Open editorialbot opened 2 months ago
Hello humans, 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
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.3389/fevo.2021.588292 is OK
- 10.25080/majora-92bf1922-011 is OK
- 10.5281/zenodo.5765804 is OK
- 10.1093/biomet/76.4.643 is OK
- 10.1214/18-aoas1177 is OK
MISSING DOIs
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: gllvm - Fast analysis of multivariate abundance da...
- No DOI given, and none found for title: Zero-inflation in the Multivariate Poisson Lognorm...
- No DOI given, and none found for title: The NLopt nonlinear-optimization package
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.90 T=0.09 s (702.9 files/s, 170255.1 lines/s)
-------------------------------------------------------------------------------
Language files blank comment code
-------------------------------------------------------------------------------
Python 30 1380 3087 6043
CSV 10 0 0 1948
Markdown 3 65 0 287
R 2 30 9 171
TeX 1 12 0 85
YAML 2 8 17 79
Jupyter Notebook 1 0 1026 64
TOML 1 6 8 53
DOS Batch 1 8 1 26
reStructuredText 7 13 56 17
Bourne Shell 1 2 0 13
make 1 4 7 9
-------------------------------------------------------------------------------
SUM: 60 1528 4211 8795
-------------------------------------------------------------------------------
Commit count by author:
636 bastien-mva
11 Julien Chiquet
9 Jean-Benoist Leger
1 Joon Kwon
Paper file info:
📄 Wordcount for paper.md
is 1064
✅ The paper includes a Statement of need
section
License info:
✅ License found: MIT License
(Valid open source OSI approved license)
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@LingfengLuo0510 @mrazomej this is the issue for the review! Let me know if you have any questions - more info can also be found here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
@editorialbot generate pdf
Figures were not displayed.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
nicer color in figure.
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
First, I must apologize for the delayed comments on this submission.
There are two main comments I would like to make about the state of the software and the paper.
quickstart
section would be greatly appreciated) or the differences between the different models. The documentation only contains the automatically generated API information from the function docstrings. Even the quickstart
section on the README.md
file does not explain anything being done.
1.a. On that note, between the paper and the documentation, it was not clear to me what the software's capabilities are. I felt that without reading the previous publication I stand no chance of understanding what your package can do, even though I have enough background knowledge on related areas. As the JOSS guidelines indicate:Documentation
There should be sufficient documentation for you, the reviewer, to understand the core functionality of the software under review. A README file (or equivalent) should include a high-level overview of this documentation.
Summary
section does not feel like an actual summary of the functionality of the software. @likeajumprope can correct me if I'm wrong, but I think of this section as the Abstract of the paper, where one can quickly assess whether the paper is relevant or not for one's intentions. Even the JOSS guidelines indicate that the paper should include:
A summary describing the high-level functionality and purpose of the software for a diverse, non-specialist audience.
2.a Fig. 2 does not have a caption that explains, among other things, what the legend labels are. Furthermore, when doing this kind of comparison, it would be handy to highlight which of the curves are directly related to your software. Something that can be added in a detailed caption or in the legend, something like model name (ours)
to guide the reader.
These are my first two initial comments. These changes are necessary for me to properly assess the software and the entire submission, as I need the most basic tools to understand the software's core functionality. From what I can get from glancing at the previous publications, this is an exciting piece of software. But my understanding is that, as a JOSS
publication, it needs to exist as a stand-alone piece of work where users (and reviewers) can utilize the software solely from the paper and the documentation information.
Thank you for your comments and suggestions. We have carefully considered them and made the necessary amendments to our manuscript and its accompanying documentation:
Documentation:
Manuscript:
We hope these revisions enhance the clarity and comprehensibility of our work.
Thank you for your time.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@Bastien-mva , thanks for the changes. In my opinion, the software is much better. @likeajumprope, I have completed my checklist.
Sorry for the delayed comments
Here are my comments: (1) Fig2 compares the running time of different packages, can you provide the code used to generate Figure 2. (2) Fig2 shows the fast computaiton speed of your porposed approach, it would be beneficial to include additional performance metrics. (3) Line 21: Consider rephrasing to "necessitating dimension reduction techniques suitable for count data." (4) Line 25: Remove the unnecessary brackets. (5) Line 34-37: Double-check the punctuation in lines 34-37 (6) When discussing GPU and CPU calculations for time comparison, please specify the exact machine type (e.g., GPU model, CPU cores) used. (7) Increase the font size in Figure 1 for better readability. (8) line 47: Verify the accuracy of the citation. (9) At the beginning of lines 52 and 56, consider adding a few sentences to introduce the other packages mentioned. (10) Rephrase the sentences in lines 72-76 for improved clarity and coherence. (11) Line 80, at the begining of a paragraph, make it more detailed. (12) Line 80: Choose between "maximizing" and "to maximize" in line 80 based on the intended meaning. (13) Line 80, "Bound" or "BOund"? (14) Maintain a consistent citation style throughout the paper, including journal names, volume numbers, and issue numbers.
Thanks you for your comments. We have carefully considered them and made the
necessary amendments to our manuscript:
(1) The code used to generate Figure 2 is available in the benchmark
folder
of the joss branch. Only the dataset must be downloaded and is available here https://zenodo.org/record/5765804/files/2k_cell_per_study_10studies.tar.bz2?download=1.
(2) We have considered incorporating figures showing the
Root Mean Squared Error (RMSE) between the estimated parameters and the true
parameters, for different number of samples $n$ and dimension $p$. However, we
do not think this is necessary as the performance claim
of this paper focus mainly on the computational efficiency of the proposed
method. Moreover, the RMSE is systematically verified each time the package is uploaded to PyPI via automated testing procedures (see
https://github.com/PLN-team/pyPLNmodels/blob/main/tests/test_common.py).
(13) It is "Evidence Lower BOund", to make the acronym "ELBO".
(14) We have maintained a uniform citation
format, which includes the title, journal, and
DOI.
All points not explicitly mentioned were satisfactorily addressed.
@mrazomej @LingfengLuo0510, We have rectified an error in the description of the optimization process in GLLVM. The optimization actually utilizes the TMB https://cran.r-project.org/web/packages/TMB/index.html library, as opposed to an alternate method previously mentioned. The necessary amendments have been made in the paper.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@Bastien-mva My comments have been addressed sufficiently. Just two more minor things: (1) Do we need to capitalize the "O" in “BOund”? (2) Line 115, the citation style is not consistent (no link provided).
Other than that, good to go here. @likeajumprope
I have added the link in the bibliography and corrected the capitalization in 'Bound'.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Submitting author: !--author-handle-->@bastien-mva<!--end-author-handle-- (Bastien Batardiere) Repository: https://github.com/PLN-team/pyPLNmodels.git Branch with paper.md (empty if default branch): joss Version: 0.0.78 Editor: !--editor-->@likeajumprope<!--end-editor-- Reviewers: @LingfengLuo0510, @mrazomej Archive: Pending
Status
Status badge code:
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
@LingfengLuo0510 & @mrazomej, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @likeajumprope know.
✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨
Checklists
📝 Checklist for @mrazomej