[REVIEW]: SIRUS.jl: Interpretable Machine Learning via Rule Extraction

[editorialbot]

Submitting author: !--author-handle-->@rikhuijzer<!--end-author-handle-- (Rik Huijzer) Repository: https://github.com/rikhuijzer/SIRUS.jl Branch with paper.md (empty if default branch): rh/paper Version: v1.3.3 Editor: !--editor-->@jbytecode<!--end-editor-- Reviewers: @sylvaticus, @gdalle Archive: 10.5281/zenodo.8398350

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7e25a1e05f1a5981f0a27fd0f2585477/status.svg)](https://joss.theoj.org/papers/7e25a1e05f1a5981f0a27fd0f2585477)

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

@sylvaticus & @gdalle, 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 @jbytecode 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 @gdalle

📝 Checklist for @sylvaticus

[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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1424.4 files/s, 176077.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           25            557            235           3043
Markdown                         5            108              0            477
TeX                              1             21              0            185
TOML                             3              4              0             89
YAML                             3              4              4             71
Bourne Shell                     2              7              0             16
-------------------------------------------------------------------------------
SUM:                            39            701            239           3881
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1997

[editorialbot]

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

OK DOIs

- 10.1016/j.inffus.2019.12.012 is OK
- 10.1214/20-EJS1792 is OK
- 10.1007/s11749-016-0481-7 is OK
- 10.21105/joss.02704 is OK
- 10.1023/A:1010933404324 is OK
- 10.1145/2939672.2939785 is OK
- 10.48550/arXiv.2305.01582 is OK
- 10.48550/arXiv.1702.08608 is OK
- 10.1111/j.1469-1809.1936.tb02137.x is OK
- 10.24432/C5XK51 is OK
- 10.1016/0095-0696(78)90006-2 is OK
- 10.1007/978-1-0716-1418-1 is OK
- 10.5281/zenodo.7359268 is OK
- 10.48550/arXiv.2001.10488 is OK
- 10.24432/C5DW2B is OK
- 10.1073/pnas.1901326117 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:

[jbytecode]

@sylvaticus, @gdalle

This is the review thread. Firstly, type

@editorialbot generate my checklist

to generate your own checklist. In that checklist, there are many check items. Whenever you complete the corresponding task, you can check off them.

Please write your comments as separate posts and do not modify your checklist descriptions.

The review process is interactive so you can always interact with the authors, reviewers, and the editor. You can also create issues and pull requests in the target repository. Please do mention this thread's URL in the issues so we can keep tracking what is going on out of our world.

Please do not hesitate to ask me about anything, anytime.

Thank you in advance!

[gdalle]

Review checklist for @gdalle

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/rikhuijzer/SIRUS.jl?
• [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 (@rikhuijzer) 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?

[gdalle]

and that is how you do it :sunglasses:

[sylvaticus]

Review checklist for @sylvaticus

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/rikhuijzer/SIRUS.jl?
• [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 (@rikhuijzer) 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?

[jbytecode]

@sylvaticus - it could may be of our editorial bot, could you please try it again?

[sylvaticus]

argh.. yep.. yust done it and worked.... I don't know why it didn't work the first time.. thanks...

[gdalle]

Just made a first pass, it is a really cool project with a very nice hand-holding documentation! Since I'm a bit picky, I opened a few issues on the repo, but hopefully they shouldn't be too hard to tackle. Well done @rikhuijzer!

[jbytecode]

@sylvaticus, @gdalle, @rikhuijzer - I want to thank you all for such a smooth reviewing and exemplary author-reviewer interaction in the thread and external issues on the target repository. Please do not hesitate to contact me if you get into any trouble.

[rikhuijzer]

Thank you for the compliment @jbytecode and thanks to the reviewers for finding various bugs and providing feedback on the project. I just wanted to let the editor and reviewers know that I appreciate the raised issues and am working on them, but am slower than I would like. Some PhD-related tasks randomly popped up, which keep me from sitting down and finding focus. Apologies for the delay from my side.

[rikhuijzer]

@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:

[rikhuijzer]

Thanks all for the patience. Above is a new version of the PDF. In summary, this updated PDF should solve many of the raised issues. We have described more commonly-used packages and how they related to SIRUS, as was raised in https://github.com/rikhuijzer/SIRUS.jl/issues/52. Furthermore, we have improved the example in the paper as well as in the documentation (https://sirus.jl.huijzer.xyz/dev/basic-example/), as was raised in https://github.com/rikhuijzer/SIRUS.jl/issues/54 and https://github.com/rikhuijzer/SIRUS.jl/issues/55. I'll keep working on the remaining issues, in particular https://github.com/rikhuijzer/SIRUS.jl/issues/51.

[rikhuijzer]

@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:

[rikhuijzer]

Issue https://github.com/rikhuijzer/SIRUS.jl/issues/51 has now been addressed as well. Let me know if there is anything else I can address.

[jbytecode]

@rikhuijzer - We have still two unresolved issues, right? Please ping us when you've done the fixing stuff with them and ping us again. Thank you in advance.

[gdalle]

Issue https://github.com/rikhuijzer/SIRUS.jl/issues/27 remains open but it is not blocking for me. Indeed, it hints at a bug on the regression part of the algorithm, but the classification part seems correct. I agree with the authors that publishing their implementation is valuable nonetheless, and may even lead to fixing the bug in question. I have checked the remaining boxes and opened a last issue for minor typos.

[sylvaticus]

Going to do the last check too..

