Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Smooth Scalar-on-Image Regression via Spatial Bayesian Variable Selection.

ABSTRACT: We develop scalar-on-image regression models when images are registered multidimensional manifolds. We propose a fast and scalable Bayes inferential procedure to estimate the image coefficient. The central idea is the combination of an Ising prior distribution, which controls a latent binary indicator map, and an intrinsic Gaussian Markov random field, which controls the smoothness of the nonzero coefficients. The model is fit using a single-site Gibbs sampler, which allows fitting within minutes for hundreds of subjects with predictor images containing thousands of locations. The code is simple and is provided in less than one page in the Appendix. We apply this method to a neuroimaging study where cognitive outcomes are regressed on measures of white matter microstructure at every voxel of the corpus callosum for hundreds of subjects.

SUBMITTER: Goldsmith J

PROVIDER: S-EPMC3979628 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Smooth Scalar-on-Image Regression via Spatial Bayesian Variable Selection.

Goldsmith Jeff J Huang Lei L Crainiceanu Ciprian M CM

Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America 20140101 1

We develop scalar-on-image regression models when images are registered multidimensional manifolds. We propose a fast and scalable Bayes inferential procedure to estimate the image coefficient. The central idea is the combination of an Ising prior distribution, which controls a latent binary indicator map, and an intrinsic Gaussian Markov random field, which controls the smoothness of the nonzero coefficients. The model is fit using a single-site Gibbs sampler, which allows fitting within minute ...[more]

PMID: 24729670

Similar Datasets

Variable Selection in Function-on-Scalar Regression.

Project description:For regression models with functional responses and scalar predictors, it is common for the number of predictors to be large. Despite this, few methods for variable selection exist for function-on-scalar models, and none account for the inherent correlation of residual curves in such models. By expanding the coefficient functions using a B-spline basis, we pose the function-on-scalar model as a multivariate regression problem. Spline coefficients are grouped within coefficient function, and group-minimax concave penalty (MCP) is used for variable selection. We adapt techniques from generalized least squares to account for residual covariance by "pre-whitening" using an estimate of the covariance matrix, and establish theoretical properties for the resulting estimator. We further develop an iterative algorithm that alternately updates the spline coefficients and covariance; simulation results indicate that this iterative algorithm often performs as well as pre-whitening using the true covariance, and substantially outperforms methods that neglect the covariance structure. We apply our method to two-dimensional planar reaching motions in a study of the effects of stroke severity on motor control, and find that our method provides lower prediction errors than competing methods.

| S-EPMC4943585 | biostudies-literature

Bayesian Scalar on Image Regression With Nonignorable Nonresponse.

Project description:Medical imaging has become an increasingly important tool in screening, diagnosis, prognosis, and treatment of various diseases given its information visualization and quantitative assessment. The aim of this article is to develop a Bayesian scalar-on-image regression model to integrate high-dimensional imaging data and clinical data to predict cognitive, behavioral, or emotional outcomes, while allowing for nonignorable missing outcomes. Such a nonignorable nonresponse consideration is motivated by examining the association between baseline characteristics and cognitive abilities for 802 Alzheimer patients enrolled in the Alzheimer's Disease Neuroimaging Initiative 1 (ADNI1), for which data are partially missing. Ignoring such missing data may distort the accuracy of statistical inference and provoke misleading results. To address this issue, we propose an imaging exponential tilting model to delineate the data missing mechanism and incorporate an instrumental variable to facilitate model identifiability followed by a Bayesian framework with Markov chain Monte Carlo algorithms to conduct statistical inference. This approach is validated in simulation studies where both the finite sample performance and asymptotic properties are evaluated and compared with the model with fully observed data and that with a misspecified ignorable missing mechanism. Our proposed methods are finally carried out on the ADNI1 dataset, which turns out to capture both of those clinical risk factors and imaging regions consistent with the existing literature that exhibits clinical significance. Supplementary materials for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.

| S-EPMC7901831 | biostudies-literature

Bayesian Approximate Kernel Regression with Variable Selection.

