% Encoding: UTF-8
% Submitted
%% 0




@article{ChenParkJeongEtAl26,
      title={Benchmarking Deep Learning-Based Reconstruction Methods for Photoacoustic Computed Tomography with Clinically Relevant Synthetic Datasets}, 
      author={Chen, Panpan  and Park, Seonyeong  and  Jeong, Gangwon and Cam, Refik~Mert  and Villa, Umberto  and Anastasio, Mark~A. },
      year={2026},
      eprint={2601.17165},
      archivePrefix={arXiv},
      primaryClass={physics.med-ph},
      url={https://arxiv.org/abs/2601.17165}, 
      classification = {pact, iqa, vi}
}

@article{CraftsVillaMowlaviEtal26,
      title={A Stabilized Path-Space Approach to Diffusion-Based Posterior Sampling}, 
      author={Scope~Crafts, Evan  and Villa, Umberto  and  Mowlavi, Saviz and  Ma, Yanting and Mansour, Hassan  and Ali, Wael~H. },
      year={2026},
      eprint={2606.12710},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      url={https://arxiv.org/abs/2606.12710}, 
      classification={ipuq}
}



@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},
classification={usct, dlirm, iqa}
}


% Techincal reports

%6
@misc{LozenskiCamAnastasioEtAl24,
      title={Technical Note: {A}n Efficient Implementation of the Spherical Radon Transform with Cylindrical Apertures}, 
      author={Lozenski, Luke  and Cam, Refik~Mert  and Anastasio, Mark~A.  and Villa, Umberto},
      year={2024},
    archivePrefix = {arXiv},
      eprint={2402.15641},
      url={https://arxiv.org/abs/2402.15641}
}

%5
@misc{VillaOLeary24,
      title={A note on the relationship between {PDE}-based precision operators and {M}at\'ern covariances}, 
      author={Villa, Umberto  and O'Leary-Roseberry, Thomas},
      year={2024},
      archivePrefix = {arXiv},
      eprint={2407.00471},
      url={https://arxiv.org/abs/2407.00471}, 
}

%4
@misc{LiangLozenskiVillaEtAl23,
      title={Technical Note: {PDE}-constrained Optimization Formulation for Tumor Growth Model Calibration}, 
      author={Liang, Baoshan  and Lozenski, Luke  and Villa, Umberto  and Faghihi, Danial},
      year={2023},
      archivePrefix = {arXiv},
      eprint={2302.06445},
      url={https://arxiv.org/abs/2302.06445}, 
}

%3
@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}
}

%2
@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},
}

%1
@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}
}


%Journal Articles

%% Classification:
% vi: Virtual imaging studies
% pact: Photoacoustic Computed Tomography
% usct: Ultrasound Computed Tomography
% iqa: Image quality assessment
% dlirm: Deep learning-based image reconstruction
% ipuq: Inverse problems, Uncertainty Quantification, and Digital Twins
% amg: Preconditioners, multigrid and numerical upscaling
% cfd: Computational Fluid Dynamics
% health: Data Science for Public Heath

%Lanza K, Chen B, Sheffield PE, Gimeno Ruiz de Porras D, Salvo D, %Villa U, Gohlke JM. (In Press). Summer heat, physical activity, %and sedentary behavior of children outdoors and indoors in an %urban setting. Journal of Urban Health.

%67
@article{ChowdaryAliSakpuntoonEtAl26,
	title = {{AI} {Based} {Cough} {Analysis} for {Pulmonary} {Tuberculosis} {Triage} and {Diagnosis}: {A} {Technical} {Review}},
	volume = {3},
	copyright = {2026 The Author(s)},
	issn = {3005-1444},
	shorttitle = {{AI} {Based} {Cough} {Analysis} for {Pulmonary} {Tuberculosis} {Triage} and {Diagnosis}},
	url = {https://www.nature.com/articles/s44385-026-00110-9},
	doi = {10.1038/s44385-026-00110-9},
	number = {1},
	urldate = {2026-09-23},
	journal = {npj Biomedical Innovations},
	publisher = {Nature Publishing Group},
	author = {Chowdary, Gutta J. and Ali, Shams Nafisa and Sakpuntoon, Varunya and Shapiro, Adrienne E. and Restrepo, Blanca I. and Pont, Stephen J. and Armitige, Lisa Y. and Kingwara, Leonard and Villa, Umberto E. and Panpradist, Nuttada},
	month = sep,
	year = {2026},
	keywords = {Biomarkers, Computational biology and bioinformatics, Diseases, Health care, Mathematics and computing, Medical research},
	pages = {56},
    classification = {health}
}


% 66
@article{KhanMarkeyVillaEtAl26,
  title={Context-specific image quality assessment for virtual histologic staining: checklist and guideline},
  author={Khan, Fadeel S and Markey, Mia K and Villa, Umberto E and Bovik, Alan C and Fox, Matthew C and Keeling, Brett H and Reichenberg, Jason S and Tunnell, James W},
  journal={Journal of Medical Imaging},
  volume={13},
  number={S1},
  pages={S11209--S11209},
  year={2026},
  publisher={Society of Photo-Optical Instrumentation Engineers},
  classification = {iqa}
}

