% Diffusion

@article{zhang20233dshape2vecset,
  title={3dshape2vecset: A 3d shape representation for neural fields and generative diffusion models},
  author={Zhang, Biao and Tang, Jiapeng and Niessner, Matthias and Wonka, Peter},
  journal={arXiv preprint arXiv:2301.11445},
  year={2023}
}

@article{ho2020denoising,
  title={Denoising diffusion probabilistic models},
  author={Ho, Jonathan and Jain, Ajay and Abbeel, Pieter},
  journal={Advances in neural information processing systems},
  volume={33},
  pages={6840--6851},
  year={2020}
}

@article{karras2022elucidating,
  title={Elucidating the design space of diffusion-based generative models},
  author={Karras, Tero and Aittala, Miika and Aila, Timo and Laine, Samuli},
  journal={Advances in Neural Information Processing Systems},
  volume={35},
  pages={26565--26577},
  year={2022}
}

@article{dhariwal2021diffusion,
  title={Diffusion models beat gans on image synthesis},
  author={Dhariwal, Prafulla and Nichol, Alexander},
  journal={Advances in neural information processing systems},
  volume={34},
  pages={8780--8794},
  year={2021}
}

@inproceedings{rombach2022high,
  title={High-resolution image synthesis with latent diffusion models},
  author={Rombach, Robin and Blattmann, Andreas and Lorenz, Dominik and Esser, Patrick and Ommer, Bj{\"o}rn},
  booktitle={Proceedings of the IEEE/CVF conference on computer vision and pattern recognition},
  pages={10684--10695},
  year={2022}
}

@inproceedings{hoogeboom2022equivariant,
  title={Equivariant diffusion for molecule generation in 3d},
  author={Hoogeboom, Emiel and Satorras, V{\i}ctor Garcia and Vignac, Cl{\'e}ment and Welling, Max},
  booktitle={International conference on machine learning},
  pages={8867--8887},
  year={2022},
  organization={PMLR}
}


% DL shape generation
@inproceedings{kalaie2023geometric,
  title={A Geometric Deep Learning Framework for Generation of Virtual Left Ventricles as Graphs},
  author={Kalaie, Soodeh and Bulpitt, Andrew J and Frangi, Alejandro F and Gooya, Ali},
  booktitle={Medical Imaging with Deep Learning},
  year={2023}
}

@inproceedings{beetz2021generating,
  title={Generating subpopulation-specific biventricular anatomy models using conditional point cloud variational autoencoders},
  author={Beetz, Marcel and Banerjee, Abhirup and Grau, Vicente},
  booktitle={International Workshop on Statistical Atlases and Computational Models of the Heart},
  pages={75--83},
  year={2021},
  organization={Springer}
}

@article{romero2021clinically,
  title={Clinically-driven virtual patient cohorts generation: An application to aorta},
  author={Romero, Pau and Lozano, Miguel and Mart{\'\i}nez-Gil, Francisco and Serra, Dolors and Sebasti{\'a}n, Rafael and Lamata, Pablo and Garc{\'\i}a-Fern{\'a}ndez, Ignacio},
  journal={Frontiers in Physiology},
  pages={1375},
  year={2021},
  publisher={Frontiers}
}

@article{bannister2022deep,
  title={A deep invertible 3-D facial shape model for interpretable genetic syndrome diagnosis},
  author={Bannister, Jordan J and Wilms, Matthias and Aponte, J David and Katz, David C and Klein, Ophir D and Bernier, Francois PJ and Spritz, Richard A and Hallgr{\'\i}msson, Benedikt and Forkert, Nils D},
  journal={IEEE Journal of Biomedical and Health Informatics},
  volume={26},
  number={7},
  pages={3229--3239},
  year={2022},
  publisher={IEEE}
}

@inproceedings{bouritsas2019neural,
  title={Neural 3d morphable models: Spiral convolutional networks for 3d shape representation learning and generation},
  author={Bouritsas, Giorgos and Bokhnyak, Sergiy and Ploumpis, Stylianos and Bronstein, Michael and Zafeiriou, Stefanos},
  booktitle={Proceedings of the IEEE/CVF International Conference on Computer Vision},
  pages={7213--7222},
  year={2019}
}

