@article{PashVillaHormuthEtAl25,
title = {Predictive Digital Twins with Quantified Uncertainty for Patient-Specific Decision Making in Oncology},
author = {Pash, Graham and Villa, Umberto and Hormuth, David~A.~II and Yankeelov,~Thomas E. and Willcox, Karen},
year = {2025},
eprint = {2505.08927},
archiveprefix = {arXiv},
primaryclass = {cs.CE},
url = {https://arxiv.org/abs/2505.08927}
}
@article{LozenskiHanchenLiEtAl24,
title = {Learned Correction Methods for Simplified Acoustic Forward Models in Ultrasound Computed Tomography},
author = {Lozenski, Luke and Wang, Hanchen and Li, Fu and Anastasio, Mark~A. and Wohlberg, Brendt and Lin, Youzuo and Villa, Umberto},
year = {2024},
journal = {\emph{submitted to} Journal of Medical Imaging}
}
@article{ChenParkCamEtAl24a,
title = {Learning a Filtered Backprojection Reconstruction Method for Photoacoustic Computed Tomography with Hemispherical Measurement Geometries},
author = {Chen, Panpan and Park, Seonyeong and Cam, Refik~Mert and Huang, Hsuan-Kai and Oraevsky, Alexander~A. and Villa, Umberto and Anastasio, Mark~A. },
year = {2024},
journal = {\emph{submitted to} IEEE Trans on Medical Imaging},
url = {https://arxiv.org/abs/2412.01971},
doi = {10.48550/arXiv.2412.01971}
}
@article{LinFengTheilerEtAl24,
title = {Physics and Deep Learning in Computational Wave Imaging},
author = {Lin, Youzou and Feng, Shihang and Theiler, James and Chen, Yinpeng and Villa, Umberto and Rao, Jing and Greenhall, John and Pantea, Cristian and Anastasio, Mark and Wohlberg, Brendt},
journal = {\emph{submitted to } Proceedings of the IEEE},
year = {2024},
url = {https://arxiv.org/abs/2410.08329},
doi = {10.48550/arXiv.2410.08329}
}
@article{CraftsVilla25,
title = {Can Diffusion Models Provide Rigorous Uncertainty Quantification for Bayesian Inverse Problems?},
author = {Scope~Crafts, Evan and Villa, Umberto},
journal = {arXiv preprint arXiv:2503.03007},
year = {2025}
}
@misc{BhadraVillaAnastasio23,
title = {Mining the manifolds of deep generative models for
multiple data-consistent solutions of ill-posed tomographic imaging problems},
author = {Bhadra, Sayantan and Villa, Umberto and Anastasio, Mark},
archiveprefix = {arXiv},
eprint = {2202.05311},
year = {2022}
}
@misc{LozenskiVilla21,
title = {Consensus ADMM for Inverse Problems Governed by Multiple PDE Models},
author = {Lozenski, Luke and Villa, Umberto},
year = {2021},
archiveprefix = {arXiv},
eprint = {2104.13899}
}
@misc{VillaMarques17,
author = {Villa, U. and Marques, A.~N.},
title = {{An UQ-ready finite element solver for a two-dimensional RANS model of free plane jets}},
year = {2017},
archiveprefix = {arXiv},
eprint = {1712.01786},
url = {https://arxiv.org/pdf/1712.01786.pdf}
}
@article{GangwonVillaAnastasio25,
title = {Revisiting the joint estimation of initial pressure and speed-of-sound distributions in photoacoustic computed tomography with consideration of canonical object constraints},
author = {Jeong, Gangwon and Villa, Umberto and Anastasio, Mark},
year = {2025},
journal = {Photoacoustics},
url = {https://doi.org/10.1016/j.pacs.2025.100700.},
doi = {10.1016/j.pacs.2025.100700.}
}
@article{HuangKuoYangEtAl25,
author = {Huang, Hsuan-Kai and Kuo, Joseph and Zhang, Yang and Aborahama, Yousuf and Cui, Manxiu and Sastry, Karteekeya and Park, Seonyeong and Villa, Umberto and Wang, Lihong V and Anastasio, Mark},
title = {Fast aberration correction in {3D} transcranial photoacoustic computed tomography via a learning-based image reconstruction method},
journal = {Photoacoustics},
year = {2025}
}
@article{MaciasMonterrubioSalmeron24,
title = {Exploring the effect of sedentary behavior on increased adiposity in middle-aged adults},
author = {Mac{\'\i}as, Nayeli and Monterrubio-Flores, Eric and Salmer{\'o}n, Jorge and Meneses-Le{\'o}n, Joacim and Flores, Yvonne N and J{\'a}uregui, Alejandra and Salvo, Deborah and Villa, Umberto and Olvera, Armando G and Gallegos-Carrillo, Katia},
journal = {BMC Public Health},
volume = {24},
number = {1},
pages = {2228},
year = {2024},
publisher = {Springer}
}
@article{CraftScopeAnastasioVilla24,
title = {Optimizing Quantitative Photoacoustic Imaging Systems: The Bayesian Cram{\'e}r-Rao Bound Approach},
author = {{Craft Scope}, Evan and Anastasio, Mark A and Villa, Umberto},
journal = {Inverse Problems},
year = {2024},
volume = {in press},
url = {https://arxiv.org/abs/2410.09557},
doi = {10.1088/1361-6420/ad910a}
}
@article{SeelingerReinarzLykkegaard24,
title = {Democratizing Uncertainty Quantification},
