brain activation and connectivity patterns from multiple subjects. In particular, fMRI measurements from each individual obtained in the form of a multi-dimensional array/tensor at each time are regressed on functions of the stimuli. We impose a low-rank parallel factorization decomposition on the tensor regression coefficients corresponding to the stimuli to achieve parsimony. Multiway stick-breaking shrinkage priors are employed to infer activation patterns and associated uncertainties in each voxel. Further, the model introduces region-specific random effects which are jointly modeled with a Bayesian Gaussian graphical prior to account for the connectivity among pairs of ROIs. Empirical investigations under various simulation studies demonstrate the effectiveness of the method as a tool to simultaneously assess brain activation and connectivity. The method is then applied to a multi-subject fMRI dataset from a balloon-analog risk-taking experiment, showing the effectiveness of the model in providing interpretable joint inference on voxel-level activations and inter-regional connectivity associated with how the brain processes risk. The proposed method is also validated through simulation studies and comparisons to other methods used within the neuroscience community.

A Case Study Competition Among Methods for Analyzing Large Spatial Data.

The Gaussian process is an indispensable tool for spatial data analysts. The onset of the "big data" era, however, has lead to the traditional Gaussian process being computationally infeasible for modern spatial data. As such, various alternatives to the full Gaussian process that are more amenable to handling big spatial data have been proposed. These modern methods often exploit low-rank structures and/or multi-core and multi-threaded computing environments to facilitate computation. This study provides, first, an introductory overview of several methods for analyzing large spatial data. Second, this study describes the results of a predictive competition among the described methods as implemented by different groups with strong expertise in the methodology. Specifically, each research group was provided with two training datasets (one simulated and one observed) along with a set of prediction locations. Each group then wrote their own implementation of their method to produce predictions at the given location and each was subsequently run on a common computing environment. The methods were then compared in terms of various predictive diagnostics. Supplementary materials regarding implementation details of the methods and code are available for this article online. ELECTRONIC SUPPLEMENTARY MATERIAL: Supplementary materials for this article are available at 10.1007/s13253-018-00348-w.

Multivariate spatial meta kriging.

This work extends earlier work on spatial meta kriging for the analysis of large multivariate spatial datasets as commonly encountered in environmental and climate sciences. Spatial meta-kriging partitions the data into subsets, analyzes each subset using a Bayesian spatial process model and then obtains approximate posterior inference for the entire dataset by optimally combining the individual posterior distributions from each subset. Importantly, as is often desired in spatial analysis, spatial meta kriging offers posterior predictive inference at arbitrary locations for the outcome as well as the residual spatial surface after accounting for spatially oriented predictors. Our current work explores spatial meta kriging idea to enhance scalability of multivariate spatial Gaussian process model that uses linear model co-regionalization (LMC) to account for the correlation between multiple components. The approach is simple, intuitive and scales multivariate spatial process models to big data effortlessly. A simulation study reveals inferential and predictive accuracy offered by spatial meta kriging on multivariate observations.

Meta-Kriging: Scalable Bayesian Modeling and Inference for Massive Spatial Datasets.

Spatial process models for analyzing geostatistical data entail computations that become prohibitive as the number of spatial locations becomes large. There is a burgeoning literature on approaches for analyzing large spatial datasets. In this article, we propose a divide-and-conquer strategy within the Bayesian paradigm. We partition the data into subsets, analyze each subset using a Bayesian spatial process model and then obtain approximate posterior inference for the entire dataset by combining the individual posterior distributions from each subset. Importantly, as often desired in spatial analysis, we offer full posterior predictive inference at arbitrary locations for the outcome as well as the residual spatial surface after accounting for spatially oriented predictors. We call this approach "Spatial Meta-Kriging" (SMK). We do not need to store the entire data in one processor, and this leads to superior scalability. We demonstrate SMK with various spatial regression models including Gaussian processes and tapered Gaussian processes. The approach is intuitive, easy to implement, and is supported by theoretical results presented in the supplementary material available online. Empirical illustrations are provided using different simulation experiments and a geostatistical analysis of Pacific Ocean sea surface temperature data.

Bayesian nonparametric areal wombling for small-scale maps with an application to urinary bladder cancer data from Connecticut.

With increasingly abundant spatial data in the form of case counts or rates combined over areal regions (eg, ZIP codes, census tracts, or counties), interest turns to formal identification of difference "boundaries," or barriers on the map, in addition to the estimated statistical map itself. "Boundary" refers to a border that describes vastly disparate outcomes in the adjacent areal units, perhaps caused by latent risk factors. This article focuses on developing a model-based statistical tool, equipped to identify difference boundaries in maps with a small number of areal units, also referred to as small-scale maps. This article proposes a novel and robust nonparametric boundary detection rule based on nonparametric Dirichlet processes, later referred to as Dirichlet process wombling (DPW) rule, by employing Dirichlet process-based mixture models for small-scale maps. Unlike the recently proposed nonparametric boundary detection rules based on false discovery rates, the DPW rule is free of ad hoc parameters, computationally simple, and readily implementable in freely available software for public health practitioners such as JAGS and OpenBUGS and yet provides statistically interpretable boundary detection in small-scale wombling. We offer a detailed simulation study and an application of our proposed approach to a urinary bladder cancer incidence rates dataset between 1990 and 2012 in the 8 counties in Connecticut.

Human papillomavirus vaccine acceptance among young men in Bangalore, India.

BACKGROUND: Human papillomavirus (HPV) is the most common sexually transmitted infection in the world. It can lead to anogenital, cervical, and head and neck cancer, with higher risk of malignant disease in patients with human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS) patients. In India, 73,000 of the 130,000 women diagnosed with cervical cancer die annually. Gardasil(®) , a vaccine available against HPV types 6, 11, 16, and 18, is approved for use in women in India but not men. A backlash to post-licensure trials has created a negative public opinion of the vaccine for women. Vaccinating boys and men is an alternate approach to prevent cervical cancer in women. This study gauges facilitators and barriers to vaccination acceptance among men in Bangalore, India. MATERIALS AND METHODS: Young men presenting to a dermatology clinic or an ART center in Bangalore, India, answered a seven-point survey assessing acceptance of the HPV vaccine, perceived barriers to vaccination, and acceptance of vaccination for their children. Ninety-three general dermatology patients and 85 patients with HIV/AIDS participated. RESULTS: There was a high degree of vaccine acceptance for both groups, 83 and 98%, respectively. Vaccine side effects and cost were cited as key barriers to vaccination, and doctor recommendation and government approval were the main facilitators. CONCLUSION: There is potential for high acceptability of the HPV vaccine among men in India. These results can facilitate further study of vaccine acceptance among males and physician opinion and knowledge about HPV vaccine use. Vaccination of males is a hopeful strategy to protect men and women from HPV-related malignancies.

Adaptive Gaussian Predictive Process Models for Large Spatial Datasets.

Large point referenced datasets occur frequently in the environmental and natural sciences. Use of Bayesian hierarchical spatial models for analyzing these datasets is undermined by onerous computational burdens associated with parameter estimation. Low-rank spatial process models attempt to resolve this problem by projecting spatial effects to a lower-dimensional subspace. This subspace is determined by a judicious choice of "knots" or locations that are fixed a priori. One such representation yields a class of predictive process models (e.g., Banerjee et al., 2008) for spatial and spatial-temporal data. Our contribution here expands upon predictive process models with fixed knots to models that accommodate stochastic modeling of the knots. We view the knots as emerging from a point pattern and investigate how such adaptive specifications can yield more flexible hierarchical frameworks that lead to automated knot selection and substantial computational benefits.