[REVIEW]: Metasyn: Transparent Generation of Synthetic Tabular Data with Privacy Guarantees

[editorialbot]

Submitting author: @vankesteren (Erik-Jan van Kesteren)
Repository: https://github.com/sodascience/metasyn
Branch with paper.md (empty if default branch):
Version: v1.0.2
Editor: @crvernon
Reviewers: @PetrKorab, @misken
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/43fd4234e18bfd94b952aea35db8b883/status.svg)](https://joss.theoj.org/papers/43fd4234e18bfd94b952aea35db8b883)

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

@PetrKorab & @misken, 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 @crvernon 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 @misken

📝 Checklist for @PetrKorab

[editorialbot]

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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 1.90  T=0.08 s (1261.0 files/s, 292075.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              5              0              0          11376
Python                          40            931           1409           3146
JSON                             3              1              0            767
reStructuredText                28            746           1002            639
Markdown                         4            118              0            351
TOML                             5             48              3            243
TeX                              1             13              0            148
YAML                             5             20             23            144
SVG                              5              0              0             98
Jupyter Notebook                 1              0           1789             68
DOS Batch                        1              8              1             26
make                             1              6              7             11
Dockerfile                       1              6              7              8
-------------------------------------------------------------------------------
SUM:                           100           1897           4241          17025
-------------------------------------------------------------------------------

Commit count by author:

    95	qubixes
    34	Erik-Jan van Kesteren
    29	Samuwhale
    26	Samuel
    13	Raoul Schram

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2230

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.7697217 is OK
- 10.18637/jss.v059.i10 is OK

MISSING DOIs

- No DOI given, and none found for title: ONS methodology working paper series number 16—Syn...
- No DOI given, and none found for title: Differential privacy
- No DOI given, and none found for title: Statistical disclosure control
- No DOI given, and none found for title: k-anonymity: A model for protecting privacy
- No DOI given, and none found for title: Guidelines for Output Checking. Eurostat
- 10.29012/jpc.v1i2.570 may be a valid DOI for title: Differential privacy for statistics: What we know ...
- 10.1007/bf02985802 may be a valid DOI for title: The elements of statistical learning: data mining,...
- 10.1007/978-1-4612-0919-5_38 may be a valid DOI for title: Information theory and an extension of the maximum...
- 10.1002/wics.199 may be a valid DOI for title: The Bayesian information criterion: background, de...
- No DOI given, and none found for title: synthpop: Bespoke creation of synthetic data in R
- No DOI given, and none found for title: Simulation of synthetic complex data: The R packag...
- No DOI given, and none found for title: Datasynthesizer: Privacy-preserving synthetic data...
- No DOI given, and none found for title: To democratize research with sensitive data, we sh...

INVALID DOIs

- None

[crvernon]

👋 @vankesteren, @PetrKorab, and @misken - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #7099 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[editorialbot]

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

[crvernon]

👋 @vankesteren - please reduce the length of your paper to around 1000 words. Thanks!

[misken]

Review checklist for @misken

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 https://github.com/sodascience/metasyn?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@vankesteren) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

[vankesteren]

👋 @vankesteren - please reduce the length of your paper to around 1000 words. Thanks!

Short version of the paper is on its way, will commit this week!

[vankesteren]

Paper has now been shortened!

[PetrKorab]

Review checklist for @PetrKorab

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 https://github.com/sodascience/metasyn?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@vankesteren) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

[PetrKorab]

@vankesteren please, update readme (#317). Thanks.

[qubixes]

@PetrKorab Thanks for spotting the broken link! I have fixed it now.

[PetrKorab]

@vankesteren Please be less technical in the second part of the paper. Instead, add examples and use cases across disciplines. Thanks!  (#321).

[vankesteren]

Thanks all for the progress on this review. Just a heads-up: I'll be on leave for the coming two weeks so I'll not be able to respond. Will do my best to pick this up soon after!

[PetrKorab]

@vankesteren Test folder contains python codes and a test titanic dataset. Please, add well-documented automated tests (Github Action, CI..) in line with the JOOS guidelines. Please, also prepare the tests for at least one other "real-world" dataset, except the titanic one. Thanks! #326

[crvernon]

👋 @vankesteren, @PetrKorab, and @misken - Just checking in to see how things are going with this review. Could you each post an update to where you are currently in this review process? Thanks!

