[PRE REVIEW]: ProbNumDiffEq.jl: Probabilistic Numerical Solvers for Ordinary Differential Equations in Julia

[editorialbot]

Submitting author: !--author-handle-->@nathanaelbosch<!--end-author-handle-- (Nathanael Bosch) Repository: https://github.com/nathanaelbosch/ProbNumDiffEq.jl Branch with paper.md (empty if default branch): paper Version: 0.16.0 Editor: !--editor-->@jbytecode<!--end-editor-- Reviewers: @PieterjanRobbe, @ranocha Managing EiC: Daniel S. Katz

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Author instructions

Thanks for submitting your paper to JOSS @nathanaelbosch. Currently, there isn't a JOSS editor assigned to your paper.

@nathanaelbosch if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.20 s (906.7 files/s, 168965.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             56              0              0          16901
Julia                           85           1158           1341           6903
Markdown                        24            833              0           6205
TeX                              2             33              0            461
YAML                            10             10             11            226
TOML                             5              9              1            161
CSS                              1              0              0             17
INI                              1              3              0             14
-------------------------------------------------------------------------------
SUM:                           184           2046           1353          30888
-------------------------------------------------------------------------------

Commit count by author:

   826  Nathanael Bosch
    93  github-actions[bot]
     4  dependabot[bot]
     2  Pietro Monticone
     1  Christopher Rackauckas
     1  CompatHelper Julia
     1  Cornelius Roemer
     1  Daniel González Arribas
     1  David Widmann
     1  Jose Storopoli
     1  Qingyu Qu
     1  Tim Holy
     1  Vedant Puri

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 894

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/s11222-017-9798-7 is OK
- 10.1007/s11222-019-09900-1 is OK
- 10.1007/s11222-020-09972-4 is OK
- 10.1007/s11222-021-09993-7 is OK

MISSING DOIs

- No DOI given, and none found for title: Probabilistic ODE Solutions in Millions of Dimensi...
- No DOI given, and none found for title: Fenrir: Physics-Enhanced Regression for Initial Va...
- No DOI given, and none found for title: Probabilistic Exponential Integrators
- No DOI given, and none found for title: Diffusion Tempering Improves Parameter Estimation ...
- No DOI given, and none found for title: ProbNum: Probabilistic Numerics in Python
- No DOI given, and none found for title: Data-Adaptive Probabilistic Likelihood Approximati...
- No DOI given, and none found for title: DifferentialEquations.jl – A Performant and Featur...
- No DOI given, and none found for title: probdiffeq: Probabilistic solvers for differential...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Parallel-in-Time Probabilistic Numerical ODE Solve...
- No DOI given, and none found for title: Differentiable Likelihoods for Fast Inversion of ’...
- No DOI given, and none found for title: A Probabilistic State Space Model for Joint Infere...
- No DOI given, and none found for title: Linear-Time Probabilistic Solution of Boundary Val...
- No DOI given, and none found for title:  Probabilistic Numerical Method of Lines for Time-...
- No DOI given, and none found for title:  Pick-and-Mix Information Operators for Probabilis...
- No DOI given, and none found for title:  Calibrated Adaptive Probabilistic ODE Solvers 
- No DOI given, and none found for title: Stable Implementation of Probabilistic ODE Solvers

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[editorialbot]

Five most similar historical JOSS papers:

NoisySignalIntegration.jl: A Julia package for uncertainty evaluation of numeric integrals Submitting author: @nluetts Handling editor: @jbytecode (Active) Reviewers: @myousefi2016, @mseri Similarity score: 0.7413

DynamicOED.jl: A Julia package for solving optimum experimental design problems Submitting author: @AlCap23 Handling editor: @diehlpk (Active) Reviewers: @KBodolai, @joshuaeh Similarity score: 0.7401

HOODESolver.jl: A Julia package for highly oscillatory problems Submitting author: @pnavaro Handling editor: @vissarion (Active) Reviewers: @ranocha, @HaoZeke Similarity score: 0.7339

GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields Submitting author: @PieterjanRobbe Handling editor: @jbytecode (Active) Reviewers: @ziyiyin97, @shahmoradi Similarity score: 0.7278

QAOA.jl: Toolkit for the Quantum and Mean-Field Approximate Optimization Algorithms Submitting author: @timbode Handling editor: @danielskatz (Active) Reviewers: @babreu-ncsa, @pkairys, @Abinashbunty Similarity score: 0.7262

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

👋 @jbytecode - I know you are at your limit, but I also wanted to see if you wanted to edit this one... If not, no worries.