author = {Seelinger, Linus and Reinarz, Anne and Lykkegaard, Mikkel~B. and Akers, Robert and Alghamdi, Amal~M.~A. and Aristoff, David and Bangerth, Wolfgang and B\'en\'ezech, Jean and Diez, Matteo and Frey, Kurt and Jakeman, John~D. and Jørgensen, Jakob~S. and Kim, Ki-Tae and Martinelli, Massimiliano and Parno, Matthew and Pellegrini, Riccardo and Petra, Noemi and Riis, Nicolai~A.~B. and Rosenfeld, Katherine and Serani, Andrea and Tamellini, Lorenzo and Villa, Umberto and Dodwell, Tim~J. and Scheichl, Robert },
year = {2024},
journal = {Journal Computational Physics},
volume = {In press, pre-proof},
doi = {10.1016/j.jcp.2024.113542},
url = {https://arxiv.org/abs/2402.13768}
}
@article{LuoHuangKarteekeyaEtAl24,
title = {Full-wave Image Reconstruction in Transcranial Photoacoustic Computed Tomography using a Multiphysics Finite Element Method},
author = {Luo, Yilin and Huang, Hsuan-Kai and Sastry, Karteekeya and Hu, Peng and Tong, Xin and Kuo, Joseph and Aborahama, Yousuf and Na, Shuai and Villa, Umberto and Anastasio, Mark.~A. and Wang, Lihong~V. },
journal = {IEEE Trans on Medical Imaging},
volume = {\emph{Early Access}},
year = {2024},
doi = {10.1109/TMI.2024.3456595}
}
@article{GangwonLiVillaEtAl24,
title = {Investigating the Use of Traveltime and Reflection Tomography for Deep Learning-Based Sound-Speed Estimation in Ultrasound Computed Tomography},
author = {Jeong, Gangwon and Li, Fu Mitcham, Trevor and Duric, Nebojsa and Villa, Umberto and Anastasio, Mark},
journal = {IEEE Trans on Ultrasonic, Ferroelectrics, and Frequency Control},
volume = {\emph{Early Access}},
doi = {10.1109/TUFFC.2024.3459391},
year = {2024}
}
@article{LozenskiCamPagelEtAl24,
title = {Prox{NF}: Neural Field Proximal Training for High-Resolution 4{D} Dynamic Image Reconstruction},
author = {Lozenski, Luke and Cam, Refik Mert and Pagel, Mark~D. and Anastasio, Mark A. and Villa, Umberto},
journal = {Transactions on Computational Imaging},
year = {2024},
volume = {10},
pages = {1368-1383},
doi = {10.1109/TCI.2024.3458397}
}
@article{LouChenOLearyEtAl24,
title = {{SOUPy: Stochastic PDE-constrained optimization under high-dimensional uncertainty in Python}},
author = {Lou, Dingchen and Chen, Peng and O'Leary-Roseberry, Thomas and Villa, Umberto and Ghattas, Omar},
journal = {Journal of Open Source Software},
year = {2024}
}
@article{CamVillaAnastasio24,
title = {Learning a Stable Approximation of an Existing but Unknown Inverse Mapping: Application to the Half-Time Circular Radon Transform},
author = {Cam, Refik M and Villa, Umberto and Anastasio, Mark A},
journal = {Inverse Problems},
volume = {40},
number = {8},
pages = {085002},
doi = {10.1088/1361-6420/ad4f0a},
year = {2024}
}
@article{PuelBeckerVillaEtAl24,
author = {Puel, Simone and Becker, Thorsten W and Villa, Umberto and Ghattas, Omar and Liu, Dunuy},
title = {Volcanic arc rigidity variations illuminated by coseismic deformation of the 2011 {T}ohoku-oki {M}9},
journal = {Science Advances},
volume = {10},
number = {23},
pages = {eadl4264},
year = {2024},
doi = {10.1126/sciadv.adl4264},
url = {https://www.science.org/doi/abs/10.1126/sciadv.adl4264},
eprint = {https://www.science.org/doi/pdf/10.1126/sciadv.adl4264}
}
@article{LiVillaLiEtAl24,
title = {Application of Learned Ideal Observers for Estimating Task-Based Performance Bounds for Computed Imaging Systems},
author = {Li, Kaiyan and Villa, Umberto and Li, Hua and Anastasio, Mark},
journal = { Journal of Medical Imaging},
volume = {11},
number = {2},
publisher = {SPIE},
pages = {026002},
year = {2024},
doi = {10.1117/1.JMI.11.2.026002},
url = {https://doi.org/10.1117/1.JMI.11.2.026002}
}
@article{LozenskiWangLiEtAl24,
title = {Learned Full Waveform Inversion Incorporating Task Information for Ultrasound Computed Tomography},
author = {Lozenski, Luke and Wang, Hanchen and Li, Fu and Anastasio, Mark and Wohlberg, Brendt and Lin, Youzuo and Villa, Umberto},
journal = {IEEE Transactions on Computational Imaging},
year = {2024},
volume = {10},
number = {},
pages = {69-82},
doi = {10.1109/TCI.2024.3351529}
}
@article{CamWangWeylanEtAl24,
title = {Spatiotemporal Image Reconstruction to Enable High-Frame Rate Dynamic Photoacoustic Tomography with Rotating-Gantry Volumetric Imagers},
author = {Cam, Refik M and Wang, Chao and Thompson, Weylan and Ermilov, Sergey A and Anastasio, Mark A and Villa, Umberto},
volume = {29},
journal = {Journal of Biomedical Optics},
number = {S1},
publisher = {SPIE},
pages = {S11516},
