82 citations · 926 across the 70 of their papers we have counts for
73 papers
Interactive Debugger for Performance Portable Python HPC Kernels
Ivan Grigorik, Gabriel Kosmacher, George Biros +1
We propose PKDB, the first interactive debugger for GPU and multithreaded low-level kernels written in Python. Python is widely used in high performance computing (HPC), with frame…
VesNet: Neural network accelerated solver for simulating Stokesian vesicle suspensions
Shan Zhong, Gokberk Kabacaoglu, George Biros
Numerical simulation of deformable particle suspensions in Stokes flow is computationally expensive due to nonlinear fluid-structure interactions, evolving interfaces, and multisca…
A performance portable fast Ewald summation for Stokes flow
Gabriel Kosmacher, Ziyu Du, Joar Bagge +1
We present GPU algorithms for Ewald summation methods for accelerating N-body Stokes flow problems in periodic domains. Like most N-body codes, Ewald sums use a near-field/far-fiel…
IV-Net: A neural network for elliptic PDEs with random and highly varying coefficients
Shan Zhong, George Biros
We introduce a novel neural operator architecture designed to approximate solutions of linear elliptic partial differential equations with high-contrast, spatially varying coeffici…
LNODE: latent dynamics reveal the shared spatiotemporal structure of amyloid- progression
Zheyu Wen, George Biros
We present and analyze LNODE, a mechanism-based phenomenological model for amyloid beta (A) dynamics, calibrated using positron emission tomography (PET) imaging. A is a key…
Proximal-IMH: Proximal Posterior Proposals for Independent Metropolis-Hastings with Approximate Operators
Youguang Chen, George Biros
We consider the problem of sampling from a posterior distribution arising in Bayesian inverse problems in science, engineering, and imaging. Our method belongs to the family of ind…
Inverse problems for history-enriched linear model reduction
Arjun Vijaywargiya, George Biros
Standard projection-based model reduction for dynamical systems incurs closure error because it only accounts for instantaneous dependence on the resolved state. From the Mori-Zwan…
Latent-IMH: Efficient Bayesian Inference for Inverse Problems with Approximate Operators
Youguang Chen, George Biros
We study sampling from posterior distributions in Bayesian linear inverse problems where , the parameters to observables operator, is computationally expensive. In many applicat…
VLCs: Managing Parallelism with Virtualized Libraries
Yineng Yan, William Ruys, Hochan Lee +11
As the complexity and scale of modern parallel machines continue to grow, programmers increasingly rely on composition of software libraries to encapsulate and exploit parallelism.…
A Portable Multi-GPU Solver for Collisional Plasmas with Coulombic Interactions
James Almgren-Bell, Nader Al Awar, Dilip S Geethakrishnan +2
We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability densit…
Extensions of the regret-minimization algorithm for optimal design
Youguang Chen, George Biros
We consider the problem of selecting a subset of points from a dataset of unlabeled examples for labeling, with the goal of training a multiclass classifier. To address this, w…
Boltzsim: A fast solver for the 1D-space electron Boltzmann equation with applications to radio-frequency glow discharge plasmas
Milinda Fernando, James Almgren-Bell, Todd Oliver +4
We present an algorithm for solving the one-dimensional space collisional Boltzmann transport equation (BTE) for electrons in low-temperature plasmas (LTPs). Modeling LTPs is usefu…
A Scalable Algorithm for Active Learning
Youguang Chen, Zheyu Wen, George Biros
FIRAL is a recently proposed deterministic active learning algorithm for multiclass classification using logistic regression. It was shown to outperform the state-of-the-art in ter…
FIRAL: An Active Learning Algorithm for Multinomial Logistic Regression
Youguang Chen, George Biros
We investigate theory and algorithms for pool-based active learning for multiclass classification using multinomial logistic regression. Using finite sample analysis, we prove that…
A fast solver for the spatially homogeneous electron Boltzmann equation
Milinda Fernando, Daniil Bochkov, James Almgren-Bell +5
We present a numerical method for the velocity-space, spatially homogeneous, collisional Boltzmann equation for electron transport in low-temperature plasma (LTP) conditions. Model…
Inverse Problem Regularization for 3D Multi-Species Tumor Growth Models
Ali Ghafouri, George Biros
We present a multi-species partial differential equation (PDE) model for tumor growth and a an algorithm for calibrating the model from magnetic resonance imaging (MRI) scans. The…
A single-snapshot inverse solver for two-species graph model of tau pathology spreading in human Alzheimer disease
Zheyu Wen, Ali Ghafouri, George Biros
We propose a method that uses a two-species ordinary differential equation (ODE) model to characterize misfolded tau (or simply tau) protein spreading in Alzheimer's disease (AD) a…
GrainGNN: A dynamic graph neural network for predicting 3D grain microstructure
Yigong Qin, Stephen DeWitt, Balasubramaniam Radhakrishnan +1
We propose GrainGNN, a surrogate model for the evolution of polycrystalline grain structure under rapid solidification conditions in metal additive manufacturing. High fidelity sim…
An O(N) distributed-memory parallel direct solver for planar integral equations
Tianyu Liang, Chao Chen, Per-Gunnar Martinsson +1
Boundary value problems involving elliptic PDEs such as the Laplace and the Helmholtz equations are ubiquitous in mathematical physics and engineering. Many such problems can be al…
Numerical simulation of an extensible capsule using regularized Stokes kernels and overset finite differences
Dhwanit Agarwal, George Biros
In this paper, we present a novel numerical scheme for simulating deformable and extensible capsules suspended in a Stokesian fluid. The main feature of our scheme is a partition-o…
CLAIRE -- Parallelized Diffeomorphic Image Registration for Large-Scale Biomedical Imaging Applications
Naveen Himthani, Malte Brunn, Jae-Youn Kim +3
We study the performance of CLAIRE -- a diffeomorphic multi-node, multi-GPU image-registration algorithm, and software -- in large-scale biomedical imaging applications with billio…
Shape dynamics of a red blood cell in Poiseuille flow
Dhwanit Agarwal, George Biros
We use numerical simulations to study the dynamics of red blood cells (RBCs) in unconfined and confined Poiseuille flow. Previous numerical studies with 3D vesicles have indicated…
Overlapping Domain Decomposition Preconditioner for Integral Equations
Chao Chen, George Biros
The discretization of certain integral equations, e.g., the first-kind Fredholm equation of Laplace's equation, leads to symmetric positive-definite linear systems, where the coeff…
Ensemble inversion for brain tumor growth models with mass effect
Shashank Subramanian, Klaudius Scheufele, Naveen Himthani +2
We propose a method for extracting physics-based biomarkers from a single multiparametric Magnetic Resonance Imaging (mpMRI) scan bearing a glioma tumor. We account for mass effect…