% 65
@article{HuangKuoParkEtAl26,
	title = {Stochastic numerical head phantoms to enable virtual imaging studies of transcranial photoacoustic computed tomography},
    pages={100859},
    year={2026},
	url = {http://arxiv.org/abs/2510.09758},
	doi = {10.1016/j.pacs.2026.100859},
	author = {Huang, Hsuan-Kai and Kuo, Joseph and Park, Seonyeong and Villa, Umberto and Wang, Lihong V. and Anastasio, Mark A.},
    journal={Photoacoustics},
    classification = {pact, vi}
}

% 64
@article{YangParkJeongEtAl26,
title={A Learning-based Framework for Spatial Impulse Response Compensation in 3D Photoacoustic Computed Tomography}, 
author={Yang, Kaiyi and Park, Seonyeong  and Jeong, Gangwon  and Huang, Hsuan-Kai  and Oraevsky, Alexander~A.  and Villa, Umberto  and Anastasio, Mark~A. },
year={2026},
doi={10.1109/TMI.2026.3717230},
journal={IEEE Transactions on Medical Imaging},
url={https://arxiv.org/abs/2601.20291}, 
classification = {pact, dlirm}
}

% 63
@article{NicholsonVuchkovVillaEtal26,
doi = {10.1088/1361-6420/ae609b},
url = {https://doi.org/10.1088/1361-6420/ae609b},
year = {2026},
month = {apr},
publisher = {IOP Publishing},
volume = {42},
number = {4},
pages = {045020},
author = {Nicholson, Ruanui and Vuchkov, Radoslav and Villa, Umberto and Petra, Noémi},
title = {Taylor approximation variance reduction for approximation errors in PDE-constrained Bayesian inverse problems},
journal = {Inverse Problems},
classification = {ipuq}
}

% 62
@article{ParkJeongVillaEtal26,
	title = {A virtual imaging framework for three-dimensional quantitative optoacoustic tomography using stochastic numerical {Breast} phantoms},
    journal = {Photoacoustics},
    pages = {100850},
    year = {2026},
    issn = {2213-5979},
    doi = {10.1016/j.pacs.2026.100850},
	url = {http://arxiv.org/abs/2510.00189},
	author = {Park, Seonyeong and Jeong, Gangwon and Villa, Umberto and Anastasio, Mark A.},
	month = Jun,
	year = {2026},
    classification = {pact, vi}
}

% 61
@ARTICLE{LinFengTheilerEtal26,
  author={Lin, Youzuo and Feng, Shihang and Theiler, James and Chen, Yinpeng and Villa, Umberto and Rao, Jing and Greenhall, John and Pantea, Cristian and Anastasio, Mark A. and Wohlberg, Brendt},
  journal={Proceedings of the IEEE}, 
  title={Survey of Deep Learning and Physics-Based Approaches in Computational Wave Imaging}, 
  year={2025},
  volume={113},
  number={12},
  pages={1384-1417},
  doi={10.1109/JPROC.2026.3684003},
  classification={pact,usct,dlirm}
  }


% 60
@article{PashVillaHormuthEtAl26,
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={2026},
journal={Journal of Computational Physics},
volume={Available on-line},
doi = {10.1016/j.jcp.2026.114937},
url={https://arxiv.org/abs/2505.08927}, 
classification={ipuq}
}

% 59
@article{CamParkVillaEtAl26,
title = {Application of a virtual imaging framework for investigating a deep learning-based reconstruction method for 3D quantitative photoacoustic computed tomography},
journal = {Photoacoustics},
volume = {48},
pages = {100792},
year = {2026},
issn = {2213-5979},
doi = {https://doi.org/10.1016/j.pacs.2025.100792},
url = {https://www.sciencedirect.com/science/article/pii/S2213597925001156},
author = {Refik Mert Cam and Seonyeong Park and Umberto Villa and Mark A. Anastasio},
classification={pact, dlirm, vi}
}

% 58
@ARTICLE{HongVillaFessler26,
  author={Hong, Tao and Villa, Umberto and Fessler, Jeffrey A.},
  journal={IEEE Transactions on Computational Imaging}, 
  title={A Convergent Generalized Krylov Subspace Method for Compressed Sensing MRI Reconstruction with Gradient-Driven Denoisers}, 
  year={2026},
  volume={},
  number={},
  pages={1-14},
  doi={10.1109/TCI.2026.3655489},
url = {http://arxiv.org/abs/2508.11219},
classification={dlirm}
}


%57
@article{CraftsVilla25,
  title={Benchmarking Diffusion Annealing-Based Bayesian Inverse Problem Solvers},
  author={Scope~Crafts, Evan and Villa, Umberto},
journal={IEEE Open Journal of Signal Processing},
year={2025},
volume={6},
number={},
pages={975-991},
doi={10.1109/OJSP.2025.3597867},
url={https://arxiv.org/abs/2503.03007},
classification={ipuq, dlirm}
}

%56
@article{ChenParkCamEtAl25,
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. },
volume={Early Access},
number={},
pages={13},
year={2025},
journal={IEEE Trans on Medical Imaging},
url={https://arxiv.org/abs/2412.01971},
doi={10.1109/TMI.2025.3591706},
classification={pact, dlirm}
}

%55
@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},
volume = {43},
pages = {100700},
url={https://doi.org/10.1016/j.pacs.2025.100700.},
doi={10.1016/j.pacs.2025.100700},
classification={pact, usct}
}