[sylvaticus]

Fine for me.. just three very minor points:

• in the paper you still refer to class 1.0 instead of 1 ("then the patient will most likely survive (class == 1.0)"
• thank you that you cite my own machine learning toolkit (BetaML), but it is not necessary.. you can keep DecisionTree.jl as example of Decision Tree/ Random Forest package, they are way more optimized (although they don't accept missing nor unordered features)
• I would rewrite the sentence "The performance scores were taken from the GitHub Actions Job Summary124 for commit 5c87eda." to "The performance scores were taken from the SIRUS.jl test job that was run following commit 5c87eda using GitHub Actions."

[rikhuijzer]

@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:

[rikhuijzer]

@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:

[rikhuijzer]

Thank you @gdalle and @sylvaticus for all the constructive comments and suggestions. It greatly improved the quality of the paper and documentation. I have responded to all comments.

I hope @jbytecode now considers the paper suitable for publication in JOSS.

[rikhuijzer]

thank you that you cite my own machine learning toolkit (BetaML), but it is not necessary..

I appreciate your humility, @sylvaticus, but I think your project is a valuable mention. It was added it in response to https://github.com/rikhuijzer/SIRUS.jl/issues/52. Your paper is definitely part of the ML field in Julia.

[jbytecode]

@rikhuijzer - Before starting my editorial stuff I have to wait our reviewer's (@sylvaticus ) tasks to be completed and corresponding checkbox to be set.

[sylvaticus]

@jbytecode : Sorry, I did it yesterday but some checkboxes didn't activated (perhaps I did click too fast). Now, there should all be checked/set... (I verified the software example yesterday)

[jbytecode]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• [ ] Double check authors and affiliations (including ORCIDs)
• [ ] 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.
• [ ] Archive the release on Zenodo/figshare/etc and post the DOI here.
• [ ] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• [ ] Make sure that the license listed for the archive is the same as the software license.

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] Check that the archive title, author list, version tag, and the license are correct
• [x] Set archive 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
• [ ] Recommend acceptance with @editorialbot recommend-accept

[jbytecode]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.14569/IJACSA.2013.041105 is OK
- 10.1016/j.inffus.2019.12.012 is OK
- 10.1214/20-EJS1792 is OK
- 10.1007/s11749-016-0481-7 is OK
- 10.21105/joss.02704 is OK
- 10.1023/A:1010933404324 is OK
- 10.1145/2939672.2939785 is OK
- 10.48550/arXiv.2305.01582 is OK
- 10.48550/arXiv.1702.08608 is OK
- 10.1111/j.1469-1809.1936.tb02137.x is OK
- 10.24432/C5XK51 is OK
- 10.1016/0095-0696(78)90006-2 is OK
- 10.1007/978-1-0716-1418-1 is OK
- 10.5281/zenodo.8363803 is OK
- 10.5281/zenodo.7359268 is OK
- 10.48550/arXiv.2001.10488 is OK
- 10.21105/joss.00602 is OK
- 10.21105/joss.02849 is OK
- 10.1145/1273496.1273598 is OK
- 10.24432/C5DW2B is OK
- 10.1073/pnas.1901326117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@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:

[jbytecode]

@rikhuijzer - The paper and bibtex seem quite good. I have added a citation for Julia in the PR (https://github.com/rikhuijzer/SIRUS.jl/pull/63). Please review and merge. Ping me when you are done. Thank you in advance.

[jbytecode]

@rikhuijzer - The other things

• please create a tagged release in the repository
• use this tagged release to create a Zenodo archive. This archive page should match the paper title, the author list, their orchids, etc.
• Please report here the version and archive url.

thank you in advance.

[rikhuijzer]

Thank you for the instructions, @jbytecode. I have followed them together with https://joss.readthedocs.io/en/latest/editing.html#after-reviewers-recommend-acceptance.

This is the Zenodo link for the record with the right paper title and author list: https://zenodo.org/record/8398350.

DOI: 10.5281/zenodo.8398350 (https://doi.org/10.5281/zenodo.8398350) Version: 1.3.3

I hope I did everything correctly. Let me know if not. I'll also trigger a new PDF build to get the Julia citation (https://github.com/rikhuijzer/SIRUS.jl/pull/63) into the article proof:

[rikhuijzer]

@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:

[jbytecode]

@editorialbot set v1.3.3 as version

[editorialbot]

Done! version is now v1.3.3

[jbytecode]

@editorialbot set 10.5281/zenodo.8398350 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8398350

[jbytecode]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.14569/IJACSA.2013.041105 is OK
- 10.1016/j.inffus.2019.12.012 is OK
- 10.1214/20-EJS1792 is OK
- 10.1007/s11749-016-0481-7 is OK
- 10.21105/joss.02704 is OK
- 10.1023/A:1010933404324 is OK
- 10.1145/2939672.2939785 is OK
- 10.48550/arXiv.2305.01582 is OK
- 10.48550/arXiv.1702.08608 is OK
- 10.1111/j.1469-1809.1936.tb02137.x is OK
- 10.24432/C5XK51 is OK
- 10.1016/0095-0696(78)90006-2 is OK
- 10.1007/978-1-0716-1418-1 is OK
- 10.5281/zenodo.8363803 is OK
- 10.5281/zenodo.7359268 is OK
- 10.48550/arXiv.2001.10488 is OK
- 10.21105/joss.00602 is OK
- 10.21105/joss.02849 is OK
- 10.1145/1273496.1273598 is OK
- 10.24432/C5DW2B is OK
- 10.1073/pnas.1901326117 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[jbytecode]

@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: