arXiv subjects

Shawn C. Shadden

Publications and source records attributed to Shawn C. Shadden.

15 recordsLinked to original sources

arXiv2026

svMultiPhysics: a finite element-based solver for cardiovascular simulations

Heart disease remains the leading cause of death in the United States, motivating extensive efforts to improve its diagnosis, treatment, and prevention. Over the past decade, computational modeling has emerged as a powerful tool to advance cardiovascular research by enabling detailed, patient-specific studies of cardiac physiology and pathology. svMultiPhysics is an open-source, parallel finite element solver written in C++ specifically designed for multiphysics cardiovascular problems. It provides a unified framework for simulating the partial differential equations that govern solid mechanics, fluid dynamics, diffusion, and cardiac electrophysiology. These equations can be solved independently or in a coupled fashion, allowing researchers to investigate interactions between physical processes in a modular yet integrated way. The solver's main strength lies in its ability to seamlessly couple multiple physics modules, enabling the study of complex, highly nonlinear systems. For example, svMultiPhysics can capture the interplay between cardiac electrophysiology, myocardial tissue mechanics, and blood flow dynamics, processes that are essential to understanding vascular and cardiac physiology and function in health and disease. Preliminary GPU-enabled simulations show up to approximately $30\times$ wall-clock speedup for selected linear solver configurations over CPU-based simulations. By offering a robust, extensible, and freely available platform, svMultiPhysics empowers researchers to explore multiphysics problems in cardiovascular science. As the primary 3D solver in the SimVascular open source project, it forms a key component of an end-to-end open source software ecosystem for image based patient specific modeling in the cardiovascular system. It is maintained and openly developed on GitHub, fostering transparency, reproducibility, and collaboration.

physics.flu-dyn↗

arXiv2026

Characterization of coherent flow structures in brain ventricles

The dynamic flow of cerebrospinal fluid (CSF) in brain ventricles exhibits flow features on several scales, both spatially and temporally. Most analysis of this complex flow and the accompanying transport has used instantaneous (Eulerian) flow variables. Such analysis makes understanding of unsteady transport challenging. Here, we analyze brain ventricular CSF flow both in a Eulerian sense and from the Lagrangian perspective -- a time-integrated view of the flow. With geometries generated from imaging data, we model CSF flow in adult human and embryonic zebrafish brain ventricles. In the human brain we model flow governed by cardiovascular pulsations, CSF secretion and motile cilia. The flow driven by cardiovascular pulsations is derived from a damped linear elastic model of brain ventricle deformations, as a result of applying displacement boundary conditions derived from experimental data. In the zebrafish brain we consider flow driven solely by motile cilia. The tissue and flow models are implemented and solved with finite element methods. We use the resulting velocity fields to compute finite-time Lyapunov exponent (FTLE) fields and use these fields to characterize Lagrangian coherent structures, which can be approximated by ridges in the FTLE fields. These coherent structures demonstrate prominent flow features in the brain ventricles congruent with findings in experimental research. In the human brain ventricles, we also investigate the role of inertia by comparing flow models governed by the Navier-Stokes and the Stokes equations. Comparisons show that solving the Stokes equations is adequate to compute integrated flow variables like stroke volumes, but that the Stokes approximation fails to resolve intricate features of flow and advective transport that are present in the solution to the Navier-Stokes equations, features that could be important to elucidating transport.

physics.flu-dyn↗

arXiv2025

SeqSeg: Learning Local Segments for Automatic Vascular Model Construction

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.

eess.IV↗

arXiv2023

A Singular Woodbury and Pseudo-Determinant Matrix Identities and Application to Gaussian Process Regression

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.

math.ST↗

arXiv2022

Development of an Efficient and Flexible Pipeline for Lagrangian Coherent Structure Computation

The computation of Lagrangian coherent structures (LCS) has become a standard tool for the analysis of advective transport in unsteady flow applications. LCS identification is primarily accomplished by evaluating measures based on the finite-time Cauchy Green (CG) strain tensor over the fluid domain. Sampling the CG tensor requires the advection of large numbers of fluid tracers, which can be computationally intensive, but presents a large degree of data parallelism. Processing can be specialized to parallel computing architectures, but on the other hand, there is compelling need for robust and flexible implementations for end users. Specifically, code that can accommodate analysis of wide-ranging fluid mechanics applications, while using a modular structure that is easily extended or modified, and facilitates visualization is desirable. We discuss the use of Visualization Toolkit (VTK) libraries as a foundation for object-oriented LCS computation, and how this framework can facilitate integration of LCS computation into flow visualization software such as ParaView. We also discuss the development of CUDA GPU kernels for efficient parallel spatial sampling of the flow map, including optimizing these kernels for better utilization.

physics.flu-dyn↗

arXiv2022

Interpolating Log-Determinant and Trace of the Powers of Matrix $\mathbf{A} + t \mathbf{B}$

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.

math.NA↗

arXiv2022

Noise Estimation in Gaussian Process Regression

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.

cs.LG↗

arXiv2021

A Deep-Learning Approach For Direct Whole-Heart Mesh Reconstruction

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

eess.IV↗

arXiv2021

Whole Heart Mesh Generation For Image-Based Computational Simulations By Learning Free-From Deformations

Image-based computer simulation of cardiac function can be used to probe the mechanisms of (patho)physiology, and guide diagnosis and personalized treatment of cardiac diseases. This paradigm requires constructing simulation-ready meshes of cardiac structures from medical image data--a process that has traditionally required significant time and human effort, limiting large-cohort analyses and potential clinical translations. We propose a novel deep learning approach to reconstruct simulation-ready whole heart meshes from volumetric image data. Our approach learns to deform a template mesh to the input image data by predicting displacements of multi-resolution control point grids. We discuss the methods of this approach and demonstrate its application to efficiently create simulation-ready whole heart meshes for computational fluid dynamics simulations of the cardiac flow. Our source code is available at https://github.com/fkong7/HeartFFDNet.

eess.IV↗

arXiv2019

Improving the Convergence of the Iterative Ensemble Kalman Filter by Resampling

The iterative ensemble Kalman filter (IEnKF) is widely used in inverse problems to estimate system parameters from limited observations. However, the IEnKF, when applied to nonlinear systems, can be plagued by poor convergence. Here we provide a comprehensive convergence analysis of the IEnKF and propose a new method to improve its convergence. A theoretical analysis of the standard IEnKF is presented and we demonstrate that the interaction between the nonlinearity of the forward model and the diminishing effect of the Kalman updates results in "early stopping" of the IEnKF, i.e. the Kalman operator converges to zero before the innovation is minimized. The steady state behavior of the early stopping phenomenon and its relation to observation uncertainty is demonstrate. We then propose an approach to prevent the early stopping by perturbing the covariance with hidden parameter ensemble resampling. The ensemble mean and covariance are kept unchanged during the resampling process, which ensures the Kalman operator at each iteration maintains a correct update direction. We briefly discuss the influence higher moments, such as kurtosis, of the resampling distribution on algorithm convergence. Parallel to the above developments, an example problem is presented to demonstrate the early stopping effect, and the application and merit of the proposed resampling scheme.

math.OC↗

arXiv2019

FEniCS Mechanics: A Package for Continuum Mechanics Simulations

FEniCS Mechanics is a Python package to facilitate computational mechanics simulations. The Python library dolfin, from the FEniCS Project, is used to formulate and numerically solve the problem in variational form. The general balance laws from continuum mechanics are used to enable rapid prototyping of different material laws. In addition to its generality, FEniCS Mechanics also checks the input provided by users to ensure that problem definitions are physically consistent. In turn, this code enables simulations of custom mechanics problems to be more accessible to those with limited programming or mechanics knowledge.

cs.CE↗

arXiv2018

Data-augmented modeling of intracranial pressure

Precise management of patients with cerebral diseases often requires intracranial pressure (ICP) monitoring, which is highly invasive and requires a specialized ICU setting. The ability to noninvasively estimate ICP is highly compelling as an alternative to, or screening for, invasive ICP measurement. Most existing approaches for noninvasive ICP estimation aim to build a regression function that maps noninvasive measurements to an ICP estimate using statistical learning techniques. These data-based approaches have met limited success, likely because the amount of training data needed is onerous for this complex applications. In this work, we discuss an alternative strategy that aims to better utilize noninvasive measurement data by leveraging mechanistic understanding of physiology. Specifically, we developed a Bayesian framework that combines a multiscale model of intracranial physiology with noninvasive measurements of cerebral blood flow using transcranial Doppler. Virtual experiments with synthetic data are conducted to verify and analyze the proposed framework. A preliminary clinical application study on two patients is also performed in which we demonstrate the ability of this method to improve ICP prediction.

physics.med-ph↗

arXiv2018

Adding Constraints to Bayesian Inverse Problems

Using observation data to estimate unknown parameters in computational models is broadly important. This task is often challenging because solutions are non-unique due to the complexity of the model and limited observation data. However, the parameters or states of the model are often known to satisfy additional constraints beyond the model. Thus, we propose an approach to improve parameter estimation in such inverse problems by incorporating constraints in a Bayesian inference framework. Constraints are imposed by constructing a likelihood function based on fitness of the solution to the constraints. The posterior distribution of the parameters conditioned on (1) the observed data and (2) satisfaction of the constraints is obtained, and the estimate of the parameters is given by the maximum a posteriori estimation or posterior mean. Both equality and inequality constraints can be considered by this framework, and the strictness of the constraints can be controlled by constraint uncertainty denoting a confidence on its correctness. Furthermore, we extend this framework to an approximate Bayesian inference framework in terms of the ensemble Kalman filter method, where the constraint is imposed by re-weighing the ensemble members based on the likelihood function. A synthetic model is presented to demonstrate the effectiveness of the proposed method and in both the exact Bayesian inference and ensemble Kalman filter scenarios, numerical simulations show that imposing constraints using the method presented improves identification of the true parameter solution among multiple local minima.

stat.ME↗

arXiv2018

A transport method for restoring incomplete ocean current measurements

Remote sensing of oceanographic data often yields incomplete coverage of the measurement domain. This can limit interpretability of the data and identification of coherent features informative of ocean dynamics. Several methods exist to fill gaps of missing oceanographic data, and are often based on projecting the measurements onto basis functions or a statistical model. Herein, we use an information transport approach inspired from an image processing algorithm. This approach aims to restore gaps in data by advecting and diffusing information of features as opposed to the field itself. Since this method does not involve fitting or projection, the portions of the domain containing measurements can remain unaltered, and the method offers control over the extent of local information transfer. This method is applied to measurements of ocean surface currents by high frequency radars. This is a relevant application because data coverage can be sporadic and filling data gaps can be essential to data usability. Application to two regions with differing spatial scale is considered. The accuracy and robustness of the method is tested by systematically blinding measurements and comparing the restored data at these locations to the actual measurements. These results demonstrate that even for locally large percentages of missing data points, the restored velocities have errors within the native error of the original data (e.g., $<10$% for velocity magnitude and $<3$% for velocity direction). Results were relatively insensitive to model parameters, facilitating a priori selection of default parameters for de novo applications.

physics.ao-ph↗

arXiv2013

Detection of coherent structures in photospheric turbulent flows

We study coherent structures in solar photospheric flows in a plage in the vicinity of the active region AR 10930 using the horizontal velocity data derived from Hinode/SOT magnetograms. Eulerian and Lagrangian coherent structures are detected by computing the Q-criterion and the finite-time Lyapunov exponents of the velocity field, respectively. Our analysis indicates that, on average, the deformation Eulerian coherent structures dominate over the vortical Eulerian coherent structures in the plage region. We demonstrate the correspondence of the network of high magnetic flux concentration to the attracting Lagrangian coherent structures (a-LCS) in the photospheric velocity based on both observations and numerical simulations. In addition, the computation of a-LCS provides a measure of the local rate of contraction/expansion of the flow.

astro-ph.SR↗