[danielskatz]

@editorialbot invite @jbytecode as editor

[editorialbot]

Invitation to edit this submission sent!

[jbytecode]

@editorialbot assign me as editor

@danielskatz - sure! thank you for inviting me, indeed, I like to edit Julia submissions and the subject perfectly fits my experiences.

[editorialbot]

Assigned! @jbytecode is now the editor

[jbytecode]

@nathanaelbosch - Hi, thank you for submitting your work to JOSS. I am the handling editor. We will be doing whole the stuff together from start to finish. Firstly, could you please try to find the DOI information for the missing ones of the bibtex entries? For example the submission

DifferentialEquations.jl – A Performant and Featur...

is resolved by using the DOI information

https://doi.org/10.5334/jors.151

and hopefully you can investigate the others. Addition to this, it seems you forgot to cite the Julia programming language. You can use the bibtex entry

@article{julia,
  doi       = {10.1137/141000671},
  url       = {https://doi.org/10.1137%2F141000671},
  year      = 2017,
  month     = {jan},
  publisher = {Society for Industrial {\&} Applied Mathematics ({SIAM})},
  volume    = {59},
  number    = {1},
  pages     = {65--98},
  author    = {Jeff Bezanson and Alan Edelman and Stefan Karpinski and Viral B. Shah},
  title     = {Julia: A Fresh Approach to Numerical Computing},
  journal   = {{SIAM} Review}
}

for Julia, in manuscript, possibly where the first use is located.

The editorial bot suggests us some potential reviewers for the submission, it lists top 10 with highest similarity scores. I will try to invite them while you are editing your bibtex.

Thank you in advance!

[jbytecode]

👋👋👋 Dear @nluetts, @AlCap23, @pnavaro 👋👋👋

I am writing here to you because you have recently published your work in JOSS which is about Julia and computational methods.

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

ProbNumDiffEq.jl: Probabilistic Numerical Solvers for Ordinary Differential Equations in Julia

You can find more information at the top of this Github issue https://github.com/openjournals/joss-reviews/issues/7015

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be about 20 check items for each single reviewer.

Thank you in advance!

[nathanaelbosch]

Hello @jbytecode, thank you for taking the time to edit this submission and for supporting me in the process!

I added the DOI for the DifferentialEquations.jl paper and a citation to the Julia paper, as well as some of the other missing DOIs. I could however not find DOIs for the any paper published by PMLR or JMLR. Do you have any suggestion for how I should proceed to find the missing DOIs, or could it also simply be that these publishers do not provide a DOI?

Thank you again for your support!

[jbytecode]

@editorialbot check references

@nathanaelbosch - Thank you, let me take a look at the changes. If any improvements are required for this issue, we can fix them after the review as well.

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.2112.02100 is OK
- 10.5334/jors.151 is OK
- 10.1007/s11222-017-9798-7 is OK
- 10.1007/s11222-019-09900-1 is OK
- 10.1007/s11222-020-09972-4 is OK
- 10.1007/s11222-021-09993-7 is OK
- 10.48550/arXiv.2310.01145 is OK
- 10.1137/141000671 is OK

MISSING DOIs

- No DOI given, and none found for title: Probabilistic ODE Solutions in Millions of Dimensi...
- No DOI given, and none found for title: Fenrir: Physics-Enhanced Regression for Initial Va...
- No DOI given, and none found for title: Diffusion Tempering Improves Parameter Estimation ...
- No DOI given, and none found for title: Data-Adaptive Probabilistic Likelihood Approximati...
- No DOI given, and none found for title: probdiffeq: Probabilistic solvers for differential...
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Differentiable Likelihoods for Fast Inversion of ’...
- No DOI given, and none found for title:  Probabilistic Numerical Method of Lines for Time-...
- No DOI given, and none found for title:  Pick-and-Mix Information Operators for Probabilis...
- No DOI given, and none found for title:  Calibrated Adaptive Probabilistic ODE Solvers 
- No DOI given, and none found for title: Stable Implementation of Probabilistic ODE Solvers

