[REVIEW]: DeepSynth: Scaling Neural Program Synthesis with Distribution-based Search

[whedon]

Submitting author: @Theomat (Théo Matricon)
Repository: https://github.com/nathanael-fijalkow/DeepSynth
Branch with paper.md (empty if default branch): joss
Version: v1.0
Editor: @arfon
Reviewers: @njuaplusplus, @bzz
Archive: 10.5281/zenodo.7194579

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Review checklist for @njuaplusplus

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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• 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.

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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?
• Contribution and authorship: Has the submitting author (@Theomat) 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 and who the target audience is?
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• 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?

Review checklist for @Kraks

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@Theomat) 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 and who the target audience is?
• 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?

Review checklist for @bzz

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@Theomat) 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 and who the target audience is?
• 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?

[whedon]

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

⚠️ JOSS reduced service mode ⚠️

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #4151 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.28 s (179.5 files/s, 46480.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          49           1225           1144           5441
SVG                              1              1              1           5177
Markdown                         1             50              0            170
-------------------------------------------------------------------------------
SUM:                            51           1276           1145          10788
-------------------------------------------------------------------------------


Statistical information for the repository 'dd71a7aa04ea7726de6bda9d' was
gathered on 2022/02/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Guillaume Lagarde                8           871            242            5.05
Nathanael Fijalkow              37          7691           3627           51.32
Theomat                        181          5705           3281           40.75
[email protected]               5           540             95            2.88

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
Guillaume Lagarde            64            7.3          6.9                0.00
Nathanael Fijalkow         4073           53.0          3.3               10.83
Theomat                    3665           64.2          4.5               10.42
[email protected]            8            1.5          5.1               37.50

[terrytangyuan]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #4151 with the following error:

 Can't find any papers to compile :-(

[terrytangyuan]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

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

[terrytangyuan]

@whedon add @bzz as reviewer

[whedon]

OK, @bzz is now a reviewer

[bzz]

HI @ Theomat.

I’ve started reviewing the submission and got a couple of questions that are not immediately related to the code, so posting it here.

“What should my paper contain” of JOSS submission guideline and “citations of relevant work” of JOSS Review Criteria mentions

list of key references, including to other software addressing related needs. Note that the references should include full names of venues, e.g., journals and conferences, not abbreviations only understood in the context of a specific discipline.

1. There is reference to Copilot, but no mention of the Codex paper that it is based on.
   In this context, would you agree that the paper would benefit for a brief description on how this popular approach with large language models is fundamentally different from the neuro-symbolic one that your work is exploring?

2. I think the paper would also benefit greatly from more references to the other published OSS software in the field of program synthesis / programming by example (PbE)

Several examples that come to mind are:

• KasraF/SnipPy: Meta-repository for SnipPy
• kensens/FrAngel: A Java program synthesizer.
• utopia-group/regel: REGEL: Regular Expression Generation from Examples and Language
• StanfordPL/stoke: STOKE: A stochastic superoptimizer and program synthesizer

That may, in turn, call for including a short exposition on the enumerative/ stochastic/constraint-based search strategies, possibly with linking in a literature review like Gulwani 2017 for further details.

I suggest all that, in the spirit of making whole program synthesis domain more legible for non-experts, but the curious souls with software engineering background who might be reading JOSS.

What do you think?

-Alex

[Theomat]

Hi Alex,
Thanks a lot for the suggestions!

1. About citing the Codex paper, we should have done it, thanks.
2. About giving a broader overview of techniques and OSS software in program synthesis, that's also a good point. However in 1000 words we won't be able to say much, so it's more about citing more relevant work? Another natural reference is the AAAI paper which uses the current tool for experiments; we did a more thorough job on related works -- we may simply refer to that section explicitly.
   One last comment: many, if not most, of the program synthesis tools target a specific domain (DSL), and one (academic) appeal of DeepSynth is to work in a general fashion, allowing users to input DSLs themselves. For that reason, it's hard to list existing program synthesis tools, as each serves a different purpose.

• Nathanaël and Théo

[whedon]

👋 @Kraks, please update us on how your review is going (this is an automated reminder).

[njuaplusplus]

Hi @Theomat,

I have some problems completing the installation as instructed in your repo, could you take a look at this issue nathanael-fijalkow/DeepSynth#2 ? Thank you.

Best,
Shengwei

[njuaplusplus]

Hi Nath & Théo,

Thank you very much for your patience. I have read your AAAI paper. It's quite interesting. The following are my suggestions on the documentation and software paper.

1. Example usage
   I couldn't find detailed complete examples in the documentation. At least one complete example which can explore most of the features is expected.

2. Functionality documentation
   No API method documentation.

3. Community guidelines
   No such guidelines.

4. State of the field
   This section mentions some packages but didn't describe the difference or comparison. Besides, I suggest citing and comparing PROSE.

Best,
Shengwei

[arfon]

👋 folks. Just checking in here to see how things are going? @terrytangyuan – what's the next step here?

[terrytangyuan]

@Theomat Did you get a chance to take a look at the feedback above?

@bzz and @Kraks Would you like to take a closer look and provide your feedback as well?

[Theomat]

Hi,

We did look at the feedback above for points 1 up to 3, we have added more documentation within the README. We believe this is enough for the targeted users.

We are currently writing something on PROSE.

Best,

Nath and Théo

[arfon]

@editorialbot set 10.5281/zenodo.7194579 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7194579

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1145/3453483.3454080 may be a valid DOI for title: DreamCoder: bootstrapping inductive program synthesis with wake-sleep library learning
- 10.1145/3517034 may be a valid DOI for title: TF-Coder: Program Synthesis for Tensor Manipulations
- 10.1145/1925844.1926423 may be a valid DOI for title: Automating string processing in spreadsheets using input-output examples
- 10.1609/aaai.v36i6.20616 may be a valid DOI for title: Scaling Neural Program Synthesis with Distribution-based Search

INVALID DOIs

- None

[arfon]

@Theomat – can you check if the DOIs that @editorialbot is suggesting are correct for your paper and if they are, could you add them to your BibTeX file please?

[editorialbot]

👋 @openjournals/joss-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#3622, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@Theomat – I've also found a few small issues with your paper that need fixing: nathanael-fijalkow/DeepSynth#4

[Theomat]

Hi,

All the missing DOIs pointed out by the bot have been added.

[arfon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1145/3453483.3454080 is OK
- 10.1145/3517034 is OK
- 10.1145/1926385.1926423 is OK
- 10.1609/aaai.v36i6.20616 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1145/3453483.3454080 is OK
- 10.1145/3517034 is OK
- 10.1145/1926385.1926423 is OK
- 10.1609/aaai.v36i6.20616 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-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#3623, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04151 joss-papers#3624
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04151
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@njuaplusplus, @bzz – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@Theomat – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

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

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.04151/status.svg)](https://doi.org/10.21105/joss.04151)

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