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[PRE REVIEW]: CBX: Python and Julia Packages for Consensus-Based Interacting Particle Methods #6526

Closed editorialbot closed 7 months ago

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@rafaelbailo<!--end-author-handle-- (Rafael Bailo) Repository: https://github.com/PdIPS/CBX Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@mstimberg<!--end-editor-- Reviewers: @AlessandroPierro, @gdalle, @kellertuer, @Bobby-Huggins Managing EiC: Daniel S. Katz

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Markdown: [![status](https://joss.theoj.org/papers/008799348e8232eb9fe8180712e2dfb8/status.svg)](https://joss.theoj.org/papers/008799348e8232eb9fe8180712e2dfb8)

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@rafaelbailo 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 8 months ago

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:

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editorialbot commented 8 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (581.1 files/s, 85531.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             53              0            483
Markdown                         2             39              0            121
YAML                             1              1              4             18
JSON                             1              0              0             17
-------------------------------------------------------------------------------
SUM:                             5             93              4            639
-------------------------------------------------------------------------------

Commit count by author:

    16  Tim Roith
    15  Dr Rafael Bailo
    10  Konstantin Riedl
     5  TimRoith
     5  ctotzeck
     4  Urbain Vaes
     2  Susana Gomes
     2  aletheaBarbaro
editorialbot commented 8 months ago

Paper file info:

📄 Wordcount for paper.md is 1857

✅ The paper includes a Statement of need section

editorialbot commented 8 months ago

License info:

🔴 Failed to discover a valid open source license

editorialbot commented 8 months ago

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

danielskatz commented 8 months ago

Submission message from the authors:

This is a first submission to JOSS of two packages for consensus-based optimisation (unconstrained, global, derivative-free optimisation). This is a combined submission of two packages (one for Python, one for Julia) with common functionality. The Python package (https://pdips.github.io/CBXpy/) is hosted at https://github.com/PdIPS/CBXpy, and the Julia package (https://pdips.github.io/ConsensusBasedX.jl/) is hosted at https://github.com/PdIPS/ConsensusBasedX.jl . We are submitting the paper from a third repository, https://github.com/PdIPS/CBX, on the suggestion of Arfon Smith. A preprint of this paper has been made available on arXiv: https://arxiv.org/abs/2403.14470 . No portion of the paper will be submitted elsewhere.

danielskatz commented 8 months ago

Re automated checks above, both repos have open source licenses (MIT).

editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.05320 is OK
- 10.5281/zenodo.1054110 is OK
- 10.21105/joss.03866 is OK
- 10.5281/zenodo.7754236 is OK
- 10.1142/S0218202518500276 is OK
- 10.1017/S0956792523000293 is OK
- 10.1142/S0218202521500342 is OK
- 10.5281/ZENODO.7738525 is OK
- 10.1007/978-3-662-12616-5 is OK
- 10.1007/s10898-024-01369-1 is OK

