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[PRE REVIEW]: Pyrimidine: An algebra-inspired Programming framework for evolutionary algorithms #6142

Closed editorialbot closed 6 months ago

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@Freakwill<!--end-author-handle-- (Congwei Song) Repository: https://github.com/Freakwill/pyrimidine Branch with paper.md (empty if default branch): Version: v1.5.4 Editor: !--editor-->@boisgera<!--end-editor-- Reviewers: @mmore500, @sjvrijn Managing EiC: Arfon Smith

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Markdown: [![status](https://joss.theoj.org/papers/60f6f831c3d0037e1aff4f5fa13bfaf5/status.svg)](https://joss.theoj.org/papers/60f6f831c3d0037e1aff4f5fa13bfaf5)

Author instructions

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

@Freakwill 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 commented 10 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:

@editorialbot generate pdf
editorialbot commented 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.20 s (802.9 files/s, 247455.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           4737           4760          17564
HTML                            16           1014             48           9376
Python                         103           2320           1188           4860
Markdown                         9            589              0           1375
CSS                              5            304             69           1291
TeX                              1             20              0            164
YAML                             5             19             27            106
reStructuredText                 6             80            150             90
DOS Batch                        1              8              1             26
TOML                             1              5              1             24
make                             1              4              7              9
INI                              1              0              0              2
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                           163           9100           6251          34888
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 2020

editorialbot commented 10 months ago

Failed to discover a Statement of need section in paper

editorialbot commented 10 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 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/gji/ggad446 is OK
- 10.1088/1742-6596/1719/1/012102 is OK
- 10.1109/ICEC.1997.592270 is OK
- 10.1007/s00500-016-2474-6 is OK

MISSING DOIs

- 10.1007/978-3-319-31204-0_9 may be a valid DOI for title: Automating Biomedical Data Science Through Tree-Based Pipeline Optimization

INVALID DOIs

- None
editorialbot commented 10 months ago

Five most similar historical JOSS papers:

Quilë: C++ genetic algorithms scientific library Submitting author: @ttarkowski Handling editor: @vissarion (Active) Reviewers: @mbarzegary, @acrlakshman Similarity score: 0.8091

pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search Submitting author: @pySRURGS Handling editor: @arokem (Retired) Reviewers: @iljah, @nicoguaro Similarity score: 0.8090

DEPP - Differential Evolution Parallel Program Submitting author: @gbertoldo Handling editor: @meg-simula (Retired) Reviewers: @HaoZeke, @dham Similarity score: 0.8087

GAIM: A C++ library for Genetic Algorithms and Island Models Submitting author: @gdetor Handling editor: @majensen (Active) Reviewers: @sjvrijn, @sarats Similarity score: 0.8062

dcgp: Differentiable Cartesian Genetic Programming made easy. Submitting author: @darioizzo Handling editor: @VivianePons (Retired) Reviewers: @Ohjeah, @shah314 Similarity score: 0.7986

⚠️ 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.

arfon commented 10 months ago

@Freakwill – you mentioned an earlier paper in your submission notes. Could you please link to it here so I can better understand what the focus/content of the earlier paper was?

Freakwill commented 10 months ago

Hi @arfon, I have translated the article to English: text.md

PS: original paper: https://pan.baidu.com/s/1IiXkm7XEaipOZ_mEeFWVng?pwd=n3a4 This is the journal (in Chinese) link: http://www.comprg.com.cn/post_show.asp?id=12947

@Freakwill – you mentioned an earlier paper in your submission notes. Could you please link to it here so I can better understand what the focus/content of the earlier paper was?

arfon commented 10 months ago

Hi @Freakwill – I'm afraid we don't have a way to deal with non-English based submissions. Could you please provide some kind of translated artifact here for us to review? Thank you.

Freakwill commented 10 months ago

I translate the article to English. It was written about 3 years ago. In these three years, the program has been greatly redesigned. @arfon Thank you for reviewing my submission. What could I do to improve the progress of reviewing or just wait?

text.md

Hi @Freakwill – I'm afraid we don't have a way to deal with non-English based submissions. Could you please provide some kind of translated artifact here for us to review? Thank you.

