[PRE REVIEW]: PolytopeWalk: Sparse MCMC Sampling over Polytopes

[editorialbot]

Submitting author: @bsun1220 (Benny Sun)
Repository: https://github.com/ethz-randomwalk/polytopewalk
Branch with paper.md (empty if default branch):
Version: v1.0.17
Editor: @vissarion
Reviewers: Pending
Managing EiC: Chris Vernon

Status

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Markdown: [![status](https://joss.theoj.org/papers/c7799a15f0b75c91e43ff4d8da5c5d85/status.svg)](https://joss.theoj.org/papers/c7799a15f0b75c91e43ff4d8da5c5d85)

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Software report:

github.com/AlDanial/cloc v 1.98  T=0.03 s (2772.8 files/s, 191922.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             27            352            101           2113
C/C++ Header                    25            230            626            460
Python                           6             99             34            326
YAML                             5             49             18            280
TeX                              1             23              0            191
Markdown                         2             66              0            177
CMake                            6             36             16            124
Jupyter Notebook                 2              0            361            111
reStructuredText                12             96            213             71
TOML                             1              7              7             43
DOS Batch                        1              8              1             26
Text                             2              0              0              9
Bourne Shell                     2             12             75              7
-------------------------------------------------------------------------------
SUM:                            92            978           1452           3938
-------------------------------------------------------------------------------

Commit count by author:

   130	Benny Sun
   102	Yuansi Chen
    35	bsun1220
     1	Ikko Eltociear Ashimine
     1	whatwilliam

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1573

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

✅ OK DOIs

- 10.1093/nar/gkv1049 is OK
- 10.32614/rj-2021-077 is OK
- 10.21105/joss.00061 is OK
- 10.1175/2007JCLI1571.1 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Approximating discrete probability distributions w...
- No DOI given, and none found for title: Sampling with Riemannian Hamiltonian Monte Carlo i...
- No DOI given, and none found for title: Fast MCMC Sampling Algorithms on Polytopes
- No DOI given, and none found for title: A Simple Analysis of the Dikin Walk
- No DOI given, and none found for title: Geometric Random Walks: A Survey
- No DOI given, and none found for title: Practical volume computation of structured convex ...
- No DOI given, and none found for title: Creation and analysis of biochemical constraint-ba...

❌ MISSING DOIs

- 10.1016/0004-3702(91)90084-w may be a valid DOI for title: Probabilistic Reasoning in Intelligent Systems:  N...
- 10.1145/3357713.3384272 may be a valid DOI for title: Strong Self-Concordance and Sampling
- 10.1561/9781680833911 may be a valid DOI for title: The many faces of degeneracy in conic optimization
- 10.1007/s101070050099 may be a valid DOI for title: Hit-and-run mixes fast
- 10.1007/s10107-003-0447-x may be a valid DOI for title: How to compute the volume in high dimension?
- 10.1016/j.ejor.2023.03.021 may be a valid DOI for title: Revisiting degeneracy, strict feasibility, stabili...
- 10.1016/j.softx.2021.100659 may be a valid DOI for title: Polyrun: A Java library for sampling from the boun...

❌ INVALID DOIs

- None

[editorialbot]

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

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[crvernon]

@editorialbot invite @vissarion as editor

👋 @vissarion will you be able to take this one on as editor?

[editorialbot]

Invitation to edit this submission sent!

[crvernon]

👋 @bsun1220 - while I am getting a topic editor assigned to your submission, please reduce the word count of your paper to <= 1000 words. Thanks.

[bsun1220]

@crvernon Sounds good, I have cut down on the paper!

[vissarion]

@editorialbot assign me as editor

[editorialbot]

Assigned! @vissarion is now the editor

[bsun1220]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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PxMCMC: A Python package for proximal Markov Chain Monte Carlo
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Software report:

github.com/AlDanial/cloc v 1.98  T=0.03 s (2800.7 files/s, 193795.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             27            352            101           2113
C/C++ Header                    25            230            626            460
Python                           6             99             34            326
YAML                             5             49             18            280
TeX                              1             23              0            191
Markdown                         2             65              0            176
CMake                            6             36             16            124
Jupyter Notebook                 2              0            361            111
reStructuredText                12             96            213             71
TOML                             1              7              7             43
DOS Batch                        1              8              1             26
Text                             2              0              0              9
Bourne Shell                     2             12             75              7
-------------------------------------------------------------------------------
SUM:                            92            977           1452           3937
-------------------------------------------------------------------------------

Commit count by author:

   130	Benny Sun
   102	Yuansi Chen
    37	bsun1220
     1	Ikko Eltociear Ashimine
     1	whatwilliam

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1255

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[bsun1220]

@bsun1220 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.

Using the reviewer suggestions from matt-graham who has a different paper on MCMC algorithms, @vissarion if you need help finding reviewers, I saw that larryshamalama, vankesteren, robmoss, njtierney and martinmodrak all had relevant profiles.