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

[editorialbot]

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: Pending Reviewers: Pending Managing EiC: Kyle Niemeyer

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (1417.1 files/s, 187171.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          65           1630           2014           6791
YAML                            40            298            101           3310
Markdown                        17            716              0           1753
TeX                              1             43             30            397
TOML                             1             10              0             47
Bourne Shell                     4             20             37             45
JSON                             2              0              0             30
Dockerfile                       1              7              7             16
-------------------------------------------------------------------------------
SUM:                           131           2724           2189          12389
-------------------------------------------------------------------------------

Commit count by author:

   141  Samuel Van Stroud
    40  Sam Van Stroud
    16  Jackson Barr
    14  Nikita Ivvan Pond
     9  Sam
     8  Philipp Gadow
     6  Dmitrii Kobylianskii
     4  Andrius Vaitkus
     4  Johannes Michael Wagner
     4  Manuel Guth
     4  Maxence Draguet
     3  Diptaparna Biswas
     3  Wei Sheng Lai
     2  Emil Haines
     2  Ivan Oleksiyuk
     2  Sebastien Rettie
     1  Chris Pollard
     1  Ema Maricic
     1  Giovanni Rupnik Boero
     1  Martino Tanasini
     1  Mathias Josef Backes
     1  Matthew Leigh
     1  Nicholas Luongo
     1  Nikita I Pond
     1  Osama Karkout
     1  Paul Philipp Gadow
     1  Wouter Max Morren
     1  samvanstroud

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1111

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[kyleniemeyer]

Hello @samvanstroud, thanks for your submission to JOSS. I noticed that the GitHub repo submitted is just a mirror of the repo at https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/salt - is that the actual repo for the software? We'd prefer to link the paper with the official repo, where people would go to submit issues, etc.

[editorialbot]

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

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

INVALID DOIs

- None

[samvanstroud]

Hi @kyleniemeyer, thanks for starting the review! Yes the GitLab repo is where most of the development takes place, but unfortunately it requires a sign-in so doesn't meet the JOSS submission requirements, hence the mirror.

For what it's worth, we are following the same approach as for a previous submission: https://github.com/openjournals/joss-reviews/issues/5833.

[kyleniemeyer]

@samvanstroud ah, I see, thanks. I saw GitLab but didn't notice that it was a CERN-specific instance.

[kyleniemeyer]

@samvanstroud unfortunately, we don't have an editor in this area who is available to handle this right now, so I have to put this on our waitlist until someone frees up.

[kyleniemeyer]

@editorialbot invite @eloisabentivegna as editor

Hi @eloisabentivegna, any chance you could take this on to edit, when your other submissions wrap up? (Unfortunately we don't have anyone else familiar with high-energy physics on the team.)

[editorialbot]

Invitation to edit this submission sent!

[eloisabentivegna]

Hello @kyleniemeyer, unfortunately I have no availability.