references.bib

@article{knuth84,
  author = {Knuth, Donald E.},
  title = {Literate Programming},
  year = {1984},
  issue_date = {May 1984},
  publisher = {Oxford University Press, Inc.},
  address = {USA},
  volume = {27},
  number = {2},
  issn = {0010-4620},
  url = {https://doi.org/10.1093/comjnl/27.2.97},
  doi = {10.1093/comjnl/27.2.97},
  journal = {Comput. J.},
  month = may,
  pages = {97–111},
  numpages = {15}
}

@book{asch2016data,
  title={Data assimilation: methods, algorithms, and applications},
  author={Asch, Mark and Bocquet, Marc and Nodet, Ma{\"e}lle},
  year={2016},
  publisher={SIAM}
}

@book{asch2022toolbox,
  title={A toolbox for digital twins: from model-based to data-driven},
  author={Asch, Mark},
  year={2022},
  publisher={SIAM}
}

@article{thelen2022comprehensivea,
  title={A comprehensive review of digital twin—part 1: modeling and twinning enabling technologies},
  author={Thelen, Adam and Zhang, Xiaoge and Fink, Olga and Lu, Yan and Ghosh, Sayan and Youn, Byeng D and Todd, Michael D and Mahadevan, Sankaran and Hu, Chao and Hu, Zhen},
  journal={Structural and Multidisciplinary Optimization},
  volume={65},
  number={12},
  pages={354},
  year={2022},
  publisher={Springer}
}

@article{thelen2023comprehensiveb,
  title={A comprehensive review of digital twin—part 2: roles of uncertainty quantification and optimization, a battery digital twin, and perspectives},
  author={Thelen, Adam and Zhang, Xiaoge and Fink, Olga and Lu, Yan and Ghosh, Sayan and Youn, Byeng D and Todd, Michael D and Mahadevan, Sankaran and Hu, Chao and Hu, Zhen},
  journal={Structural and multidisciplinary optimization},
  volume={66},
  number={1},
  pages={1},
  year={2023},
  publisher={Springer}
}

@article{national2023foundational,
  title={Foundational Research Gaps and Future Directions for Digital Twins},
  author={National Academies of Sciences, Engineering, and Medicine and others},
  year={2023}
}

@book{wright2006numerical,
  title={Numerical optimization},
  author={Wright, Stephen J},
  year={2006}
}

@book{troltzsch2010optimal,
  title={Optimal control of partial differential equations: theory, methods, and applications},
  author={Tr{\"o}ltzsch, Fredi},
  volume={112},
  year={2010},
  publisher={American Mathematical Soc.}
}

@article{louboutin2023learned,
  title={Learned multiphysics inversion with differentiable programming and machine learning},
  author={Louboutin, Mathias and Yin, Ziyi and Orozco, Rafael and Grady, Thomas J and Siahkoohi, Ali and Rizzuti, Gabrio and Witte, Philipp A and M{\o}yner, Olav and Gorman, Gerard J and Herrmann, Felix J},
  journal={The Leading Edge},
  volume={42},
  number={7},
  pages={474--486},
  year={2023},
  publisher={Society of Exploration Geophysicists}
}

@article{li2020coupled,
  title={Coupled time-lapse full-waveform inversion for subsurface flow problems using intrusive automatic differentiation},
  author={Li, Dongzhuo and Xu, Kailai and Harris, Jerry M and Darve, Eric},
  journal={Water Resources Research},
  volume={56},
  number={8},
  pages={e2019WR027032},
  year={2020},
  publisher={Wiley Online Library}
}

@article{Baydin2018,
  title={Automatic differentiation in machine learning: a survey},
  author={Baydin, Atilim Gunes and Pearlmutter, Barak A and Radul, Alexey Andreyevich and Siskind, Jeffrey Mark},
  journal={Journal of Marchine Learning Research},
  volume={18},
  pages={1--43},
  year={2018},
  publisher={Microtome Publishing}
}

@article{innes2019differentiable,
  title={A differentiable programming system to bridge machine learning and scientific computing},
  author={Innes, Mike and Edelman, Alan and Fischer, Keno and Rackauckas, Chris and Saba, Elliot and Shah, Viral B and Tebbutt, Will},
  journal={arXiv preprint arXiv:1907.07587},
  year={2019}
}
@article{rackauckas2017differentialequations,
  title={Differentialequations.jl--a performant and feature-rich ecosystem for solving differential equations in julia},
  author={Rackauckas, Christopher and Nie, Qing},
  journal={Journal of Open Research Software},
  volume={5},
  number={1},
  pages={15},
  year={2017},
  publisher={Ubiquity Press}
}

@article{law2015data,
  title={Data assimilation},
  author={Law, Kody and Stuart, Andrew and Zygalakis, Kostas},
  journal={Cham, Switzerland: Springer},
  volume={214},
  pages={52},
  year={2015},
  publisher={Springer}
}

@book{sarkka2023bayesian,
  title={Bayesian filtering and smoothing},
  author={S{\"a}rkk{\"a}, Simo and Svensson, Lennart},
  volume={17},
  year={2023},
  publisher={Cambridge university press}
}

@book{sarkka2013,
  title={Bayesian filtering and smoothing},
  author={S{\"a}rkk{\"a}, Simo and Svensson, Lennart},
  volume={17},
  year={2023},
  publisher={Cambridge university press}
}

@book{evensen2009data,
  title={Data assimilation: the ensemble Kalman filter},
  author={Evensen, Geir and others},
  volume={2},
  year={2009},
  publisher={Springer}
}

@article{li2001optimality,
  title={Optimality of variational data assimilation and its relationship with the Kalman filter and smoother},
  author={Li, Zhijin and Navon, IM},
  journal={Quarterly Journal of the Royal Meteorological Society},
  volume={127},
  number={572},
  pages={661--683},
  year={2001},
  publisher={Wiley Online Library}
}

@article{doucet2009tutorial,
  title={A tutorial on particle filtering and smoothing: Fifteen years later},
  author={Doucet, Arnaud and Johansen, Adam M and others},
  journal={Handbook of nonlinear filtering},
  volume={12},
  number={656-704},
  pages={3},
  year={2009}
}

@article{tatsis2022sequential,
  title={Sequential bayesian inference for uncertain nonlinear dynamic systems: A tutorial},
  author={Tatsis, Konstantinos E and Dertimanis, Vasilis K and Chatzi, Eleni N},
  journal={arXiv preprint arXiv:2201.08180},
  year={2022}
}

@book{prince2023understanding,
author = "Simon J.D. Prince",
title = "Understanding Deep Learning",
publisher = "MIT Press",
year = 2023,
url = "http://udlbook.com"
}