Project description:Nonlinear kernel regression models are often used in statistics and machine learning because they are more accurate than linear models. Variable selection for kernel regression models is a challenge partly because, unlike the linear regression setting, there is no clear concept of an effect size for regression coefficients. In this paper, we propose a novel framework that provides an effect size analog for each explanatory variable in Bayesian kernel regression models when the kernel is shift-invariant - for example, the Gaussian kernel. We use function analytic properties of shift-invariant reproducing kernel Hilbert spaces (RKHS) to define a linear vector space that: (i) captures nonlinear structure, and (ii) can be projected onto the original explanatory variables. This projection onto the original explanatory variables serves as an analog of effect sizes. The specific function analytic property we use is that shift-invariant kernel functions can be approximated via random Fourier bases. Based on the random Fourier expansion, we propose a computationally efficient class of Bayesian approximate kernel regression (BAKR) models for both nonlinear regression and binary classification for which one can compute an analog of effect sizes. We illustrate the utility of BAKR by examining two important problems in statistical genetics: genomic selection (i.e. phenotypic prediction) and association mapping (i.e. inference of significant variants or loci). State-of-the-art methods for genomic selection and association mapping are based on kernel regression and linear models, respectively. BAKR is the first method that is competitive in both settings.

| S-EPMC6383716 | biostudies-literature

Scalar-on-Image Regression via the Soft-Thresholded Gaussian Process.

Project description:This work concerns spatial variable selection for scalar-on-image regression. We propose a new class of Bayesian nonparametric models and develop an efficient posterior computational aigorithm. The proposed soft-thresholded Gaussian process provides large prior support over the class of piecewise-smooth, sparse, and continuous spatially-varying regression coefficient functions. In addition, under some mild regularity conditions the soft-thresholded Gaussian proess prior leads to the posterior consistency for parameter estimation and variable selection for scalar-on-image regression, even when the number of predictors is larger than the sample size. The proposed method is compared to alternatives via simulation and applied to an electroen-cephalography study of alcoholism.

| S-EPMC6345249 | biostudies-literature

Bayesian Variable Selection for Gaussian copula regression models.

Project description:We develop a novel Bayesian method to select important predictors in regression models with multiple responses of diverse types. A sparse Gaussian copula regression model is used to account for the multivariate dependencies between any combination of discrete and/or continuous responses and their association with a set of predictors. We utilize the parameter expansion for data augmentation strategy to construct a Markov chain Monte Carlo algorithm for the estimation of the parameters and the latent variables of the model. Based on a centered parametrization of the Gaussian latent variables, we design a fixed-dimensional proposal distribution to update jointly the latent binary vectors of important predictors and the corresponding non-zero regression coefficients. For Gaussian responses and for outcomes that can be modeled as a dependent version of a Gaussian response, this proposal leads to a Metropolis-Hastings step that allows an efficient exploration of the predictors' model space. The proposed strategy is tested on simulated data and applied to real data sets in which the responses consist of low-intensity counts, binary, ordinal and continuous variables.

| S-EPMC7614421 | biostudies-literature

A spatial Bayesian latent factor model for image-on-image regression.

Project description:Image-on-image regression analysis, using images to predict images, is a challenging task, due to (1) the high dimensionality and (2) the complex spatial dependence structures in image predictors and image outcomes. In this work, we propose a novel image-on-image regression model, by extending a spatial Bayesian latent factor model to image data, where low-dimensional latent factors are adopted to make connections between high-dimensional image outcomes and image predictors. We assign Gaussian process priors to the spatially varying regression coefficients in the model, which can well capture the complex spatial dependence among image outcomes as well as that among the image predictors. We perform simulation studies to evaluate the out-of-sample prediction performance of our method compared with linear regression and voxel-wise regression methods for different scenarios. The proposed method achieves better prediction accuracy by effectively accounting for the spatial dependence and efficiently reduces image dimensions with latent factors. We apply the proposed method to analysis of multimodal image data in the Human Connectome Project where we predict task-related contrast maps using subcortical volumetric seed maps.

| S-EPMC8236065 | biostudies-literature

Bayesian variable selection logistic regression with paired proteomic measurements.