% DL shape for vessels

@inproceedings{danu2019deep,
  title={Deep learning based generation of synthetic blood vessel surfaces},
  author={Danu, Manuela and Nita, Cosmin-Ioan and Vizitiu, Anamaria and Suciu, Constantin and Itu, Lucian Mihai},
  booktitle={2019 23rd International Conference on System Theory, Control and Computing (ICSTCC)},
  pages={662--667},
  year={2019},
  organization={IEEE}
}

@article{wolterink2018blood,
  title={Blood vessel geometry synthesis using generative adversarial networks},
  author={Wolterink, Jelmer M and Leiner, Tim and Isgum, Ivana},
  journal={arXiv preprint arXiv:1804.04381},
  year={2018}
}

% Importance of Stroke research
@article{phipps2020management,
  title={Management of acute ischemic stroke},
  author={Phipps, Michael S and Cronin, Carolyn A},
  journal={Bmj},
  volume={368},
  year={2020},
  publisher={British Medical Journal Publishing Group}
}

@article{viceconti2016silico,
  title={In silico clinical trials: how computer simulation will transform the biomedical industry},
  author={Viceconti, Marco and Henney, Adriano and Morley-Fletcher, Edwin},
  journal={International Journal of Clinical Trials},
  volume={3},
  number={2},
  pages={37--46},
  year={2016},
  publisher={Medip Academy}
}

% SSM approaches
@article{cosentino2020statistical,
  title={Statistical shape analysis of ascending thoracic aortic aneurysm: correlation between shape and biomechanical descriptors},
  author={Cosentino, Federica and Raffa, Giuseppe M and Gentile, Giovanni and Agnese, Valentina and Bellavia, Diego and Pilato, Michele and Pasta, Salvatore},
  journal={Journal of Personalized Medicine},
  volume={10},
  number={2},
  pages={28},
  year={2020},
  publisher={MDPI}
}

@article{gooya2017mixture,
  title={Mixture of probabilistic principal component analyzers for shapes from point sets},
  author={Gooya, Ali and Lekadir, Karim and Castro-Mateos, Isaac and Pozo, Jose Maria and Frangi, Alejandro F},
  journal={IEEE transactions on pattern analysis and machine intelligence},
  volume={40},
  number={4},
  pages={891--904},
  year={2017},
  publisher={IEEE}
}

@inproceedings{lamecker2002statistical,
  title={A statistical shape model for the liver},
  author={Lamecker, Hans and Lange, Thomas and Seebass, Martin},
  booktitle={Medical Image Computing and Computer-Assisted Intervention—MICCAI 2002: 5th International Conference Tokyo, Japan, September 25--28, 2002 Proceedings, Part II 5},
  pages={421--427},
  year={2002},
  organization={Springer}
}

@article{bridio2023generation,
  title={Generation of a Virtual Cohort of Patients for in Silico Trials of Acute Ischemic Stroke Treatments},
  author={Bridio, Sara and Luraghi, Giulia and Ramella, Anna and Rodriguez Matas, Jose Felix and Dubini, Gabriele and Luisi, Claudio A and Neidlin, Michael and Konduri, Praneeta and Arrarte Terreros, Nerea and Marquering, Henk A and others},
  journal={Applied Sciences},
  volume={13},
  number={18},
  pages={10074},
  year={2023},
  publisher={MDPI}
}

% AIS causes
@article{zivin1998factors,
  title={Factors determining the therapeutic window for stroke},
  author={Zivin, Justin A},
  journal={Neurology},
  volume={50},
  number={3},
  pages={599--603},
  year={1998},
  publisher={AAN Enterprises}
}

@article{heiss1999targets,
  title={Which targets are relevant for therapy of acute ischemic stroke?},
  author={Heiss, Wolf-Dieter and Thiel, Alexander and Grond, Martin and Graf, Rudolf},
  journal={Stroke},
  volume={30},
  number={7},
  pages={1486--1489},
  year={1999},
  publisher={Am Heart Assoc}
}

