[REVIEW]: UnlockNN: Uncertainty quantification for neural network models of chemical systems #3700

whedon · 2021-09-07T13:34:24Z

Submitting author: @a-ws-m (Alexander Moriarty)
Repository: https://github.com/a-ws-m/unlockNN/
Branch with paper.md (empty if default branch):
Version: v2.0.2
Editor: @osorensen
Reviewers: @TahiriNadia, @pmeier, @Het-Shah
Archive: 10.5281/zenodo.6799685

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Markdown: [![status](https://joss.theoj.org/papers/b00df538a159c4b6816ec24d4d1716fb/status.svg)](https://joss.theoj.org/papers/b00df538a159c4b6816ec24d4d1716fb)

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Reviewer instructions & questions

@TahiriNadia & @pmeier & @Het-Shah, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @TahiriNadia

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@a-ws-m) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is? #3793
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems). #3796
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)? #3798
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified? #3799
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages? #3797
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @pmeier

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@a-ws-m) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @Het-Shah

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@a-ws-m) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

The text was updated successfully, but these errors were encountered:

whedon · 2021-09-07T13:34:28Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @TahiriNadia, @pmeier, @Het-Shah it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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whedon · 2021-09-07T13:34:49Z

Wordcount for paper.md is 555

whedon · 2021-09-07T13:34:50Z

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

OK DOIs

- 10.1038/s41586-018-0337-2 is OK
- 10.1021/acs.chemmater.9b01294 is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.1021/acs.jctc.7b00577 is OK
- 10.1557/mrc.2019.78 is OK
- 10.1038/s41524-017-0056-5 is OK
- 10.1038/s41524-019-0221-0 is OK
- 10.1063/1.5019779 is OK
- 10.1088/2632-2153/ab7e1a is OK
- 10.1103/PhysRevLett.120.145301 is OK
- 10.1038/ncomms11241 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2021-09-07T13:34:51Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.11 s (387.6 files/s, 37189.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            408            521           1165
Jupyter Notebook                 1              0            538            379
TeX                              1             16              0            232
Markdown                         4             42              0            160
YAML                             6             15             17            129
reStructuredText                 8             76             55            125
SVG                              1              1              1             53
DOS Batch                        1              8              1             26
INI                              1              2              1             22
JSON                             2              0              0             17
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            42            572           1141           2317
-------------------------------------------------------------------------------


Statistical information for the repository '554da9444b0d05b9d5db864d' was
gathered on 2021/09/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alex Moriarty                  184          6006           2821           52.15
a-ws-m                         155          3504           4595           47.85

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
a-ws-m                     2094           59.8          1.3                9.89

whedon · 2021-09-07T13:35:10Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

osorensen · 2021-09-07T13:35:36Z

@TahiriNadia, @pmeier, @Het-Shah thanks for agreeing to review this submission. This is the review issue, andd you find your review checklist above. Please reach out to me if you have any questions.

whedon · 2021-09-21T13:34:32Z

👋 @Het-Shah, please update us on how your review is going (this is an automated reminder).

whedon · 2021-09-21T13:34:32Z

👋 @pmeier, please update us on how your review is going (this is an automated reminder).

whedon · 2021-09-21T13:34:32Z

👋 @TahiriNadia, please update us on how your review is going (this is an automated reminder).

osorensen · 2021-09-26T19:29:49Z

@Het-Shah, could you please update us on how it is going with the review? If you have any suggestions for improvement of the software or the paper, feel free to post it here or to open an issue in the source repository.

osorensen · 2021-09-26T19:29:57Z

@pmeier, could you please update us on how it is going with the review? If you have any suggestions for improvement of the software or the paper, feel free to post it here or to open an issue in the source repository.

osorensen · 2021-09-26T19:30:09Z

@TahiriNadia, could you please update us on how it is going with the review? If you have any suggestions for improvement of the software or the paper, feel free to post it here or to open an issue in the source repository.

pmeier · 2021-09-27T12:09:25Z

@osorensen I've checked all the basic things and so far everything looks good. The paper is well written. The only thing left for me is to check its functionality and the documentation thereof. This might take some time, since I'm neither familiar with TensorFlow / keras nor have any domain knowledge. Regarding the latter, I fail to see how I should provide an opinion if the literature references are complete or not.

osorensen · 2021-09-27T12:21:05Z

Thanks for replying, @pmeier! Regarding the literature references, I assume you're referring to this part:

Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

I suggest you can interpret this as asking whether papers/datasets/software mentioned inside the paper are properly cited, and whether the citation syntax is correct. So if you don't have an overview of this particular application area, you may still check off the box if the citations are done formally correct.

