2025
Performance Characterization of Python Runtimes for Multi-device Task Parallel Programming.
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Int. J. Parallel Program., April, 2025
KNN-DBSCAN: a DBSCAN in high dimensions.
ACM Trans. Parallel Comput., March, 2025
Extensions of regret-minimization algorithm for optimal design.
CoRR, March, 2025
Boltzsim: A fast solver for the 1D-space electron Boltzmann equation with applications to radio-frequency glow discharge plasmas.
CoRR, February, 2025
Speeding up the Local C++ Development Cycle with Header Substitution.
Proceedings of the 23rd ACM/IEEE International Symposium on Code Generation and Optimization, 2025
2024
GrainGNN: A dynamic graph neural network for predicting 3D grain microstructure.
J. Comput. Phys., 2024
Numerical simulation of an extensible capsule using regularized Stokes kernels and overset finite differences.
J. Comput. Phys., 2024
A fast solver for the spatially homogeneous electron Boltzmann equation.
CoRR, 2024
Inverse Problem Regularization for 3D Multi-Species Tumor Growth Models.
CoRR, 2024
GrainGNN: A dynamic graph neural network for predicting 3D grain microstructure.
CoRR, 2024
A Scalable Algorithm for Active Learning.
Proceedings of the International Conference for High Performance Computing, 2024
Biophysics-Based Data Assimilation of Longitudinal Tau and Amyloid-β PET Scans.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2024, 2024
Single-Scan mpMRI Calibration of Multi-species Brain Tumor Dynamics with Mass Effect.
Proceedings of the Simulation and Synthesis in Medical Imaging, 2024
A Deep Dive into Task-Based Parallelism in Python.
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Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2024
An O(N) distributed-memory parallel direct solver for planar integral equations.
Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2024
2023
Ensemble Inversion for Brain Tumor Growth Models With Mass Effect.
IEEE Trans. Medical Imaging, April, 2023
Inverse Biophysical Modeling and Machine Learning in Personalized Oncology (Dagstuhl Seminar 23022).
Dagstuhl Reports, January, 2023
A distributed-memory parallel algorithm for discretized integral equations using Julia.
CoRR, 2023
A GPU Algorithm for Detecting Strongly Connected Components.
Proceedings of the International Conference for High Performance Computing, 2023
FIRAL: An Active Learning Algorithm for Multinomial Logistic Regression.
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
A Two-Species Model for Abnormal Tau Dynamics in Alzheimer's Disease.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2023 Workshops, 2023
A 3D Inverse Solver for a Multi-species PDE Model of Glioblastoma Growth.
Proceedings of the Computational Mathematics Modeling in Cancer Analysis, 2023
2022
Overlapping Domain Decomposition Preconditioner for Integral Equations.
SIAM J. Sci. Comput., 2022
CLAIRE - Parallelized Diffeomorphic Image Registration for Large-Scale Biomedical Imaging Applications.
J. Imaging, 2022
Parla: A Python Orchestration System for Heterogeneous Architectures.
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Proceedings of the SC22: International Conference for High Performance Computing, 2022
A GPU-Accelerated AMR Solver for Gravitational Wave Propagation.
Proceedings of the SC22: International Conference for High Performance Computing, 2022
A Multi-GPU Python Solver for Low-Temperature Non-Equilibrium Plasmas.
Proceedings of the 2022 IEEE 34th International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), 2022
PyKokkos: Performance Portable Kernels in Python.
Proceedings of the 44th IEEE/ACM International Conference on Software Engineering: Companion Proceedings, 2022
2021
Hardware Accelerator Integration Tradeoffs for High-Performance Computing: A Case Study of GEMM Acceleration in N-Body Methods.
IEEE Trans. Parallel Distributed Syst., 2021
Fully Automatic Calibration of Tumor-Growth Models Using a Single mpMRI Scan.
IEEE Trans. Medical Imaging, 2021
Modeling of Glioma Growth With Mass Effect by Longitudinal Magnetic Resonance Imaging.
IEEE Trans. Biomed. Eng., 2021
RCHOL: Randomized Cholesky Factorization for Solving SDD Linear Systems.
SIAM J. Sci. Comput., 2021
Fast Approximation of the Gauss-Newton Hessian Matrix for the Multilayer Perceptron.
SIAM J. Matrix Anal. Appl., 2021
Fast GPU 3D diffeomorphic image registration.
