[REVIEW]: GeometricFlux.jl: a geometric deep learning library in Julia

[whedon]

Submitting author: !--author-handle-->@yuehhua<!--end-author-handle-- (Yueh-Hua Tu) Repository: https://github.com/yuehhua/GeometricFlux.jl Branch with paper.md (empty if default branch): Version: Editor: !--editor-->@ranjanan<!--end-editor-- Reviewers: !--reviewers-list-->@jpfairbanks<!--end-reviewers-list-- Archive: Pending

Status

Status badge code:

HTML: <a href="https://proceedings.juliacon.org/papers/71f2b389ec88ef7107978a6fc9505614"><img src="https://proceedings.juliacon.org/papers/71f2b389ec88ef7107978a6fc9505614/status.svg"></a>
Markdown: [![status](https://proceedings.juliacon.org/papers/71f2b389ec88ef7107978a6fc9505614/status.svg)](https://proceedings.juliacon.org/papers/71f2b389ec88ef7107978a6fc9505614)

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

@DhairyaLGandhi, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @ranjanan 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 ✨

Review checklist for @DhairyaLGandhi

Conflict of interest

• [ ] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [ ] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

• [ ] Repository: Is the source code for this software available at the repository url?
• [ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [ ] Authorship: Has the submitting author (@yuehhua) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [ ] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [ ] 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

• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [ ] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [ ] 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

Paper format

• [ ] Authors: Does the paper.tex file include a list of authors with their affiliations?
• [ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
• [ ] Page limit: Is the page limit for full papers respected by the submitted document?

Content

• [ ] Context: is the scientific context motivating the work correctly presented?
• [ ] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
• [ ] Results: are the results presented and compared to approaches with similar goals?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @DhairyaLGandhi it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/JuliaCon/proceedings-review) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/JuliaCon/proceedings-review:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.14 s (540.2 files/s, 53893.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           36            532             56           2490
TeX                              9            249            177           2399
Markdown                        13            179              0            452
SVG                              1              0              0            251
YAML                             6              9              9            216
Lisp                             5             43              0            210
TOML                             2              5              0             47
Ruby                             1              8              4             45
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                            74           1025            246           6111
-------------------------------------------------------------------------------

Statistical information for the repository '28d96408eb7602dd057943c4' was
gathered on 2021/02/09.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Yueh-Hua Tu                      1            57              0          100.00

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
Yueh-Hua Tu                  57          100.0          0.0                7.02

[whedon]

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

[whedon]

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

OK DOIs

- 10.1088/1367-2630/15/9/095003 is OK
- 10.1609/aimag.v29i3.2157 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[ranjanan]

@dhairyalgandhi look over JuliaCon guide and start your review.

Just as a first point, @yuehhua, I would improve the quality of plots in the paper. They do not look publication quality.

[yuehhua]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #70 with the following error:

rm: cannot remove '*.aux': No such file or directory Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex'

Run number 1 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation battaglia2018' on page 1 undefined on input line 36 Citationgilmer2017' on page 1 undefined on input line 36 Latexmk: Summary of warnings: Latex failed to resolve 2 citation(s) Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'paper.aux'

Run number 2 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation battaglia2018' on page 1 undefined on input line 36 Citationgilmer2017' on page 1 undefined on input line 36 Latexmk: Summary of warnings: Latex failed to resolve 2 citation(s) Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'paper.out'

Run number 3 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation battaglia2018' on page 1 undefined on input line 36 Citationgilmer2017' on page 1 undefined on input line 36 Latexmk: Summary of warnings: Latex failed to resolve 2 citation(s) Failure to make 'paper.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'paper.log' for details Looks like we failed to compile the PDF

[yuehhua]

@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:

[yuehhua]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #70 with the following error:

rm: cannot remove '*.aux': No such file or directory Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex'

Run number 1 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

===========Latexmk: Missing input file: 'svg.sty' from line '! LaTeX Error: File svg.sty' not found.' Latexmk: Missing input file: 'svg.sty' from line '! LaTeX Error: Filesvg.sty' not found.' Failure to make 'paper.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'paper.log' for details Looks like we failed to compile the PDF