%54
@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},
    volume = {43},
    pages = {100698},
    year = {2025},
    doi = {10.1016/j.pacs.2025.100698},
    classification={pact, dlirm}
}

%53
@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},
  classification={health}
}

%52
@article{CraftScopeAnastasioVilla24,
title={Optimizing Quantitative Photoacoustic Imaging Systems: The Bayesian Cram{\'e}r-Rao Bound Approach},
author={Scope~Crafts, Evan and Anastasio, Mark A and Villa, Umberto},
journal={Inverse Problems},
year={2024},
volume = {40},
number = {12},
pages = {125012},
url={https://arxiv.org/abs/2410.09557},
doi={10.1088/1361-6420/ad910a},
classification={pact, ipuq}
}

%51
@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}, 
classification={ipuq}
}

%50
@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},
classification={pact}
}


%49
@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},
year={2024},
volume={71},
number={11},
pages={1358-1376},
doi={10.1109/TUFFC.2024.3459391},
classification={usct, dlirm}
}

%48
@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},
       classification={pact, dlirm}   
}

%47
@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},
classification={ipuq}
}

%46
@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},
classification={pact, dlirm}
}

%45
@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},
classification={ipuq}
}


%44
@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},
classification={iqa}
}

%43
@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},
classification={usct, dlirm, iqa}
}

%42
@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},
  classification = {pact}
}

%41
@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},
  classification={ipuq}
}

% 40
@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},
  classification={ipuq}
}

%39
@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},
  classification={usct, vi}
}

% 38
@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},
classification={iqa}
}

%37
@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},
classification={pact, vi}
}

%36
@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},
  classification={ipuq}
}

%35
@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},
    classification={ipuq}
}

%34
@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},
  classification={amg}
}

%33
@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},
  classification={health}
}

%32
@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},
  classification={ipuq}
}

%31
@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},
      classification={ipuq}
}

%30
@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},
  classification={pact, dlirm}
}

%29
@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},
classification={pact}
}

%28
@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},
  classification={ipuq}
}

%27
@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},
  classification={ipuq}
}

%26
@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},
classification={iqa}
}

%%25
@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},
  classification={ipuq}
}

%%24
@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},
  classification={usct, vi}
}

%% 23
@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},
classification={amg, ipuq}
}

%% 22
@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},
classification={ipuq}
}

%% 21
@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},
classification= {ipuq}
}

%% 20
@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},
classification={ipuq}
}

%% 19
@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},
classification={ipuq}
}

%% 18
@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},
classification={health}
}

%% 17
@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},
classification={ipuq}
}

%% 16
@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},
classification={ipuq}
}

%% 15
@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},
classification={ipuq}
}

%% 14
@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},
classification={amg, ipuq}
}

%% 13
@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},
classification={amg}
}

%% 12
@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},
  classification={ipuq}
}

%% 11
@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},
classification={ipuq}
}

%% 10
@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},
classification={amg, ipuq}
}

%% 9
@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},
classification={amg}
}

%% 8
@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},
classification={amg}
}

%% 7
@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},
classification={cfd}
}

%% 6
@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},
  classification={health}
}

%% 5
@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},
  classification={amg}
}

%% 4
@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},
  classification={amg}
}

%% 3
@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},
  classification={cfd}
}

%% 2
@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},
  classification={cfd}
}

%% 1
@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},
   classification={cfd}
}



%%%% Proceedings

%46
@inproceedings{JeongParkVillaEtal26p,
author = {Jeong, Gangwon  and Park, Seonyeong  and Villa, Umberto  and Anastasio, Mark~A.},
title = {{Joint reconstruction of initial pressure and sound speed distributions in 3D photoacoustic computed tomography using object constraints}},
volume = {13851},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2026},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {138510P},
year = {2026},
doi = {10.1117/12.3087156},
URL = {https://doi.org/10.1117/12.3087156}
}

%45
@inproceedings{ChenParkJeongEtal26p,
author = {Chen, Panpan  and Park, Seonyeong  and Jeong, Gangwon  and Cam, Refik~Mert  and Villa, Umberto and Anastasio, Mark~A.},
title = {{Assessment of image reconstruction methods for photoacoustic computed tomography based on signal detection performance}},
volume = {13851},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2026},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {138510O},
year = {2026},
doi = {10.1117/12.3088388},
URL = {https://doi.org/10.1117/12.3088388}
}

%44
@inproceedings{YangParkJeongEtal26p,
author = {Yang, Kaiyi  and Park, Seonyeong  and Jeong, Gangwon  and Liu, CindyZ.  and Tong, Xin and Cui, Manxiu  and Ku, Geng  and Villa, Umberto  and Wang, Lihong~V.  and Anastasio, Mark~A.},
title = {{Application of a learned SIR compensation method to improve elevational resolution in ring-array-based photoacoustic computed tomography}},
volume = {13851},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2026},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {138510J},
year = {2026},
doi = {10.1117/12.3088475},
URL = {https://doi.org/10.1117/12.3088475}
}

%43
@inproceedings{CamParkAnastasioEtal26p,
author = {Cam, Refik~Mert  and Park, Seonyeong  and Anastasio, Mark~A.  and Villa, Umberto},
title = {{Quantitative evaluation of DCE-PACT reconstruction methods using virtual imaging studies}},
volume = {13851},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2026},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {138510I},
year = {2026},
doi = {10.1117/12.3087833},
URL = {https://doi.org/10.1117/12.3087833}
}