doi = {10.1117/1.JBO.29.S1.S11516},
year = {2024}
}
@article{PuelBeckerVillaEtAl23,
title = {An adjoint-based optimization method for jointly inverting heterogeneous material properties and fault slip from earthquake surface deformation data},
author = {Puel, Simone and Becker, Thorsten W and Villa, Umberto and Ghattas, Omar and Liu, Dunyu},
year = {2023},
journal = {Geophysical Journal International},
volume = {236},
issue = {2},
pages = {778--797},
url = {https://doi.org/10.31223/X5JW9R},
doi = {10.1093/gji/ggad442}
}
@article{OLearyChenVillaEtAl23,
title = {Derivative Informed Neural Operator: An Efficient Framework for High-Dimensional Parametric Derivative Learning},
author = {O'Leary-Roseberry, Thomas and Chen, Peng and Villa, Umberto and Ghattas, Omar},
journal = {Journal of Computational Physics},
pages = {112555},
year = {2023},
issn = {0021-9991},
doi = {10.1016/j.jcp.2023.112555}
}
@article{LiVillaDuricEtAl23,
url = {https://arxiv.org/abs/2301.07787},
author = {Li, Fu and Villa, Umberto and Duric, Nebojsa and Anastasio, Mark A.},
title = {A forward model incorporating elevation-focused transducer properties for 3{D} full-waveform inversion in ultrasound computed tomography},
journal = {IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control},
volume = {70},
number = {10},
pages = {1339-1354},
doi = {10.1109/TUFFC.2023.3313549},
year = {2023}
}
@article{ZhouVillaAnastasio23,
author = {Zhou, Weimin and Villa, Umberto and Anastasio, Mark A.},
title = {Ideal Observer Computation by use of Markov-Chain Monte Carlo with Generative Adversarial Networks},
journal = {IEEE Transactions on Medical Imaging},
volume = {42},
number = {12},
pages = {3715-3724},
doi = {10.1109/TMI.2023.3304907},
url = {https://arxiv.org/abs/2304.00433},
year = {2023}
}
@article{ParkVillaLiEtAl23,
author = {Park, Seonyeong and Villa, Umberto and Cam, Refik Mert and Oraevsky, Alexander and Anastasio, Mark},
title = {Stochastic three-dimensional numerical phantoms to enable computational studies in quantitative optoacoustic tomography of breast cancer},
volume = {28},
journal = {Journal of Biomedical Optics},
number = {6},
publisher = {SPIE},
pages = {066002},
keywords = {Numerical breast phantoms, optical breast phantoms, acoustic breast phantoms, optoacoustic computed tomography, photoacoustic computed tomography, virtual imaging trials, Breast, Tissues, Acoustics, Anatomy, Blood, Tissue optics, Blood vessels, Imaging systems, Stochastic processes, Tumors},
year = {2023},
doi = {10.1117/1.JBO.28.6.066002},
url = {https://doi.org/10.1117/1.JBO.28.6.066002}
}
@article{BaoshanLozenskiHormuthEtAl23,
title = {Bayesian Inference of Tissue Heterogeneity for Individualized Prediction of Glioma Growth},
author = {Liang, Baoshan and Tan, Jingye and Lozenski, Luke and Hormuth II, David A and Yankeelov, Thomas E and Villa, Umberto and Faghihi, Danial},
year = {2023},
journal = {IEEE Transactions on Medical Imaging},
volume = {42},
number = {10},
pages = {2865-2875},
url = {https://arxiv.org/abs/2209.12089},
doi = {10.1109/TMI.2023.3267349}
}
@article{NicholsonPetraVillaEtAl23,
author = {Nicholson, Ruanui and Petra, Noemi and Villa, Umberto and Kaipio, Jari P.},
title = {On global normal linear approximations for nonlinear Bayesian inverse problems},
journal = {Inverse Problems},
url = {http://iopscience.iop.org/article/10.1088/1361-6420/acc129},
volume = {39},
issue = {5},
pages = {4001},
year = {2023}
}
@article{KalchevVassilevskiVilla23,
cc = {\ec},
title = {Parallel Element-based Algebraic Multigrid for {H}(curl) and {H}(div) Problems Using the {P}ar{ELAG} Library},
author = {Kalchev, Delyan Z and Vassilevski, Panayot S and Villa, Umberto},
journal = {SIAM Journal on Scientific Computing},
volume = {45},
number = {3},
pages = {S371-S400},
year = {2023},
doi = {10.1137/21M1433253},
url = {https://arxiv.org/abs/2107.05613}
}
@article{LanzaAlcazarDurandEtAl22,
title = {Heat-Resilient Schoolyards: Relations Between Temperature, Shade, and Physical Activity of Children During Recess},
author = {Lanza, Kevin and Alcazar, Melody and Durand, Casey P and Salvo, Deborah and Villa, Umberto and Kohl, Harold W},
journal = {Journal of Physical Activity and Health},
volume = {1},
number = {aop},
pages = {1--8},
year = {2022},
publisher = {Human Kinetics}
}
@article{LeeBuiVillaEtAl22,
title = {Forward and inverse modeling of fault transmissibility in subsurface flows},
author = {Lee, Jeonghun J and Bui-Thanh, Tan and Villa, Umberto and Ghattas, Omar},
