Shawn C. Shadden

Siavash Ameli, Shawn C. Shadden

We develop a computational procedure to estimate the covariance hyperparameters for semiparametric Gaussian process regression models with additive noise. Namely, the presented method can be used to efficiently estimate the variance of the correlated error, and the variance of the noise based on maximizing a marginal likelihood function. Our method involves suitably reducing the dimensionality of the hyperparameter space to simplify the estimation procedure to a univariate root-finding problem. Moreover, we derive bounds and asymptotes of the marginal likelihood function and its derivatives, which are useful to narrowing the initial range of the hyperparameter search. Using numerical examples, we demonstrate the computational advantages and robustness of the presented approach compared to traditional parameter optimization.

Siavash Ameli, Shawn C. Shadden

We study a matrix that arises from a singular form of the Woodbury matrix identity. We present generalized inverse and pseudo-determinant identities for this matrix, which have direct applications for Gaussian process regression, specifically its likelihood representation and precision matrix. We extend the definition of the precision matrix to the Bott-Duffin inverse of the covariance matrix, preserving properties related to conditional independence, conditional precision, and marginal precision. We also provide an efficient algorithm and numerical analysis for the presented determinant identities and demonstrate their advantages under specific conditions relevant to computing log-determinant terms in likelihood functions of Gaussian process regression.

Fanwei Kong, Nathan Wilson, Shawn C. Shadden

Automated construction of surface geometries of cardiac structures from volumetric medical images is important for a number of clinical applications. While deep-learning-based approaches have demonstrated promising reconstruction precision, these approaches have mostly focused on voxel-wise segmentation followed by surface reconstruction and post-processing techniques. However, such approaches suffer from a number of limitations including disconnected regions or incorrect surface topology due to erroneous segmentation and stair-case artifacts due to limited segmentation resolution. We propose a novel deep-learning-based approach that directly predicts whole heart surface meshes from volumetric CT and MR image data. Our approach leverages a graph convolutional neural network to predict deformation on mesh vertices from a pre-defined mesh template to reconstruct multiple anatomical structures in a 3D image volume. Our method demonstrated promising performance of generating whole heart reconstructions with as good or better accuracy than prior deep-learning-based methods on both CT and MR data. Furthermore, by deforming a template mesh, our method can generate whole heart geometries with better anatomical consistency and produce high-resolution geometries from lower resolution input image data. Our method was also able to produce temporally consistent surface mesh predictions for heart motion from CT or MR cine sequences, and therefore can potentially be applied for efficiently constructing 4D whole heart dynamics. Our code and pre-trained networks are available at https://github.com/fkong7/MeshDeformNet

Numi Sveinsson Cepero, Shawn C. Shadden

Computational modeling of cardiovascular function has become a critical part of diagnosing, treating and understanding cardiovascular disease. Most strategies involve constructing anatomically accurate computer models of cardiovascular structures, which is a multistep, time-consuming process. To improve the model generation process, we herein present SeqSeg (sequential segmentation): a novel deep learning based automatic tracing and segmentation algorithm for constructing image-based vascular models. SeqSeg leverages local U-Net-based inference to sequentially segment vascular structures from medical image volumes. We tested SeqSeg on CT and MR images of aortic and aortofemoral models and compared the predictions to those of benchmark 2D and 3D global nnU-Net models, which have previously shown excellent accuracy for medical image segmentation. We demonstrate that SeqSeg is able to segment more complete vasculature and is able to generalize to vascular structures not annotated in the training data.

Siavash Ameli, Shawn C. Shadden

We develop heuristic interpolation methods for the functions $t \mapsto \log \det \left( \mathbf{A} + t \mathbf{B} \right)$ and $t \mapsto \operatorname{trace}\left( (\mathbf{A} + t \mathbf{B})^{p} \right)$ where the matrices $\mathbf{A}$ and $\mathbf{B}$ are Hermitian and positive (semi) definite and $p$ and $t$ are real variables. These functions are featured in many applications in statistics, machine learning, and computational physics. The presented interpolation functions are based on the modification of sharp bounds for these functions. We demonstrate the accuracy and performance of the proposed method with numerical examples, namely, the marginal maximum likelihood estimation for Gaussian process regression and the estimation of the regularization parameter of ridge regression with the generalized cross-validation method.