%42
@inproceedings{HuangCuiZhuEtal26p,
author = {Huang, Hsuan-Kai  and Cui, Manxiu  and Zhu, Junhao  and Park, Seonyeong  and Villa, Umberto  and Wang, Lihong~V.  and Anastasio, Mark~A.},
title = {{Joint estimation of a CT-informed skull model and initial pressure distribution in transcranial photoacoustic computed tomography}},
volume = {13851},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2026},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {138510G},
year = {2026},
doi = {10.1117/12.3080016},
URL = {https://doi.org/10.1117/12.3080016}
}

%41
@inproceedings{JeongParkVillaEtal26p,
author = {Jeong, Gangwon  and Park, Seonyeong  and Villa, Umberto  and Anastasio, Mark~A.},
title = {{Impact of modeling transducer spatial impulse response and acoustic heterogeneity on image reconstruction accuracy in photoacoustic computed tomography}},
volume = {13851},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2026},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {1385107},
year = {2026},
doi = {10.1117/12.3087273},
URL = {https://doi.org/10.1117/12.3087273}
}

%40
@inproceedings{HongShahLozenskiEtal26p,
author = {Hong, Tao and Shah, Jenil  and Lozenski, Luke  and Cam, Refik~Mert and  Anastasio, Mark and Villa, Umberto },
title = {{A virtual imaging framework for DCE-PACT estimation of tumor perfusion}},
volume = {13924},
booktitle = {Medical Imaging 2026: Physics of Medical Imaging},
editor = {Ke Li and Shiva Abbaszadeh and Arundhuti Ganguly},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {1392415},
year = {2026},
doi = {10.1117/12.3087895},
URL = {https://doi.org/10.1117/12.3087895}
}

%39
@inproceedings{ShahLozenskiAnastasioEtal25p,
author = {Shah, Jenil  and Lozenski, Luke  and Anastasio, Mark  and Pagel, Mark  and Villa, Umberto },
title = {{A low-rank-based image reconstruction method for dynamic contrast-enhanced multispectral optoacoustic tomography (DCE-MSOT)}},
volume = {13412},
booktitle = {Medical Imaging 2025: Ultrasonic Imaging and Tomography},
editor = {Christian Boehm and Mohammad Mehrmohammadi},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {134120I},
year = {2025},
doi = {10.1117/12.3047128},
URL = {https://doi.org/10.1117/12.3047128}
}

%38
@inproceedings{JeongLiMitchamEtal25p,
author = {Jeong, Gangwon  and Li, Fu  and Mitcham,  Trevor~M.  and Duric, Nebojsa and Villa, Umberto  and Anastasio, Mark~A.},
title = {{A deep-learning-based high-resolution sound-speed reconstruction method for USCT that employs traveltime and reflection tomography images: applications to clinical data (Conference Presentation)}},
volume = {13412},
booktitle = {Medical Imaging 2025: Ultrasonic Imaging and Tomography},
editor = {Christian Boehm and Mohammad Mehrmohammadi},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {134120S},
year = {2025},
doi = {10.1117/12.3048476},
URL = {https://doi.org/10.1117/12.3048476}
}

%37
@inproceedings{JeongVillaAnastasio25p,
author = {Jeong, Gangwon  and Villa, Umberto  and Anastasio, Mark~A.},
title = {{Investigating the use of canonical object constraints for the joint estimation of initial pressure and speed-of-sound distributions in photoacoustic computed tomography (Conference Presentation)}},
volume = {13412},
booktitle = {Medical Imaging 2025: Ultrasonic Imaging and Tomography},
editor = {Christian Boehm and Mohammad Mehrmohammadi},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {134120H},
year = {2025},
doi = {10.1117/12.3048661},
URL = {https://doi.org/10.1117/12.3048661}
}

%36
@inproceedings{YangParkHuangEtal25p,
author = {Yang, Kaiyi and  Park, Seonyeong and  Huang, Hsuan-Kai and  Villa, Umberto and Anastasio, Mark~A. },
title = {{Compensating for the spatial impulse response in 3D photoacoustic computed tomography using a learned data space restoration method}},
volume = {13319},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2025},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {133190L},
keywords = {Photoacoustic computed tomography (PACT), acoustic inversion, spatial impulse response (SIR), finite aperture effect, data restoration, deep learning, image reconstruction, Optoacoustic computed tomography},
year = {2025},
doi = {10.1117/12.3049239},
URL = {https://doi.org/10.1117/12.3049239}
}

%35
@inproceedings{HuangParkVillaEtAl25p,
author = {Huang, Hsuan-Kai and  Park, Seonyeong and Villa, Umberto  and  Wang, Lihong~V. and Anastasio,Mark~A.},
title = {{Gradient-free joint reconstruction of initial pressure distribution and wave speeds in transcranial photoacoustic computed tomography}},
volume = {13319},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2025},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {133190K},
keywords = {Transcranial imaging, Photoacoustic computed tomography, Joint reconstruction, Derivative-free optimization, Image reconstruction},
year = {2025},
doi = {10.1117/12.3049081},
URL = {https://doi.org/10.1117/12.3049081}
}

