[PRE REVIEW]: multipers: Multiparameter Persistence for Machine Learning

[editorialbot]

Submitting author: @DavidLapous (David Loiseaux)
Repository: https://github.com/DavidLapous/multipers
Branch with paper.md (empty if default branch):
Version: v2.0.0
Editor: @RMeli
Reviewers: @yossibokorbleile, @peekxc
Managing EiC: Chris Vernon

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/73e33046702c27dbb1cc76841e7d5fba"><img src="https://joss.theoj.org/papers/73e33046702c27dbb1cc76841e7d5fba/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/73e33046702c27dbb1cc76841e7d5fba/status.svg)](https://joss.theoj.org/papers/73e33046702c27dbb1cc76841e7d5fba)

Author instructions

Thanks for submitting your paper to JOSS @DavidLapous. Currently, there isn't a JOSS editor assigned to your paper.

@DavidLapous if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.21 s (957.4 files/s, 313614.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                   115           5233           6257          33181
Python                          46           1346           1994           7478
Cython                          13            295            609           1455
Jupyter Notebook                13              0           5445            929
XML                              1              0              0            693
TeX                              2             41              0            583
Markdown                         2             40              0            156
YAML                             2             12             31            146
reStructuredText                 3             54             74             42
JSON                             1              0              0             30
TOML                             1              1              0             14
make                             1              6              7             10
Bourne Shell                     2              0              0              9
-------------------------------------------------------------------------------
SUM:                           202           7028          14417          44726
-------------------------------------------------------------------------------

Commit count by author:

   144	David Loiseaux
    46	DavidLapous

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1321

🔴 Failed to discover a Statement of need section in paper

[editorialbot]

License info:

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

[editorialbot]

⚠️ An error happened when generating the pdf.

[editorialbot]

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

OK DOIs

- 10.48550/arXiv.2203.14289 is OK
- 10.21105/joss.05022 is OK
- 10.1137/20M1353605 is OK
- 10.1137/1.9781611977561.ch3 is OK
- 10.1007/978-3-662-44199-2_28 is OK
- 10.4230/LIPIcs.SoCG.2022.19 is OK

MISSING DOIs

- No DOI given, and none found for title: Euler Characteristic Tools For Topological Data An...
- 10.1137/1.9781611977912.173 may be a valid DOI for title: Delaunay Bifiltrations of Functions on Point Cloud...
- No DOI given, and none found for title: GRIL: A \2\-Parameter Persistence Based Vectorizat...
- No DOI given, and none found for title: GUDHI
- No DOI given, and none found for title: Fast, Stable and Efficient Approximation of Multi-...
- No DOI given, and none found for title: A Framework for Fast and Stable Representations of...
- 10.1137/1.9781611976472.16 may be a valid DOI for title: Fast Minimal Presentations of Bi-graded Persistenc...
- No DOI given, and none found for title: Multiparameter Persistence Landscapes
- No DOI given, and none found for title: Stable and Consistent Density-Based Clustering via...
- No DOI given, and none found for title: POT: Python Optimal Transport
- No DOI given, and none found for title: Kernel Operations on the GPU, with Autodiff, witho...
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: Interactive Visualization of 2-D Persistence Modul...
- No DOI given, and none found for title: Stable Vectorization of Multiparameter Persistent ...
- No DOI given, and none found for title: Scikit-Learn: Machine Learning in Python
- 10.1137/22m1489150 may be a valid DOI for title: On the Stability of Multigraded Betti Numbers and ...
- No DOI given, and none found for title: Differentiability and Convergence of Filtration Le...

INVALID DOIs

- None

[crvernon]

@editorialbot invite @RMeli as editor

👋 @RMeli - would you like to take this one on as editor?

[editorialbot]

Invitation to edit this submission sent!

[DavidLapous]

if you have any suggestions for potential reviewers then please mention them here in this thread

There are a few JOSS papers in Topological Data Analysis (TDA)-Machine Learning (ML) in Python, whose authors / previous reviewer could be possible reviewers:

• Giotto : https://joss.theoj.org/papers/10.21105/joss.04846
• Persistable : https://joss.theoj.org/papers/10.21105/joss.05022 (Although Luis Scoccola could have a conflict of interest)
• Ripser: https://joss.theoj.org/papers/10.21105/joss.00925

Also, from the list of reviewer having TDA,ML, python as keywords,

• Yossi Bokor
• Matt Piekenbrock
• EduPH
• sauln
• leotrs

seem to be good candidates.