J. Parallel Distributed Comput., 2021
CLAIRE: Constrained Large Deformation Diffeomorphic Image Registration on Parallel Computing Architectures.
J. Open Source Softw., 2021
Ensemble inversion for brain tumor growth models with mass effect.
CoRR, 2021
Quantitative in vivo imaging to enable tumor forecasting and treatment optimization.
CoRR, 2021
A performance portability framework for Python.
Proceedings of the ICS '21: 2021 International Conference on Supercomputing, 2021
2020
Image-Driven Biophysical Tumor Growth Model Calibration.
SIAM J. Sci. Comput., 2020
An efficient method for modeling flow in porous media with immersed faults.
CoRR, 2020
Multi-node multi-GPU diffeomorphic image registration for large-scale imaging problems.
Proceedings of the International Conference for High Performance Computing, 2020
Multiatlas Calibration of Biophysical Brain Tumor Growth Models with Mass Effect.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020
Estimating Glioblastoma Biophysical Growth Parameters Using Deep Learning Regression.
Proceedings of the Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries, 2020
2019
CLAIRE: A Distributed-Memory Solver for Constrained Large Deformation Diffeomorphic Image Registration.
SIAM J. Sci. Comput., 2019
Fast Evaluation and Approximation of the Gauss-Newton Hessian Matrix for the Multilayer Perceptron.
CoRR, 2019
ANODEV2: A Coupled Neural ODE Evolution Framework.
CoRR, 2019
ANODEV2: A Coupled Neural ODE Framework.
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
Distributed O(N) Linear Solver for Dense Symmetric Hierarchical Semi-Separable Matrices.
Proceedings of the 13th IEEE International Symposium on Embedded Multicore/Many-core Systems-on-Chip, 2019
ANODE: Unconditionally Accurate Memory-Efficient Gradients for Neural ODEs.
Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence, 2019
2018
Low-resolution simulations of vesicle suspensions in 2D.
J. Comput. Phys., 2018
Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge.
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et al.
CoRR, 2018
PDE-constrained optimization in medical image analysis.
CoRR, 2018
Distributed-memory hierarchical compression of dense SPD matrices.
Proceedings of the International Conference for High Performance Computing, 2018
A Novel Domain Adaptation Framework for Medical Image Segmentation.
Proceedings of the Brainlesion: Glioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries, 2018
2017
A Semi-Lagrangian Two-Level Preconditioned Newton-Krylov Solver for Constrained Diffeomorphic Image Registration.
SIAM J. Sci. Comput., 2017
Geometry-oblivious FMM for compressing dense SPD matrices.
Proceedings of the International Conference for High Performance Computing, 2017
A framework for scalable biophysics-based image analysis.
Proceedings of the International Conference for High Performance Computing, 2017
An N log N Parallel Fast Direct Solver for Kernel Matrices.
Proceedings of the 2017 IEEE International Parallel and Distributed Processing Symposium, 2017
2016
Algorithm 967: A Distributed-Memory Fast Multipole Method for Volume Potentials.
ACM Trans. Math. Softw., 2016
Parallel Algorithms for Nearest Neighbor Search Problems in High Dimensions.
SIAM J. Sci. Comput., 2016
ASKIT: An Efficient, Parallel Library for High-Dimensional Kernel Summations.
SIAM J. Sci. Comput., 2016
FFT, FMM, or Multigrid? A comparative Study of State-Of-the-Art Poisson Solvers for Uniform and Nonuniform Grids in the Unit Cube.
SIAM J. Sci. Comput., 2016
Constrained H<sup>1</sup>-Regularization Schemes for Diffeomorphic Image Registration.
SIAM J. Imaging Sci., 2016
Adaptive time stepping for vesicle suspensions.
J. Comput. Phys., 2016
Inv-ASKIT: A Parallel Fast Diret Solver for Kernel Matrices.
CoRR, 2016
Research and Education in Computational Science and Engineering.
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CoRR, 2016
Distributed-memory large deformation diffeomorphic 3D image registration.
Proceedings of the International Conference for High Performance Computing, 2016
A parallel arbitrary-order accurate AMR algorithm for the scalar advection-diffusion equation.
Proceedings of the International Conference for High Performance Computing, 2016
INV-ASKIT: A Parallel Fast Direct Solver for Kernel Matrices.
Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium, 2016
Optimizing GPGPU Kernel Summation for Performance and Energy Efficiency.
Proceedings of the 45th International Conference on Parallel Processing Workshops, 2016
2015
ASKIT: Approximate Skeletonization Kernel-Independent Treecode in High Dimensions.
