arXiv subjects

Yu Ryan Yue

Publications and source records attributed to Yu Ryan Yue.

4 recordsLinked to original sources

arXiv2020

A spatial template independent component analysis model for subject-level brain network estimation and inference

Independent component analysis is commonly applied to functional magnetic resonance imaging (fMRI) data to extract independent components (ICs) representing functional brain networks. While ICA produces reliable group-level estimates, single-subject ICA often produces noisy results. Template ICA (tICA) is a hierarchical ICA model using empirical population priors to produce reliable subject-level IC estimates. However, this and other hierarchical ICA models assume unrealistically that subject effects are spatially independent. Here, we propose spatial template ICA (stICA), which incorporates spatial process priors into tICA. This results in greater estimation efficiency of ICs and subject effects. Additionally, the joint posterior distribution can be used to identify engaged areas using an excursions set approach. By leveraging spatial dependencies and avoiding massive multiple comparisons, stICA has high power to detect true effects. We derive an efficient expectation-maximization algorithm to obtain maximum likelihood estimates of the model parameters and posterior moments of the latent fields. Based on analysis of simulated data and fMRI data from the Human Connectome Project, we find that stICA produces estimates that are more accurate and reliable than benchmark approaches, and identifies larger and more reliable areas of engagement. The algorithm is quite tractable, achieving convergence within 7 hours in our fMRI analysis.

stat.ME↗

arXiv2017

A Bayesian General Linear Modeling Approach to Cortical Surface fMRI Data Analysis

Cortical surface fMRI (cs-fMRI) has recently grown in popularity versus traditional volumetric fMRI, as it allows for more meaningful spatial smoothing and is more compatible with the common assumptions of isotropy and stationarity in Bayesian spatial models. However, as no Bayesian spatial model has been proposed for cs-fMRI data, most analyses continue to employ the classical, voxel-wise general linear model (GLM) (Worsley and Friston 1995). Here, we propose a Bayesian GLM for cs-fMRI, which employs a class of sophisticated spatial processes to flexibly model latent activation fields. We use integrated nested Laplacian approximation (INLA), a highly accurate and efficient Bayesian computation technique (Rue et al. 2009). To identify regions of activation, we propose an excursions set method based on the joint posterior distribution of the latent fields, which eliminates the need for multiple comparisons correction. Finally, we address a gap in the existing literature by proposing a novel Bayesian approach for multi-subject analysis. The methods are validated and compared to the classical GLM through simulation studies and a motor task fMRI study from the Human Connectome Project. The proposed Bayesian approach results in smoother activation estimates, more accurate false positive control, and increased power to detect truly active regions.

stat.AP↗

arXiv2012

Bayesian Adaptive Smoothing Spline using Stochastic Differential Equations

The smoothing spline is one of the most popular curve-fitting methods, partly because of empirical evidence supporting its effectiveness and partly because of its elegant mathematical formulation. However, there are two obstacles that restrict the use of smoothing spline in practical statistical work. Firstly, it becomes computationally prohibitive for large data sets because the number of basis functions roughly equals the sample size. Secondly, its global smoothing parameter can only provide constant amount of smoothing, which often results in poor performances when estimating inhomogeneous functions. In this work, we introduce a class of adaptive smoothing spline models that is derived by solving certain stochastic differential equations with finite element methods. The solution extends the smoothing parameter to a continuous data-driven function, which is able to capture the change of the smoothness of underlying process. The new model is Markovian, which makes Bayesian computation fast. A simulation study and real data example are presented to demonstrate the effectiveness of our method.

math.ST↗

arXiv2012

Meta-analysis of functional neuroimaging data using Bayesian nonparametric binary regression

In this work we perform a meta-analysis of neuroimaging data, consisting of locations of peak activations identified in 162 separate studies on emotion. Neuroimaging meta-analyses are typically performed using kernel-based methods. However, these methods require the width of the kernel to be set a priori and to be constant across the brain. To address these issues, we propose a fully Bayesian nonparametric binary regression method to perform neuroimaging meta-analyses. In our method, each location (or voxel) has a probability of being a peak activation, and the corresponding probability function is based on a spatially adaptive Gaussian Markov random field (GMRF). We also include parameters in the model to robustify the procedure against miscoding of the voxel response. Posterior inference is implemented using efficient MCMC algorithms extended from those introduced in Holmes and Held [Bayesian Anal. 1 (2006) 145--168]. Our method allows the probability function to be locally adaptive with respect to the covariates, that is, to be smooth in one region of the covariate space and wiggly or even discontinuous in another. Posterior miscoding probabilities for each of the identified voxels can also be obtained, identifying voxels that may have been falsely classified as being activated. Simulation studies and application to the emotion neuroimaging data indicate that our method is superior to standard kernel-based methods.

stat.AP↗