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[PRE REVIEW]: TorchSurv: A Lightweight Package for Deep Survival Analysis #7032

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editorialbot opened this issue Jul 24, 2024 · 49 comments
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[PRE REVIEW]: TorchSurv: A Lightweight Package for Deep Survival Analysis #7032

editorialbot opened this issue Jul 24, 2024 · 49 comments
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pre-review Python R TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented Jul 24, 2024 •
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Submitting author: @melodiemonod (Mélodie Monod)
Repository: https://github.com/Novartis/torchsurv
Branch with paper.md (empty if default branch): 45-joss-submission
Version: v0.1.2
Editor: @kanishkan91
Reviewers: @WeakCha, @LingfengLuo0510
Managing EiC: Chris Vernon

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/02d7496da2b9cc34f9a6e04cabf2298d"><img src="https://joss.theoj.org/papers/02d7496da2b9cc34f9a6e04cabf2298d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/02d7496da2b9cc34f9a6e04cabf2298d/status.svg)](https://joss.theoj.org/papers/02d7496da2b9cc34f9a6e04cabf2298d)

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

@melodiemonod 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.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Jul 24, 2024
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Hello human, 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:

@editorialbot commands

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

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.18 s (377.5 files/s, 67094.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           1224           2067           4133
Markdown                         7            271              0            679
R                                7            221            158            520
TeX                              2             47              0            520
Jupyter Notebook                 2              0           1551            238
YAML                             6             34              6            201
TOML                             1              8              0             49
Bourne Shell                     4             20              3             40
reStructuredText                 5             16             37             13
make                             1              5              8             10
JSON                             7              0              0              7
-------------------------------------------------------------------------------
SUM:                            68           1846           3830           6410
-------------------------------------------------------------------------------

Commit count by author:

    29	Peter Krusche
    17	Thibaud Coroller
     9	melodiemonod
     7	Mélodie Monod
     6	corolth1
     2	Peter Krusche (Novartis)
     1	Ikko Eltociear Ashimine

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Paper file info:

📄 Wordcount for paper.md is 1911

✅ The paper includes a Statement of need section

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License info:

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

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⚠️ An error happened when generating the pdf.

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

OK DOIs

- 10.1016/s0197-2456(03)00072-2 is OK
- 10.1093/bioinformatics/btr511 is OK
- 10.1111/j.0006-341x.2000.00337.x is OK
- 10.1111/j.0006-341x.2005.030814.x is OK
- 10.1002/bimj.201200045 is OK
- 10.1198/016214507000000149 is OK
- 10.1093/biostatistics/kxy006 is OK
- 10.1002/sim.4154 is OK
- 10.1002/(sici)1097-0258(19960229)15:4<361::aid-sim168>3.0.co;2-4 is OK
- 10.1002/(sici)1097-0258(19990915/30)18:17/18<2529::aid-sim274>3.0.co;2-5 is OK
- 10.1080/01621459.1977.10480613 is OK
- 10.2307/1402659 is OK

MISSING DOIs

- 10.21105/joss.01317 may be a valid DOI for title: lifelines: survival analysis in Python
- No DOI given, and none found for title: Package ‘survival’
- No DOI given, and none found for title: Pytorch: An imperative style, high-performance dee...
- No DOI given, and none found for title: scikit-survival: A Library for Time-to-Event Analy...
- No DOI given, and none found for title: Package ‘survAUC’
- 10.1109/cvpr42600.2020.00975 may be a valid DOI for title: Momentum contrast for unsupervised visual represen...
- 10.1186/s12874-018-0482-1 may be a valid DOI for title: DeepSurv: personalized treatment recommender syste...
- No DOI given, and none found for title: Time-to-Event Prediction with Neural Networks and ...
- No DOI given, and none found for title: auton-survival: An open-source package for regress...
- 10.1007/978-1-4612-4380-9_37 may be a valid DOI for title: Regression Models and Life‐Tables
- No DOI given, and none found for title: The Weibull Distribution
- No DOI given, and none found for title: A Package for Survival Analysis in R
- No DOI given, and none found for title: torchlife: Survival Analysis using pytorch
- No DOI given, and none found for title: Estimators of prediction accuracy for time-to-even...
- No DOI given, and none found for title: Time-Dependent ROC Curve and AUC for Censored Surv...
- No DOI given, and none found for title: Riskset ROC Curve Estimation from Censored Surviva...
- No DOI given, and none found for title: Time-Dependent ROC Curve Estimation from Censored ...
- No DOI given, and none found for title: Risk Regression Models and Prediction Scores for S...
- No DOI given, and none found for title: Predictive Evaluation Metrics in Survival Analysis
- No DOI given, and none found for title: Prediction Error Curves for Risk Prediction Models...

