[REVIEW]: DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@ayuei@arfon<!--end-editor-- Reviewers: @KonradHoeffner, @amitkumarj441 Archive: 10.5281/zenodo.8103783

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editorialbot commented 1 year ago

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (730.7 files/s, 203354.8 lines/s)
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SUM:                           184           5920           2282          43006
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gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1261

arfon commented 1 year ago

@KonradHoeffner – This is the review thread for the paper. All of our communications will happen here from now on.

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editorialbot commented 1 year ago

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

arfon commented 1 year ago

@amitkumarj441 @JacksonMaxfield @shruti-singh – would any of you be willing to review this submission for JOSS? The submission under consideration is DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval, a Python package for information retrieval and natural language processing.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

editorialbot commented 1 year ago

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- Errored finding suggestions for "Cost-effective Selection of Pretraining Data: A Ca...", please try later
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- 10.1145/2363.2708 may be a valid DOI for title: Generalizing specifications for uniformly implemented loops
- 10.1145/3318.3321 may be a valid DOI for title: Towards monolingual programming environments
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- 10.1093/nar/gky1064 may be a valid DOI for title: Stemformatics: visualize and download curated stem cell data
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- https://doi.org/10.1137/080734467 is INVALID because of 'https://doi.org/' prefix
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- https://doi.org/10.1016/j.jbi.2022.104005 is INVALID because of 'https://doi.org/' prefix

KonradHoeffner commented 1 year ago

Review checklist for @KonradHoeffner

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/Ayuei/DeBEIR?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@ayuei) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
API documentation exists but is not complete, see https://github.com/Ayuei/DeBEIR/issues/9
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)? Writing quality and structure is OK but, there needs to be a correction pass for language. For example, there are spaces in front of full stops: "DeBeIR .", "issues .". "github" -> "GitHub". Hugggingface -> Huggingface.
[x] 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?

KonradHoeffner commented 1 year ago

@ayuei: The paper has three authors but you are the only contributor of the repository. Can you clarify the contribution of your coauthors?

KonradHoeffner commented 1 year ago

@Ayuei: Is it “DeBIR” or “DeBEIR”? The paper is titled DeBIR but the repository title and README contains “DeBEIR”. The code in the paper uses both. Please use a consistent name. Or are they actually two different things?

KonradHoeffner commented 1 year ago

Success in information retrieval was limited until 2021

@Ayuei: A paper from 2019 is cited next, which talks about how the breakthrough came in 2018 or 2019. Please confirm that 2021 is indeed the correct year.

KonradHoeffner commented 1 year ago

Additional hackability

@Ayuei: I didn’t know the word “hackability” in this context but I’m not a native speaker and had to look it up to find out that it has two different meanings. If possible I would use a less ambiguous term to not confuse other non-native speakers.

KonradHoeffner commented 1 year ago

Please describe author affiliation in more detail. I had to Google “CSIRO’s Data61” to understand what it is. “Australian National University” is also very general. Which department and research group? You could move part of that from the acknowledgements.

KonradHoeffner commented 1 year ago

A brief summary of the pipeline stages are

Summary is singular so it should be “is”, not “are”. Also please refer to figure 1 here, which illustrates the stages.

“Figure” is repeated several times as “Figure Figure”

Similar libraries that exist include sentence-transformers, openNIR

Add “such as”, cite publication

but have less of a focus on all stages of the dense retrieval pipeline

Please explain in more detail which stages of the pipeline are not covered enough by all existing libraries and what the benefits of DeBIR over those existing libraries are. This is important to clarify, how exactly it "either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler)." as part of the "substantial scholarly effort" criterion and for the statement of need criterion.

arfon commented 1 year ago

@Ayuei – please shorten your BibTeX file to include only those entries cited by this paper.

Ayuei commented 1 year ago

@arfon Hi, I've shortened the BibTex and recompiled the paper.

@KonradHoeffner Thank you for taking time to review the work and for the detailed comments, I'm still working on addressing concerns and issues.

arfon commented 1 year ago

:wave: @kuutsav would you be willing to review this submission for JOSS? The submission under consideration is DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval, a Python package for information retrieval and natural language processing.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

kuutsav commented 1 year ago

👋 @kuutsav would you be willing to review this submission for JOSS? The submission under consideration is DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval, a Python package for information retrieval and natural language processing.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

@arfon Thanks for reaching out. I have a very busy schedule this month. If you are still looking for a reviewer at the end of the month, please reach out to me again. All the best!

arfon commented 1 year ago

:wave: @nreimers @blvns – would either of you be willing to review this submission for JOSS? The submission under consideration is DeBIR: A Python Package for Dense Bi-Encoder Information Retrieval, a Python package for information retrieval and natural language processing.

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. You can learn more about the process in these guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Based on your experience, we think you might be able to provide a great review of this submission. Please let me know if you think you can help us out!

Many thanks Arfon

nreimers commented 1 year ago

Sorry, I'm currently completely busy

KonradHoeffner commented 1 year ago

@arfon I need some help deciding about this criterion:

JOSS requires that software should be [...] packaged appropriately according to common community standards for the programming language being used.

According to https://github.com/Ayuei/DeBEIR/issues/7, DeBEIR cannot be published on PyPi because of git dependencies but releases of the built wheel will be added to the repository. Is this enough to satisfy the criterion?

KonradHoeffner commented 1 year ago

@Ayuei: Where are the HTML docs published? Please add a link to that to the README. Right now I can only preview it at https://raw.githack.com/Ayuei/DeBEIR/main/docs/debeir.html.

Ayuei commented 1 year ago

@Ayuei: Where are the HTML docs published? Please add a link to that to the README. Right now I can only preview it at https://raw.githack.com/Ayuei/DeBEIR/main/docs/debeir.html.

Hi, I set up a GitHub pages here: https://ayuei.github.io/DeBEIR/debeir.html

arfon commented 1 year ago

:wave: @kuutsav – if it's OK, I'd still love to have you as a reviewer here? We've not managed to find a second reviewer yet.

arfon commented 1 year ago

According to https://github.com/Ayuei/DeBEIR/issues/7, DeBEIR cannot be published on PyPi because of git dependencies but releases of the built wheel will be added to the repository. Is this enough to satisfy the criterion?

@KonradHoeffner – yes, I think this is acceptable. Thanks for checking.

kuutsav commented 1 year ago

:wave: @kuutsav – if it's OK, I'd still love to have you as a reviewer here? We've not managed to find a second reviewer yet.

Sure. I'll go over the thread tomorrow. Anything i should focus on while getting up to speed?

Ayuei commented 1 year ago

Thank you once again for taking the time to review the paper.

@Ayuei: The paper has three authors but you are the only contributor of the repository. Can you clarify the contribution of your coauthors?

The co-authors helped with the writing of this paper (Sarvnaz Karimi). And with the original paper/ that the idea was from and projection supervision and direction (Zhenchang Xing + Sarvaz Karimi).

@Ayuei: Is it “DeBIR” or “DeBEIR”? The paper is titled DeBIR but the repository title and README contains “DeBEIR”. The code in the paper uses both. Please use a consistent name. Or are they actually two different things?

This is indeed a typo, I've fixed this in the paper.

@Ayuei: A paper from 2019 is cited next, which talks about how the breakthrough came in 2018 or 2019. Please confirm that 2021 is indeed the correct year.

2021 is the incorrect year, the paper I cited was published in 2021 but was submitted in 2019. This is fixed in the current commit.

Additional hackability

@Ayuei: I didn’t know the word “hackability” in this context but I’m not a native speaker and had to look it up to find out that it has two different meanings. If possible I would use a less ambiguous term to not confuse other non-native speakers.

I'll replace "hackability" with extendability, as it's intended to mean that a user can use the building blocks in the library to create their own classes or are able to use the batteries-included pipeline class.

Summary is singular so it should be “is”, not “are”. Also please refer to figure 1 here, which illustrates the stages. “Figure” is repeated several times as “Figure Figure” Add “such as”, cite publication

Fixed in the revised paper bef8baa

but have less of a focus on all stages of the dense retrieval pipeline

Please explain in more detail which stages of the pipeline are not covered enough by all existing libraries and what the benefits of DeBIR over those existing libraries are. This is important to clarify, how exactly it "either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler)." as part of the "substantial scholarly effort" criterion and for the statement of need criterion.