TahiriNadia · 2021-09-27T12:50:43Z

Sorry, I started to revise the article this weekend, however, I can't do anything, no update!

osorensen · 2021-09-27T13:01:28Z

Sorry, @TahiriNadia, I didn't really understand. Is there a technical issue which means you cannot do anything?

TahiriNadia · 2021-09-27T13:38:54Z

Sorry, My ckeck list is not clikeable (see below).

danielskatz · 2021-09-27T13:47:53Z

@whedon re-invite @TahiriNadia as reviewer

whedon · 2021-09-27T13:47:56Z

The reviewer already has a pending invite.

@TahiriNadia please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

danielskatz · 2021-09-27T13:49:03Z

If that doesn't work (as there's a weird bug that sometimes marks the invitation as expired late), let us know and we'll re-issue it - this should let you check the boxes...

TahiriNadia · 2021-09-27T15:11:44Z

If that doesn't work (as there's a weird bug that sometimes marks the invitation as expired late), let us know and we'll re-issue it - this should let you check the boxes...

Thank you @whedon and @danielskatz. It's exactly my case.

danielskatz · 2021-09-27T15:12:23Z

@whedon re-invite @TahiriNadia as reviewer

whedon · 2021-09-27T15:12:27Z

OK, the reviewer has been re-invited.

@TahiriNadia please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

editorialbot · 2022-07-05T19:15:01Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

editorialbot · 2022-07-05T19:15:03Z

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

OK DOIs

- 10.1038/s41586-018-0337-2 is OK
- 10.1021/acs.chemmater.9b01294 is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.1021/acs.jctc.7b00577 is OK
- 10.1557/mrc.2019.78 is OK
- 10.1038/s41524-017-0056-5 is OK
- 10.1038/s41524-019-0221-0 is OK
- 10.1063/1.5019779 is OK
- 10.1103/PhysRevLett.120.145301 is OK
- 10.1038/ncomms11241 is OK

MISSING DOIs

- 10.1088/2632-2153/ab7e1a may be a valid DOI for title: Methods for Comparing Uncertainty Quantifications for Material Property Predictions

INVALID DOIs

- None

Related to [JOSS submission](openjournals/joss-reviews#3700). I think this might be the correct reference for Tran et al. (2020)? If not, let's keep the arXiv reference as is.

osorensen · 2022-07-05T19:48:18Z

Thanks @a-ws-m. Could you please check the latest PR I made in the source repository?

a-ws-m · 2022-07-05T19:52:53Z

Done, thanks for the correction!

osorensen · 2022-07-05T20:16:31Z

@editorialbot generate pdf

osorensen · 2022-07-05T20:16:40Z

@editorialbot check references

editorialbot · 2022-07-05T20:16:47Z

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

OK DOIs

- 10.1038/s41586-018-0337-2 is OK
- 10.1021/acs.chemmater.9b01294 is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.1021/acs.jctc.7b00577 is OK
- 10.1557/mrc.2019.78 is OK
- 10.1038/s41524-017-0056-5 is OK
- 10.1038/s41524-019-0221-0 is OK
- 10.1063/1.5019779 is OK
- 10.1088/2632-2153/ab7e1a is OK
- 10.1103/PhysRevLett.120.145301 is OK
- 10.1038/ncomms11241 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-07-05T20:17:53Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

osorensen · 2022-07-05T20:19:55Z

@editorialbot recommend-accept

editorialbot · 2022-07-05T20:19:56Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-07-05T20:20:06Z

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

OK DOIs

- 10.1038/s41586-018-0337-2 is OK
- 10.1021/acs.chemmater.9b01294 is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.1021/acs.jctc.7b00577 is OK
- 10.1557/mrc.2019.78 is OK
- 10.1038/s41524-017-0056-5 is OK
- 10.1038/s41524-019-0221-0 is OK
- 10.1063/1.5019779 is OK
- 10.1088/2632-2153/ab7e1a is OK
- 10.1103/PhysRevLett.120.145301 is OK
- 10.1038/ncomms11241 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-07-05T20:21:58Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3347, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2022-07-05T20:33:30Z

@editorialbot recommend-accept

thanks, this looks ready to go

editorialbot · 2022-07-05T20:33:31Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-07-05T20:33:39Z