INVALID DOIs

- None

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👋 @melodiemonod - Thanks for your submission to JOSS. While I am getting you set up with a topic editor, please see if you can fix the PDF compile issue flagged in a comment above due to their being an error in your paper or bib file. Also, please reduce the length of your paper to right around 1000 words and try to fix as many of the missing DOI listed above as you can. Thanks!

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@editorialbot invite @kanishkan91 as editor

👋 @kanishkan91 - can you take this one on?

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Invitation to edit this submission sent!

@kanishkan91
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@crvernon I can edit this!

@crvernon
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@editorialbot assign @kanishkan91 as editor

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Assigned! @kanishkan91 is now the editor

@tcoroller tcoroller mentioned this issue Jul 29, 2024
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Hello @tcoroller, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

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@editorialbot check references

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

OK DOIs

- 10.32614/CRAN.package.survival is OK
- 10.32614/CRAN.package.survAUC is OK
- 10.1109/cvpr42600.2020.00975 is OK
- 10.1186/s12874-018-0482-1 is OK
- 10.1007/978-1-4612-4380-9_37 is OK
- 10.1016/s0197-2456(03)00072-2 is OK
- 10.32614/CRAN.package.survival is OK
- 10.32614/CRAN.package.survAUC is OK
- 10.32614/CRAN.package.timeROC is OK
- 10.32614/CRAN.package.risksetROC is OK
- 10.32614/CRAN.package.survivalROC is OK
- 10.1093/bioinformatics/btr511 is OK
- 10.32614/CRAN.package.riskRegression is OK
- 10.32614/CRAN.package.SurvMetrics is OK
- 10.32614/CRAN.package.pec is OK
- 10.1111/j.0006-341x.2000.00337.x is OK
- 10.1111/j.0006-341x.2005.030814.x is OK
- 10.1002/bimj.201200045 is OK
- 10.1198/016214507000000149 is OK
- 10.1093/biostatistics/kxy006 is OK
- 10.1002/sim.4154 is OK
- 10.1002/(sici)1097-0258(19960229)15:4<361::aid-sim168>3.0.co;2-4 is OK
- 10.1002/(sici)1097-0258(19990915/30)18:17/18<2529::aid-sim274>3.0.co;2-5 is OK
- 10.1080/01621459.1977.10480613 is OK
- 10.2307/1402659 is OK

MISSING DOIs

- No DOI given, and none found for title: scikit-survival: A Library for Time-to-Event Analy...
- No DOI given, and none found for title: Time-to-Event Prediction with Neural Networks and ...
- No DOI given, and none found for title: The Weibull Distribution
- No DOI given, and none found for title: A Package for Survival Analysis in R

INVALID DOIs

- https://doi.org/10.21105/joss.01317 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.48550/arXiv.1912.01703 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.48550/arXiv.2204.07276 is INVALID because of 'https://doi.org/' prefix

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@editorialbot check repository

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.18 s (370.1 files/s, 65740.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           1224           2067           4133
Markdown                         7            263              0            660
TeX                              2             47              0            540
R                                7            221            158            520
Jupyter Notebook                 2              0           1551            238
YAML                             6             34              6            201
TOML                             1              8              0             49
Bourne Shell                     4             20              3             40
reStructuredText                 5             16             37             13
make                             1              5              8             10
JSON                             7              0              0              7
-------------------------------------------------------------------------------
SUM:                            68           1838           3830           6411
-------------------------------------------------------------------------------

Commit count by author:

    29	Peter Krusche
    17	Thibaud Coroller
     9	melodiemonod
     8	corolth1
     7	Mélodie Monod
     2	Peter Krusche (Novartis)
     1	Ikko Eltociear Ashimine

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Paper file info:

📄 Wordcount for paper.md is 1372

✅ The paper includes a Statement of need section

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License info:

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

@tcoroller
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@editorialbot check references

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

OK DOIs

- 10.21105/joss.01317 is OK
- 10.32614/CRAN.package.survival is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.5281/zenodo.3352342 is OK
- 10.32614/CRAN.package.survAUC is OK
- 10.1109/cvpr42600.2020.00975 is OK
- 10.1186/s12874-018-0482-1 is OK
- 10.48550/arXiv.2204.07276 is OK
- 10.1007/978-1-4612-4380-9_37 is OK
- 10.1016/s0197-2456(03)00072-2 is OK
- 10.32614/CRAN.package.survival is OK
- 10.32614/CRAN.package.survival is OK
- 10.32614/CRAN.package.survAUC is OK
- 10.32614/CRAN.package.timeROC is OK
- 10.32614/CRAN.package.risksetROC is OK
- 10.32614/CRAN.package.survivalROC is OK
- 10.1093/bioinformatics/btr511 is OK
- 10.32614/CRAN.package.riskRegression is OK
- 10.32614/CRAN.package.SurvMetrics is OK
- 10.32614/CRAN.package.pec is OK
- 10.1111/j.0006-341x.2000.00337.x is OK
- 10.1111/j.0006-341x.2005.030814.x is OK
- 10.1002/bimj.201200045 is OK
- 10.1198/016214507000000149 is OK
- 10.1093/biostatistics/kxy006 is OK
- 10.1002/sim.4154 is OK
- 10.1002/(sici)1097-0258(19960229)15:4<361::aid-sim168>3.0.co;2-4 is OK
- 10.1002/(sici)1097-0258(19990915/30)18:17/18<2529::aid-sim274>3.0.co;2-5 is OK
- 10.1080/01621459.1977.10480613 is OK
- 10.2307/1402659 is OK