%34
@inproceedings{HuangKuoZhangEtAl25p,
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~A. },
title = {{Experimental validation of learning-based compensation for skull-induced aberrations in transcranial photoacoustic computed tomography}},
volume = {13319},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2025},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {133190H},
keywords = {Transcranial imaging, Photoacoustic computed tomography, Deep learning, Image reconstruction},
year = {2025},
doi = {10.1117/12.3048984},
URL = {https://doi.org/10.1117/12.3048984}
}

%33
@inproceedings{ChenParkJeongEtAl25p,
author = {Chen, Panpan and Park, Seonyeong and Jeong, Gangwon and Cam, Refik~Mert and Huang, Hsuan-Kai and Villa, Umberto  and Anastasio, Mark~A. },
title = {{Benchmarking deep learning-based reconstruction in photoacoustic computed tomography with clinically relevant synthetic datasets}},
volume = {13319},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2025},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {133190F},
keywords = {photoacoustic computed tomography, optoacoustic computed tomography, benchmarking, deep learning, image reconstruction, virtual imaging studies},
year = {2025},
doi = {10.1117/12.3049244},
URL = {https://doi.org/10.1117/12.3049244}
}

%32
@inproceedings{CamHuangLozenskiEtAl25b,
author = {Cam, Refik~Mert and Huang, Hsuan-Kai and Lozenski, Luke and Park, Seonyeong and Anastasio, Mark~A. and Villa, Umberto},
title = {{Numerical mouse phantoms for multispectral dynamic contrast-enhanced photoacoustic computed tomography}},
volume = {13319},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2025},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {133190C},
keywords = {dynamic contrast enhanced imaging, photoacoustic, computed tomography, numerical phantom, small animal imaging, Tofts model},
year = {2025},
doi = {10.1117/12.3049240},
URL = {https://doi.org/10.1117/12.3049240}
}

%31
@inproceedings{LiVillaAnastasio24p,
author = {Li, Fu and Villa, Umberto  and Anastasio, Mark A. },
title = {{A learning-based method for compensating 3D-2D model mismatch in ring-array ultrasound computed tomography}},
volume = {12932},
booktitle = {Medical Imaging 2024: Ultrasonic Imaging and Tomography},
editor = {Christian Boehm and Nick Bottenus},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {129321E},
keywords = {Ultrasound computed tomography, Full waveform inversion, Breast imaging, Deep learning},
year = {2024},
doi = {10.1117/12.3006968},
URL = {https://doi.org/10.1117/12.3006968}
}

%30
@inproceedings{FanWangZhangEtAl24p,
author = {Zong Fan and Zhimin Wang and Chaojie Zhang and Muzaffer {\"O}zbey and Umberto Villa and Yao Hao and Zhongwei Zhang and Xiaowei Wang and Hua Li},
title = {{Self-supervised learning based on StyleGAN for medical image classification on small labeled dataset}},
volume = {12926},
booktitle = {Medical Imaging 2024: Image Processing},
editor = {Olivier Colliot and Jhimli Mitra},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {1292630},
keywords = {Image classification, Self-supervised learning, Generative model, Adversarial attack, Attention mechanism},
year = {2024},
doi = {10.1117/12.3006959},
URL = {https://doi.org/10.1117/12.3006959}
}

%29
@inproceedings{LozenskiWangWohlbergEtAl24p,
author = {Luke Lozenski and Hanchen Wang and Brendt Wohlberg and Umberto Villa and Youzuo Lin},
title = {{Learned measurement correction for simplified acoustic forward models in ultrasound computed tomography}},
volume = {12932},
booktitle = {Medical Imaging 2024: Ultrasonic Imaging and Tomography},
editor = {Christian Boehm and Nick Bottenus},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {129320I},
keywords = {Ultrasound computed tomography, Deep learning-based image reconstruction, Physics-informed machine learning, Full waveform inversion, Born approximation, Numerical breast phantoms},
year = {2024},
doi = {10.1117/12.3006948},
URL = {https://doi.org/10.1117/12.3006948}
}

%28
@inproceedings{ScopeCraftsAnastasioVilla24p,
author = {{Scope Crafts}, Evan D.  and Anastasio, Mark A.  and Villa, Umberto},
title = {{Bayesian Cramér-Rao bound optimization of the illumination pattern in quantitative photoacoustic computed tomography}},
volume = {12925},
booktitle = {Medical Imaging 2024: Physics of Medical Imaging},
editor = {Rebecca Fahrig and John M. Sabol and Ke Li},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {129254A},
keywords = {Quantitative imaging, Photoacoustic computed tomography, Bayesian Cramer-Rao bound, Optimal experimental design, Virtual imaging studies},
year = {2024},
doi = {10.1117/12.3005856},
URL = {https://doi.org/10.1117/12.3005856}
}


%27
@inproceedings{HuangKuoParkEtAl24,
author = {Huang, Hsuan-Kai and  Kuo, Joseph and Park, Seonyeong  and Villa, Umberto  and  Wang, Lihong V. and Anastasio, Mark A.},
title = {{A learning-based image reconstruction method for skull-induced aberration compensation in transcranial photoacoustic computed tomography}},
volume = {12842},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2024},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {128420C},
keywords = {Photoacoustic computed tomography, Transcranial imaging, Image reconstruction, Deep learning},
year = {2024},
doi = {10.1117/12.3008569},
URL = {https://doi.org/10.1117/12.3008569}
}