journal = {Computers \& Mathematics with Applications},
volume = {128},
pages = {354--367},
year = {2022},
publisher = {Elsevier}
}
@article{KimVillaParnoEtAl23,
title = {h{IPPYlib}-{MUQ}: A {B}ayesian Inference Software Framework for Integration of Data with Complex Predictive Models under Uncertainty},
author = {Kim , Ki-Tae and Villa, Umberto and Parno, Matthew and Marzouk, Youssef and Ghattas, Omar and Petra, Noemi},
year = {2023},
journal = {ACM Trans. Math. Softw.},
url = {https://arxiv.org/abs/2112.00713},
volume = {49},
number = {2},
articleno = {17},
numpages = {31},
doi = {10.1145/3580278}
}
@article{LozenskiAnastasioVilla22,
author = {Lozenski, Luke and Anastasio, Mark A. and Villa, Umberto},
journal = {IEEE Transactions on Computational Imaging},
title = {A Memory-Efficient Self-Supervised Dynamic Image Reconstruction Method Using Neural Fields},
year = {2022},
volume = {8},
number = {},
pages = {879-892},
doi = {10.1109/TCI.2022.3208511},
url = {https://arxiv.org/abs/2205.05585}
}
@article{ParkBrooksVillaEtAl22,
author = {Park, Seonyeong and Brooks, Frank and Villa, Umberto and Su, Richard and Anastasio, Mark and Oraevsky, Alexander},
title = {Normalization of optical fluence distribution for three-dimensional functional optoacoustic tomography of the breast},
journal = {Journal of Biomedical Optics},
volume = {27},
issue = {3},
year = {2022}
}
@article{PuelKhattatovVillaEtAl22,
cc = {\scon},
title = {A Mixed, Unified Forward/Inverse Framework for Earthquake Problems: Fault Implementation and Coseismic Slip Estimate},
author = {Puel, Simone and Khattatov, Eldar and Villa, Umberto and Liu, Dunyu and Ghattas, Omar and Becker, Thorsten W},
year = {2022},
journal = {Geophysical Journal International},
volume = {230},
issue = {2},
pages = {733--758},
url = {https://doi.org/10.31223/X5262V}
}
@article{TanMalekiAnEtAl22,
cc = {\scon},
title = {A Predictive Multiphase Model of Silica Aerogels for Building Envelope Insulations},
author = {Tan, Jingye and Maleki, Pedram and An, Lu and Di Luigi, Massimigliano and Villa, Umberto and Zhou, Chi and Ren, Shenqiang and Faghihi, Danial},
journal = {Computational Mechanics},
volume = {69},
issue = {6},
pages = {1457--1479},
year = {2022},
url = {https://arxiv.org/abs/2107.12182}
}
@article{KuoGranstedtVillaEtAl22,
cc = {\scon},
title = {Computing a Projection Operator onto the Null Space of a Linear Imaging Operator: {T}utorial},
author = {Kuo, Joseph and Granstedt, Jason and Villa, Umberto and Anastasio, Mark A.},
journal = {Journal of the Optical Society of America A},
doi = {10.1364/JOSAA.443443},
volume = {39},
issue = {3},
pages = {470--481},
year = {2022}
}
@article{OLearyVillaChenEtAl21,
cc = {\scon},
title = {Derivative-Informed Projected Neural Networks for High-Dimensional Parametric Maps Governed by {PDE}s},
author = {O'Leary-Roseberry, T. and Villa, U. and Chen, P. and Ghattas, O.},
journal = {Computer Methods in Applied Mechanics and Engineering},
volume = {388},
pages = {114199},
year = {2022},
issn = {0045-7825},
doi = {10.1016/j.cma.2021.114199},
url = {https://arxiv.org/abs/2011.15110}
}
@article{LiVillaParkEtAl21,
cc = {\scon},
title = {Three-dimensional stochastic numerical breast phantoms for enabling virtual imaging trials of ultrasound computed tomography},
author = {Li, Fu and Villa, Umberto and Park, Seonyeong and Anastasio, Mark A},
year = {2022},
volume = {69},
number = {1},
pages = {135--146},
doi = {10.1109/TUFFC.2021.3112544},
journal = {IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control},
url = {https://arxiv.org/abs/2106.02744}
}
@article{FairbanksVillaVassilevski21,
cc = {\ec},
title = {{Multilevel Hierarchical Decomposition of Finite Element White Noise with Application to Multilevel Markov Chain Monte Carlo}},
author = {Fairbanks, H.~R. and Villa, U. and Vassilevski, P. S.},
year = {2021},
journal = {SIAM Journal on Scientific Computing},
volume = {43},
number = {5},
pages = {S293-S316},
doi = {10.1137/20M1349606},
url = {https://arxiv.org/abs/2007.14440}
}
@article{AlghamdiHesseChenEtAl21,
cc = {\scon},
author = {Alghamdi, A and Hesse, M. and Chen, J. and Villa, U. and Ghattas, O.},
title = {Bayesian Poroelastic Aquifer Characterization from {I}n{SAR} Surface Deformation Data Part {II}: {Q}uantifying the Uncertainty},
journal = {Water Resources Research},
volume = {57},
number = {11},
pages = {e2021WR029775},
year = {2021},
doi = {10.1029/2021WR029775}
}
@article{BabaniyiNicholsonVilla21,
cc = {\scon},