[yuehhua]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #70 with the following error:

rm: cannot remove '*.aux': No such file or directory Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex'

Run number 1 of rule 'pdflatex'

---

Running 'pdflatex -recorder "paper.tex"'

===========Latexmk: Missing input file: 'svg.sty' from line '! LaTeX Error: File svg.sty' not found.' Latexmk: Missing input file: 'svg.sty' from line '! LaTeX Error: Filesvg.sty' not found.' Failure to make 'paper.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'paper.log' for details Looks like we failed to compile the PDF

[yuehhua]

I tried several times compiling pdf but not success. I just upload my compilation version.

[yuehhua]

@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:

[whedon]

:wave: @DhairyaLGandhi, please update us on how your review is going (this is an automated reminder).

[ranjanan]

@DhairyaLGandhi could you let us know how your review is going?

[ranjanan]

@DhairyaLGandhi any update on your review?

[DhairyaLGandhi]

Yes sorry about the delay.

[DhairyaLGandhi]

Thanks @yuehhua

Here are some thoughts on the paper that would be good to be addressed

1. Comparison of capabilities with other similar software - there needs to be a more complete feature comparison taking multiple such packages into account
2. The references don't show up correctly
3. The motivation behind the ScatterNNlib package and what it borrows from the graphs ecosystem isnt established
4. There should be some examples of the modeling achieved by GeometricFlux. While one can conceivably assume some kinds of popular graph learning possibilities, it would be important to state the kinds of models that it has already been used to build (with examples) and ones there is support for
5. How is the Flux and CUDA integration handled? Section 4 needs some clarity.
6. What is the future direction for this package and how does its current flexibility compare with other packages beyond pytorch-scatter

[ranjanan]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

[ranjanan]

@whedon assign @jpfairbanks as reviewer

[whedon]

OK, @jpfairbanks is now a reviewer

[jpfairbanks]

1. Writing is telegraphic.
2. Introduction does not motivate graph learning or properly contextualize it in the tradition of graph algorithms or graph data mining
3. Benchmarks refer only to the message passing primitives and not to any learning algorithm or accuracy on a dataset.
4. I don't see anything geometric in this paper, there is no implementation of spaces or embedded graphs or anything else geometric. Graphs are combinatorial objects, not geometric structures. Graphs can be viewed as finite metric spaces, but this work does not engage with that viewpoint. The shortest path metric is not directly being used in the computation of the message passing microbenchmark.
5. There is no learning in this paper, Section 4 states that the GNN layers are compatible with flux layers. I would expect this to be demonstrated with an end-to-end example using Flux to solve a classification or regression problem.

Overall, I think this is a paper reporting a micro-benchmark of message passing on graphs. I would advise a revise and resubmit.

[yuehhua]

If I'd like to revise this work, what should I do next?

[ranjanan]

You’re welcome to just update the latex source with changes or a new paper from the ground up too. We’ll just use whedon to regenerate your paper whenever you’re done.

On Sat, 22 May 2021 at 8:24 PM, Yueh-Hua Tu @.***> wrote:

If I'd like to revise this work, what should I do next?

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/JuliaCon/proceedings-review/issues/70#issuecomment-846480880, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACFOAQMRR37TO4IYA2R7YN3TPBDKPANCNFSM4XLILWKQ .

-- Best, Ranjan Anantharaman

[yuehhua]

@ranjanan Sorry! I am recently too busy to work on the paper. I'd like to withdraw paper review and revise a new version for later re-submission. @jpfairbanks Thank you for your comment. It really helps. Thank you for your time.

[ranjanan]

Thanks for the update @yuehhua , and for considering the JuliaCon proceedings. Looking forward to your resubmission!

[ranjanan]

@whedon withdraw

[whedon]

I'm sorry @ranjanan, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[ranjanan]

@matbesancon could you withdraw this please? Thank you.

[matbesancon]

@whedon withdraw

[whedon]

Paper withdrawn.