[REVIEW]: High-performance neural population dynamics modeling enabled by scalable computational infrastructure

[editorialbot]

Submitting author: !--author-handle-->@a9p<!--end-author-handle-- (Aashish Patel) Repository: https://github.com/TNEL-UCSD/autolfads-deploy Branch with paper.md (empty if default branch): Version: v1.1.0 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @richford, @tachukao Archive: 10.5281/zenodo.7719505

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@richford & @tachukao, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @emdupre know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @richford

📝 Checklist for @tachukao

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.35 s (751.3 files/s, 252409.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                           956            816           3611         332355
Python                          10            208            286           1386
Markdown                        29            441              0           1118
Bourne Shell                    12            133            200            496
TeX                              1             14              0            141
make                             5             25             14             58
JSON                             3              0              0             51
-------------------------------------------------------------------------------
SUM:                          1016           1637           4111         335605
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2035

[editorialbot]

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

OK DOIs

- 10.1038/nn.3776 is OK
- 10.1101/2021.01.13.426570 is OK
- 10.1038/s41592-018-0109-9 is OK
- 10.48550/arXiv.1711.09846 is OK
- 10.48550/arXiv.1712.05889 is OK
- 10.48550/arXiv.2006.02085 is OK
- 10.48550/arXiv.2109.04463 is OK
- 10.1038/s41586-021-03506-2 is OK
- 10.7554/eLife.66410 is OK
- 10.1146/annurev-neuro-092619-094115 is OK
- 10.1038/s41593-018-0095-3 is OK
- 10.1523/JNEUROSCI.0508-17.2018 is OK

MISSING DOIs

- None

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:

[emdupre]

👋 Hi @richford and @tachukao !

Thank you again for agreeing to review this submission ! The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @\editorialbot generate my checklist.

⭐ I know that the holiday season is here, so just to flag : We ask that reviewers provide their feedback within six weeks. If you anticipate any difficulties in working with this timeline, please let me know !

Otherwise, in working through the checklist, you're likely to have specific feedback on autolfads-deploy. Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !

If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !

[richford]

Review checklist for @richford

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/TNEL-UCSD/autolfads-deploy?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@a9p) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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, who the target audience is, and its relation to other work?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[tachukao]

@\editorialbot generate my checklist

[emdupre]

Sorry @tachukao , you'll need to remove the slash ! I just included it so that I didn't trigger the bot myself 🙂

If you enter the updated text in a new comment in-thread, it should trigger your checklist creation !

[tachukao]

Review checklist for @tachukao

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/TNEL-UCSD/autolfads-deploy?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@a9p) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• [x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• [x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• [x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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, who the target audience is, and its relation to other work?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[emdupre]

Hi @richford and @tachukao,

I just wanted to check-in on how this review process is going for you. Please let me know if you're having any difficulties in working through your reviewer checklist or interacting with autolfads-deploy.

[yarikoptic]

note: if reviewers do not emerge -- I would be happy to review, let me know @emdupre . Cheers.

[tachukao]

I just wanted to check-in on how this review process is going for you. Please let me know if you're having any difficulties in working through your reviewer checklist or interacting with autolfads-deploy.

Hi @emdupre, thanks for following up. Still working through the checklist

[tachukao]

Hi @emdupre, the citations look good to me in the proofs, but I'm a bit confused about how I should be checking the citation syntax in the text? Thanks for your help!

[richford]

Hi @emdupre, thanks for following up with me as well. I'm still working through the checklist and will aim to have it completed by Feb 10.

[emdupre]

Hi everyone,

Thanks for your updates !

@yarikoptic I appreciate the offer, and I will certainly keep you in mind for future reviews. Though I'm sure that the authors would appreciate your feedback regardless 😸

Hi @emdupre, the citations look good to me in the proofs, but I'm a bit confused about how I should be checking the citation syntax in the text? Thanks for your help!

Thanks for your attention on this, @tachukao ! If the citations are rendering appropriately in the proof, then they're in the appropriate syntax. As an editor, I'll make sure that all of the formatting information in the actual References section is correct once you and @richford can confirm that all of the relevant work is cited !

[emdupre]

Hi @tachukao and @richford , thank you for your opened issues to date !

