[REVIEW]: Efficiently Collecting Relative Similarity Judgments from Humans #4517

editorialbot · 2022-06-27T07:35:10Z

Submitting author: @stsievert (Scott Sievert)
Repository: https://github.com/stsievert/salmon/
Branch with paper.md (empty if default branch): master
Version: v1.0.2
Editor: @ajstewartlang
Reviewers: @hoechenberger, @stain, @jorgedch
Archive: 10.5281/zenodo.7832431

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/00e003e1cd7c632f80d4097a66a58c69"><img src="https://joss.theoj.org/papers/00e003e1cd7c632f80d4097a66a58c69/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/00e003e1cd7c632f80d4097a66a58c69/status.svg)](https://joss.theoj.org/papers/00e003e1cd7c632f80d4097a66a58c69)

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

@hoechenberger,@jorgedch, & @stain, 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:

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

📝 Checklist for @jorgedch

📝 Checklist for @stain

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-06-27T07:35:11Z

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:

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

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editorialbot · 2022-06-27T07:35:15Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (775.8 files/s, 118657.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          50           1856           2614           6491
HTML                             5             93             12           1246
reStructuredText                15            547            600            811
CSS                              2            178              0            783
YAML                            26             35             49            554
Jupyter Notebook                 3              0           1391            245
TeX                              1             20              0            181
Markdown                         6             58              0            165
Bourne Shell                     3             20             48             73
make                             2             14             10             39
DOS Batch                        1              8              1             26
Dockerfile                       2              6              2             22
SVG                              3              0              0              3
-------------------------------------------------------------------------------
SUM:                           119           2835           4727          10639
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-06-27T07:35:16Z

Wordcount for paper.md is 887

editorialbot · 2022-06-27T07:35:28Z

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

OK DOIs

- 10.1137/1.9781611974010.31 is OK
- 10.1109/MLSP.2012.6349720 is OK
- 10.1007/s42761-020-00024-8 is OK
- 10.1109/BTAS.2016.7791205 is OK
- 10.1109/IJCNN.2019.8852059 is OK
- 10.1111/cogs.12744 is OK
- 10.25080/shinma-7f4c6e7-010 is OK
- 10.1109/TKDE.2019.2956700 is OK
- 10.1109/Allerton.2011.6120287 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-06-27T07:36:27Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

ajstewartlang · 2022-06-27T09:40:06Z

@editorialbot add @jorgedch as reviewer

editorialbot · 2022-06-27T09:40:08Z

@jorgedch added to the reviewers list!

jorgedch · 2022-07-07T11:34:10Z

Review checklist for @jorgedch

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/stsievert/salmon/?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@stsievert) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

jorgedch · 2022-07-07T13:40:24Z

@stsievert

Functionality

Installation:

Fails to run local installation stsievert/salmon#135
I'll go through the Functionality and Performance checklist items once the Installation is fixed 👍

Functionality:

Documentation

Automated tests:

Fails to run unit tests stsievert/salmon#136

Software paper

Quality of writing:

Typo stsievert/salmon#137

References:

Incorrect DOI stsievert/salmon#138

stsievert · 2022-07-08T02:51:40Z

Salmon's documentation mentions an install process on Amazon AWS: https://docs.stsievert.com/salmon/installation.html#experimentalist. I've reached out to the reviewers (@hoechenberger, @stain, @jorgedch) to provide an Amazon AWS account so they can more easily verify that process works and because Amazon EC2 machines have a non-zero cost.

@ajstewartlang let me know if that violates any ethics rules; I can revoke their permissions at any time. The relevant AMI is public (see Amazon AWS Dashboard screenshot below), so the fact I created their accounts should not provide privileged access not available to the public.

ajstewartlang · 2022-07-08T07:45:19Z

Thanks @stsievert - for the purpose of facilitating the review process, I'm comfortable with that. I'll assume that @hoechenberger, @stain, and @jorgedch are too unless I hear otherwise.

jorgedch · 2022-08-23T14:53:43Z

@stsievert the solutions to the following issues are already posted in their corresponding threads:

Functionality:
stsievert/salmon#140
stsievert/salmon#141

Feel free to copy/paste the code in the relevant files and close the issues. Other than that, everything else is approved from my side and the code is ready for publication. All the best, Jorge

ajstewartlang · 2022-09-12T17:00:48Z

👋

@stain and @hoechenberger - just checking in to see how your reviews of this submission are going?

hoechenberger · 2022-09-14T10:50:37Z

@ajstewartlang I'm sorry for the delay, I'm working on the review right now and will submit ASAP!

hoechenberger · 2022-09-14T10:51:56Z

Review checklist for @hoechenberger

Conflict of interest

I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/stsievert/salmon/?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@stsievert) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

hoechenberger · 2022-09-14T12:56:10Z

Hello @stsievert @ajstewartlang,

I am happy with everything except with the installation procedure. I managed to get Salmon to run on an AWS instance, but local installation failed, both via Docker and via conda.

There is a problem when running docker-compose build. I'm pasting the relevant parts here:

#0 219.1 Installing pip dependencies: ...working... Pip subprocess error:
#0 317.7 ERROR: Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
...
#0 317.7   Attempting uninstall: pyyaml
#0 317.7     Found existing installation: PyYAML 5.1.2
#0 317.7
#0 317.7 failed
#0 317.7
#0 317.7 CondaEnvException: Pip failed
#0 317.7
------
failed to solve: executor failed running [/bin/sh -c conda env update -n base --file /salmon/salmon.yml --prune]: exit code: 1

And for installation from the salmon.yaml file via conda, I run into:

Encountered problems while solving:
  - nothing provides requested bokeh 2.0.1

This is on macOS 12.6 on an Apple Silicon machine.

Since the AWS installation worked flawlessly, I was still able to review functionality of the software.

editorialbot · 2023-04-17T08:02:13Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-04-17T08:04:22Z

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4130, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2023-04-17T08:09:15Z

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

OK DOIs

- 10.1137/1.9781611974010.31 is OK
- 10.1109/MLSP.2012.6349720 is OK
- 10.1007/s42761-020-00024-8 is OK
- 10.1109/BTAS.2016.7791205 is OK
- 10.1109/IJCNN.2019.8852059 is OK
- 10.1111/cogs.12744 is OK
- 10.25080/shinma-7f4c6e7-010 is OK
- 10.1109/TKDE.2019.2956700 is OK
- 10.1109/Allerton.2011.6120287 is OK

MISSING DOIs

- Errored finding suggestions for "Adaptively Learning the Crowd Kernel", please try later

INVALID DOIs

- None

oliviaguest · 2023-04-17T09:10:05Z

what's up with this error @gkthiruvathukal? 😅

oliviaguest · 2023-04-17T09:12:51Z

I think it's just a book and the bot is struggling for some reason? Anyway, it looks good in the PDF to me. Is that all good for you too @stsievert?

stsievert · 2023-04-17T12:11:58Z

@editorialbot generate pdf

editorialbot · 2023-04-17T12:13:16Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

stsievert · 2023-04-17T12:27:08Z

Huh, I haven't changed the DOIs in a while. Both errors are with conference articles ("Adaptively learning ..." is from ICML, "NEXT: A System ..." is from NeurIPS). Both links resolve to the expected article.

Also, I've reviewed the paper again and noticed a typo in paper/paper.md. I've published a new release (v1.0.3), on Zenodo at 10.5281/zenodo.7837296 (latest release: 10.5281/zenodo.7832320). I apologize for the late edit!

oliviaguest · 2023-04-17T15:37:05Z

@editorialbot recommend-accept

editorialbot · 2023-04-17T15:37:06Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-04-17T15:38:32Z

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4135, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot · 2023-04-17T15:40:29Z

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

OK DOIs

- 10.1137/1.9781611974010.31 is OK
- 10.1109/MLSP.2012.6349720 is OK
- 10.1007/s42761-020-00024-8 is OK
- 10.1109/BTAS.2016.7791205 is OK
- 10.1109/IJCNN.2019.8852059 is OK
- 10.1111/cogs.12744 is OK
- 10.25080/shinma-7f4c6e7-010 is OK
- 10.1109/TKDE.2019.2956700 is OK
- 10.1109/Allerton.2011.6120287 is OK

MISSING DOIs

- None

INVALID DOIs

- None

oliviaguest · 2023-04-17T15:56:42Z

@editorialbot accept

editorialbot · 2023-04-17T15:56:44Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2023-04-17T15:58:25Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Sievert
  given-names: Scott
  orcid: "https://orcid.org/0000-0002-4275-3452"
- family-names: Nowak
  given-names: Robert
- family-names: Rogers
  given-names: Timothy
  orcid: "https://orcid.org/0000-0001-6304-755X"
doi: 10.5281/zenodo.7832431
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sievert
    given-names: Scott
    orcid: "https://orcid.org/0000-0002-4275-3452"
  - family-names: Nowak
    given-names: Robert
  - family-names: Rogers
    given-names: Timothy
    orcid: "https://orcid.org/0000-0001-6304-755X"
  date-published: 2023-04-17
  doi: 10.21105/joss.04517
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4517
  title: Efficiently Learning Relative Similarity Embeddings with
    Crowdsourcing
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04517"
  volume: 8
title: Efficiently Learning Relative Similarity Embeddings with
  Crowdsourcing

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2023-04-17T15:58:29Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-04-17T15:58:30Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-04-17T15:58:31Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04517 joss-papers#4136
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04517
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

oliviaguest · 2023-04-17T16:02:22Z

@stsievert congratulations! And a big thanks for the reviews to @hoechenberger, @stain, and @jorgedch! 🥳

editorialbot · 2023-04-17T16:02:24Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04517/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04517/status.svg
   :target: https://doi.org/10.21105/joss.04517

This is how it will look in your documentation:

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stsievert · 2023-04-17T21:04:26Z

Thank you for your reviews/help @oliviaguest @hoechenberger, @stain, and @jorgedch!

editorialbot added Dockerfile Makefile review Shell labels Jun 27, 2022

editorialbot assigned ajstewartlang Jun 27, 2022

editorialbot mentioned this issue Jun 27, 2022

[PRE REVIEW]: Efficiently Collecting Relative Similarity Judgments from Humans #4445

Closed

This was referenced Jul 7, 2022

Fails to run local installation stsievert/salmon#135

Closed

Fails to run unit tests stsievert/salmon#136

Closed

Typo stsievert/salmon#137

Closed

Incorrect DOI stsievert/salmon#138

Closed

stsievert mentioned this issue Jul 8, 2022

Feedback from JOSS review stsievert/salmon#139

Merged

13 tasks

This was referenced Jul 30, 2022

Missing import stsievert/salmon#140

Closed

Example code for generating embeddings stsievert/salmon#141

Closed

editorialbot added the Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences label Sep 10, 2022

editorialbot added accepted published Papers published in JOSS labels Apr 17, 2023

oliviaguest closed this as completed Apr 17, 2023

This was referenced Sep 28, 2023

[PRE REVIEW]: cblearn: Comparison-based Machine Learning in Python #5896

Closed

[PRE REVIEW]: Learning from Crowds with Crowd-Kit #5898

Closed

editorialbot mentioned this issue Oct 22, 2023

[PRE REVIEW]: Machine Learning Validation via Rational Dataset Sampling with astartes #5970

Closed

This was referenced Jan 26, 2024

[PRE REVIEW]: CCS-Lib: A Python package to elicit latent knowledge from LLMs #6135

Closed

[PRE REVIEW]: ReLax: Efficient and Scalable Recourse Explanation Benchmarking using JAX #6289

Closed

editorialbot mentioned this issue Sep 9, 2024

[PRE REVIEW]: wiserank: a platform for running pairwise comparison experiments #7168

Closed

[REVIEW]: Efficiently Collecting Relative Similarity Judgments from Humans #4517

[REVIEW]: Efficiently Collecting Relative Similarity Judgments from Humans #4517

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jorgedch commented Jul 7, 2022 • edited Loading

Review checklist for @jorgedch

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

jorgedch commented Jul 7, 2022 • edited Loading

Functionality

Documentation

Software paper

stsievert commented Jul 8, 2022

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jorgedch commented Aug 23, 2022

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hoechenberger commented Sep 14, 2022

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Review checklist for @hoechenberger

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

hoechenberger commented Sep 14, 2022

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