Freakwill commented 10 months ago

@editorialbot generate pdf

@editorialbot generate pdf

Freakwill commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago

My name is now @editorialbot

Freakwill commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/gji/ggad446 is OK
- 10.1088/1742-6596/1719/1/012102 is OK
- 10.1109/ICEC.1997.592270 is OK
- 10.1007/s00500-016-2474-6 is OK

MISSING DOIs

- 10.1007/978-3-319-31204-0_9 may be a valid DOI for title: Automating Biomedical Data Science Through Tree-Based Pipeline Optimization

INVALID DOIs

- None
editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-319-31204-0_9 is OK
- 10.1093/gji/ggad446 is OK
- 10.1088/1742-6596/1719/1/012102 is OK
- 10.1109/ICEC.1997.592270 is OK
- 10.1007/s00500-016-2474-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None
Freakwill commented 10 months ago

@editorialbot commands

editorialbot commented 10 months ago

Hello @Freakwill, 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

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

# Perform checks on the repository
@editorialbot check repository

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

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

# 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
Freakwill commented 10 months ago

@editorialbot list reviewers

editorialbot commented 10 months ago

Please log in the JOSS Reviewers site to search through the list of current reviewers.

Freakwill commented 10 months ago

@editorialbot generate my checklist

editorialbot commented 10 months ago

Checklists can only be created once the review has started in the review issue

Freakwill commented 10 months ago

@editorialbot check repository

editorialbot commented 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.24 s (736.3 files/s, 224301.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           4737           4760          17564
HTML                            17           1189             51          11082
Python                         110           2487           1275           5172
Markdown                        11            675              0           1529
CSS                              5            304             69           1291
TeX                              1             20              0            165
reStructuredText                 7             99            190            108
YAML                             5             19             27            106
DOS Batch                        1              8              1             26
TOML                             1              5              1             24
make                             1              4              7              9
INI                              1              0              0              2
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                           174           9547           6381          37079
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 1992

Freakwill commented 10 months ago

@editorialbot check repository

editorialbot commented 10 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (709.7 files/s, 216252.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           4737           4760          17564
HTML                            17           1189             51          11082
Python                         110           2489           1275           5181
Markdown                        11            675              0           1528
CSS                              5            304             69           1291
TeX                              1             20              0            165
reStructuredText                 7             99            190            108
YAML                             5             19             27            106
DOS Batch                        1              8              1             26
TOML                             1              5              1             24
make                             1              4              7              9
INI                              1              0              0              2
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                           174           9549           6381          37087
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 10 months ago

Wordcount for paper.md is 1926

Freakwill commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 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 10 months ago

Five most similar historical JOSS papers:

pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search Submitting author: @pySRURGS Handling editor: @arokem (Retired) Reviewers: @iljah, @nicoguaro Similarity score: 0.8047

DEPP - Differential Evolution Parallel Program Submitting author: @gbertoldo Handling editor: @meg-simula (Retired) Reviewers: @HaoZeke, @dham Similarity score: 0.7977

Quilë: C++ genetic algorithms scientific library Submitting author: @ttarkowski Handling editor: @vissarion (Active) Reviewers: @mbarzegary, @acrlakshman Similarity score: 0.7951

GAIM: A C++ library for Genetic Algorithms and Island Models Submitting author: @gdetor Handling editor: @majensen (Active) Reviewers: @sjvrijn, @sarats Similarity score: 0.7921

dcgp: Differentiable Cartesian Genetic Programming made easy. Submitting author: @darioizzo Handling editor: @VivianePons (Retired) Reviewers: @Ohjeah, @shah314 Similarity score: 0.7846

⚠️ 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.

Freakwill commented 10 months ago

Author instructions

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

@Freakwill 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.

I suggest the following potential reviewers: professoralkmin shah314 AlessandroPierro sjvrijn JJ benjamin-lee jmadera HaoZeke dham acrlakshman mbarzegary Ohjeah

and the authors: gbertoldo ttarkowski

Freakwill commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/978-3-319-31204-0_9 is OK
- 10.1093/gji/ggad446 is OK
- 10.1088/1742-6596/1719/1/012102 is OK
- 10.1109/ICEC.1997.592270 is OK
- 10.1007/s00500-016-2474-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None
Freakwill commented 10 months ago

@editorialbot generate my checklist

editorialbot commented 10 months ago

Checklists can only be created once the review has started in the review issue

Freakwill commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 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 10 months ago

Five most similar historical JOSS papers:

DEPP - Differential Evolution Parallel Program Submitting author: @gbertoldo Handling editor: @meg-simula (Retired) Reviewers: @HaoZeke, @dham Similarity score: 0.8131

pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search Submitting author: @pySRURGS Handling editor: @arokem (Retired) Reviewers: @iljah, @nicoguaro Similarity score: 0.8071

GAIM: A C++ library for Genetic Algorithms and Island Models Submitting author: @gdetor Handling editor: @majensen (Active) Reviewers: @sjvrijn, @sarats Similarity score: 0.8058

Quilë: C++ genetic algorithms scientific library Submitting author: @ttarkowski Handling editor: @vissarion (Active) Reviewers: @mbarzegary, @acrlakshman Similarity score: 0.8042

dcgp: Differentiable Cartesian Genetic Programming made easy. Submitting author: @darioizzo Handling editor: @VivianePons (Retired) Reviewers: @Ohjeah, @shah314 Similarity score: 0.8021

⚠️ 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.

arfon commented 10 months ago

I translate the article to English. It was written about 3 years ago. In these three years, the program has been greatly redesigned.

