[PRE REVIEW]: BART-Survival: A Bayesian machine learning approach to survival analyses in Python

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@twj8CDC@mahfuz05062<!--end-editor-- Reviewers: @turgeonmaxime, @WeakCha Managing EiC: Kevin M. Moerman

Status

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Author instructions

Thanks for submitting your paper to JOSS @twj8CDC. Currently, there isn't a JOSS editor assigned to your paper.

@twj8CDC if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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editorialbot commented 2 months ago

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editorialbot commented 2 months ago

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

OK DOIs

- 10.1002/bimj.202200178 is OK
- 10.1214/19-AOS1889 is OK
- 10.1177/0962280217746191 is OK
- 10.1136/bmjopen-2023-077137 is OK
- 10.1038/s41598-020-77220-w is OK
- 10.1177/0962280218822140 is OK
- 10.18637/jss.v097.i01 is OK
- 10.1002/sim.6893 is OK
- 10.3390/stats5030038 is OK
- 10.18637/jss.v097.i01 is OK
- 10.7717/peerj-cs.1516 is OK
- 10.1136/bmj.317.7156.468 is OK
- 10.1038/sj.bjc.6601119 is OK
- 10.1214/09-AOAS285 is OK
- 10.1111/j.2517-6161.1972.tb00899.x is OK
- 10.1182/blood.V122.21.1728.1728 is OK
- 10.1007/978-3-319-19425-7 is OK
- 10.1214/08-AOAS169 is OK
- 10.1002/sim.6893 is OK
- 10.18637/jss.v097.i01 is OK

MISSING DOIs

- No DOI given, and none found for title: Bayesian Additive Regression Trees for Probabilist...
- No DOI given, and none found for title: Variable Selection with Random Survival Forest and...

INVALID DOIs

- None

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (591.4 files/s, 477343.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            11           3755             28          23030
SVG                              3              0              0           2689
CSS                              9            425             87           1761
JavaScript                      13            150            252            945
Python                           9            206            429            884
Jupyter Notebook                 5              0          22547            607
Markdown                        12            137              0            481
TeX                              1             22              0            342
DOS Batch                        1              8              1             26
TOML                             1              4              0             25
reStructuredText                 5             16             15             14
JSON                             1              0              0              9
make                             1              4              7              9
YAML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            73           4727          23366          30825
-------------------------------------------------------------------------------

Commit count by author:

    56  twj8CDC
     8  dependabot[bot]
     1  Boris Ning

editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 587

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot commented 2 months ago

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

editorialbot commented 2 months ago

Five most similar historical JOSS papers:

aorsf: An R package for supervised learning using the oblique random survival forest Submitting author: @bcjaeger Handling editor: @danielskatz (Active) Reviewers: @danielskatz Similarity score: 0.7521

SurPyval: Survival Analysis with Python Submitting author: @derrynknife Handling editor: @dfm (Active) Reviewers: @CamDavidsonPilon, @MatthewReid854 Similarity score: 0.7347

BayesMFSurv: An R Package to Estimate Bayesian Split-Population Survival Models With (and Without) Misclassified Failure Events Submitting author: @Nicolas-Schmidt Handling editor: @marcosvital (Active) Reviewers: @alletsee, @andybega Similarity score: 0.7268

MatSurv: Survival analysis and visualization in MATLAB Submitting author: @jhcreed Handling editor: @cMadan (Retired) Reviewers: @dsurujon, @ManuelaS Similarity score: 0.7239

survPen: an R package for hazard and excess hazard modelling with multidimensional penalized splines Submitting author: @fauvernierma Handling editor: @csoneson (Active) Reviewers: @corybrunson, @seabbs Similarity score: 0.7205

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman commented 2 months ago

@twj8CDC- thanks for your submission to JOSS. Unfortunately, given the small size of this submission, it doesn't meet our substantial scholarly effort criterion. We will therefore proceed to reject this submission.

One possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot reject

editorialbot commented 2 months ago

Paper rejected.

Kevin-Mattheus-Moerman commented 2 months ago

@twj8CDC apologies I appear to have acted too soon. I misread the above code report (looked at the number of blank lines by accident). I will work to re-open this submission. I will however query the scope as the submission is relatively small in terms of number of lines of code. So the board will review if this submission is in scope.