MISSING DOIs

- No DOI given, and none found for title: Time-to-Event Prediction with Neural Networks and ...
- No DOI given, and none found for title: The Weibull Distribution

INVALID DOIs

- None

@tcoroller
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Paper file info:

📄 Wordcount for paper.md is 1372

✅ The paper includes a Statement of need section

Hi @crvernon , thank you for helping us prepare the review. I will take over the process while Melodie is away.

  • I have fixed the DOIs - with two that I just cannot find
  • I have trimmed the text to 1040 words, excluding the markdown tags (authors, affiliations) and the two table links. Please let me know if thats acceptable to you now

@tcoroller
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@editorialbot generate pdf

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⚠️ An error happened when generating the pdf.

@tcoroller
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@editorialbot generate pdf

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⚠️ An error happened when generating the pdf.

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

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Five most similar historical JOSS papers:

lifelines: survival analysis in Python
Submitting author: @CamDavidsonPilon
Handling editor: @trallard (Retired)
Reviewers: @becarioprecario, @sunhwan
Similarity score: 0.6930

survxai: an R package for structure-agnostic explanations of survival models
Submitting author: @AleksandraDabrowska
Handling editor: @yochannah (Retired)
Reviewers: @hiendn, @dirmeier
Similarity score: 0.6579

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: 0.6557

aorsf: An R package for supervised learning using the oblique random survival forest
Submitting author: @bcjaeger
Handling editor: @danielskatz (Active)
Reviewers: @danielskatz
Similarity score: 0.6373

PyMSM: Python package for Competing Risks and Multi-State models for Survival Data
Submitting author: @hrossman
Handling editor: @majensen (Active)
Reviewers: @CamDavidsonPilon, @stefanocoretta
Similarity score: 0.6355

⚠️ 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.

@crvernon
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Thanks @tcoroller, @kanishkan91 will get you set up with some reviewers soon.

@tcoroller
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Thanks!

@kanishkan91
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@tcoroller I was away on paternity leave. I'l make sure this review gets started in the next week. My apologies for the delay.

@tcoroller
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@kanishkan91 welcome back and thank you for the update! I came back myself recently from one, so I fully understand how busy you may be right now. Thanks again

@kanishkan91
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@tcoroller, @crvernon Quick update. I just got back from medical leave. I am in the process of finding a second reviewer for this. After that, I can get the review started. Moving forward feel free to ping me in this thread in case you need an update. My hope is that after the review gets started, you'll have review comments within the next month. Let me know what you think.

@kanishkan91
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@WeakCha given your experience with JOSS and your recent reviews, would you be interested in reviewing this paper? I know you just got done with a review 3 weeks ago. Let me know what you think.

@kanishkan91
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@RhysPeploe would you be interested in reviewing this paper given your previous experience with JOSS and interests? It seemed like a good fit.

@WeakCha
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WeakCha commented Oct 3, 2024 via email

@kanishkan91
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@editorialbot add @WeakCha as reviewer

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@WeakCha added to the reviewers list!

@kanishkan91
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@mhu48 Given your previous experience reviewing for JOSS, would you be interested in reviewing this paper? It seems like a good fit given your interests and profile. Let me know what you think.

@kanishkan91
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@LingfengLuo0510 would you be interested in reviewing this manuscript for JOSS? I see that you just got done with another review review a month ago. Let me know what you think.

@LingfengLuo0510
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LingfengLuo0510 commented Oct 10, 2024 via email

@kanishkan91
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@editorialbot add @LingfengLuo0510 as reviewer

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@LingfengLuo0510 added to the reviewers list!

@kanishkan91
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@WeakCha , @LingfengLuo0510 - Thanks so much for agreeing to review. We are ready to get this review started.

@kanishkan91
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@editorialbot start review

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OK, I've started the review over in #7341.

@mhu48
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mhu48 commented Oct 10, 2024 via email

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@kanishkan91 kanishkan91

@LingfengLuo0510 LingfengLuo0510

@WeakCha WeakCha

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