author = {Babaniyi, O. and Nicholson, R. and Villa, U. and Petra, N.},
title = {Inferring the basal sliding coefficient field for the Stokes ice sheet model under rheological uncertainty},
journal = {The Cryosphere},
volume = {15},
year = {2021},
number = {4},
pages = {1731--1750},
url = {https://tc.copernicus.org/articles/15/1731/2021/},
doi = {10.5194/tc-15-1731-2021}
}
@article{FaghihiTanVillaEtAl21,
cc = {\scon},
author = {Faghihi, D. and Tan, J. and Villa, U. and Shamsaei, N. and Shao, S. and Zbib, H.},
title = {A Predictive Discrete-Continuum Multiscale Model of Plasticity With Quantified Uncertainty},
journal = {International Journal of Plasticity},
year = {2021},
volume = {138},
pages = {102935},
issn = {0749-6419},
doi = {10.1016/j.ijplas.2021.102935},
url = {https://arxiv.org/pdf/2012.10823}
}
@article{VillaPetraGhattas21,
cc = {\fac},
author = {{Villa}, U. and {Petra}, N. and {Ghattas}, O.},
title = {{hIPPYlib: An Extensible Software Framework for Large-Scale Inverse Problems Governed by PDEs; Part I: Deterministic Inversion and Linearized Bayesian Inference}},
year = {2021},
issue_date = {March 2021},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
volume = {47},
number = {2},
issn = {0098-3500},
doi = {10.1145/3428447},
journal = {ACM Trans. Math. Softw.},
month = apr,
articleno = {16},
numpages = {34},
url = {https://arxiv.org/abs/1909.03948}
}
@article{JaureguiSalvoGarciaEtAl19,
author = {J\'auregui, A. and Salvo, D. and Garc\'ia-Olvera, A. and Villa, U. and T\'ellez-Rojo, M.~M. and Schnaas, L.~M. and Svensson, K. and Oken, E. and Wright, R.~O. and Baccarelli, A.~A. and Cantoral, A.},
title = {Physical activity, sedentary time and cardiometabolic health indicators among Mexican children},
year = {2019},
journal = {Clinical Obesity},
pages = {e12346},
doi = {10.1111/cob.12346},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/cob.12346}
}
@article{KramerMarquesPeherstorferEtAl19,
cc = {\scon},
author = {Kramer, B. and Marques, A.~N. and Peherstorfer, B. and Villa, U. and Willcox, K.},
title = {Multifidelity probability estimation via fusion of estimators},
journal = {Journal of Computational Physics},
volume = {392},
pages = {385--402},
doi = {10.1016/j.jcp.2019.04.071},
url = {http://web.mit.edu/bokramer/www/img/pubs/KramerMarquesPeherstorferVillaWillcox17-fusedIS-TR.pdf},
year = {2019}
}
@article{ChenVillaGhattas19,
cc = {\scon},
author = {Chen, P. and Villa, U. and Ghattas, O.},
title = {Taylor approximation and variance reduction for {PDE}-constrained optimal control under uncertainty},
journal = {Journal of Computational Physics},
pages = {163--186},
volume = {385},
doi = {10.1016/j.jcp.2019.01.047},
year = {2019},
url = {https://arxiv.org/pdf/1804.04301.pdf}
}
@article{VillaPetraGhattas18,
cc = {\fac},
title = {{hIPPYlib: an Extensible Software Framework for Large-scale Deterministic and Bayesian Inverse Problems}},
author = {Villa, U. and Petra, N. and Ghattas, O.},
journal = {Journal of Open Source Software},
volume = {3},
number = {30},
pages = {940},
doi = {10.21105/joss.00940},
year = {2018}
}
@article{OsbornZulianBensonEtAl18,
cc = {\scon},
author = {Osborn, S. and Zulian, P. and Benson, T. and Villa, U. and Krause, R. and Vassilevski, P.},
title = {Scalable hierarchical PDE sampler for generating spatially correlated random fields using non-matching meshes},
journal = {Numerical Linear Algebra with Applications},
issn = {1099-1506},
doi = {10.1002/nla.2146},
eprint = {1712.06758},
volume = {25},
number = {3},
pages = {e2146},
year = {2018}
}
@article{ChristensenVassilevskiVilla17,
cc = {\lac},
author = {Christensen, M. and Vassilevski, P.~S. and Villa, U.},
title = {{Nonlinear Multigrid solvers exploiting AMGe coarse spaces with approximation properties}},
journal = {Journal of Computational and Applied Mathematics},
volume = {340},
pages = {691 - 708},
year = {2018},
issn = {0377-0427},
doi = {10.1016/j.cam.2017.10.029}
}
@article{ChenVillaGhattas17,
cc = {\scon},
author = {Chen, P. and Villa, U. and Ghattas, O.},
title = {{Hessian-based adaptive sparse quadrature for infinite-dimensional Bayesian inverse problems}},
journal = {Computer Methods in Applied Mechanics and Engineering},
year = {2017},
volume = {327},
pages = {147--172},
eprint = {1706.06692},
doi = {10.1016/j.cma.2017.08.016}
}
@article{AlgerVillaBuiEtAl17,
cc = {\scon},
author = {{Alger}, N. and {Villa}, U. and {Bui-Thanh}, T. and {Ghattas}, O. },
title = {{A data scalable augmented Lagrangian KKT preconditioner for large scale inverse problems}},
