A more complete list of publications can be found on my Google Scholar profile.
- with Sahidul Islam & Maxim Olshanskii, Tensor-Based Reduced-Order Modeling for Optimization-Based Inverse Problems. arXiv preprint
- with Asikul Islam, Md Rezwan Bin Mizan & Maxim Olshanskii, Tensorial reduced-order models for parametric coupled reaction-diffusion systems: Application to brain tumor growth modeling. arXiv preprint
- with Xiaoyu Wang, Alexandra Valavanis, Azhir Mahmood, Martin Benning & Audrey Repetti, A unified framework for lifted training and inversion approaches. Handbook of Numerical Analysis, Volume 27, 2026, Pages 425-485. doi arXiv chapter
- with Ji Shi, Nicolas Charon, Demetrio Labate & Robert Azencott, Fast k-means clustering in Riemannian manifolds via Fréchet maps: Applications to large-dimensional SPD matrices. arXiv preprint
- with Zhongjie Zhou, Bao Zhao & Guojun Liao, VPreg: An optimal control formulation for diffeomorphic image registration based on the variational principle grid generation method. arXiv preprint
- with Yunhui He, A generalized alternating NGMRES method for PDE-constrained optimization problems governed by transport equations. arXiv preprint
- with German Villalobos & Johann Rudi, Neural networks for Bayesian inverse problems governed by a nonlinear ODE. SIAM Journal on Scientific Computing, 48(3):C415-C452, 2025. doi arXiv journal
- with Yingxue Su, Brett Geiger, Ilya Timofeyev & Robert Azencott, Rare events analysis and computation for stochastic evolution of bacterial populations. Stochastic Analysis and Applications, 2025. doi arXiv journal
- with Hossein Dabirian, Radmir Sultamuratov, James Herring, Carlos El-Tallawi, William Zoghbi & Robert Azencott, Classification of Deformable Smooth Shapes Through Geodesic Flows of Diffeomorphisms. Journal of Mathematical Imaging and Vision, 2024. doi arXiv journal
- CLAIRE: Scalable GPU-Accelerated Algorithms for Diffeomorphic Image Registration in 3D. Explorations in the Mathematics of Data Science. Applied and Numerical Harmonic Analysis, 167-215, 2024. doi arXiv chapter
- with Jiwen He & Robert Azencott, An operator-splitting approach for variational optimal control formulations for diffeomorphic shape matching. Journal of Computational Physics, 493:112463, 2023. doi arXiv journal
- with Naveen Himthani, Malte Brunn, Jae Youn Kim, Miriam Schulte & George Biros, CLAIRE: Parallelized diffeomorphic image registration for large-scale biomedical imaging applications. Journal of Imaging, 8(9):251, 2022. doi arXiv journal
- with Saeed Sarmadi, Joel J. Winkle, Razan N. Alnahhas, Matthew R. Bennett, Kresimir Josic & Robert Azencott, Stochastic Neural Networks for Automatic Cell Tracking in Microscopy Image Sequences of Bacterial Colonies. Mathematical and Computational Applications, 27(2):22, 2022. doi arXiv journal
- with Peng Zhang, Jiwen He, Robert Azencott, Carlos El-Tallawi & William Zoghbi, Diffeomorphic Shape Matching by Operator Splitting in 3D Cardiology Imaging. Journal of Optimization Theory and Applications, 188(1):143-168, 2021. doi arXiv journal
- with M. Brunn, N. Himthani, G. Biros & M. Mehl, CLAIRE: Constrained large deformation diffeomorphic image registration on parallel computing architectures. Journal of Open Source Software, 6(61):3038, 2021. doi journal
- with Malte Brunn, Naveen Himthani, George Biros & Miriam Mehl, Fast GPU 3D diffeomorphic image registration. Journal of Parallel and Distributed Computing, 149:149-162, 2021. doi arXiv journal
- with Spyridon Bakas, Shashank Subramanian, Christos Davatzikos & George Biros, Integrated biophysical modeling and image analysis: Application to neuro-oncology. Annual Review of Biomedical Engineering, 22:309-341, 2020. doi arXiv journal
- with Klaudius Scheufele, Shashank Subramanian, George Biros & Miriam Mehl, Image-driven biophysical tumor growth model calibration. SIAM Journal on Scientific Computing, 42(3):B549-B580, 2020. doi arXiv journal
- with Malte Brunn, Naveen Himthani, George Biros & Miriam Mehl, Multi-node multi-GPU diffeomorphic image registration for large-scale imaging problems. Proc ACM/IEEE Conference on Supercomputing, pp. 523-539, 2020. doi arXiv conference
- with Spyridon Bakas, Mauricio Reyes, Andras Jakab et al., Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge. arXiv:1811.02629, 2019. arXiv preprint
- with Amir Gholami, Christos Davatzikos & George Biros, CLAIRE: A distributed-memory solver for constrained large deformation diffeomorphic image registration. SIAM Journal on Scientific Computing, 41(5):C548-C584, 2019. doi arXiv journal
- with Klaudius Scheufele, Amir Gholami, Christos Davatzikos, George Biros & Miriam Mehl, Coupling brain-tumor biophysical models and diffeomorphic image registration. Computer Methods in Applied Mechanics and Engineering, 347:533-567, 2019. doi arXiv journal
- with Amir Gholami, Christos Davatzikos & George Biros, PDE-constrained optimization in medical image analysis. Optimization and Engineering, 19:765-812, 2018. doi arXiv journal
- with Lars Ruthotto, A Lagrangian Gauss-Newton-Krylov solver for intensity- and mass-preserving diffeomorphic image registration. SIAM Journal on Scientific Computing, 39(5):B860-B885, 2017. doi arXiv journal
- with George Biros, A semi-Lagrangian two-level preconditioned Newton-Krylov solver for constrained diffeomorphic image registration. SIAM Journal on Scientific Computing, 39(6):B1064-B1101, 2017. doi arXiv journal
- with Amir Gholami, Klaudius Scheufele, Christos Davatzikos, Miriam Mehl & George Biros, A framework for scalable biophysics-based image analysis. Proc ACM/IEEE Conference on Supercomputing, 19, 2017. doi conference
- with George Biros, Constrained H1 regularization schemes for diffeomorphic image registration. SIAM Journal on Imaging Sciences, 9(3):1154-1194, 2016. doi arXiv journal
- with Amir Gholami & George Biros, An inverse problem formulation for parameter estimation of a reaction-diffusion model for low grade gliomas. Journal of Mathematical Biology, 72(1):409-433, 2016. doi arXiv journal
- with Amir Gholami & George Biros, Distributed-memory large deformation diffeomorphic 3D image registration. Proc ACM/IEEE Conference on Supercomputing, 72:842-853, 2016. doi arXiv conference
- with George Biros, An inexact Newton-Krylov algorithm for constrained diffeomorphic image registration. SIAM Journal on Imaging Sciences, 8(2):1030-1069, 2015. doi arXiv journal
- Methoden zur numerischen Simulation der Progression von Gliomen. Springer Verlag, 2014. doi book
- with A. Toma, T. A. Schuetz, S. Becker, C. Mohr, T. Eckey, D. Petersen & T. M. Buzug, Biophysical modeling of brain tumor progression: From unconditionally stable explicit time integration to an inverse problem with parabolic PDE constraints for model calibration. Medical Physics, 39(7):4444-4460, 2012. doi journal
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