MISSING DOIs

- 10.1142/s0218202517400061 may be a valid DOI for title: A consensus-based model for global optimization an...
- 10.1007/978-3-662-38527-2_55 may be a valid DOI for title: On Bayesian methods for seeking the extremum
- No DOI given, and none found for title: Studien ueber das Gleichgewicht der lebenden Kraft
- 10.1016/j.eswa.2011.09.076 may be a valid DOI for title: A survey: Ant Colony Optimization based recent res...
- 10.1007/s10462-012-9328-0 may be a valid DOI for title: A comprehensive survey: artificial bee colony (ABC...
- 10.1007/978-3-642-04944-6_14 may be a valid DOI for title: Firefly algorithms for multimodal optimization
- No DOI given, and none found for title: The wind driven optimization technique and its app...
- No DOI given, and none found for title: Particle swarm optimization
- No DOI given, and none found for title: The theory and practice of simulated annealing
- No DOI given, and none found for title: The convergence of the random search method in the...
- No DOI given, and none found for title: Planning experiments seeking maxima
- No DOI given, and none found for title: "Direct Search" Solution of Numerical and Statisti...
- No DOI given, and none found for title: Consensus-based optimization methods converge glob...
- No DOI given, and none found for title: Trends in consensus-based optimization
- No DOI given, and none found for title: Consensus-based sampling
- 10.1007/978-1-4613-1997-9 may be a valid DOI for title: A connectionist machine for genetic hillclimbing
- 10.21105/joss.00433 may be a valid DOI for title: PySwarms: a research toolkit for Particle Swarm Op...
- No DOI given, and none found for title: scikit-opt
- No DOI given, and none found for title: DEAP: Evolutionary Algorithms Made Easy
- No DOI given, and none found for title: cbo-in-python
- No DOI given, and none found for title: polarcbo
- No DOI given, and none found for title: PyPop7: A Pure-Python Library for Population-Based...
- No DOI given, and none found for title: Polarized consensus-based dynamics for optimizatio...
- 10.21105/joss.00615 may be a valid DOI for title: Optim: A mathematical optimization package for Jul...
- 10.21105/joss.04723 may be a valid DOI for title: Metaheuristics: A Julia package for single-and mul...
- 10.1051/cocv/2020046 may be a valid DOI for title: A consensus-based global optimization method for h...
- No DOI given, and none found for title: Pytorch: An imperative style, high-performance dee...
- 10.1007/978-3-031-02462-7_46 may be a valid DOI for title: Convergence of Anisotropic Consensus-Based Optimiz...
- No DOI given, and none found for title: On the global convergence of particle swarm optimi...
- No DOI given, and none found for title: Gradient is All You Need?
- No DOI given, and none found for title: FedCBO: Reaching Group Consensus in Clustered Fede...
- 10.1007/s10898-024-01369-1 may be a valid DOI for title: Consensus-Based Optimization for Multi-Objective P...
- No DOI given, and none found for title: An adaptive consensus based method for multi-objec...
- No DOI given, and none found for title: Consensus-based optimization on the sphere: conver...
- No DOI given, and none found for title: Constrained consensus-based optimization
- No DOI given, and none found for title: On the mean-field limit for the consensus-based op...
- No DOI given, and none found for title: Consensus-based optimization for saddle point prob...
- No DOI given, and none found for title: Consensus-Based Optimization with Truncated Noise
- No DOI given, and none found for title: Large deviations techniques and applications
- No DOI given, and none found for title: Consensus-based rare event estimation

INVALID DOIs

- None
danielskatz commented 8 months ago

@rafaelbailo - thanks for your submission. Please add countries to all affiliations in your .md file when you get a chance. I'll look for an editor for this submission next.

danielskatz commented 8 months ago

@mstimberg - Do you think you would be able to take on editing this submission? Note that it's a bit more complicated than most, with two repos for Python and Julia packages.

danielskatz commented 8 months ago

@editorialbot invite @mstimberg as editor

editorialbot commented 8 months ago

Invitation to edit this submission sent!

danielskatz commented 8 months ago

@rafaelbailo - In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

mstimberg commented 8 months ago

@editorialbot assign me as editor

Happy to edit this submission !

editorialbot commented 8 months ago

Assigned! @mstimberg is now the editor

mstimberg commented 8 months ago

@rafaelbailo I will handle this submission process as the editor. The first step will be to find reviewers. If you have any suggestions, please mention them here (without tagging their username with @).

rafaelbailo commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

rafaelbailo commented 8 months ago

Thank you @danielskatz for setting up the review and @mstimberg for agreeing to be the handling editor. I have added the country information to the affiliations. I have also added the missing DOIs as suggested. I shall follow up shortly with reviewer suggestions.

rafaelbailo commented 8 months ago

@mstimberg for Julia, we suggest Oliver Dunbar and Guillaume Dalle. For Python, we suggest Alessandro Pierro and Mathieu Besançon.

mstimberg commented 8 months ago

@editorialbot add @AlessandroPierro as reviewer

Thanks again for helping out!

editorialbot commented 8 months ago

@AlessandroPierro added to the reviewers list!

mstimberg commented 8 months ago

Hi @rafaelbailo Thank you for your suggestions. I have contacted several potential reviewers over mail, and I am waiting for their reply (as you can see above, I do have one positive reply already). Please note that I will be out-of-office until April 7th, so I might be slow to reply during that time. Most likely, the review process will not start before I am back. Many thanks for your patience!

rafaelbailo commented 8 months ago

No problem @mstimberg , thanks for all the work!

