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[REVIEW]: Salt: Multimodal Multitask Machine Learning for High Energy Physics #7217

Open editorialbot opened 2 months ago

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@samvanstroud<!--end-author-handle-- (Samuel Van Stroud) Repository: https://github.com/umami-hep/salt Branch with paper.md (empty if default branch): Version: v0.5 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: !--reviewers-list-->@divijghose<!--end-reviewers-list-- Archive: Pending

Status

status

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HTML: <a href="https://joss.theoj.org/papers/6a39e80165a9b936710c8a345604a0ff"><img src="https://joss.theoj.org/papers/6a39e80165a9b936710c8a345604a0ff/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6a39e80165a9b936710c8a345604a0ff/status.svg)](https://joss.theoj.org/papers/6a39e80165a9b936710c8a345604a0ff)

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

@tkoyama010 & @divijghose, 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 @arfon 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 @divijghose

📝 Checklist for @tkoyama010

editorialbot commented 2 months ago

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 commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (1356.9 files/s, 187348.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          67           1776           2228           7566
YAML                            41            314            130           3432
Markdown                        17            720              0           1773
TeX                              1             43             30            397
Bourne Shell                     5             21             38             48
TOML                             1             10              0             47
JSON                             2              0              0             33
Dockerfile                       1              8              8             18
-------------------------------------------------------------------------------
SUM:                           135           2892           2434          13314
-------------------------------------------------------------------------------

Commit count by author:

   150  Samuel Van Stroud
    41  Sam Van Stroud
    21  Nikita Ivvan Pond
    18  Jackson Barr
     9  Sam
     8  Philipp Gadow
     6  Dmitrii Kobylianskii
     5  Johannes Michael Wagner
     4  Andrius Vaitkus
     4  Manuel Guth
     4  Maxence Draguet
     4  Nicholas Luongo
     4  Wei Sheng Lai
     3  Diptaparna Biswas
     3  Emil Haines
     3  Ivan Oleksiyuk
     2  Giovanni Rupnik Boero
     2  Mathias Josef Backes
     2  Matthew Leigh
     2  Sebastien Rettie
     1  Chris Pollard
     1  Ema Maricic
     1  Jackson Carl Burzynski
     1  Lucio Derin
     1  Martino Tanasini
     1  Neelam Kumari
     1  Nikita I Pond
     1  Osama Karkout
     1  Paul Philipp Gadow
     1  Wouter Max Morren
     1  jdegens
     1  samvanstroud
editorialbot commented 2 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1088/1748-0221/3/08/S08001 is OK
- 10.1088/1748-0221/3/08/S08003 is OK
- 10.5281/ZENODO.6467676 is OK
- 10.5281/ZENODO.7806395 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1146/annurev-nucl-101917-021019 is OK
- 10.3390/app122010574 is OK
- 10.1088/1748-0221/15/12/p12012 is OK
- 10.1103/physrevd.101.056019 is OK
- 10.5281/ZENODO.6619768 is OK
- 10.1038/nature14539 is OK
- 10.5281/zenodo.3828935 is OK
- 10.48550/arXiv.1706.03762 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The ATLAS Collaboration Software and Firmware
- No DOI given, and none found for title: Python 3 Reference Manual
- No DOI given, and none found for title: Style Guide for Python Code
- No DOI given, and none found for title: YAML Ain’t Markup Language (YAML™) version 1.2
- No DOI given, and none found for title: Setuptools
- No DOI given, and none found for title: Flake8
- No DOI given, and none found for title: Black
- No DOI given, and none found for title: pytest 7.3
- No DOI given, and none found for title: MkDocs
- No DOI given, and none found for title: Sphinx
- No DOI given, and none found for title: Docker: lightweight linux containers for consisten...
- No DOI given, and none found for title:  TensorFlow: Large-Scale Machine Learning on Heter...
- No DOI given, and none found for title: Hierarchical Data Format, version 5
- No DOI given, and none found for title: ATLAS flavour-tagging algorithms for the LHC Run 2...
- No DOI given, and none found for title: Particle Transformer for Jet Tagging
- No DOI given, and none found for title: Adam: A Method for Stochastic Optimization
- No DOI given, and none found for title: Deep Sets
- No DOI given, and none found for title: A Unified Approach to Interpreting Model Predictio...
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: Graph Neural Network Jet Flavour Tagging with the ...
- No DOI given, and none found for title: Transformer Neural Networks for Identifying Booste...
- No DOI given, and none found for title: ONNX: Open Neural Network Exchange
- No DOI given, and none found for title: Umami: A Python toolkit for jet flavour tagging

❌ MISSING DOIs

- 10.1163/2214-8647_dnp_e612900 may be a valid DOI for title: Keras

❌ INVALID DOIs

- None
editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1126

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

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

arfon commented 2 months ago

@tkoyama010, @divijghose – 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. Please create your checklist typing: 

@editorialbot generate my checklist

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 https://github.com/openjournals/joss-reviews/issues/7217 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 commented 2 months ago

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

divijghose commented 2 months ago

Review checklist for @divijghose

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

tkoyama010 commented 2 months ago

Review checklist for @tkoyama010

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

tkoyama010 commented 2 months ago

The documentation shows how to install this library directly from the repository. Is there a way to install from PyPI and conda-forge?

samvanstroud commented 2 months ago

Hi @tkoyama010! We don't currently offer this since there hasn't been a clear need from users, but it's certainly something we could add if you think it would be useful. Thanks

tkoyama010 commented 2 months ago

Hi @tkoyama010! We don't currently offer this since there hasn't been a clear need from users, but it's certainly something we could add if you think it would be useful. Thanks

Awesome. I am registering with them is recommended as it lowers the psychological hurdle for users.

samvanstroud commented 1 month ago

Thanks @tkoyama010. It's now available on PyPI: https://pypi.org/project/salt-ml/

tkoyama010 commented 1 month ago

Last week, I was diagnosed with ulcerative colitis by a doctor. I will be taking some time to recover, so my responses will be significantly delayed. I will return to the community when I am recover. If it is not possible to extend the review deadline, I would be very sorry, but I would like to be removed from the reviewer list.

samvanstroud commented 1 month ago

@tkoyama010 I'm very sorry to hear that - wishing you a swift recovery and please don't feel any pressure whatsoever with the review. I agree it would be best to find someone else to take a look at this so it's not hanging over you. I really appreciate the feedback that you gave so far.

arfon commented 1 month ago

No problem at all @tkoyama010 – wishing you a speedy recovery here! I'll go ahead and remove you as a reviewer and work with @samvanstroud to find an alternative.

arfon commented 1 month ago

@editorialbot remove @tkoyama010 as reviewer

editorialbot commented 1 month ago

@tkoyama010 removed from the reviewers list!

samvanstroud commented 2 weeks ago

@editorialbot generate preprint

editorialbot commented 2 weeks ago

:page_facing_up: Preprint file created: Find it here in the Artifacts list :page_facing_up:

arfon commented 2 weeks ago

@pikarpov-lanl @asogaard – would you be willing to review this submission for JOSS? The submission under consideration is Salt: Multimodal Multitask Machine Learning for High Energy Physics

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, and past papers published in JOSS, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

asogaard commented 2 weeks ago

Hi @arfon, Thanks for considering me for reviewing this paper. I very much appreciated the JOSS review process myself. However, as I have left academia, I think you'd be better off finding a reviewer who is more active in the field and can provide a better review. Best, Andreas