Kevin-Mattheus-Moerman commented 2 months ago

@openjournals/dev is there a way to "unreject" this submission? Or do the authors need to resubmit?

twj8CDC commented 2 months ago

@twj8CDC apologies I appear to have acted too soon. I misread the above code report (looked at the number of blank lines by accident). I will work to re-open this submission. I will however query the scope as the submission is relatively small in terms of number of lines of code. So the board will review if this submission is in scope.

@Kevin-Mattheus-Moerman Hi Kevin, thanks starting the review process. If it helps, I understand the LOC is lower than normal, however we believe that we meet scientific contribution qualification based on the following factors:

There is currently no other Bayesian Additive Regression Tree (BART) for survival analysis packages ready-made in python.
The associated BART-Survival algorithm is complex enough that an applied practitioner would not be able to or would not want to implement the algorithm from scratch.
The BART-Survival algorithm is a general solution that it can be applied to most Survival modeling problems (so it is not a niche use case)

Thanks! Jake

Kevin-Mattheus-Moerman commented 2 months ago

@openjournals/dev :wave:

xuanxu commented 2 months ago

There is no editorialbot command it but I've just unrejected manually

Kevin-Mattheus-Moerman commented 2 months ago

@xuanxu great, thanks

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot query scope

editorialbot commented 2 months ago

Submission flagged for editorial review.

danielskatz commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

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

editorialbot commented 2 months ago

Five most similar historical JOSS papers:

aorsf: An R package for supervised learning using the oblique random survival forest Submitting author: @bcjaeger Handling editor: @danielskatz (Active) Reviewers: @danielskatz Similarity score: 0.7522

SurPyval: Survival Analysis with Python Submitting author: @derrynknife Handling editor: @dfm (Active) Reviewers: @CamDavidsonPilon, @MatthewReid854 Similarity score: 0.7341

BayesMFSurv: An R Package to Estimate Bayesian Split-Population Survival Models With (and Without) Misclassified Failure Events Submitting author: @Nicolas-Schmidt Handling editor: @marcosvital (Active) Reviewers: @alletsee, @andybega Similarity score: 0.7265

MatSurv: Survival analysis and visualization in MATLAB Submitting author: @jhcreed Handling editor: @cMadan (Retired) Reviewers: @dsurujon, @ManuelaS Similarity score: 0.7237

survPen: an R package for hazard and excess hazard modelling with multidimensional penalized splines Submitting author: @fauvernierma Handling editor: @csoneson (Active) Reviewers: @corybrunson, @seabbs Similarity score: 0.7209

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot invite @mahfuz05062 as editor

editorialbot commented 2 months ago

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman commented 2 months ago

@twj8CDC I am pleased to inform you this work passed the initial scope review. I have just invited an editor who can hopefully handle this submission. In the mean time can you work on the below:

[ ] Some editors noted your README and paper are rather terse. Could you review these, and extend them where possible. I would recommend adding a brief (nearly lay person) description of the software's purpose and applications. Next I would clearly link to the documentation and testing, it may mean having to briefly reiterate some information from the documentation, but it will make the README more complete and user friendly.
[ ] Can you try to address the potential DOI issues reported above :point_up: ? You can call @editorialbot check references to check them again. Also if you make changes to the paper you can call @editorialbot generate pdf.

twj8CDC commented 2 months ago

@Kevin-Mattheus-Moerman thats great! I will address these issues as soon as possible. Thanks!

mahfuz05062 commented 2 months ago

@editorialbot assign @mahfuz05062 as editor

editorialbot commented 2 months ago

Assigned! @mahfuz05062 is now the editor

mahfuz05062 commented 1 month ago

Hi @twj8CDC , do you have any suggestions for potential reviewers? If so, please mention them here (without tagging them with an @). You can search the list of people who have already agreed to review and may be suitable for this submission. I will then reach out to the potential reviewers to finalize the reviewers for this submission.

twj8CDC commented 1 month ago

Hi @mahfuz05062. I think L. Liu and turgeonmaxime could be potential reviewers based on their interest in Survival analysis.

How many reviewers will be selected? I can try to identify a few more if needed.

Also I am still working on updating the readme and paper per Kevins comment. I should have it updated in the next day or two.