%26
@inproceedings{ChenParkCamEtAl24,
author = {Chen, Panpan  and Park, Seonyeong  and Cam, Refik Mert  and Huang, Hsuan-Kai  and Villa, Umberto  and Anastasio, Mark A.},
title = {{Learning a semi-analytic reconstruction method for photoacoustic computed tomography with hemispherical measurement geometries}},
volume = {12842},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2024},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {128420U},
keywords = {photoacoustic computed tomography , optoacoustic computed tomography, three-dimensional breast imaging, learned filtered backprojection, deep learning, image reconstruction, inverse problem},
year = {2024},
doi = {10.1117/12.3008778},
URL = {https://doi.org/10.1117/12.3008778}
}

%25
@inproceedings{MarshallBrechtThompsonEtAl24,
author = {Marshall, Nathanael  and Brecht, Hans-Peter  and Thompson, Weylan  and Lawrence, Dylan J.  and Marshall, Vanessa  and Toler, Samuel and Emelianov, Stanislav  and Yu, Anthony  and Anastasio, Mark  and Villa, Umberto  and Maxwell,  Joshua  and Ermilov, Sergey},
title = {{High-throughput photoacoustic tomography by integrated robotics and automation}},
volume = {12842},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2024},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {128420I},
keywords = {Photoacoustic tomography, High-throughput, Robotics, Automation, Preclinical, Murine},
year = {2024},
doi = {10.1117/12.3005569},
URL = {https://doi.org/10.1117/12.3005569}
}

%24
@inproceedings{CamParkVillaEtAl24,
author = {Cam, Refik Mert  and Park, Seonyeong  and Villa,  Umberto  and Anastasio, Mark A.},
title = {{Investigation of a learned image reconstruction method for three-dimensional quantitative photoacoustic tomography of the breast}},
volume = {12842},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2024},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {128420M},
keywords = {quantitative photoacoustic imaging, three-dimensional breast imaging, oxygen saturation estimation, learning-based image reconstruction, realistic numerical breast phantoms, deep-learning, photoacoustic computed tomography, multi-spectral imaging},
year = {2024},
doi = {10.1117/12.3008904},
URL = {https://doi.org/10.1117/12.3008904}
}

%23
@inproceedings{CamWangThompsonEtAl23a,
author = {Refik Mert Cam and Chao Wang and Weylan Thompson and Sergey A. Ermilov and Mark A. Anastasio and Umberto Villa},
title = {{Low-rank matrix estimation-based spatiotemporal image reconstruction from few tomographic measurements per frame for dynamic photoacoustic computed tomography}},
volume = {12463},
booktitle = {Medical Imaging 2023: Physics of Medical Imaging},
editor = {Lifeng Yu and Rebecca Fahrig and John M. Sabol},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {124630R},
year = {2023},
doi = {10.1117/12.2654199},
URL = {https://doi.org/10.1117/12.2654199}
}


%% 22
@inproceedings{LiVillaDuricEtAl23a,
author = {Li, Fu and Villa, Umberto and Duric, Nebojsa and Anastasio, Mark},
title={3{D} full-waveform inversion in ultrasound computed tomography employing a ring-array},
volume = {12470},
booktitle = {Medical Imaging 2023: Ultrasonic Imaging and Tomography},
editor = {Christian Boehm and Nick Bottenus},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {124700K},
year = {2023},
doi = {10.1117/12.2654406},
URL = {https://doi.org/10.1117/12.2654406}
}

%% 21
@inproceedings{LozenskiWangWohlbergEtAl23,
author={Lozenski, Luke and Wang, Hanchen and Wohlberg, Brendt and Villa, Umberto and Lin, Youzou},
title={Data driven methods for ultrasound computed tomography},
volume = {12463},
booktitle = {Medical Imaging 2023: Physics of Medical Imaging},
editor = {Lifeng Yu and Rebecca Fahrig and John M. Sabol},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {124630Q},
keywords = {Ultrasound Computed Tomography, Full Waveform Inversion, Convolutional Neural Network, Image Reconstruction, Learned Reconstruction Methods},
year = {2023},
doi = {10.1117/12.2654442},
URL = {https://doi.org/10.1117/12.2654442}
}

%% 20
@inproceedings{ZhaiKuoAnastasioEtAl23,
author = {Zhai, Albert and Kuo, Joseph and Anastasio, Mark and Villa, Umberto},
title={Memory-efficient self-supervised learning of null space projection operators},
volume = {12463},
booktitle = {Medical Imaging 2023: Physics of Medical Imaging},
editor = {Lifeng Yu and Rebecca Fahrig and John M. Sabol},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {124631I},
year = {2023},
doi = {10.1117/12.2654260},
URL = {https://doi.org/10.1117/12.2654260}
}

%% 19
@inproceedings{JeongLiVillaEtAl23,
author = {Jeong, Gangwon and Li, Fu and Villa, Umberto and Anastasio, Mark},
title = {A deep learning-based image reconstruction method for {USCT} that employs multimodality inputs },
volume = {12470},
booktitle = {Medical Imaging 2023: Ultrasonic Imaging and Tomography},
editor = {Christian Boehm and Nick Bottenus},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {124700M},
year = {2023},
doi = {10.1117/12.2654564},
URL = {https://doi.org/10.1117/12.2654564}
}

