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24 changes: 24 additions & 0 deletions .github/workflows/draft-pdf.yml
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name: Draft PDF
on: [push]

jobs:
paper:
runs-on: ubuntu-latest
name: Paper Draft
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Build draft PDF
uses: openjournals/openjournals-draft-action@master
with:
journal: joss
# This should be the path to the paper within your repo.
paper-path: paper/paper.md
- name: Upload
uses: actions/upload-artifact@v4
with:
name: paper
# This is the output path where Pandoc will write the compiled
# PDF. Note, this should be the same directory as the input
# paper.md
path: paper/paper.pdf
238 changes: 233 additions & 5 deletions paper/paper.bib
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@InProceedings{krämer2021probabilistic,
@InProceedings{krämer2021highdim,
title = {Probabilistic {ODE} Solutions in Millions of Dimensions},
author = {Kr{\"a}mer, Nicholas and Bosch, Nathanael and Schmidt,
Jonathan and Hennig, Philipp},
Expand Down Expand Up @@ -57,7 +55,6 @@ @inproceedings{beck2024diffusion
url = {https://openreview.net/forum?id=43HZG9zwaj}
}


@misc{wenger2021probnum,
title = {ProbNum: Probabilistic Numerics in Python},
author = {Jonathan Wenger and Nicholas Krämer and Marvin Pförtner and
Expand All @@ -68,4 +65,235 @@ @misc{wenger2021probnum
eprint = {2112.02100},
archivePrefix ={arXiv},
primaryClass = {cs.MS}
}
}

@InProceedings{dalton2024,
title = {Data-Adaptive Probabilistic Likelihood Approximation for Ordinary Differential Equations},
author = {Wu, Mohan and Lysy, Martin},
booktitle = {Proceedings of The 27th International Conference on Artificial Intelligence and Statistics},
pages = {1018--1026},
year = {2024},
editor = {Dasgupta, Sanjoy and Mandt, Stephan and Li, Yingzhen},
volume = {238},
series = {Proceedings of Machine Learning Research},
month = {02--04 May},
publisher = {PMLR},
pdf = {https://proceedings.mlr.press/v238/wu24b/wu24b.pdf},
url = {https://proceedings.mlr.press/v238/wu24b.html},
}

@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,
year = 2017,
publisher = {Ubiquity Press}
}

@misc{probdiffeq,
author = {Kr{\"a}mer, Nicholas},
title = {probdiffeq: Probabilistic solvers for differential equations in JAX},
year = {2023},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/pnkraemer/probdiffeq}
}

@misc{jax2018github,
author = {James Bradbury and Roy Frostig and Peter Hawkins and Matthew
James Johnson and Chris Leary and Dougal Maclaurin and George
Necula and Adam Paszke and Jake Vander{P}las and Skye
Wanderman-{M}ilne and Qiao Zhang},
title = {{JAX}: composable transformations of {P}ython+{N}um{P}y
programs},
version = {0.2.5},
year = 2018,
}

@article{schober19,
author = "Schober, Michael and S{\"a}rkk{\"a}, Simo and Hennig, Philipp",
title = "A probabilistic model for the numerical solution of initial
value problems",
journal = "Statistics and Computing",
year = 2019,
month = "Jan",
day = 01,
volume = 29,
number = 1,
pages = "99--122",
issn = "1573-1375",
doi = "10.1007/s11222-017-9798-7",
url = "https://doi.org/10.1007/s11222-017-9798-7"
}

@article{tronarp19,
author = {Filip Tronarp and Hans Kersting and Simo S{\"{a}}rkk{\"{a}}
and Philipp Hennig},
title = {Probabilistic solutions to ordinary differential equations as
nonlinear {B}ayesian filtering: a new perspective},
year = 2019,
volume = 29,
number = 6,
pages = {1297-1315},
doi = {10.1007/s11222-019-09900-1},
url = {https://doi.org/10.1007/s11222-019-09900-1},
journal = {Statistics and Computing},
timestamp = {Wed, 25 Mar 2020 09:31:58 +0100},
biburl = {https://dblp.org/rec/journals/sac/TronarpKSH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}

@article{kersting20,
author = {Kersting, Hans and Sullivan, T. J. and Hennig, Philipp},
title = {Convergence rates of Gaussian ODE filters},
journal = {Statistics and Computing},
year = 2020,
month = {Nov},
day = 01,
volume = 30,
number = 6,
pages = {1791-1816},
issn = {1573-1375},
doi = {10.1007/s11222-020-09972-4},
url = {https://doi.org/10.1007/s11222-020-09972-4}
}

@article{tronarp21,
author = {Tronarp, Filip and S{\"a}rkk{\"a}, Simo and Hennig, Philipp},
title = {Bayesian ODE solvers: the maximum a posteriori estimate},
journal = {Statistics and Computing},
year = 2021,
month = {Mar},
day = 03,
volume = 31,
number = 3,
pages = 23,
issn = {1573-1375},
doi = {10.1007/s11222-021-09993-7},
url = {https://doi.org/10.1007/s11222-021-09993-7}
}

