[REVIEW]: A Java Library for Itemset Mining with Choco-solver

[editorialbot]

Submitting author: !--author-handle-->@ChaVer<!--end-author-handle-- (Charles Vernerey) Repository: https://gitlab.com/chaver/choco-mining Branch with paper.md (empty if default branch): Version: v1.0.2 Editor: !--editor-->@danielskatz<!--end-editor-- Reviewers: @skadio, @jgFages Archive: 10.5281/zenodo.8263971

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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

@skadio & @jgFages, 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 @danielskatz 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 @jgFages

📝 Checklist for @skadio

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (1302.5 files/s, 83740.1 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Java                            102            800           1336           4257
SVG                               2              1             52            284
Maven                             1              8              6            193
TeX                               1              0              0            166
Markdown                          3             57              0            161
Bourne Again Shell                1              0              0              2
Bourne Shell                      1              0              0              2
JSON                              2              0              0              2
make                              1              0              0              2
--------------------------------------------------------------------------------
SUM:                            114            866           1394           5069
--------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1388

[editorialbot]

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

OK DOIs

- 10.1007/978-3-319-66158-2_34 is OK
- 10.1137/1.9781611975673.15 is OK
- 10.24963/ijcai.2019/149 is OK
- 10.1016/j.artint.2011.05.002 is OK
- 10.24963/ijcai.2022/261 is OK
- 10.21105/joss.04708 is OK
- 10.1007/978-3-030-67658-2_3 is OK
- 10.1093/bioinformatics/btn490 is OK
- 10.3390/e18050164 is OK
- 10.1016/j.artint.2015.04.003 is OK
- 10.1007/978-3-319-44953-1_22 is OK
- 10.1002/widm.1207 is OK
- 10.14257/ijhit.2013.6.6.30 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:

[danielskatz]

@skadio and @jgFages - Thanks for agreeing to review this submission. This is the review thread for the paper. All of our communications will happen here from now on.

As you can see above, you each should use the command @editorialbot generate my checklist to create your review checklist. @editorialbot commands need to be the first thing in a new comment.

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#5654 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 reviews to be completed within about 2-4 weeks. Please let me know if either of you require some more time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@danielskatz) if you have any questions/concerns.

[danielskatz]

reminder to self: @skadio said when accepting this review "I might take some time (~8 weeks)."

[jgFages]

Review checklist for @jgFages

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://gitlab.com/chaver/data-mining?
• [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 (@ChaVer) 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?

[jgFages]

Data Mining with Constraint Programming is indeed an interesting topic of Research. The paper is well written, and well illustrated. The literature review is good and the tool is well motivated.

I have however a few remarks regarding both the paper and the software :

• I recommend to follow Choco Solver implementation standards, by : -- Prefixing propagators by Prop, as it is done in Choco Solver (CoverSize -> PropCoverSize) to emphasize the difference between a constraint and a propagator -- Regrouping these constraints within a Factory, that would be the main entry point of the library -- Keeping the post() instruction at the end of the line : model.arithm(...).post() is more common than model.post(model.arithm(...))
• More generally, as the software name includes Choco and therefore sounds "official" from the chocoteam (see https://github.com/chocoteam/), I would recommend to have to some kind of code review with @cprudhom. If he is a co-worker, I guess it would be easy to organize. Maybe the project should be hosted in that repo.
• What is the software license ?

Minor : data mining to Constraint Programming -> Data Mining to Constraint Programming

[skadio]

Review checklist for @skadio

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://gitlab.com/chaver/data-mining?
• [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 (@ChaVer) 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?

[skadio]

@chaver congratulations on your IJCAI'22 paper and turning it into a library.

This submission is clearly relevant to JOSS and almost there in terms of publication, with a few suggestions that needs to be accounted for:

• typo in summary: "task ," remove extra space

• The readme needs a major update. Luckily you have all that information in the WIKI and the Paper

The current readme is not in sync with the wiki.

A user looking at the Readme would not understand that this is a "library" which was my main confusion initially. It almost seems like a standalone command line tool, which is not the case here, it is indeed a library. Even worse, it first looked like a repo to me to reproduce the experiments from the IJCAI'22 paper.

Compared to that; the Wiki does a much better job. https://gitlab.com/chaver/data-mining/-/wikis/home

My recommendation is creating a lean / subset of the Wiki to replace the current Readme. You can cite the IJCAI paper at top but push the commentary about reproducing experiments to the bottom (or better, leave in a section in the detailed Wiki).