[vankesteren]

Hey @crvernon thanks for asking;

Until now, we have responded to several issues that have come out of this review (e.g., sodascience/metasyn#317, sodascience/metasyn#324) and we are working on changes based on the other issues. For example, we have included a medical example dataset in the package (sodascience/metasyn#330) as a partial response to sodascience/metasyn#321 and sodascience/metasyn#326.

I have gotten in a bit of a time-crunch with teaching, but I'm committed to update the paper itself over the next weeks to include more examples and fewer technical details, for which we can refer to the documentation. In the meantime, we are also slightly updating the documentation to have a better flow through these technical details.

In summary, I haven't responded much over the past weeks but we have been hard at work! Let me know if you require something additional.

[PetrKorab]

@vankesteren The medical dataset is ok, but for the reviewer, it is complicated to evaluate Metasyn without well-documented GitHub actions or unit tests in other CI. Please place everything into a single folder. Thanks!

[vankesteren]

@PetrKorab I have now left a comment on your main issue on this, here: sodascience/metasyn#326 (comment)

We have also updated the paper, making it more legible and with better examples based on reviewer feedback, while keeping it as short as possible. The new paper is available here: https://github.com/sodascience/metasyn/blob/develop/docs/paper/paper.pdf

We are currently in the process of updating the documentation once more and then we will release Metasyn version 1.1! I will ping this thread when we do our release, that would be a good moment to have another "round" of reviews (where hopefully we will check all the boxes 😉)

[PetrKorab]

@vankesteren Thanks for adding the tests, domain datasets and updating the paper!

[vankesteren]

@crvernon @misken @PetrKorab We have now released version 1.1! This is a good time to get back to the review process 😄

[misken]

In the left sidebar for the updated paper, the links to the Review and Repository aren't pointing to the correct places (or I'm missing something).

…

On Fri, Nov 15, 2024 at 6:28 AM Erik-Jan van Kesteren < ***@***.***> wrote: @PetrKorab <https://github.com/PetrKorab> I have now left a comment on your main issue on this, here: sodascience/metasyn#326 (comment) <sodascience/metasyn#326 (comment)> We have also updated the paper, making it more legible and with better examples based on reviewer feedback, while keeping it as short as possible. The new paper is available here: https://github.com/sodascience/metasyn/blob/develop/docs/paper/paper.pdf We are currently in the process of updating the documentation once more and then we will release Metasyn version 1.1! I will ping this thread when we do our release, that would be a good moment to have another "round" of reviews (where hopefully we will check all the boxes 😉) — Reply to this email directly, view it on GitHub <#7099 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAFBGPXYEBQXZYA3UAHJUPL2AXLEPAVCNFSM6AAAAABMNGGOAKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINZYGYYTANRRGA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[misken]

My checklist is complete. I've used the software locally but did not do a dev install to run the tests - I'm an Anaconda user and ran into some issues. I'm fine with recommending publication at this point.

[PetrKorab]

For me, as well. I now also recommend the paper for publication.

[crvernon]

@editorialbot generate pdf

[crvernon]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1007/11787006_1 is OK
- 10.1002/9781118348239 is OK
- 10.1142/S0218488502001648 is OK
- 10.1007/978-0-387-84858-7 is OK
- 10.1002/wics.199 is OK
- 10.5281/zenodo.7697217 is OK
- 10.18637/jss.v059.i10 is OK
- 10.18637/jss.v074.i11 is OK
- 10.18637/jss.v079.i10 is OK
- 10.1145/3085504.3091117 is OK
- 10.1016/j.patter.2024.101049 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: ONS methodology working paper series number 16—Syn...
- No DOI given, and none found for title: Guidelines for the checking of output based on mic...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

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

[vankesteren]

@crvernon is there anything I can do?

[crvernon]

@vankesteren no, I've just been tied up in meetings from dawn till dusk this week. I'll get you some feedback ASAP. Thanks!

[vankesteren]

Oh that does not sound particularly fun... No worries, we can wait!