SIAM J. Sci. Comput., 2015
An Inexact Newton-Krylov Algorithm for Constrained Diffeomorphic Image Registration.
SIAM J. Imaging Sci., 2015
Comparison of multigrid algorithms for high-order continuous finite element discretizations.
Numer. Linear Algebra Appl., 2015
On preconditioners for the Laplace double-layer in 2D.
Numer. Linear Algebra Appl., 2015
Boundary integral method for the flow of vesicles with viscosity contrast in three dimensions.
J. Comput. Phys., 2015
Controlling the deformation map in diffeomorphic image registration.
CoRR, 2015
AccFFT: A library for distributed-memory FFT on CPU and GPU architectures.
CoRR, 2015
Performance optimization for the k-nearest neighbors kernel on x86 architectures.
Proceedings of the International Conference for High Performance Computing, 2015
A kernel-independent FMM in general dimensions.
Proceedings of the International Conference for High Performance Computing, 2015
Robust Treecode Approximation for Kernel Machines.
Proceedings of the 21th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2015
An Algebraic Parallel Treecode in Arbitrary Dimensions.
Proceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium, 2015
2014
High-volume fraction simulations of two-dimensional vesicle suspensions.
J. Comput. Phys., 2014
Far-Field Compression for Fast Kernel Summation Methods in High Dimensions.
CoRR, 2014
FFT, FMM, or MULTIGRID? A comparative study of state-of-the-art poisson solvers.
CoRR, 2014
A Volume Integral Equation Stokes Solver for Problems with Variable Coefficients.
Proceedings of the International Conference for High Performance Computing, 2014
Performance analysis of HPC applications with irregular tree data structures.
Proceedings of the 20th IEEE International Conference on Parallel and Distributed Systems, 2014
2013
A geodesic-active-contour-based variational model for short-axis cardiac MR image segmentation.
Int. J. Comput. Math., 2013
HykSort: a new variant of hypercube quicksort on distributed memory architectures.
Proceedings of the International Conference on Supercomputing, 2013
2012
GLISTR: Glioma Image Segmentation and Registration.
IEEE Trans. Medical Imaging, 2012
Dynamic Data Driven Methods for Self-aware Aerospace Vehicles.
Proceedings of the International Conference on Computational Science, 2012
FaIMS: A fast algorithm for the inverse medium problem with multiple frequencies and multiple sources for the scalar Helmholtz equation.
J. Comput. Phys., 2012
A massively parallel adaptive fast multipole method on heterogeneous architectures.
Commun. ACM, 2012
Parallel geometric-algebraic multigrid on unstructured forests of octrees.
Proceedings of the SC Conference on High Performance Computing Networking, 2012
2011
Deformable Registration of Glioma Images Using EM Algorithm and Diffusion Reaction Modeling.
IEEE Trans. Medical Imaging, 2011
A fast algorithm for simulating vesicle flows in three dimensions.
J. Comput. Phys., 2011
Poster: parallel algorithms for clustering and nearest neighbor search problems in high dimensions.
Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis, 2011
Towards Extra-Luminal Blood Detection from Intravascular Ultrasound Radio Frequency Data.
Proceedings of the Medical Image Computing and Computer-Assisted Intervention - MICCAI 2011, 2011
Joint Segmentation and Deformable Registration of Brain Scans Guided by a Tumor Growth Model.
Proceedings of the Medical Image Computing and Computer-Assisted Intervention - MICCAI 2011, 2011
2010
A Parallel Geometric Multigrid Method for Finite Elements on Octree Meshes.
SIAM J. Sci. Comput., 2010
Fast Algorithms for Source Identification Problems with Elliptic PDE Constraints.
SIAM J. Imaging Sci., 2010
Dynamic simulation of locally inextensible vesicles suspended in an arbitrary two-dimensional domain, a boundary integral method.
J. Comput. Phys., 2010
Petascale Direct Numerical Simulation of Blood Flow on 200K Cores and Heterogeneous Architectures.
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Proceedings of the Conference on High Performance Computing Networking, 2010
Optimizing and tuning the fast multipole method for state-of-the-art multicore architectures.
Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010
An EM algorithm for brain tumor image registration: A tumor growth modeling based approach.
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, 2010
2009
Non-diffeomorphic registration of brain tumor images by simulating tissue loss and tumor growth.