I've added more detail to the paper in commits (79e70e1, https://github.com/Ayuei/DeBEIR/commit/66f8d42482ac3644cdaf3987c9188bb5c1852cc4), which hopefully clarifies this point. The point being made is that a library solely for bi-encoder IR research does not yet exist. Though apart from that, effort was made to make sure the library is as fast (execution-wise and ease-of-use-wise) as possible for experimentation.

arfon commented 1 year ago

@editorialbot add @kuutsav as reviewer

editorialbot commented 1 year ago

@kuutsav added to the reviewers list!

arfon commented 1 year ago

@kuutsav – This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5017 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

As you work through your checklist, it's probably worth catching up on @KonradHoeffner's review to see which issues/questions have already been flagged.

Many thanks again for helping out here!

KonradHoeffner commented 1 year ago

The co-authors helped with the writing of this paper (Sarvnaz Karimi). And with the original paper/ that the idea was from and projection supervision and direction (Zhenchang Xing + Sarvaz Karimi).

If both did specific project supervision and direction the criteria seem to be fulfilled and I will mark the appropriate checkbox, thanks for clarifying!

KonradHoeffner commented 1 year ago

Community guidelines exist now, checked the box. @Ayuei please convert your reference to ./CONTRIBUTING.md in the readme file into a link. Using GitHub Markdown syntax, `<./CONTRIBUTING.md> or something similar should work with relative links to files in the repository.

KonradHoeffner commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

KonradHoeffner commented 1 year ago

@Ayuei: Is it “DeBIR” or “DeBEIR”? The paper is titled DeBIR but the repository title and README contains “DeBEIR”. The code in the paper uses both. Please use a consistent name. Or are they actually two different things?

This is indeed a typo, I've fixed this in the paper.

I just regenerated the paper but it still has many occurrences of both "debir" and "debeir".

KonradHoeffner commented 1 year ago

The reference "openNIR(opennir?)" on line 83 is displayed incorrectly.

Ayuei commented 1 year ago

@Ayuei: Is it “DeBIR” or “DeBEIR”? The paper is titled DeBIR but the repository title and README contains “DeBEIR”. The code in the paper uses both. Please use a consistent name. Or are they actually two different things?

This is indeed a typo, I've fixed this in the paper.

I just regenerated the paper but it still has many occurrences of both "debir" and "debeir".

Sorry, I thought the typos were only in the code examples. Fixed throughout the paper now.

The reference "openNIR(opennir?)" on line 83 is displayed incorrectly.

Forgot to commit the bibtex, added it now.

Community guidelines exist now, checked the box. @Ayuei please convert your reference to ./CONTRIBUTING.md in the readme file into a link. Using GitHub Markdown syntax, `<./CONTRIBUTING.md> or something similar should work with relative links to files in the repository.

Added to the repository. Thanks!

KonradHoeffner commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

KonradHoeffner commented 1 year ago

There are still spaces in front of full stops: "DeBeIR .", "issues .". Also "github" *-> "GitHub". Hugggingface -> Huggingface.

KonradHoeffner commented 1 year ago

Reference lin-neural-recentation is broken.

Ayuei commented 1 year ago

@KonradHoeffner thank you again for your time.

There are still spaces in front of full stops: "DeBeIR .", "issues .". Also "github" *-> "GitHub". Hugggingface -> Huggingface.

Fixed. There was an issue with links in the final pdf which caused the spacing issue.

Reference lin-neural-recentation is broken.

Fixed this typo.

Additionally, fixed grammar mistakes, and refined explanations in the text. Currently working on refining the documentation.

Ayuei commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

KonradHoeffner commented 1 year ago

I would recommend doing another correction pass as there are still many writing issues remaining, for example:

"openNIR(": missing space
accurate/effective": use a word instead of a slash or choose one
"encoded at ranking time) (Lin, 2019)": I would include the citation in the parenthesis and not open another set of parentheses there
"opening a thread in DeBEIR issue": I think creating an issue sounds better than opening a thread in issues.
the" neural hype" in references

KonradHoeffner commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

arfon commented 1 year ago

:wave: @kuutsav – just checking in to see how you're getting on here?

kuutsav commented 1 year ago

@arfon it's not going good. I have not been able to take out the time for the review here. Request you to find another reviewer as I don't want to delay this because of me. Sorry for the late notice and not being of help here ☹️.

Ayuei commented 1 year ago

@editorialbot generate pdf

Thanks for the patience, the co-authors and myself did some correction passes over the text.

openjournals / joss-reviews