%% 18
@inproceedings{ParkVillaOraevskyEtAl23,
author = {Seonyeong Park and Umberto Villa and Alexander Oraevsky and Mark Anastasio},
title = {Numerical investigation of impact of skin phototype on three-dimensional optoacoustic tomography of the breast},
volume = {PC12379},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2023},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {PC123790E},
keywords = {Photoacoustic computed tomography, Optoacoustic tomography, Breast imaging, Skin color, Virtual imaging trials, Numerical breast phantom},
year = {2023},
doi = {10.1117/12.2650740},
URL = {https://doi.org/10.1117/12.2650740}
}

%% 17
@inproceedings{CamWangParkEtAl23,
author = {Refik Mert Cam and Chao Wang and Seonyeong Park and Weylan Thompson and Sergey A. Ermilov and Mark A. Anastasio and Umberto Villa},
title = {Dynamic image reconstruction to monitor tumor vascular perfusion in small animals using 3{D} photoacoustic computed-tomography imagers with rotating gantries},
volume = {12379},
booktitle = {Photons Plus Ultrasound: Imaging and Sensing 2023},
editor = {Alexander A. Oraevsky and Lihong V. Wang},
organization = {International Society for Optics and Photonics},
publisher = {SPIE},
pages = {123790F},
keywords = {Photoacoustic computed tomography (PACT), Small animal imaging, Image reconstruction, Dynamic contract enhanced imaging, Tumor vascular perfusion, Low-rankness, Iterative reconstruction, Inverse problems},
year = {2023},
doi = {10.1117/12.2647663},
URL = {https://doi.org/10.1117/12.2647663}
}

%% 16
@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},
}

%% 15
@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},
}

%% 14
@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},
}

%% 13
@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},
}

%% 12
@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}
}

%% 11
@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}
}

%% 10
@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}
}

%% 9
@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}
}

%% 8
@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}
}

%% 7
@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}
}

%% 6
@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}
}

%% 5
@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}
}


%% 4
@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}
}

%% 3
@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},
}

%% 2
@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}
}

%% 1
@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}
}


%% Datasets

@data{illinoisdatabankIDB-1071666,
doi = {10.13012/B2IDB-1071666_V1},
url = {https://doi.org/10.13012/B2IDB-1071666_V1},
author = {Park, Seonyeong and Jeong, Gangwon and Villa, Umberto and Anastasio, Mark},
publisher = {University of Illinois Urbana-Champaign},
title = {Stochastic Optoacoustic Numerical Breast Phantoms with Multiple Skin Tones and Simulated OAT Measurement Data},
year = {2026}
}

@data{nhp26,
doi = {10.13012/B2IDB-5613691_V1},
url = {https://doi.org/10.13012/B2IDB-5613691_V1},
author = {Huang, Hsuan-Kai and Kuo, Joseph and Zhou, Bozhen and Park, Seonyeong and Villa, Umberto and Anastasio, Mark},
publisher = {University of Illinois Urbana-Champaign},
title = {Stochastic Photoacoustic Numerical Head Phantoms and Simulated PACT Measurement Data},
year = {2026}
}

@data{pact_nbp_3d_multi,
doi = {10.13012/B2IDB-8164905_V1},
url = {https://doi.org/10.13012/B2IDB-8164905_V1},
author = {Park, Seonyeong and Jeong, Gangwon and Villa, Umberto and Anastasio, Mark},
publisher = {University of Illinois Urbana-Champaign},
title = {Anatomy-Matched Multi-Variant Stochastic Optoacoustic Numerical Breast Phantoms and Simulated OAT Measurement Data},
year = {2026}
}

@data{pact_jr_2d,
doi = {10.13012/B2IDB-9572729_V1},
url = {https://doi.org/10.13012/B2IDB-9572729_V1},
author = {Jeong, Gangwon and Villa, Umberto and Park, Seonyeong and Anastasio, Mark A.},
publisher = {University of Illinois Urbana-Champaign},
title = {2D Acoustic Numerical Breast Phantoms and Measurement Data for Joint Reconstruction in PACT},
year = {2025}
}

@data{usct2d_phantom,
doi = {10.13012/B2IDB-5648161_V1},
url = {https://doi.org/10.13012/B2IDB-5648161_V1},
author = {Li, Fu and Villa, Umberto and Park, Seonyeong and Jeong, Gangwon and Anastasio, Mark A.},
publisher = {University of Illinois Urbana-Champaign},
title = {2D Acoustic Numerical Breast Phantoms for Ultrasound Computed Tomography},
year = {2025}
}

@data{perfusion2d,
author = {Villa, Umberto and Lozenski, Luke and Park, Seonyeong and Mert Cam, Refik},
publisher = {Harvard Dataverse},
title = {{2D tumor perfusion numerical phantom for dynamic contrast enhanced photoacoustic tomography virtual imaging studies}},
year = {2024},
version = {V1},
doi = {10.7910/DVN/P7ZVJO},
url = {https://doi.org/10.7910/DVN/P7ZVJO}
}