NeuroImage, 2009
Corrigendum to "Non-diffeomorphic registration of brain tumor images by simulating tissue loss and tumor growth" [NeuroImage 46 (2009) 762-774].
NeuroImage, 2009
A boundary integral method for simulating the dynamics of inextensible vesicles suspended in a viscous fluid in 2D.
J. Comput. Phys., 2009
A numerical method for simulating the dynamics of 3D axisymmetric vesicles suspended in viscous flows.
J. Comput. Phys., 2009
Biomechanically-Constrained 4D Estimation of Myocardial Motion.
Proceedings of the Medical Image Computing and Computer-Assisted Intervention, 2009
An Inverse Scattering Algorithm for the Segmentation of the Luminal Border on Intravascular Ultrasound Data.
Proceedings of the Medical Image Computing and Computer-Assisted Intervention, 2009
2008
A Comparative Study of Biomechanical Simulators in Deformable Registration of Brain Tumor Images.
IEEE Trans. Biomed. Eng., 2008
Bottom-Up Construction and 2: 1 Balance Refinement of Linear Octrees in Parallel.
SIAM J. Sci. Comput., 2008
Brain--Tumor Interaction Biophysical Models for Medical Image Registration.
SIAM J. Sci. Comput., 2008
Multigrid Algorithms for Inverse Problems with Linear Parabolic PDE Constraints.
SIAM J. Sci. Comput., 2008
The Chebyshev fast Gauss and nonuniform fast Fourier transforms and their application to the evaluation of distributed heat potentials.
J. Comput. Phys., 2008
Dendro: parallel algorithms for multigrid and AMR methods on 2: 1 balanced octrees.
Proceedings of the ACM/IEEE Conference on High Performance Computing, 2008
Parallel optimization of tumor model parameters for fast registration of brain tumor images.
Proceedings of the Medical Imaging 2008: Image Processing, 2008
2007
A High-Order Solver for the Heat Equation in 1D domains with Moving Boundaries.
SIAM J. Sci. Comput., 2007
Low-constant parallel algorithms for finite element simulations using linear octrees.
Proceedings of the ACM/IEEE Conference on High Performance Networking and Computing, 2007
Robust Computation of Mutual Information Using Spatially Adaptive Meshes.
Proceedings of the Medical Image Computing and Computer-Assisted Intervention - MICCAI 2007, 10th International Conference, Brisbane, Australia, October 29, 2007
Modeling Glioma Growth and Mass Effect in 3D MR Images of the Brain.
Proceedings of the Medical Image Computing and Computer-Assisted Intervention - MICCAI 2007, 10th International Conference, Brisbane, Australia, October 29, 2007
2006
A high-order 3D boundary integral equation solver for elliptic PDEs in smooth domains.
J. Comput. Phys., 2006
Estimating myocardial fiber orientations by template warping.
Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2006
Correspondence detection in diffusion tensor images.
Proceedings of the 2006 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2006
Inversion of Airborne Contaminants in a Regional Model.
Proceedings of the Computational Science, 2006
Parallel Algorithms for PDE-Constrained Optimization.
Proceedings of the Parallel Processing for Scientific Computing, 2006
2005
Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. Part II: The Lagrange-Newton Solver and Its Application to Optimal Control of Steady Viscous Flows.
SIAM J. Sci. Comput., 2005
Parallel Lagrange-Newton-Krylov-Schur Methods for PDE-Constrained Optimization. Part I: The Krylov-Schur Solver.
SIAM J. Sci. Comput., 2005
Dynamic Data-Driven Inversion For Terascale Simulations: Real-Time Identification Of Airborne Contaminants.
Proceedings of the ACM/IEEE SC2005 Conference on High Performance Networking and Computing, 2005
2004
A Framework for Online Inversion-Based 3D Site Characterization.
Proceedings of the Computational Science, 2004
2003
A New Parallel Kernel-Independent Fast Multipole Method.
Proceedings of the ACM/IEEE SC2003 Conference on High Performance Networking and Computing, 2003
High Resolution Forward And Inverse Earthquake Modeling on Terascale Computers.
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Proceedings of the ACM/IEEE SC2003 Conference on High Performance Networking and Computing, 2003
2002
Parallel multiscale Gauss-Newton-Krylov methods for inverse wave propagation.
Proceedings of the 2002 ACM/IEEE conference on Supercomputing, 2002
1999
Parallel Netwon-Krylov Methods for PDE-Constrained Optimization.
Proceedings of the ACM/IEEE Conference on Supercomputing, 1999