rafaelbailo commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.21105/joss.05320 is OK
- 10.5281/zenodo.1054110 is OK
- 10.21105/joss.03866 is OK
- 10.5281/zenodo.7754236 is OK
- 10.1142/S0218202518500276 is OK
- 10.1017/S0956792523000293 is OK
- 10.1142/S0218202521500342 is OK
- 10.5281/ZENODO.7738525 is OK
- 10.1007/978-3-662-12616-5 is OK
- 10.1142/s0218202517400061 is OK
- 10.1007/978-3-662-38527-2_55 is OK
- 10.1016/j.eswa.2011.09.076 is OK
- 10.1007/s10462-012-9328-0 is OK
- 10.1007/978-3-642-04944-6_14 is OK
- 10.1007/978-1-4613-1997-9 is OK
- 10.21105/joss.00433 is OK
- 10.21105/joss.00615 is OK
- 10.21105/joss.04723 is OK
- 10.1051/cocv/2020046 is OK
- 10.1007/978-3-031-02462-7_46 is OK
- 10.1007/s10898-024-01369-1 is OK

MISSING DOIs

- No DOI given, and none found for title: Studien ueber das Gleichgewicht der lebenden Kraft
- No DOI given, and none found for title: The wind driven optimization technique and its app...
- No DOI given, and none found for title: Particle swarm optimization
- No DOI given, and none found for title: The theory and practice of simulated annealing
- No DOI given, and none found for title: The convergence of the random search method in the...
- No DOI given, and none found for title: Planning experiments seeking maxima
- No DOI given, and none found for title: "Direct Search" Solution of Numerical and Statisti...
- No DOI given, and none found for title: Consensus-based optimization methods converge glob...
- No DOI given, and none found for title: Trends in consensus-based optimization
- No DOI given, and none found for title: Consensus-based sampling
- No DOI given, and none found for title: scikit-opt
- No DOI given, and none found for title: DEAP: Evolutionary Algorithms Made Easy
- No DOI given, and none found for title: cbo-in-python
- No DOI given, and none found for title: polarcbo
- No DOI given, and none found for title: PyPop7: A Pure-Python Library for Population-Based...
- No DOI given, and none found for title: Polarized consensus-based dynamics for optimizatio...
- No DOI given, and none found for title: Pytorch: An imperative style, high-performance dee...
- No DOI given, and none found for title: On the global convergence of particle swarm optimi...
- No DOI given, and none found for title: Gradient is All You Need?
- No DOI given, and none found for title: FedCBO: Reaching Group Consensus in Clustered Fede...
- No DOI given, and none found for title: An adaptive consensus based method for multi-objec...
- No DOI given, and none found for title: Consensus-based optimization on the sphere: conver...
- No DOI given, and none found for title: Constrained consensus-based optimization
- No DOI given, and none found for title: On the mean-field limit for the consensus-based op...
- No DOI given, and none found for title: Consensus-based optimization for saddle point prob...
- No DOI given, and none found for title: Consensus-Based Optimization with Truncated Noise
- No DOI given, and none found for title: Large deviations techniques and applications
- No DOI given, and none found for title: Consensus-based rare event estimation

INVALID DOIs

- None
mstimberg commented 7 months ago

@editorialbot add @gdalle as reviewer

Thanks again for helping with this review!

editorialbot commented 7 months ago

@gdalle added to the reviewers list!

gdalle commented 7 months ago

Just to make sure that it is part of the public record as well (I have informed the editor): the last author of the paper @urbainvaes was a colleague of mine at École des Ponts. I left this institution very recently (2022) and will come back to it in 2025. However, we have never written anything together, and I don't believe this will affect my ability to judge the present paper.

mstimberg commented 7 months ago

I confirm that we waive this potential conflict of interest in accordance with the JOSS policy (CC @danielskatz)

mstimberg commented 7 months ago

@editorialbot add @kellertuer as reviewer

editorialbot commented 7 months ago

@kellertuer added to the reviewers list!

mstimberg commented 7 months ago

@editorialbot add @Bobby-Huggins as reviewer

editorialbot commented 7 months ago

@Bobby-Huggins added to the reviewers list!

mstimberg commented 7 months ago

Many thanks again to all reviewers (@Bobby-Huggins and @AlessandroPierro will focus on the Python package; @kellertuer and @gdalle will review on the Julia side) for agreeing to help out. I will now start the official review issue, all future discussions will take place over there :wave:

mstimberg commented 7 months ago

@editorialbot start review

editorialbot commented 7 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6611.