MISSING DOIs

I've updated the DOIs I could, but it seems that, e.g., NeurIPS and JMLR do not provide DOIs. Should I do something about it ?

⚠️ An error happened when generating the pdf

From the logs, the paper.jats file create some conflict and some pictures were missing; I've fixed that.

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

@DavidLapous for the references, it is OK to not have a DOI for references that do not provide them. All good.

[crvernon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.48550/arXiv.2203.14289 is OK
- 10.21105/joss.05022 is OK
- 10.1137/20M1353605 is OK
- 10.48550/arxiv.2303.14040 is OK
- 10.1137/1.9781611977561.ch3 is OK
- 10.1137/1.9781611977912.173 is OK
- 10.1007/978-3-662-44199-2_28 is OK
- 10.48550/arXiv.2206.02026 is OK
- 10.1137/1.9781611976472.16 is OK
- 10.48550/arXiv.2005.09048 is OK
- 10.48550/arXiv.1512.00180 is OK
- 10.4230/LIPIcs.SoCG.2022.19 is OK
- 10/gtt7dq is OK

MISSING DOIs

- No DOI given, and none found for title: GRIL: A \2\-Parameter Persistence Based Vectorizat...
- No DOI given, and none found for title: GUDHI
- No DOI given, and none found for title: A Framework for Fast and Stable Representations of...
- No DOI given, and none found for title: Multiparameter Persistence Landscapes
- No DOI given, and none found for title: POT: Python Optimal Transport
- No DOI given, and none found for title: Kernel Operations on the GPU, with Autodiff, witho...
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: Stable Vectorization of Multiparameter Persistent ...
- No DOI given, and none found for title: Scikit-Learn: Machine Learning in Python
- No DOI given, and none found for title: Differentiability and Convergence of Filtration Le...

INVALID DOIs

- None

[RMeli]

@editorialbot assign @RMeli as editor

[editorialbot]

Assigned! @RMeli is now the editor

[RMeli]

Hi @ulupo 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6749.

The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages, with a formal peer-review process that is designed to improve the quality of the software submitted.

Thank you in advance!

[RMeli]

Hi @yossibokor 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6749.

The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages, with a formal peer-review process that is designed to improve the quality of the software submitted.

Thank you in advance!

[RMeli]

Hi @lmcinnes 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6749.

The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages, with a formal peer-review process that is designed to improve the quality of the software submitted.

Thank you in advance!

[yossibokorbleile]

Hi @RMeli

Sure thing.

[RMeli]

@editorialbot add @yossibokorbleile as reviewer

Thank you!

[editorialbot]

@yossibokorbleile added to the reviewers list!

[ulupo]

Thank you @RMeli for your consideration! Unfortunately, I won't be able to do a good job due to a convergence of commitments these days. I'll have to decline, sorry! Nice work, though!

[RMeli]

No worries @ulupo, thank you for coming back to me.

[lmcinnes]

Thanks @RMeli for reaching out. I would like to take this on -- it looks like a great package. Unfortunately I have a lot of commitments right now and would not be able to get to a review in a timely fashion. Sorry!

[RMeli]

I totally understand @lmcinnes, thank you for getting back to me.

[RMeli]

Hi @peekxc 👋

Would you be interested in reviewing this submission for JOSS (Journal of Open Source Software)?

You can find more information about the submission at the top of this Github issue #6749.

The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages, with a formal peer-review process that is designed to improve the quality of the software submitted.

Thank you in advance!

[peekxc]

@RMeli I would be interested in reviewing this

[RMeli]

@editorialbot add @peekxc as reviewer

That's great to hear, thank you!

[editorialbot]

@peekxc added to the reviewers list!

[RMeli]

Thank you @yossibokorbleile and @peekxc for agreeing to review for JOSS. I'll soon start the review process, closing this PRE-REVIEW issue and opening a REVIEW issue for the actual review.

If it's your first time reviewing for JOSS, please have a look at the following pages:

• Reviewing for JOSS
• Review criteria
• Review checklist

A good way to review is to open issues in the software repository, and link them to the (soon-to-be-open) review issue.

Do not hesitate to ping me with any questions you might have.

[RMeli]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6773.