journal = {SIAM Journal on Scientific Computing},
year = {2017},
volume = {39},
number = {5},
pages = {A2365--A2393},
doi = {10.1137/16M1084365},
eprint = {1607.03556}
}
@article{OsbornVassilevskiVilla17,
cc = {\ec},
author = {Osborn, S. and Vassilevski, P.~S. and Villa, U.},
title = {{A Multilevel Hierarchical Sampling Technique for Spatially Correlated Random Fields}},
journal = {SIAM Journal on Scientific Computing},
year = {2017},
volume = {39},
number = {5},
pages = {S543--S562},
doi = {10.1137/16M1082688},
eprint = {1703.08498}
}
@article{ChristensenVillaEngsigEtAl17,
cc = {\scon},
author = {Christensen, M. and Villa, U. and Engsig-Karup, A. and Vassilevski, P.~S.},
title = {{Numerical upscaling for incompressible flow in reservoir simulation: an element-based algebraic multigrid (AMGe) approach}},
journal = {SIAM Journal on Scientific Computing},
year = {2017},
volume = {39},
number = {1},
doi = {10.1137/140988991},
pages = {B102--B137}
}
@article{KalchevLeeVillaEtAl16,
cc = {\scon},
author = {Kalchev, D. and Lee, C.~S. and Villa, U. and Efendiev, Y. and Vassilevski, P.~S.},
title = {{Upscaling of mixed finite element discretization problems by the spectral AMGe method}},
journal = {SIAM Journal on Scientific Computing},
year = {2016},
volume = {38},
number = {5},
pages = {A2912--A2933},
doi = {10.1137/15M1036683},
url = {https://e-reports-ext.llnl.gov/pdf/799767.pdf}
}
@article{GuzzettiPasseriniSlawinskiVillaEtAl16,
author = {Guzzetti, S. and Passerini, T. and Slawinski, J. and Villa, U. and Veneziani, A. and Sunderam, V.},
title = {{Platform and algorithm effects on computational fluid dynamics applications in life sciences}},
journal = {Future Generation Computer Systems},
volume = {67},
number = {},
pages = {382 -- 396},
year = {2017},
doi = {10.1016/j.future.2016.03.024},
url = {http://www.mathcs.emory.edu/technical-reports/techrep-00272.pdf}
}
@article{SalvoTorresVillaEtAl15,
cc = {\scon},
author = {Salvo, D. and Torres, C. and Villa, U. and Rivera, J.~A. and Sarmiento, O.~L. and Reis, R.~S. and Pratt, M.},
title = {{Accelerometer-based physical activity levels among Mexican adults and their relation with sociodemographic characteristics and BMI: a cross-sectional study}},
journal = {Int. J. Behavioral Nutrition and Physical Activity},
volume = {12},
number = {79},
pages = {1--11},
year = {2015},
publisher = {BioMed Central},
url = {https://ijbnpa.biomedcentral.com/articles/10.1186/s12966-015-0243-z}
}
@article{VassilevskiVilla14,
cc = {\fac},
title = {{A mixed formulation for the Brinkman problem}},
author = {Vassilevski, P.~S. and Villa, U.},
journal = {SIAM Journal on Numerical Analysis},
volume = {52},
number = {1},
pages = {258--281},
year = {2014},
publisher = {SIAM},
doi = {10.1137/120884109},
url = {https://e-reports-ext.llnl.gov/pdf/625743.pdf}
}
@article{VassilevskiVilla13,
cc = {\fac},
author = {Vassilevski, P.~S. and Villa, U.},
title = {{A block-diagonal algebraic multigrid preconditioner for the Brinkman problem}},
journal = {SIAM Journal on Scientific Computing},
volume = {35},
number = {5},
pages = {S3--S17},
year = {2013},
publisher = {SIAM},
doi = {10.1137/120882846},
url = {https://e-reports-ext.llnl.gov/pdf/625849.pdf}
}
@article{DesmondVillaNeweyEtAl13,
cc = {\scon},
author = {Desmond, K.~W. and Villa, U. and Newey, M. and Losert, W.},
title = {Characterizing the rheology of fluidized granular matter},
journal = {Physical Review E},
volume = {88},
number = {3},
pages = {032202},
year = {2013},
publisher = {APS},
url = {http://journals.aps.org/pre/abstract/10.1103/PhysRevE.88.032202},
eprint = {1107.0357}
}
@article{PasseriniQuainiVillaEtAl13,
author = {Passerini, T. and Quaini, A. and Villa, U. and Veneziani, A. and Canic, S.},
title = {Validation of an open source framework for the simulation of blood flow in rigid and deformable vessels},
journal = {Int. J. Numerical Methods in Biomedical Engineering},
volume = {29},
number = {11},
pages = {1192--1213},
year = {2013},
publisher = {Wiley Online Library},
doi = {10.1002/cnm.2568},
url = {http://www.mathcs.emory.edu/technical-reports/techrep-00246.pdf}
}
@article{VenezianiVilla13,
cc = {\fac},
author = {Veneziani, A. and Villa, U.},
title = {{ALADINS: An ALgebraic splitting time ADaptive solver for the Incompressible Navier--Stokes equations}},
journal = {Journal of Computational Physics},
volume = {238},
pages = {359--375},
year = {2013},
publisher = {Elsevier},
doi = {10.1016/j.jcp.2012.11.049},