@data{RingArray,
author = {Li, Fu and Villa, Umberto},
publisher = {Harvard Dataverse},
title = {{3D Numerical Breast Phantoms and Ring-Array USCT measurements (3 rings)}},
year = {2023},
version = {V1},
doi = {10.7910/DVN/8JVLAE},
url = {https://doi.org/10.7910/DVN/8JVLAE}
}

@data{OAT1,
author = {Park, Seonyeong and Villa, Umberto and Li, Fu and Cam, Refik and Oraevsky, Alexander and Anastasio, Mark},
publisher = {Harvard Dataverse},
title = {{3D optoacoustic numerical breast phantoms and simulated OAT measurement data (natural shape, 2 lesions)}},
year = {2023},
version = {V1},
doi = {10.7910/DVN/OZRVX6},
url = {https://doi.org/10.7910/DVN/OZRVX6}
}

@data{OAT2,
author = {Park, Seonyeong and Villa, Umberto and Li, Fu and Cam, Refik and Oraevsky, Alexander and Anastasio, Mark},
publisher = {Harvard Dataverse},
title = {{3D optoacoustic numerical breast phantoms and simulated OAT measurement data (hemispherical shape, 4 lesions)}},
year = {2023},
version = {V1},
doi = {10.7910/DVN/AQZE3H},
url = {https://doi.org/10.7910/DVN/AQZE3H}
}

@data{OAT3,
author = {Park, Seonyeong and Villa, Umberto and Li, Fu and Cam, Refik and Oraevsky, Alexander and Anastasio, Mark},
publisher = {Harvard Dataverse},
title = {{3D optoacoustic numerical breast phantoms and simulated OAT measurement data (natural shape, 4 lesions)}},
year = {2023},
version = {V1},
doi = {10.7910/DVN/1ZF0OW},
url = {https://doi.org/10.7910/DVN/1ZF0OW}
}


@data{mobyDPACT2D,
author = {Lozenski, Luke and Anastasio, Mark and Villa, Umberto},
publisher = {Harvard Dataverse},
title = {{2D numerical mouse phantom for dynamic photoacoustic tomography virtual imaging studies of small animal models}},
year = {2022},
version = {V1},
doi = {10.7910/DVN/3DXS18},
url = {https://doi.org/10.7910/DVN/3DXS18}
}

@data{aNBPs3D,
author = {Li, Fu and Villa, Umberto and Park, Seonyeong and Anastasio, Mark},
publisher = {Harvard Dataverse},
title = {{3D Acoustic Numerical Breast Phantoms}},
year = {2021},
version = {DRAFT VERSION},
doi = {10.7910/DVN/KBYQQ7},
url = {https://doi.org/10.7910/DVN/KBYQQ7}
}

@data{aNBPs2D,
author = {Li, Fu and Villa, Umberto and Park, Seonyeong and Anastasio, Mark},
publisher = {Harvard Dataverse},
title = {{2D Acoustic Numerical Breast Phantoms and USCT Measurement Data}},
year = {2021},
version = {V1},
doi = {10.7910/DVN/CUFVKE},
url = {https://doi.org/10.7910/DVN/CUFVKE}
}

@data{oatBreast3D,
author = {Park, Seonyeong and Brooks, Frank and Villa, Umberto and Su, Richard and Anastasio, Mark and Oraevsky, Alexander},
publisher = {Harvard Dataverse},
title = {{3D numerical breast phantom: Normalization of optical fluence distribution for 3D functional OAT}},
year = {2022},
version = {V1},
doi = {10.7910/DVN/1FW2I6},
url = {https://doi.org/10.7910/DVN/1FW2I6}
}

% Thesis
@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{VillaASP08,
author = {Villa, U.},
title = {Environment \& energy - {H}ydrogen: opportunities and utilization},
type = {Alta Scuola Politecnica diploma},
school = {Politecnico di Milano \& Politecnico di Torino},
year = {2008},
note = {Advisors: F. Profumo, E. Paolucci, A. Tenconi. External Institutions: Centro Estero Camere di Commercio Piemontesi, STEP Ricerche S.r.l.}
}

@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}
}

@article{siamnews,
author={Ghattas,  Omar  and Marzouk, Youssef and Parno, Matt  and Petra, Noemi  and Stadler, Georg and Villa, Umberto},
title={Students Tackle Bayesian Inverse Problems in the Colorado Rockies: Reflections on the 2018 Gene Golub Summer School},
journal={Siam News},
issue={January/February},
year={2019},
classification={ipuq}
}

% Software
@misc{hippylib,
title = "{hIPPYlib: an Extensible Software Framework for Large-scale Deterministic and Bayesian Inversion}",
author = {Villa, U. and Petra, N. and Ghattas, O.},
year = {2016},
url = {http://hippylib.github.io},
doi = {10.5281/zenodo.596931}
}

@Misc{mfem,
title={{MFEM}: modular finite element methods},
note={\url{http://mfem.org}}
}

@Misc{lifev,
author = {LifeV Team},
title = {Life{V}: a parallel finite element library},
note = {\url{http://lifev.org}}
}

@Misc{tminres,
author = {U. Villa},
title = {t{MINRES}: A templated parallel {C}++ implementation of the {MINRES} algorithm},
note = {\url{https://code.google.com/archive/p/tminres/}}
}



@Comment{jabref-meta: databaseType:bibtex;}