% DL methods

@inproceedings{lee2019set,
  title={Set transformer: A framework for attention-based permutation-invariant neural networks},
  author={Lee, Juho and Lee, Yoonho and Kim, Jungtaek and Kosiorek, Adam and Choi, Seungjin and Teh, Yee Whye},
  booktitle={International conference on machine learning},
  pages={3744--3753},
  year={2019},
  organization={PMLR}
}

@article{vaswani2017attention,
  title={Attention is all you need},
  author={Vaswani, Ashish and Shazeer, Noam and Parmar, Niki and Uszkoreit, Jakob and Jones, Llion and Gomez, Aidan N and Kaiser, {\L}ukasz and Polosukhin, Illia},
  journal={Advances in neural information processing systems},
  volume={30},
  year={2017}
}

@inproceedings{xiong2020layer,
  title={On layer normalization in the transformer architecture},
  author={Xiong, Ruibin and Yang, Yunchang and He, Di and Zheng, Kai and Zheng, Shuxin and Xing, Chen and Zhang, Huishuai and Lan, Yanyan and Wang, Liwei and Liu, Tieyan},
  booktitle={International Conference on Machine Learning},
  pages={10524--10533},
  year={2020},
  organization={PMLR}
}

@article{kingma2013auto,
  title={Auto-encoding variational bayes},
  author={Kingma, Diederik P and Welling, Max},
  journal={arXiv preprint arXiv:1312.6114},
  year={2013}
}

@article{goodfellow2020generative,
  title={Generative adversarial networks},
  author={Goodfellow, Ian and Pouget-Abadie, Jean and Mirza, Mehdi and Xu, Bing and Warde-Farley, David and Ozair, Sherjil and Courville, Aaron and Bengio, Yoshua},
  journal={Communications of the ACM},
  volume={63},
  number={11},
  pages={139--144},
  year={2020},
  publisher={ACM New York, NY, USA}
}

@article{loshchilov2017decoupled,
  title={Decoupled weight decay regularization},
  author={Loshchilov, Ilya and Hutter, Frank},
  journal={arXiv preprint arXiv:1711.05101},
  year={2017}
}

# Stroke

@article{luraghi2021first,
  title={The first virtual patient-specific thrombectomy procedure},
  author={Luraghi, Giulia and Bridio, Sara and Matas, Jose Felix Rodriguez and Dubini, Gabriele and Boodt, Nikki and Gijsen, Frank JH and van der Lugt, Aad and Fereidoonnezhad, Behrooz and Moerman, Kevin M and McGarry, Patrick and others},
  journal={Journal of Biomechanics},
  volume={126},
  pages={110622},
  year={2021},
  publisher={Elsevier}
}

@article{miller2023silico,
  title={In silico thrombectomy trials for acute ischemic stroke},
  author={Miller, Claire and Konduri, Praneeta and Bridio, Sara and Luraghi, Giulia and Terreros, Nerea Arrarte and Boodt, Nikki and Samuels, Noor and Matas, Jose F Rodriguez and Migliavacca, Francesco and Lingsma, Hester and others},
  journal={Computer Methods and Programs in Biomedicine},
  volume={228},
  pages={107244},
  year={2023},
  publisher={Elsevier}
}

@article{konduri2020silico,
  title={In-silico trials for treatment of acute ischemic stroke},
  author={Konduri, Praneeta R and Marquering, Henk A and Van Bavel, Ed E and Hoekstra, Alfons and Majoie, Charles BLM and Insist Investigators},
  journal={Frontiers in Neurology},
  volume={11},
  pages={558125},
  year={2020},
  publisher={Frontiers Media SA}
}


% Misc

@article{chen2018development,
  title={Development of a quantitative intracranial vascular features extraction tool on 3 D MRA using semiautomated open-curve active contour vessel tracing},
  author={Chen, Li and Mossa-Basha, Mahmud and Balu, Niranjan and Canton, Gador and Sun, Jie and Pimentel, Kristi and Hatsukami, Thomas S and Hwang, Jenq-Neng and Yuan, Chun},
  journal={Magnetic resonance in medicine},
  volume={79},
  number={6},
  pages={3229--3238},
  year={2018},
  publisher={Wiley Online Library}
}