Joss-reviews: [REVIEW]: GENRE (GPU Elastic-Net REgression): A CUDA-Accelerated Package for Massively Parallel Linear Regression with Elastic-Net Regularization

[whedon]

Submitting author: @Christopher-Khan (Christopher Khan)
Repository: https://github.com/VU-BEAM-Lab/GENRE
Version: v1.0.2
Editor: @sjpfenninger
Reviewer: @marouenbg, @krystophny
Archive: 10.5281/zenodo.4076520

:warning: JOSS reduced service mode :warning:

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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ba7eaa02926a24344a680cbd0c5ac87f"><img src="https://joss.theoj.org/papers/ba7eaa02926a24344a680cbd0c5ac87f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ba7eaa02926a24344a680cbd0c5ac87f/status.svg)](https://joss.theoj.org/papers/ba7eaa02926a24344a680cbd0c5ac87f)

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

@marouenbg & @krystophny, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @marouenbg

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 repository url?
• [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 (@Christopher-Khan) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [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?

Review checklist for @krystophny

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 repository url?
• [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 (@Christopher-Khan) 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

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @marouenbg, @krystophny it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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

@whedon commands

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

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1111/j.1467-9868.2005.00503.x is OK
- 10.18637/jss.v033.i01 is OK
- 10.1109/tuffc.2014.2928 is OK
- 10.1109/tuffc.2015.007004 is OK
- 10.1109/tuffc.2017.2729944 is OK
- 10.1186/1753-6561-6-s2-s10 is OK
- 10.3389/fgene.2013.00270 is OK
- 10.1016/j.neuroimage.2008.08.020 is OK
- 10.1109/isbi.2014.6868131 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Christopher-Khan]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[marouenbg]

@whedon generate pdf

[whedon]

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

[marouenbg]

@whedon generate pdf

[whedon]

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

[marouenbg]

@whedon generate pdf

[whedon]

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

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[marouenbg]

Hi @sjpfenninger ,
I finished my review, @Christopher-Khan addressed all of the comments either through additional experiments and implementation, new manuscript sections, and through point-by-point rebuttal.

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[Christopher-Khan]

Hi @marouenbg. I just added one more result to the manuscript. The glmnet software package has two algorithm options to choose from, so I also included the benchmark result for the other option as well. It was slower than the option whose benchmark result I had already reported though. In addition, thank you again for doing this review! Your comments were very helpful in improving this submission!

[sjpfenninger]

Thanks @marouenbg for the extensive review and @Christopher-Khan for addressing everything thoroughly! krystophny's review is slightly delayed, but we expect by end of month, so stay tuned.

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[krystophny]

@sjpfenninger I have finished reviewing the paper and testing the software and support the publication in JOSS after two minor changes in the README https://github.com/VU-BEAM-Lab/GENRE/issues/3 . As mentioned the package is relatively small (1000-2000 lines of code) and not very well known yet, but it looks very useful with its unique capability to solve multiple GLMs with elastic net regularization in parallel on GPUs and has the potential as a standard code for that task. The description is done well, and comparable software (without the special parallel feature) is referenced.

[Christopher-Khan]

Hi @krystophny. Thank you for your review! In regards to the minor points, my responses are below.

For adding the folders to the MATLAB path, in the bullet point under Windows and Linux installation in the README, I have the following statement, "Assuming the repository is on your system, go to the MATLAB directory that contains the repository folders and add them to your MATLAB path."

In regards to not needing to specify the cuda path for Linux, I have the following statement in the second bullet point under Linux compilation in the README, "Note that mexcuda might find the CUDA toolkit library even if you do not explicitly type out its path. In addition, note that there might be differences in your path compared to the one shown above, such as in regards to the version of the CUDA toolkit that is being used."

Did you want me to still modify those statements?

[krystophny]

@Christopher-Khan in that case it’s fine, now I understand that these things are correct already now. I was too hasty when reading. So all issues resolved!

[Christopher-Khan]

@krystophny Great! Thank you!

[sjpfenninger]

@marouenbg @krystophny Thanks both for your reviews. Can you both confirm that you recommend to accept the submission? @krystophny can you close VU-BEAM-Lab/GENRE#3 if it is resolved?

[krystophny]

@sjpfenninger everything resolved, I confirm the recommendation to accept the submission!

[marouenbg]

Hi @sjpfenninger, I have no further comments, I recommend the publication of the software.

[sjpfenninger]

@Christopher-Khan I have made some minor edits to the paper in VU-BEAM-Lab/GENRE#4 -- can you check and merge (ideally squash into single commit)? Also - could you adjust the table captions such that they differentiate what we see in the two tables rather than just saying "Benchmark times"?

[Christopher-Khan]

Hi @sjpfenninger. I have squashed the edits into a single commit and merged them. I have also changed the title in the second table to differentiate it from the first table's title.

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[sjpfenninger]

@Christopher-Khan Great, we're ready to accept this. Can you make a tagged release on GitHub and archive that release, for example on Zenodo or figshare, then report the version number and archive DOI back here in the review issue?

