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[REVIEW]: A Hyperbolic "Crystal Ball" #1240

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whedon opened this Issue Feb 8, 2019 · 35 comments

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whedon commented Feb 8, 2019

Submitting author: @benjaminwilson (Benjamin Wilson)
Repository: https://github.com/lateral/crystal-ball
Version: v1.0.1
Editor: @poulson
Reviewer: @HaoZeke
Archive: Pending

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/033b265ce2f8562dc1148b534a09275c"><img src="http://joss.theoj.org/papers/033b265ce2f8562dc1148b534a09275c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/033b265ce2f8562dc1148b534a09275c/status.svg)](http://joss.theoj.org/papers/033b265ce2f8562dc1148b534a09275c)

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) 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

@HaoZeke, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @poulson know.

Please try and complete your review in the next two weeks

Review checklist for @HaoZeke

Conflict of interest

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?
  • Version: Does the release version given match the GitHub release (v1.0.1)?
  • Authorship: Has the submitting author (@benjaminwilson) 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

Software paper

  • Authors: Does the paper.md 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)?
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whedon commented Feb 8, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @HaoZeke it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) 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/openjournals/joss-reviews:

watching

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

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

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whedon commented Feb 8, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 8, 2019

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benjaminwilson commented Feb 8, 2019

@HaoZeke thanks for your initial feedback over on the other issue. I'll address that today!

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benjaminwilson commented Feb 8, 2019

Hi @HaoZeke , I've added a section that gives a high-level view of the algorithms for computing the updates to the point configurations to paper.md, and added a small note about the performance to README.md.

I think this addresses the bulk of your points from previously - but not all of them - I'm afraid I'll have to leave those until Monday.

Thanks already for the comments to date!

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HaoZeke commented Feb 9, 2019

@whedon generate pdf

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whedon commented Feb 9, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 9, 2019

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HaoZeke commented Feb 9, 2019

@benjaminwilson, thank you for the extensions, I will check when your additions are completed. In general, for the review process I will be opening issues on the project tracker, or where the solution is unambiguous, I shall be opening pull requests. Also, please check the references of the article.

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HaoZeke commented Feb 9, 2019

@whedon check references

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whedon commented Feb 9, 2019

Attempting to check references...
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whedon commented Feb 9, 2019


OK DOIs

- None

MISSING DOIs

- https://doi.org/10.2172/1209543 may be missing for title: Neural Embeddings of Graphs in Hyperbolic Space
- https://doi.org/10.2172/963444 may be missing for title: Hyperbolic Neural Networks

INVALID DOIs

- None
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benjaminwilson commented Feb 12, 2019

@whedon generate pdf

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whedon commented Feb 12, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 12, 2019

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benjaminwilson commented Feb 12, 2019

@whedon check references

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whedon commented Feb 12, 2019

Attempting to check references...
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whedon commented Feb 12, 2019


OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1039/c5cc90276b may be missing for title: Neural Embeddings of Graphs in Hyperbolic Space
- https://doi.org/10.1016/0893-6080(88)90120-7 may be missing for title: Hyperbolic Neural Networks

INVALID DOIs

- None
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benjaminwilson commented Feb 12, 2019

@whedon check references

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whedon commented Feb 12, 2019

Attempting to check references...
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whedon commented Feb 12, 2019


OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None
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benjaminwilson commented Feb 12, 2019

@HaoZeke thanks for your patience! I think I've now addressed all issues raised in the pre-review.

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HaoZeke commented Feb 12, 2019

Excellent work @benjaminwilson, I believe this is ready for submission now, @poulson .

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poulson commented Feb 12, 2019

@benjaminwilson It seems that the DOIs were removed rather than fixed. Would you mind making sure that each of the references has a DOI?

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benjaminwilson commented Feb 13, 2019

Hi @poulson, I've indeed removed some entries from the .bib file that I wasn't using. For all but one of the remainder, I am afraid that I am really stumped on getting DOIs for any of them. I was surprised that I couldn't find either on the paper itself or in published BibTeX or on crossref.org. I don't know if this is because they are all either arXiv (1) or conference proceedings (rest). Do you know of somewhere else I can look?

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poulson commented Feb 15, 2019

@benjaminwilson Hi Benjamin, I am still relatively new to whedon's check references, but you might try mirroring the DOI formatting of a recently completed review, such as https://github.com/sivaramambikasaran/HODLR/blob/master/docs/paper/paper.bib.

The DOI links are surrounded by curly braces and only contain the latter part of the address. Could you try this approach to see if the DOI's are picked up?

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benjaminwilson commented Feb 15, 2019

Hi! The problem is rather that I can't find the DOIs for those articles anywhere.

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benjaminwilson commented Feb 15, 2019

@whedon check references

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whedon commented Feb 15, 2019

Attempting to check references...
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whedon commented Feb 15, 2019


OK DOIs

- None

MISSING DOIs

- https://doi.org/10.4414/saez.2013.01498 may be missing for title: Skip-gram word embeddings in hyperbolic space

INVALID DOIs

- None
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benjaminwilson commented Feb 15, 2019

whedon sure does come up with some crazy suggestions for what the missing DOI might be!

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poulson commented Feb 18, 2019

@whedon generate pdf

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whedon commented Feb 18, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Feb 18, 2019

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poulson commented Feb 18, 2019

Thanks @benjaminwilson; I proofread and everything looks great. Would you mind creating a Zenodo archive and reporting the DOI here?

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