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

OK DOIs

- 10.1038/s41586-018-0337-2 is OK
- 10.1021/acs.chemmater.9b01294 is OK
- 10.1038/s41524-020-00406-3 is OK
- 10.1021/acs.jctc.7b00577 is OK
- 10.1557/mrc.2019.78 is OK
- 10.1038/s41524-017-0056-5 is OK
- 10.1038/s41524-019-0221-0 is OK
- 10.1063/1.5019779 is OK
- 10.1088/2632-2153/ab7e1a is OK
- 10.1103/PhysRevLett.120.145301 is OK
- 10.1038/ncomms11241 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-07-05T20:35:02Z

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3348, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2022-07-05T20:35:10Z

@editorialbot accept

sorry, this is what I meant to do...

editorialbot · 2022-07-05T20:35:12Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2022-07-05T20:37:14Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-07-05T20:37:15Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03700 joss-papers#3349
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03700
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2022-07-05T20:58:24Z

Congratulations to @a-ws-m (Alexander Moriarty) and co-authors!!

And thanks to @TahiriNadia, @pmeier, and @Het-Shah for reviewing, and to @osorensen for editing!
We couldn't do this without you

editorialbot · 2022-07-05T20:58:26Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03700/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03700/status.svg
   :target: https://doi.org/10.21105/joss.03700

This is how it will look in your documentation:

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a-ws-m · 2022-07-05T21:25:40Z

Thank you all for your time and feedback! Feels great to have this published :)

whedon added Python review TeX labels Sep 7, 2021

whedon assigned osorensen Sep 7, 2021

whedon mentioned this issue Sep 7, 2021

[PRE REVIEW]: UnlockNN: Uncertainty quantification for neural network models of chemical systems #3692

Closed

whedon assigned Het-Shah and pmeier Sep 8, 2021

osorensen mentioned this issue Jul 5, 2022

Journal reference to arXiv preprint a-ws-m/unlockNN#40

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 5, 2022

editorialbot added accepted published Papers published in JOSS labels Jul 5, 2022

danielskatz closed this as completed Jul 5, 2022

editorialbot mentioned this issue Jan 12, 2024

[PRE REVIEW]: GrainLearning: A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials #6225

Closed

[REVIEW]: UnlockNN: Uncertainty quantification for neural network models of chemical systems #3700

[REVIEW]: UnlockNN: Uncertainty quantification for neural network models of chemical systems #3700

Comments

whedon commented Sep 7, 2021 • edited by editorialbot Loading

Status

Reviewer instructions & questions

Review checklist for @TahiriNadia

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @pmeier

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @Het-Shah

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Sep 7, 2021

whedon commented Sep 7, 2021

whedon commented Sep 7, 2021

whedon commented Sep 7, 2021

whedon commented Sep 7, 2021

osorensen commented Sep 7, 2021

whedon commented Sep 21, 2021

whedon commented Sep 21, 2021

whedon commented Sep 21, 2021

osorensen commented Sep 26, 2021

osorensen commented Sep 26, 2021

osorensen commented Sep 26, 2021

pmeier commented Sep 27, 2021

osorensen commented Sep 27, 2021

TahiriNadia commented Sep 27, 2021

osorensen commented Sep 27, 2021

TahiriNadia commented Sep 27, 2021

danielskatz commented Sep 27, 2021

whedon commented Sep 27, 2021

danielskatz commented Sep 27, 2021 • edited Loading

TahiriNadia commented Sep 27, 2021

danielskatz commented Sep 27, 2021

whedon commented Sep 27, 2021

editorialbot commented Jul 5, 2022

editorialbot commented Jul 5, 2022

osorensen commented Jul 5, 2022

a-ws-m commented Jul 5, 2022

osorensen commented Jul 5, 2022

osorensen commented Jul 5, 2022

editorialbot commented Jul 5, 2022

editorialbot commented Jul 5, 2022

osorensen commented Jul 5, 2022

editorialbot commented Jul 5, 2022

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editorialbot commented Jul 5, 2022

danielskatz commented Jul 5, 2022

editorialbot commented Jul 5, 2022

editorialbot commented Jul 5, 2022

editorialbot commented Jul 5, 2022

danielskatz commented Jul 5, 2022

editorialbot commented Jul 5, 2022

editorialbot commented Jul 5, 2022

editorialbot commented Jul 5, 2022

danielskatz commented Jul 5, 2022

editorialbot commented Jul 5, 2022

a-ws-m commented Jul 5, 2022

whedon commented Sep 7, 2021 •

edited by editorialbot

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danielskatz commented Sep 27, 2021 •

edited

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