Thanks!

mahfuz05062 commented 1 month ago

@twj8CDC We need a minimum of two reviewers to agree to review to start the review process. Also, where are you on the suggested updates/changes?

twj8CDC commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1002/bimj.202200178 is OK
- 10.1214/19-AOS1889 is OK
- 10.1177/0962280217746191 is OK
- 10.1136/bmjopen-2023-077137 is OK
- 10.1038/s41598-020-77220-w is OK
- 10.1177/0962280218822140 is OK
- 10.18637/jss.v097.i01 is OK
- 10.1002/sim.6893 is OK
- 10.3390/stats5030038 is OK
- 10.18637/jss.v097.i01 is OK
- 10.7717/peerj-cs.1516 is OK
- 10.1136/bmj.317.7156.468 is OK
- 10.1038/sj.bjc.6601119 is OK
- 10.1214/09-AOAS285 is OK
- 10.1111/j.2517-6161.1972.tb00899.x is OK
- 10.1182/blood.V122.21.1728.1728 is OK
- 10.1007/978-3-319-19425-7 is OK
- 10.1214/08-AOAS169 is OK
- 10.1002/sim.6893 is OK
- 10.18637/jss.v097.i01 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Bayesian Additive Regression Trees for Probabilist...
- No DOI given, and none found for title: Variable Selection with Random Survival Forest and...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

twj8CDC commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1002/bimj.202200178 is OK
- 10.48550/arXiv.2206.03619 is OK
- 10.1214/19-AOS1889 is OK
- 10.1177/0962280217746191 is OK
- 10.1136/bmjopen-2023-077137 is OK
- 10.1038/s41598-020-77220-w is OK
- 10.1177/0962280218822140 is OK
- 10.18637/jss.v097.i01 is OK
- 10.1002/sim.6893 is OK
- 10.3390/stats5030038 is OK
- 10.18637/jss.v097.i01 is OK
- 10.48550/arXiv.1910.02160 is OK
- 10.7717/peerj-cs.1516 is OK
- 10.1136/bmj.317.7156.468 is OK
- 10.1038/sj.bjc.6601119 is OK
- 10.1214/09-AOAS285 is OK
- 10.1111/j.2517-6161.1972.tb00899.x is OK
- 10.1182/blood.V122.21.1728.1728 is OK
- 10.1007/978-3-319-19425-7 is OK
- 10.1214/08-AOAS169 is OK
- 10.1002/sim.6893 is OK
- 10.18637/jss.v097.i01 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

twj8CDC commented 1 month ago

@mahfuz05062 I have updated the readme and paper. Everything should be ready for the review process now. Thanks!

mahfuz05062 commented 1 month ago

Hi @turgeonmaxime and @WeakCha, are you interested in reviewing this article? Thanks!

WeakCha commented 1 month ago

Sure!

Best wishes, RL

On Tue, Sep 10, 2024 at 1:00 PM Mahfuzur Rahman @.***> wrote:

Hi @turgeonmaxime https://github.com/turgeonmaxime and @WeakCha https://github.com/WeakCha, are you interested in reviewing this article? Thanks!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7115#issuecomment-2341623969, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALQQQRZQ4S52USCXFGUSTBLZV4XUNAVCNFSM6AAAAABMXSPESSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBRGYZDGOJWHE . You are receiving this because you were mentioned.Message ID: @.***>

turgeonmaxime commented 1 month ago

Hi @mahfuz05062 yes, I'm available and interested

mahfuz05062 commented 1 month ago

Thank you @WeakCha and @turgeonmaxime. As two reviewers agreed to perform the peer review, I will start the review process now!

mahfuz05062 commented 1 month ago

@editorialbot start review

editorialbot commented 1 month ago

Can't start a review without reviewers

mahfuz05062 commented 1 month ago

@editorialbot add @turgeonmaxime as reviewer

editorialbot commented 1 month ago

@turgeonmaxime added to the reviewers list!

mahfuz05062 commented 1 month ago

@editorialbot add @WeakCha as reviewer

editorialbot commented 1 month ago

@WeakCha added to the reviewers list!

mahfuz05062 commented 1 month ago

@editorialbot start review

editorialbot commented 1 month ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7213.

openjournals / joss-reviews

[PRE REVIEW]: BART-Survival: A Bayesian machine learning approach to survival analyses in Python #7115

Status