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[REVIEW]: PySS3: A new interpretable and simple machine learning model for text classification #3934

Closed whedon closed 2 years ago

whedon commented 2 years ago

Submitting author: !--author-handle-->@sergioburdisso<!--end-author-handle-- (Sergio Gastón Burdisso) Repository: https://github.com/sergioburdisso/pyss3 Branch with paper.md (empty if default branch): Version: v0.6.4 Editor: !--editor-->@bmcfee<!--end-editor-- Reviewers: @hbaniecki, @kmichael08 Archive: Pending

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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

@hbaniecki & @kmichael08, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @hbaniecki

✨ 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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @kmichael08

✨ 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

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @hbaniecki, @kmichael08 it looks like you're currently assigned to review this paper :tada:.

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whedon commented 2 years ago

Wordcount for paper.md is 1642

whedon commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1371/journal.pone.0168344 is OK
- 10.1016/j.eswa.2017.07.040 is OK
- 10.1007/978-3-319-44564-9_3 is OK
- 10.1007/978-3-319-65813-1_30 is OK
- 10.1016/j.eswa.2019.05.023 is OK
- 10.1016/j.patrec.2020.07.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 2 years ago

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

whedon commented 2 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=10.48 s (6.5 files/s, 3055.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSS                              6           1361            375           7369
Python                          10           1460           2144           5469
HTML                             5            429              6           4772
reStructuredText                20           1452           1207           1017
JavaScript                      10             85            193            897
Markdown                         6            208              0            392
Jupyter Notebook                 6              0           2668            276
TeX                              1             12              0            117
YAML                             2              8              5             46
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            68           5027           6606          20390
-------------------------------------------------------------------------------

Statistical information for the repository 'a31d62b5a31d0b1d086992e7' was
gathered on 2021/11/19.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Florian Angermeir                1            19             19            0.20
Sergio Burdisso                202         14552           4147           99.80

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
Florian Angermeir            18           94.7         16.4               22.22
Sergio Burdisso           10258           70.5         10.0                6.19
whedon commented 2 years ago

:wave: @kmichael08, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

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

kmichael08 commented 2 years ago

wave @kmichael08, please update us on how your review is going (this is an automated reminder).

I'll get to it within a week, thanks for checking

hbaniecki commented 2 years ago

Overall, the PySS3 package is mature and of high quality. It comes with extensive documentation and easy-to-follow tutorials. Over two years of development, it steadily gathered a recognizable user-base (55k downloads, 200+ stars). The core functionalities are a valuable and needed contribution to interpretable machine learning, especially in the context of model monitoring and interactive analysis.

Comment on substantial scholarly effort: As highlighted both in the software paper and documentation, two articles of the authors preceded this work:

"A text classification framework for simple and effective early depression detection over social media streams" (Expert Systems with Applications, 2019), https://doi.org/10.1016/j.eswa.2019.05.023, "τ-SS3: A text classifier with dynamic n-grams for early risk detection over text streams" (Pattern Recognition Letters, 2020), https://doi.org/10.1016/j.patrec.2020.07.001.

These focus mainly on introducing, evaluating and applying novel algorithms. At the same time, the software (paper) implements a convenient API for the machine learning models and contributes interactive (server, visual) tools to work with them.

Comment on contribution and authorship: From what I can tell looking at the GitHub repository, the submitting author made major contributions to the software, and is the only such in a strict sense of contributing code and documentation. Nevertheless, the full list of paper authors seems appropriate and complete, as the two other authors also contribute to this project, e.g. looking at the two preceding papers.

The authors addressed my issues on Functionality and Documentation. I will now proceed to review the paper contents.

bmcfee commented 2 years ago

Checking in on this as there hasn't been much action in the past week. @hbaniecki and @kmichael08 . Any updates here?

I know we're going into holidays and it's a busy time of year, but I'd like to know where this one stands and whether we should expect to pause until the new year.

hbaniecki commented 2 years ago

Hi, I have posted comments to the paper in the above issue and the initiative is on the authors' side to respond/address them. Edit. Then I could mark the missing checks on my list.

kmichael08 commented 2 years ago

I will do it the first week of January. Unfortunately, can't do it any faster

bmcfee commented 2 years ago

Happy new year everyone! I hope everyone's doing alright.

@kmichael08 have you had a chance to get started on this one yet?

@sergioburdisso have you been able to address @hbaniecki 's comments?

kmichael08 commented 2 years ago

I started with the section related to the software paper. My comments are in the issue linked above. Just a quick check. This paper is a shorter version of an arXiv preprint from 2019, and this preprint is referenced in this work. @bmcfee is this all good with the JOSS guidelines?

bmcfee commented 2 years ago

@kmichael08 yes, that should be fine. The JOSS preprint policy is listed here: https://joss.readthedocs.io/en/latest/submitting.html#preprint-policy

Authors are welcome to submit their papers to a preprint server (arXiv, bioRxiv, SocArXiv, PsyArXiv etc.) at any point before, during, or after the submission and review process.

Submission to a preprint server is not considered a previous publication.

bmcfee commented 2 years ago

@sergioburdisso checking in again - can you give us a quick update on progress in response to @hbaniecki 's comments?

sergioburdisso commented 2 years ago

Hi @bmcfee, @hbaniecki @kmichael08 ! First of all, thanks for taking the time to review our paper! I'm having a pretty rough "new year" so far, and couldn't manage to take care of the JOSS issues, but I'll try to do it this weekend, would it be OK if that's the case?

bmcfee commented 2 years ago

Sure, that's fine. Thanks for the update, and I hope your new year smooths out soon!

bmcfee commented 2 years ago

:wave: @sergioburdisso no pressure, just checking in again to see how things are going.

sergioburdisso commented 2 years ago

@bmcfee Last weekend couldn't make it, but I think that tomorrow I'll be finally able to do it! :muscle: (and thanks for checking in again :sunglasses:)

bmcfee commented 2 years ago

Great, thanks for the quick response!

bmcfee commented 2 years ago

Just checking in again - how are things going here?

bmcfee commented 2 years ago

@sergioburdisso checking in again. It's been over a month since we've heard from you.

bmcfee commented 2 years ago

Thanks @sergioburdisso for keeping this moving forward - how are things now regarding reviewer comments?

https://github.com/sergioburdisso/pyss3/issues/21 https://github.com/sergioburdisso/pyss3/issues/24

bmcfee commented 2 years ago

It looks like there's been no movement here since early April. Is there anything we can help with to keep this moving?

bmcfee commented 2 years ago

:wave: @sergioburdisso how is this one doing?

kyleniemeyer commented 2 years ago

Hi @sergioburdisso, it's been a while since we have heard from you. Are you still planning on working on this submission? If we do not hear from you in the next few days, either here or via email, we will have to withdraw this submission.

arfon commented 2 years ago

@editorialbot reject

@bmcfee – this submission seems to be abandoned. As such, I'm proceeding to reject. Thanks for your work here @bmcfee and reviewers @hbaniecki & @kmichael08. Sorry this submission didn't work out.

editorialbot commented 2 years ago

Paper rejected.