url = {http://www.sciencedirect.com/science/article/pii/S0021999112007310}
}
@inproceedings{GranstedtVillaAnastasio22,
cc = {\scon},
author = {Granstedt, Jason and Villa, Umberto and Anastasio, Mark},
title = {{Learned Hotelling Observers for use with Multi-Modal Data}},
volume = {12035},
pages = {262--268},
booktitle = {Medical Imaging 2022: Image Perception, Observer Performance, and Technology Assessment},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
year = {2022}
}
@inproceedings{LozenskiAnastasioVilla22a,
cc = {\scon},
author = {Lozenski, Luke and Anastasio, Mark and Villa, Umberto},
title = {{Implicit Neural Representation for Dynamic Imaging}},
volume = {12031},
pages = {231-238},
booktitle = {Medical Imaging 2022: Physics of Medical Imaging},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
year = {2022}
}
@inproceedings{CamVillaAnastasio22,
cc = {\scon},
author = {Cam, Refik and Villa, Umberto and Anastasio, Mark},
title = {{A Learned Filtered Backprojection Method for use with Half-Time Circular Radon Transform Data}},
volume = {12031},
pages = {787--792},
booktitle = {Medical Imaging 2022: Physics of Medical Imaging},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
year = {2022}
}
@inproceedings{LiVillaDuricEtAl22,
cc = {\scon},
author = {Li, Fu and Villa, Umberto and Duric, Neb and Anastasio, Mark A. },
title = {{Investigation of an elevationally focused transducer model for three-dimensional full-waveform inversion in ultrasound computed tomography}},
volume = {12038},
pages = {206--214},
booktitle = {Medical Imaging 2022: Ultrasonic Imaging and Tomography},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
year = {2022}
}
@inproceedings{ParkVillaBrooksEtAl21,
cc = {\scon},
author = {Park, Seonyeong and Villa, Umberto and Brooks, Frank J. and Su, Richard and Oraevsky, Alexander A. and Anastasio, Mark A.},
title = {{Three-dimensional quantitative functional optoacoustic tomography to estimate vascular blood oxygenation of the breast}},
volume = {11642},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2021},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
year = {2021},
doi = {10.1117/12.2585341},
url = {https://doi.org/10.1117/12.2585341}
}
@inproceedings{KuoGranstedtVillaEtAl21a,
cc = {\scon},
author = {Kuo, Joseph and Granstedt, Jason and Villa, Umberto and Anastasio, Mark A. },
title = {{Learning a projection operator onto the null space of a linear imaging operator}},
volume = {11595},
booktitle = {Medical Imaging 2021: Physics of Medical Imaging},
editor = {Hilde Bosmans and Wei Zhao and Lifeng Yu},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {1019 -- 1025},
year = {2021},
doi = {10.1117/12.2582263},
url = {https://doi.org/10.1117/12.2582263}
}
@inproceedings{WangVillaThompsonEtAl21,
cc = {\scon},
author = {Wang, Chao and Villa, Umberto and Thompson, Weylan and Park, Seonyeong and Ermilov, Sergey A. and Anastasio, Mark A. },
title = {{Dynamic reconstruction of three-dimensional photoacoustic tomography from few projections}},
volume = {11642},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2021},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
year = {2021},
doi = {10.1117/12.2585344},
url = {https://doi.org/10.1117/12.2585344}
}
@inproceedings{LiVillaParkEtAl21a,
cc = {\scon},
author = {Li, Fu and Villa, Umberto and Park, Seonyeong and He, Shenghua and Anastasio, Mark A. },
title = {{A framework for ultrasound computed tomography virtual imaging trials that employs anatomically realistic numerical breast phantoms}},
volume = {11602},
booktitle = {Medical Imaging 2021: Ultrasonic Imaging and Tomography},
editor = {Brett C. Byram and Nicole V. Ruiter},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
year = {2021},
doi = {10.1117/12.2582260},
url = {https://doi.org/10.1117/12.2582260}
}
@inproceedings{ParkVillaSuEtAl20,
cc = {\scon},
author = {Park, Seonyeong and Villa, Umberto and Su, Richard and Oraevsky, Alexander and Brooks, Frank J. and Anastasio, Mark A.},
title = {{Realistic three-dimensional optoacoustic tomography imaging trials using the VICTRE breast phantom of FDA (Conference Presentation)}},
volume = {11240},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2020},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
keywords = {Optoacoustic tomography, Photoacoustic computed tomography, Imaging trials, Breast imaging, Breast phantom},
year = {2020},
doi = {10.1117/12.2552380},
url = {https://doi.org/10.1117/12.2552380}
}
@inproceedings{GeVillaKamilovEtAl20,