@misc{bosch2023parallelintime,
title = {Parallel-in-Time Probabilistic Numerical {ODE} Solvers},
author = {Nathanael Bosch and Adrien Corenflos and Fatemeh Yaghoobi and
Filip Tronarp and Philipp Hennig and Simo Särkkä},
year = 2023,
eprint = {2310.01145},
archivePrefix ={arXiv},
primaryClass = {math.NA}
}

@InProceedings{kersting20invprob,
title = {Differentiable Likelihoods for Fast Inversion of
’{L}ikelihood-Free’ Dynamical Systems},
author = {Kersting, Hans and Kr{\"a}mer, Nicholas and Schiegg, Martin
and Daniel, Christian and Tiemann, Michael and Hennig,
Philipp},
booktitle = {Proceedings of the 37th International Conference on Machine
Learning},
pages = {5198--5208},
year = 2020,
editor = {Hal Daumé III and Aarti Singh},
volume = 119,
series = {Proceedings of Machine Learning Research},
month = {13--18 Jul},
publisher = {PMLR},
pdf = {http://proceedings.mlr.press/v119/kersting20a/kersting20a.pdf},
url = {http://proceedings.mlr.press/v119/kersting20a.html},
}

@inproceedings{schmidt21,
author = {Schmidt, Jonathan and Kr\"{a}mer, Nicholas and Hennig,
Philipp},
booktitle = {Advances in Neural Information Processing Systems},
editor = {M. Ranzato and A. Beygelzimer and Y. Dauphin and P.S. Liang
and J. Wortman Vaughan},
pages = {12374--12385},
publisher = {Curran Associates, Inc.},
title = {A Probabilistic State Space Model for Joint Inference from
Differential Equations and Data},
url =
{https://proceedings.neurips.cc/paper/2021/file/6734fa703f6633ab896eecbdfad8953a-Paper.pdf},
volume = 34,
year = 2021
}

@inproceedings{kraemer202bvp,
author = {Kr\"{a}mer, Nicholas and Hennig, Philipp},
booktitle = {Advances in Neural Information Processing Systems},
editor = {M. Ranzato and A. Beygelzimer and Y. Dauphin and P.S. Liang
and J. Wortman Vaughan},
pages = {11160--11171},
publisher = {Curran Associates, Inc.},
title = {Linear-Time Probabilistic Solution of Boundary Value Problems},
url =
{https://papers.nips.cc/paper/2021/hash/5ca3e9b122f61f8f06494c97b1afccf3-Abstract.html},
volume = 34,
year = 2021
}

@InProceedings{kraemer22mol,
title = { Probabilistic Numerical Method of Lines for Time-Dependent
Partial Differential Equations },
author = {Kr\"amer, Nicholas and Schmidt, Jonathan and Hennig, Philipp},
booktitle = {Proceedings of The 25th International Conference on Artificial
Intelligence and Statistics},
pages = {625--639},
year = 2022,
editor = {Camps-Valls, Gustau and Ruiz, Francisco J. R. and Valera,
Isabel},
volume = 151,
series = {Proceedings of Machine Learning Research},
month = {28--30 Mar},
publisher = {PMLR},
pdf = {https://proceedings.mlr.press/v151/kramer22a/kramer22a.pdf},
url = {https://proceedings.mlr.press/v151/kramer22a.html},
}

@InProceedings{bosch22pick,
title = { Pick-and-Mix Information Operators for Probabilistic {ODE}
Solvers },
author = {Bosch, Nathanael and Tronarp, Filip and Hennig, Philipp},
booktitle = {Proceedings of The 25th International Conference on Artificial
Intelligence and Statistics},
pages = {10015--10027},
year = 2022,
editor = {Camps-Valls, Gustau and Ruiz, Francisco J. R. and Valera,
Isabel},
volume = 151,
series = {Proceedings of Machine Learning Research},
month = {28--30 Mar},
publisher = {PMLR},
pdf = {https://proceedings.mlr.press/v151/bosch22a/bosch22a.pdf},
url = {https://proceedings.mlr.press/v151/bosch22a.html},
}

@InProceedings{bosch21capos,
title = { Calibrated Adaptive Probabilistic {ODE} Solvers },
author = {Bosch, Nathanael and Hennig, Philipp and Tronarp, Filip},
booktitle = {Proceedings of The 24th International Conference on Artificial
Intelligence and Statistics},
pages = {3466--3474},
year = 2021,
editor = {Banerjee, Arindam and Fukumizu, Kenji},
volume = 130,
series = {Proceedings of Machine Learning Research},
month = {13--15 Apr},
publisher = {PMLR},
pdf = {http://proceedings.mlr.press/v130/bosch21a/bosch21a.pdf},
url = {http://proceedings.mlr.press/v130/bosch21a.html},
}

@article{kraemer24stableimp,
author = {Nicholas Kr{{\"a}}mer and Philipp Hennig},
title = {Stable Implementation of Probabilistic ODE Solvers},
journal = {Journal of Machine Learning Research},
year = 2024,
volume = 25,
number = 111,
pages = {1--29},
url = {http://jmlr.org/papers/v25/20-1423.html}
}
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