My major concern about the paper is: I am not sure if an outsider would immediately understand what are these constraints are. Currently the in the Readme, the constraints are listed under "Installation" which is not right. My recommendation is: create a specific section in the README for this and mimic what's in the Wiki. I almost tempted to say use the Wiki as the Readme.

The paper does an adequate job of description the tasks (like, what is skypattern mining) but the Readme and Wiki don't do that.

My overall comment is:

• We need to clearly describe the Constraints
• We need to clearly describe the Tasks

where the ultimate goal is, once this is published in JOSS, an informed outsider (not a pattern mining expert) can leverage your library. You have all this material across the Paper, Readme, and Wiki but need to refresh the Readme and Wiki with a lens to cater to an outsider. The example in the paper is great so I would highly suggest adding a "Quick Start Example" to the very top of the README.

• state-of-the-field + references: please also mention the Seq2Pat library which is immediately relevant for declarative (sequential) pattern mining cite its relevant references from AI Mag'23 and AAAI'22. You might also consider citing the dichotomic pattern mining framework from Frontiers'22. These are listed here https://github.com/fidelity/seq2pat#citation

• I would also argue for taking that paper folder "outside" of this library. You can have your reproducibility repo in standalone and use your own library from there to show/reproduce the results. Then, you can link to that paper repo from the references here. As a "user" of the "library" I am not immediately interested in paper reproducing scripts. Notice also, down the road, your reproducibility scripts needs to stay identical whereas the library will move.

Hope this helps you improve your submission.

Serdar

[skadio]

Happy to take another quick look once you update the library

[ChaVer]

@editorialbot commands

[editorialbot]

Hello @ChaVer, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[ChaVer]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/978-3-319-66158-2_34 is OK
- 10.1137/1.9781611975673.15 is OK
- 10.24963/ijcai.2019/149 is OK
- 10.1016/j.artint.2011.05.002 is OK
- 10.24963/ijcai.2022/261 is OK
- 10.21105/joss.04708 is OK
- 10.1007/978-3-030-67658-2_3 is OK
- 10.1093/bioinformatics/btn490 is OK
- 10.3390/e18050164 is OK
- 10.1016/j.artint.2015.04.003 is OK
- 10.1007/978-3-319-44953-1_22 is OK
- 10.1002/widm.1207 is OK
- 10.14257/ijhit.2013.6.6.30 is OK

MISSING DOIs

- 10.1609/aaai.v36i11.21542 may be a valid DOI for title: Seq2Pat: Sequence-to-Pattern Generation for Constraint-based Sequential Pattern Mining
- 10.3389/frai.2022.868085 may be a valid DOI for title: Dichotomic Pattern Mining Integrated with Constraint Reasoning for Digital Behaviour Analyses

INVALID DOIs

- https://doi.org/10.1002/aaai.12081 is INVALID because of 'https://doi.org/' prefix

[ChaVer]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1007/978-3-319-66158-2_34 is OK
- 10.1137/1.9781611975673.15 is OK
- 10.24963/ijcai.2019/149 is OK
- 10.1016/j.artint.2011.05.002 is OK
- 10.24963/ijcai.2022/261 is OK
- 10.21105/joss.04708 is OK
- 10.1007/978-3-030-67658-2_3 is OK
- 10.1093/bioinformatics/btn490 is OK
- 10.3390/e18050164 is OK
- 10.1016/j.artint.2015.04.003 is OK
- 10.1007/978-3-319-44953-1_22 is OK
- 10.1002/widm.1207 is OK
- 10.14257/ijhit.2013.6.6.30 is OK
- 10.1002/aaai.12081 is OK
- 10.1609/aaai.v36i11.21542 is OK
- 10.3389/frai.2022.868085 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[ChaVer]

@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:

[ChaVer]

Dear reviewers,

Thank you for your valuable comments and suggestions for improving both the paper and the library.

@jgFages :

• We have carefully considered your observations concerning the implementation standards of Choco Solver and made the necessary updates to the library accordingly.
• The software license of the library is MIT, which can be verified at the following link: https://gitlab.com/chaver/data-mining/-/blob/master/LICENSE.txt.
• As for the potential code review with Charles Prudhomme and the possibility of hosting the library in the Choco Solver repository, we will promptly discuss this matter with him.

@skadio :

• We have made revisions to the README to accurately represent Choco-Mining as a library rather than a repository for reproducing IJCAI experiments.
• A clear and comprehensive description of the constraints along with their associated tasks has been provided in the README.
• We have included an illustrative example in the README to demonstrate the proper utilization of the library.
• References to the Seq2Pat library have been included both in the README and the paper, specifically in the "CP and Pattern Mining" section.

[skadio]

@ChaVer thank you for the updates! The readme is much improved now, and better reflects the power of the tool to an interested user now. Same for the manuscript.