INVALID DOIs

- 10.5555/3666122.3667881 is INVALID
- 10.5555/3540261.3541208 is INVALID
- 10.5555/3540261.3541114 is INVALID

[jbytecode]

@nathanaelbosch - you can use the https://www.crossref.org/ tool to search DOIs (if exist). You can trigger our editorial bot to check the references by typing

@editorialbot check references

[nathanaelbosch]

@jbytecode I removed the invalid DOIs again and unfortunately I was not able to find DOIs for the remaining papers (I suspect that these ML conferences simply do not attribute a DOI to each paper).

@editorialbot check references

[jbytecode]

@nathanaelbosch - editorial bot commands should place at the start of the posts.

That's okay to leave conference items in bibtex as they were.

[jbytecode]

👋👋👋 Dear @PieterjanRobbe and @timbode 👋👋👋

I am writing here to you because you have recently published your work in JOSS which is about Julia and computational methods.

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

ProbNumDiffEq.jl: Probabilistic Numerical Solvers for Ordinary Differential Equations in Julia

You can find more information at the top of this Github issue https://github.com/openjournals/joss-reviews/issues/7015

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be about 20 check items for each single reviewer.

Thank you in advance!

[pnavaro]

Sorry I'm in vacation and will be very busy in September. Best regards.

[nluetts]

Dear @jbytecode, dear @nathanaelbosch,

I am currently on vacation and could start the review process in two weeks time at the earliest. Also, I am not familiar with the topic and could provide merely a perspective from a newcomer. If this is acceptable, I would be happy to take part in the review, but I think it would be advisable to have two other reviewers who are active in this field.

[jbytecode]

@pnavaro, @nluetts - Thank you for the reply.

@nathanaelbosch - Do you have any suggestions for the potential reviewers? The list (https://reviewers.joss.theoj.org/lookup) contains a list of potential reviewers that are willing to review in JOSS. If so, you can mention their GitHub handles without using the @ character to avoid unwanted notifications.

Thank you in advance!

[PieterjanRobbe]

@jbytecode Sure, I'm happy to provide a review.

[jbytecode]

@editorialbot add @PieterjanRobbe as reviewer

@PieterjanRobbe - Thank you! Whenever we assign at least one more reviewer, I will inform you.

[editorialbot]

@PieterjanRobbe added to the reviewers list!

[nathanaelbosch]

@jbytecode I do not have any direct recommendation in mind, but filtering for "Julia" as a programming language and "differential equations" as keyword see 16 reviewers that could be suited. These also include some names I know from the SciML ecosystem in Julia, such as avik-pal, ranocha, or ChrisRackauckas, but I suppose this could both qualify then as being very well-suited topic-wise, but potentially also being too close to the project. I also found matt-graham who might be well-suited as they list both "numerical simulation" and also more probabilistic topics as their topc areas.

[jbytecode]

👋👋👋 Dear @avik-pal 👋👋👋

I am writing here to you because you have recently published your work in JOSS which is about Julia and computational methods.

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

ProbNumDiffEq.jl: Probabilistic Numerical Solvers for Ordinary Differential Equations in Julia

You can find more information at the top of this Github issue https://github.com/openjournals/joss-reviews/issues/7015

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be about 20 check items for each single reviewer.

Thank you in advance!

[jbytecode]

👋👋👋 Dear @ranocha 👋👋👋

I am writing here to you because you have recently published your work in JOSS which is about Julia and computational methods.

I need a second reviewer!

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

ProbNumDiffEq.jl: Probabilistic Numerical Solvers for Ordinary Differential Equations in Julia

You can find more information at the top of this Github issue https://github.com/openjournals/joss-reviews/issues/7015

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be about 20 check items for each single reviewer.

Thank you in advance!

[ranocha]

I can review the submission (but it may take a few weeks)

[jbytecode]

@editorialbot add @ranocha as reviewer

@ranocha - Thank you for accepting our invitation

@PieterjanRobbe, @ranocha, @nathanaelbosch - Now I'am starting the review in a new thread. I will introduce the instructions there.

See you!

[editorialbot]

@ranocha added to the reviewers list!

[jbytecode]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7048.