[Christopher-Khan]

Hi @sjpfenninger. Great! Here is the Zenodo information: DOI 10.5281/zenodo.4050385. Before archiving, I also made 3 minor edits to the paper unrelated to your edits (just reworded 3 sentences). Thank you!

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[sjpfenninger]

@Christopher-Khan great thanks. Can you edit the Zenodo item such that title and author list are the same as for the JOSS paper?

[Christopher-Khan]

Hi @sjpfenninger. Sorry for the late response. I made one more edit to the paper. I forgot for the benchmarks to account for the fact that MATLAB code can sometimes run slower the first time it is called than subsequent calls due to MATLAB's execution engine. Therefore, I reran and updated the benchmarks in order to account for this. The times didn't change much, but I still wanted to update them in the paper. I made a new release on Zenodo and detailed the change on there. I have also updated the metadata. Here is the new Zenodo DOI. DOI: 10.5281/zenodo.4057940

Thank you!

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[Christopher-Khan]

Hi @sjpfenninger. I was just following up. Was there anything else on my end that you needed me to do regarding the submission or the Zenodo archive? Thank you!

[sjpfenninger]

@whedon set doi as 10.5281/zenodo.4057940

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[sjpfenninger]

@whedon set 10.5281/zenodo.4057940 as archive

[whedon]

OK. 10.5281/zenodo.4057940 is the archive.

[sjpfenninger]

@whedon set v1.0.1 as version

[whedon]

OK. v1.0.1 is the version.

[sjpfenninger]

@Christopher-Khan Apologies for the delay. This looks good now!

[sjpfenninger]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1111/j.1467-9868.2005.00503.x is OK
- 10.18637/jss.v033.i01 is OK
- 10.1109/tuffc.2014.2928 is OK
- 10.1109/tuffc.2015.007004 is OK
- 10.1109/tuffc.2017.2729944 is OK
- 10.1186/1753-6561-6-s2-s10 is OK
- 10.3389/fgene.2013.00270 is OK
- 10.1016/j.neuroimage.2008.08.020 is OK
- 10.1109/isbi.2014.6868131 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1790

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1790, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kthyng]

Hi @Christopher-Khan! I see that you archive and version are set and up to date. I just looked at your paper and unfortunately it is far too long. A JOSS paper is to be between 250 and 1000 words. Can you move some of the content from the paper to your documentation?

[Christopher-Khan]

Hi @kthyng! Sure. I can move the section titled "Example Benchmark Comparing GENRE with glmnet" to my documentation on GitHub. That will make the paper two pages shorter. Do you want me to make a new Zenodo archive then and give the DOI for that one? I ask because I don't think Zenodo allows for files in archives to be updated if the archive is more than a week old. Thank you!

[krystophny]

@Christopher-Khan if you make a new release on github, Zenodo will create a new version of the same entry with a new doi. Probably that’s better than creating a new archive

[Christopher-Khan]

@whedon generate pdf

[whedon]

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

[Christopher-Khan]

@krystophny thank you. That's what I meant actually instead of creating a new archive. @kthyng I have moved the section in the JOSS paper titled "Example Benchmark Comparing GENRE with glmnet" from the paper to the section in the README.md file titled "Comparing with Other Packages". The new DOI is below. I hope the paper is better now in terms of its length.

DOI: 10.5281/zenodo.4076520

Thank you for your time.

[kthyng]

@Christopher-Khan Yes looks good! We can proceed now.

[kthyng]

@whedon set 10.5281/zenodo.4076520 as archive

[whedon]

OK. 10.5281/zenodo.4076520 is the archive.

[kthyng]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1111/j.1467-9868.2005.00503.x is OK
- 10.18637/jss.v033.i01 is OK
- 10.1109/tuffc.2014.2928 is OK
- 10.1109/tuffc.2015.007004 is OK
- 10.1109/tuffc.2017.2729944 is OK
- 10.1186/1753-6561-6-s2-s10 is OK
- 10.3389/fgene.2013.00270 is OK
- 10.1016/j.neuroimage.2008.08.020 is OK
- 10.1109/isbi.2014.6868131 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1797

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1797, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1798
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02644
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? Notify your editorial technical team...

[kthyng]

Congrats on the new publication @Christopher-Khan! Thanks to editor @sjpfenninger and reviewers @marouenbg and @krystophny for your time and expertise!!

(will close this issue once doi resolves)

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.02644/status.svg)](https://doi.org/10.21105/joss.02644)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02644">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02644/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02644/status.svg
   :target: https://doi.org/10.21105/joss.02644

This is how it will look in your documentation:

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[Christopher-Khan]

Awesome! Thank you @kthyng, @sjpfenninger, @marouenbg, and @krystophny! This review process has been great!

[Christopher-Khan]

@whedon set v1.0.2 as version

[whedon]

I'm sorry @Christopher-Khan, I'm afraid I can't do that. That's something only editors are allowed to do.

[Christopher-Khan]

@sjpfenninger. Last thing. Do I need to set the version at the top of this review from v1.0.1 to v1.0.2 because that's the newest version that actually got accepted? If so, I believe only editors can do that. Thank you!

[arfon]

@whedon set v1.0.2 as version

[whedon]

OK. v1.0.2 is the version.

[Christopher-Khan]

@arfon Great! Thank you!