I just wanted to confirm that you're each still working through your individual reviewer checklists. If you are instead done with your initial round of comments and waiting on author feedback, please let me know !

@a9p, just to note : you are welcome to begin addressing reviewer comments as they come in, or you can wait until the reviewers have completed their initial reviews.

[emdupre]

Hi @a9p, I wanted to check in and confirm how the response is going for you. I believe @richford and @tachukao have now completed their original reviews -- though please correct me if that is not the case ! -- so you should be able to proceed with addressing all of the raised points, as I see you have done in https://github.com/TNEL-UCSD/autolfads-deploy/issues/10.

If you have any questions at this point, please don't hesitate to let me know.

[a9p]

Hi @emdupre! Thank you (and the reviewers) for the update - we are working on addressing the filed issues. I'll drop a note here once we've had a chance to address them all.

[a9p]

Hi @emdupre, we have addressed all of the comments raised from the original reviews!

[richford]

@a9p, thanks for your response!

@emdupre, I approve of the authors' responses to the issues that I raised. I approve for publication.

[emdupre]

Thank you @a9p for actioning these reviewer comments, and @richford for confirming your completed review !

@tachukao, please let us know when you have reviewed the associated updates on this submission. While we wait for these additional comments, I'll perform a few editorial checks.

[emdupre]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/nn.3776 is OK
- 10.1101/2021.01.13.426570 is OK
- 10.1038/s41592-018-0109-9 is OK
- 10.48550/arXiv.1711.09846 is OK
- 10.48550/arXiv.1712.05889 is OK
- 10.48550/arXiv.2006.02085 is OK
- 10.48550/arXiv.2109.04463 is OK
- 10.1038/s41586-021-03506-2 is OK
- 10.7554/eLife.66410 is OK
- 10.1146/annurev-neuro-092619-094115 is OK
- 10.1038/s41593-018-0095-3 is OK
- 10.1523/JNEUROSCI.0508-17.2018 is OK
- 10.1087/20150211 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[emdupre]

@editorialbot generate pdf

[editorialbot]

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

[tachukao]

@a9p thanks for the response

@emdupre, the authors have addressed all my concerns. I also approve for publication.

[emdupre]

Thank you for confirming and for your review, @tachukao !

@a9p, I've finished reviewing the software and paper, and I'm also very happy with the submission. I do have a few editorial requests on the paper itself :

On figures and tables :

• On line 51, a reference to Figure 1 is included though its connection to the surrounding text is not explicit. Could you please amend to something like "and on managed or cloud compute, as illustrated in Figure 1." ?
• On line 92, the text is rendering as tableTable 1. Could you please remove the word 'table' before the reference ?
• Currently, Table 2 is not referenced in text. Could you please update the text to include this reference or remove the table ?

On references :

• Could you please update the jaderberg2017population reference as:

  @article{jaderberg2017population,
  doi = {10.48550/ARXIV.2201.11941},
  url = {http://arxiv.org/abs/1711.09846},
  author = {Jaderberg, Max and Dalibard, Valentin and Osindero, Simon and Czarnecki, Wojciech M and Donahue, Jeff and Razavi, Ali and Vinyals, Oriol and Green, Tim and Dunning, Iain and Simonyan, Karen and others},
  title = {Population Based Training of Neural Networks},
  year = {2017},
  eprint={1711.09846},
  archivePrefix={arXiv},
  primaryClass={cs.LG}
  }

• Could you please update the churchland2021mc_maze reference to include the version of the dataset used ? Based on the included URL, I assume you used the Version 'draft', but it would be important to note that explicitly.
• The keshtkaran2021large reference has Nature Methods, in press as the journal ; please update to Nature Methods.
• Could you please update the keshtkaran2019enabling reference as:

  @inproceedings{keshtkaran2019enabling,
  author = {Keshtkaran, Mohammad Reza and Pandarinath, Chethan},
  booktitle = {Advances in Neural Information Processing Systems},
  editor = {H. Wallach and H. Larochelle and A. Beygelzimer and F. d\textquotesingle Alch\'{e}-Buc and E. Fox and R. Garnett},
  pages = {},
  publisher = {Curran Associates, Inc.},
  title = {Enabling hyperparameter optimization in sequential autoencoders for spiking neural data},
  url = {https://proceedings.neurips.cc/paper/2019/file/6948bd44c91acd2b54ecdd1b132f10fb-Paper.pdf},
  volume = {32},
  year = {2019}
  }

On general formatting:

• Please add a comma after 'e.g.' on lines 24, 28, 61, 69, 80, and in the Figure 1 caption.

