[PRE REVIEW]: Testing the Julia SciML ecosystem through Physics-Informed Machine Learning applied to wildfire propagation

[whedon]

Submitting author: @francescocalisto (Francesco Calisto) Repository: https://github.com/MachineLearningJournalClub/MLJC-UniTo-ProjectX-2020-public.git Version: Editor: @carstenbauer Reviewers: @sloede Managing EiC: Valentin Churavy

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[whedon]

PDF failed to compile for issue #81 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:72:in `block in build_affiliation_string': Problem with affiliations for Simone Azeglio, perhaps the affiliations index need quoting? (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:71:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:71:in `build_affiliation_string'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:17:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:205:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:205:in `block in parse_authors'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:202:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:202:in `parse_authors'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:93:in `initialize'
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    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Wordcount for paper.tex is 4551

[whedon]

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

OK DOIs

- 10.5065/1DFH-6P97 is OK
- 10.1007/s10584-014-1183-3 is OK
- 10.7930/nca4.2018 is OK
- 10.1126/science.1259100 is OK
- 10.3390/rs10121950 is OK
- 10.5194/gmd-4-591-2011 is OK
- 10.1016/0893-6080(92)90012-8 is OK
- 10.1287/ijoc.2014.0623 is OK

MISSING DOIs

- 10.21203/rs.3.rs-55125/v1 may be a valid DOI for title: Universal differential equations for scientific machine learning
- 10.1016/j.ymeth.2019.04.008 may be a valid DOI for title: Deep learning in bioinformatics: Introduction, application, and perspective in the big data era
- 10.1016/j.jcp.2018.10.045 may be a valid DOI for title: Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations
- 10.1016/j.tcs.2011.01.039 may be a valid DOI for title: The directed Hausdorff distance between imprecise point sets

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=1.26 s (205.2 files/s, 134088.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Fortran 77                     154           1868          20046          22372
Julia                           37           1552           1618           4472
TeX                              8            315            177           2618
TOML                             4            455              2           2138
Jupyter Notebook                19              0         107222           1363
C                                9            169            432            947
Markdown                        15            257              0            528
make                             4             55             40            149
C++                              2             29             46             71
C Shell                          1             13              0             49
Prolog                           1              1              0             44
OCaml                            1              0              0             42
Ruby                             1              7              3             37
YAML                             1              1              0             32
C/C++ Header                     2              4             12             22
-------------------------------------------------------------------------------
SUM:                           259           4726         129598          34884
-------------------------------------------------------------------------------

Statistical information for the repository '26666763464e5ce00b4b95a7' was
gathered on 2021/09/16.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Francesco Calisto                1            47              0            2.16
Martina Scauda                   2          1929            197           97.84

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Francesco Calisto            47          100.0          0.0                6.38
Martina Scauda             1732           89.8          0.0               29.97

[francescocalisto]

matbesancon might be an available reviewer, according to the list

[carstenbauer]

@whedon assign @carstenbauer as editor

[whedon]

OK, the editor is @carstenbauer

[ranjanan]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #81 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:72:in `block in build_affiliation_string': Problem with affiliations for Simone Azeglio, perhaps the affiliations index need quoting? (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:71:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:71:in `build_affiliation_string'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/author.rb:17:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:205:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:205:in `block in parse_authors'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:202:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:202:in `parse_authors'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:93:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:131:in `<top (required)>'
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    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

[carstenbauer]

@whedon generate pdf

[whedon]

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

[carstenbauer]

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[carstenbauer]

@whedon add @sloede as reviewer

[whedon]

OK, @sloede is now a reviewer

[carstenbauer]

@francescocalisto While I'm already in the process of looking out for reviewers, can you suggest a few reviewers without conflict of interest from the scientific machine learning community? Could also be someone from a different open source community, e.g. from the Python community.

[francescocalisto]

@carstenbauer I can point out Chris Rackauckas, Kirill Zubov, Zoe McCarthy (whom I worked with on an other paper but not on this one, I don't know if that's considered conflict of interest), and Vaibhav Dixit. I'm afraid I don't have many other ideas but I will mention other ones in case I find them.

[ChrisRackauckas]

Wasn't this published in the AAAI-MLPS 2021 archival proceedings already? https://sites.google.com/view/aaai-mlps/proceedings?authuser=0

[francescocalisto]

Yes, it is the same work, although the paper was revised a bit. Isn't it allowed? In that case I'm sorry, I didn't know.

[ChrisRackauckas]

Generally no, that would be frowned upon. But also for yourself, what's the next story to tell? There may be more to say, and so that could be a whole new paper on this topic.

[francescocalisto]

I didn't know, sorry! I agree on that. I thought it was possible to submit the paper to the proceedings because we gave a talk at JuliaCon 2021. Then I think we can close the issue. Thank you.

[vchuravy]

@whedon withdraw

[whedon]

Paper withdrawn.