cc = {\scon},
title = {Proximal {N}ewton Methods for {X}-Ray Imaging with Non-Smooth
Regularization},
author = {Ge,T. and Villa, U. and Kamilov, U.~S. and O’Sullivan, J.~A.},
booktitle = {Proc Electronic Imaging},
publisher = {Society for Imaging Science and Technology},
doi = {10.2352/ISSN.2470-1173.2020.14.COIMG-007},
year = {2020},
url = {https://arxiv.org/abs/1912.01738}
}
@inproceedings{ChenVillaGhattas18,
cc = {\scon},
author = {Chen, P. and Villa, U. and Ghattas, O.},
title = {Taylor approximation for {PDE}-constrained optimization under uncertainty: {A}pplication to turbulent jet flow},
booktitle = {Proceedings in Applied Mathematics and Mechanics - 89th GAMM Annual Meeting},
pages = {e201800466},
volume = {18},
issue = {1},
year = {2018},
doi = {10.1002/pamm.201800466}
}
@inbook{NeumuellerVassilevskiVilla17,
cc = {\scon},
author = {Neum{\"u}ller, M. and Vassilevski, P.~S. and Villa, U.},
editor = {Lee, C.~-O. and Cai, X.~C. and Keyes, D.~E. and Kim, H.~H. and Klawonn, A. and Park, E.~J. and Widlund, O.~B.},
title = {{Space-time constrained First Order Systems Least Squares (CFOSLS) with AMGe upscaling}},
booktitle = {{Domain Decomposition Methods in Science and Engineering XXIII}},
year = {2017},
publisher = {Springer},
pages = {253--260},
isbn = {978-3-319-52389-7},
doi = {10.1007/978-3-319-52389-7_25},
url = {https://e-reports-ext.llnl.gov/pdf/807942.pdf}
}
@inproceedings{ChristensenVillaVassileski15,
cc = {\scon},
author = {Christensen, M. and Villa, U. and Vassilevski, P.~S.},
title = {Multilevel techniques lead to accurate numerical upscaling and scalable robust solvers for reservoir simulation},
booktitle = {SPE Reservoir Simulation Symposium},
year = {2015},
organization = {Society of Petroleum Engineers},
note = {23-25 February, Houston, Texas, USA, SPE-173257-MS},
url = {https://www.onepetro.org/conference-paper/SPE-173257-MS}
}
@inproceedings{PasseriniSlawinskiVillaEtAl14,
author = {Passerini, T. and Slawinski, J. and Villa, U. and Sunderam, V.},
title = {Experiences with {C}ost and {U}tility {T}rade-offs on {I}aa{S} {C}louds, {G}rids, and {O}n-{P}remise {R}esources},
booktitle = {Proc. IEEE Intl. Conference on Cloud Engineering (IC2E) - Cloud Analytics Workshop},
pages = {391--396},
year = {2014},
organization = {IEEE},
doi = {10.1109/IC2E.2014.51}
}
@inproceedings{SlawinskiVillaPasseriniEtAl13,
cc = {\scon},
author = {Slawinski, J. and Villa, U. and Passerini, T. and Veneziani, A. and Sunderam, V.},
title = {Issues in {C}ommunication {H}eterogeneity for {M}essage-{P}assing {C}oncurrent {C}omputing},
booktitle = {27th IEEE Intl. Parallel and Distributed Processing Symposium Workshops \& PhD Forum (IPDPSW)},
pages = {93--102},
year = {2013},
organization = {IEEE},
doi = {10.1109/IPDPSW.2013.140}
}
@inproceedings{SlawinskiVillaPasseriniEtAl12,
author = {Slawinski, J. and Villa, U. and Passerini, T. and Veneziani, A. and Sunderam, V.},
title = {Experiences with {T}arget-{P}latform {H}eterogeneity in {C}louds, {G}rids, and {O}n-{P}remises {R}esources},
booktitle = {26th IEEE Intl. Parallel and Distributed Processing Symposium Workshops \& PhD Forum (IPDPSW)},
pages = {41--52},
year = {2012},
organization = {IEEE},
doi = {10.1109/IPDPSW.2012.20},
url = {http://www.mathcs.emory.edu/technical-reports/techrep-00230.pdf}
}
@phdthesis{VillaPhD12,
author = {Villa, U.},
title = {{S}calable {E}fficient {M}ethods for {I}ncompressible {F}luid-dynamics in {E}ngineering {P}roblems},
school = {Emory University},
year = {2012},
address = {Atlanta, GA},
note = {Advisor: A. Veneziani},
url = {https://etd.library.emory.edu/view/record/pid/emory:cqthc}
}
@mastersthesis{VillaMS07,
author = {Villa, U.},
title = {{F}inite {E}lement {A}nalysis of the {B}rake {P}ad {S}ystem and {M}ultibody {M}odeling of {M}otor {V}ehicles in {B}raking-{P}hase},
school = {Politecnico di Milano},
year = {2007},
address = {Milan, Italy},
note = {Advisor: A. Veneziani; Committee: L. Trainelli, A. Vigliani},
url = {http://www.mate.polimi.it/biblioteca/?pp=fulltext2&qid=4&L=e&file=tsi119.pdf}
}
@mastersthesis{VillaBS05,
author = {Vele, S. and Villa, U.},
title = {Mathematical modeling and numerical simulation of hemodynamics problems in one dimension},
school = {Politecnico di Milano},
type = {Bachelor's thesis},
year = {2005},
address = {Milan, Italy},
note = {Advisor: A. Veneziani},
url = {http://www.mate.polimi.it/biblioteca/?pp=fulltext2&qid=4&L=e&file=tsi12.pdf}
}
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