[emdupre]

After making these changes, could you then please:

• [ ] Make a tagged release of your software, and list the version tag of the archived version here.
• [ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• [ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata (e.g., the JOSS paper and software archive have the same title and author listing)
• [ ] List the DOI of the archived version here.

[a9p]

Hi @emdupre, thank you for your suggestions - they should all be addressed with https://github.com/TNEL-UCSD/autolfads-deploy/pull/20. The above checklist is also complete with the requested information provided below:

• Release: TNEL-UCSD/autolfads-deploy v1.1.0
• Zenodo snapshot confirmed with correct metadata
• v1.1.0 DOI: 10.5281/zenodo.7719505

[emdupre]

@editorialbot set v1.1.0 as version

[editorialbot]

Done! version is now v1.1.0

[emdupre]

@editorialbot set 10.5281/zenodo.7719505 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7719505

[emdupre]

@editorialbot generate pdf

[editorialbot]

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

[emdupre]

Thank you, @a9p !

Could you please update the title of the Zenodo archive to exactly match the paper ? That is, currently the paper is titled "High-performance neural population dynamics modeling enabled by scalable computational infrastructure" while the archive is titled "Deployment strategies for scaling AutoLFADS to model neural population dynamics".

This can be done without minting a new DOI by editing the metadata of the existing record. Please let me know if you have any issues with this !

[a9p]

Oh no, terribly sorry about that! Metadata updated! The DOI looks to be the same - 10.5281/zenodo.7719505

[emdupre]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• [x] Double check authors and affiliations (including ORCIDs)
• [x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• [x] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.

Editor Tasks Prior to Acceptance

• [x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
• [x] Check the references in the paper for corrections (e.g. capitalization)
• [x] Set article DOI with @editorialbot set <DOI here> as archive
• [x] Set version with @editorialbot set <version here> as version
• [x] Double check rendering of paper with @editorialbot generate pdf
• [x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• [x] Recommend acceptance with @editorialbot recommend-accept

[emdupre]

Thank you, @a9p !

Apologies, but I have one more request on updating the Zenodo metadata. On the paper Andrew Sedler has their ORCID linked, but it is not linked on the Zenodo archive. Could you please add that to the author metadata ?

[a9p]

Updated!

[emdupre]

Thank you @a9p ; this now looks right on my end !

I'm now happy to recommend autolfads-deploy to the EIC team for publication (!), and I just want to add my congratulations on such an impressive effort 🎉✨

Thank you to @tachukao and @richford for your reviews !! Your volunteer efforts are what keep JOSS moving forward.

[emdupre]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1038/nn.3776 is OK
- 10.1038/s41592-022-01675-0 is OK
- 10.1038/s41592-018-0109-9 is OK
- 10.48550/ARXIV.2201.11941 is OK
- 10.48550/arXiv.1712.05889 is OK
- 10.48550/arXiv.2006.02085 is OK
- 10.48550/arXiv.2109.04463 is OK
- 10.1038/s41586-021-03506-2 is OK
- 10.7554/eLife.66410 is OK
- 10.1146/annurev-neuro-092619-094115 is OK
- 10.1038/s41593-018-0095-3 is OK
- 10.1523/JNEUROSCI.0508-17.2018 is OK
- 10.1087/20150211 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Syntax of value for attribute rid of xref is not valid
Syntax of value for attribute rid of xref is not valid
Syntax of value for attribute id of aff is not valid

[emdupre]

👋 Hi @openjournals/joss-eics -- I don't think I've seen this error before ! It looks like there's an error in two cross references and one affiliation, but this is only in the JATS validation, not the CrossRef XML validation. Any suggestions on how to debug these errors ?

[a9p]

@emdupre https://github.com/TNEL-UCSD/autolfads-deploy/pull/22 should fix this issue! It looks like the root cause was our using a symbol in affiliations: valid for tex/pdf generation, but non-compliant with JATS.

[emdupre]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...