My only final comment would the order of sections in the readme. Currently, it starts with the Architecture, Installation, and then the Illustrative Example, and Documents. Why not bring the Example to the top? So in my mind, you have the intro (as a reader I am thinking, what does this tool do?), the example (show me how it looks), installation (example is cool, how can I use this?), and documentation (where do I go to with questions and more details). Small change, but I think it would help you.

@danielskatz this is good to go from my side.

[danielskatz]

@jgFages - I look forward to your thoughts when you get a chance, and thanks to @skadio for yours

[jgFages]

@ChaVer Thank you for your answer and for the good work.

There is still one propagator to rename : Overlap -> PropOverlap.

Also the library is named Choco-Mining but the project repo and artifact is data-mining, which can be confusing. I would suggest to rename it choco-mining (maybe after the discussion with @cprudhom).

[ChaVer]

@skadio I moved the illustrative example to the top of the README as suggested. Thanks for your help!

@jgFages:

• Regarding the Overlap propagator, I suggest not changing its name since it is both a propagator and a solution monitor (used to filter out non-diverse patterns in the history). Similar to the ParetoMaximizer class in Choco Solver, I think it makes more sense not to add the "Prop" at the beginning.
• The name "data-mining" is indeed confusing, I will rename both the repository and the artifact with the approval of @cprudhom.

[danielskatz]

👋 @skadio and @jgFages - Any comments on this? I see that both of you have complete checklists, which might mean that you are satisfied with this to be accepted, but I would appreciate if you could confirm this, or let me know what else you think is needed.

[danielskatz]

@ChaVer - if you are changing the repo name, please tell me here

[jgFages]

Regarding the review process it is fine on my side. I just don't know whether or not we should wait for the decision regarding the repo name / artifact name (I guess we should).

Additionnal remark for @ChaVer : regarding the Overlap, I get your point, but then I have a few suggestions :

• creating a Constraint class "Overlap" to handle the solution monitor part (data access, storage and updates) so that the propagator remains "pure". This would simplify models : the unique entrypoint for the user would be the ConstraintFactory.
• pluging the monitor automatically upon creation (to prevent the user from forgetting it)

[skadio]

@danielskatz confirm that the submission is good to go from my end!

[ChaVer]

I agree with @jgFages that we should wait for the decision on the repo/artifact name before completing the review process. Regarding the overlap constraint, I think your idea is very relevant, so I have updated the code accordingly. Now the user can simply invoke the constraint with the following block of code: Overlap overlap = ConstraintFactory.overlap(database, x, jmax, theta); overlap.post() The monitor is automatically plugged to the solver during the Overlap object creation. The user can retrieve the history of itemsets after solving the model with this line of code: List<int[]> itemsets = overlap.getItemsetsHistory();

[danielskatz]

ok, I'll keep waiting until there's a decision on the possible name change

[danielskatz]

@ChaVer - any news on the name?

[ChaVer]

@danielskatz I got a positive answer from @cprudhom so I renamed the repository and the projet artifact to choco-mining. The new repo url is https://gitlab.com/chaver/choco-mining.

[danielskatz]

@editorialbot set https://gitlab.com/chaver/choco-mining as repository

[editorialbot]

Done! repository is now https://gitlab.com/chaver/choco-mining

[danielskatz]

@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:

[danielskatz]

@ChaVer - I think this change has been made. Does anything in the paper need to change?

[ChaVer]

@danielskatz the paper does not need to change, I think that we can go ahead, thank you !

[danielskatz]

@ChaVer - At this point could you:

• 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. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with proofreading and then recommending acceptance of the submission.

[ChaVer]

@danielskatz :

• The tagged release of the software is available at https://gitlab.com/chaver/choco-mining/-/releases/v1.0.2 and the version tag is v1.0.2
• The doi of the archive of the reviewed software in Zenodo is 10.5281/zenodo.8263971

[danielskatz]

@editorialbot set v1.0.2 as version

[editorialbot]

Done! version is now v1.0.2

[danielskatz]

@editorialbot set 10.5281/zenodo.8263971 as archive

[editorialbot]

That doesn't look like a valid DOI value

[danielskatz]

@ChaVer - https://doi.org/10.5281/zenodo.8263971 does seem to work. Can you share the URL to the archive so that I can take a look at it that way for now?

[ChaVer]

@danielskatz the url of the archive is https://zenodo.org/record/8263971

[danielskatz]

I guess there's something slow in zenodo/datacite today - I'll check again in a few hours

[danielskatz]

@editorialbot set 10.5281/zenodo.8263971 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8263971