Project description:We explore the problem of variable selection in a case-control setting with mass spectrometry proteomic data consisting of paired measurements. Each pair corresponds to a distinct isotope cluster and each component within pair represents a summary of isotopic expression based on either the intensity or the shape of the cluster. Our objective is to identify a collection of isotope clusters associated with the disease outcome and at the same time assess the predictive added-value of shape beyond intensity while maintaining predictive performance. We propose a Bayesian model that exploits the paired structure of our data and utilizes prior information on the relative predictive power of each source by introducing multiple layers of selection. This allows us to make simultaneous inference on which are the most informative pairs and for which-and to what extent-shape has a complementary value in separating the two groups. We evaluate the Bayesian model on pancreatic cancer data. Results from the fitted model show that most predictive potential is achieved with a subset of just six (out of 1289) pairs while the contribution of the intensity components is much higher than the shape components. To demonstrate how the method behaves under a controlled setting we consider a simulation study. Results from this study indicate that the proposed approach can successfully select the truly predictive pairs and accurately estimate the effects of both components although, in some cases, the model tends to overestimate the inclusion probability of the second component.

| S-EPMC6175404 | biostudies-literature

Integrative variable selection via Bayesian model uncertainty.

Project description:We are interested in developing integrative approaches for variable selection problems that incorporate external knowledge on a set of predictors of interest. In particular, we have developed an integrative Bayesian model uncertainty (iBMU) method, which formally incorporates multiple sources of data via a second-stage probit model on the probability that any predictor is associated with the outcome of interest. Using simulations, we demonstrate that iBMU leads to an increase in power to detect true marginal associations over more commonly used variable selection techniques, such as least absolute shrinkage and selection operator and elastic net. In addition, iBMU leads to a more efficient model search algorithm over the basic BMU method even when the predictor-level covariates are only modestly informative. The increase in power and efficiency of our method becomes more substantial as the predictor-level covariates become more informative. Finally, we demonstrate the power and flexibility of iBMU for integrating both gene structure and functional biomarker information into a candidate gene study investigating over 50 genes in the brain reward system and their role with smoking cessation from the Pharmacogenetics of Nicotine Addiction and Treatment Consortium.

| S-EPMC4085544 | biostudies-literature

Variable selection using a smooth information criterion for distributional regression models.

Project description:Modern variable selection procedures make use of penalization methods to execute simultaneous model selection and estimation. A popular method is the least absolute shrinkage and selection operator, the use of which requires selecting the value of a tuning parameter. This parameter is typically tuned by minimizing the cross-validation error or Bayesian information criterion, but this can be computationally intensive as it involves fitting an array of different models and selecting the best one. In contrast with this standard approach, we have developed a procedure based on the so-called "smooth IC" (SIC) in which the tuning parameter is automatically selected in one step. We also extend this model selection procedure to the distributional regression framework, which is more flexible than classical regression modelling. Distributional regression, also known as multiparameter regression, introduces flexibility by taking account of the effect of covariates through multiple distributional parameters simultaneously, e.g., mean and variance. These models are useful in the context of normal linear regression when the process under study exhibits heteroscedastic behaviour. Reformulating the distributional regression estimation problem in terms of penalized likelihood enables us to take advantage of the close relationship between model selection criteria and penalization. Utilizing the SIC is computationally advantageous, as it obviates the issue of having to choose multiple tuning parameters.Supplementary informationThe online version contains supplementary material available at 10.1007/s11222-023-10204-8.

| S-EPMC10121547 | biostudies-literature

Bayesian sparse multiple regression for simultaneous rank reduction and variable selection.

Project description:We develop a Bayesian methodology aimed at simultaneously estimating low-rank and row-sparse matrices in a high-dimensional multiple-response linear regression model. We consider a carefully devised shrinkage prior on the matrix of regression coefficients which obviates the need to specify a prior on the rank, and shrinks the regression matrix towards low-rank and row-sparse structures. We provide theoretical support to the proposed methodology by proving minimax optimality of the posterior mean under the prediction risk in ultra-high dimensional settings where the number of predictors can grow sub-exponentially relative to the sample size. A one-step post-processing scheme induced by group lasso penalties on the rows of the estimated coefficient matrix is proposed for variable selection, with default choices of tuning parameters. We additionally provide an estimate of the rank using a novel optimization function achieving dimension reduction in the covariate space. We exhibit the performance of the proposed methodology in an extensive simulation study and a real data example.

| S-EPMC7584295 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data