Many thanks. Refactors/redesign of software doesn't necessarily mean a follow-on publication in JOSS would be permitted by us. Could you say more about what significant new capabilities have been added since the original release/publication, and what sorts of research challenges can be addressed by them?

I'm also curious to learn more about community use here. Does the original paper have many citations? Are people using this package for their research already?

Freakwill commented 9 months ago

I translate the article to English. It was written about 3 years ago. In these three years, the program has been greatly redesigned.

Many thanks. Refactors/redesign of software doesn't necessarily mean a follow-on publication in JOSS would be permitted by us. Could you say more about what significant new capabilities have been added since the original release/publication, and what sorts of research challenges can be addressed by them?

I'm also curious to learn more about community use here. Does the original paper have many citations? Are people using this package for their research already?

In addition to refactoring the original code, we have adopted algebraic programming more thoroughly, greatly improving scalability, and making it easy to any iterative simulation. It has a natural way to implement the multi-population genetic algorithms (even multi-multi-population), since we make use of the similar algebraic structures of the two. We have implemented a variety of intelligent algorithms, including quantum GA, PSO, DE; designed specialized chromosomes for special variables such as probability distributions and permutations; designed a caching system to accelerate computation; and initially implemented parallel computing, although currently limited to parallel computation of fitness. Combined with machine learning models, we provide scikit-learn-style APIs, such as the GAMLPRegressor with the same APIs of MLPRegressor, which implements the evoluationary neural network.

Currently, this package has not been officially applied to research. However, I have used it to solve real-world problems (such as movie scheduling). We have produced instructional videos to allow more people to understand this package. I am also persuading my colleagues to use this package.

The journal I published had little influence in itself; my papers also seemed to be cited by no one. That was my first attempt to let people know about my immature works.

Freakwill commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 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 9 months ago

Five most similar historical JOSS papers:

pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search Submitting author: @pySRURGS Handling editor: @arokem (Retired) Reviewers: @iljah, @nicoguaro Similarity score: 0.8089

DEPP - Differential Evolution Parallel Program Submitting author: @gbertoldo Handling editor: @meg-simula (Retired) Reviewers: @HaoZeke, @dham Similarity score: 0.8086

GAIM: A C++ library for Genetic Algorithms and Island Models Submitting author: @gdetor Handling editor: @majensen (Active) Reviewers: @sjvrijn, @sarats Similarity score: 0.8073

Quilë: C++ genetic algorithms scientific library Submitting author: @ttarkowski Handling editor: @vissarion (Active) Reviewers: @mbarzegary, @acrlakshman Similarity score: 0.8043

dcgp: Differentiable Cartesian Genetic Programming made easy. Submitting author: @darioizzo Handling editor: @VivianePons (Retired) Reviewers: @Ohjeah, @shah314 Similarity score: 0.8017

⚠️ 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.

Freakwill commented 9 months ago

@editorialbot generate pdf

editorialbot commented 9 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 9 months ago

Five most similar historical JOSS papers:

pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search Submitting author: @pySRURGS Handling editor: @arokem (Retired) Reviewers: @iljah, @nicoguaro Similarity score: 0.8084

DEPP - Differential Evolution Parallel Program Submitting author: @gbertoldo Handling editor: @meg-simula (Retired) Reviewers: @HaoZeke, @dham Similarity score: 0.8081

GAIM: A C++ library for Genetic Algorithms and Island Models Submitting author: @gdetor Handling editor: @majensen (Active) Reviewers: @sjvrijn, @sarats Similarity score: 0.8061

Quilë: C++ genetic algorithms scientific library Submitting author: @ttarkowski Handling editor: @vissarion (Active) Reviewers: @mbarzegary, @acrlakshman Similarity score: 0.8039

dcgp: Differentiable Cartesian Genetic Programming made easy. Submitting author: @darioizzo Handling editor: @VivianePons (Retired) Reviewers: @Ohjeah, @shah314 Similarity score: 0.8003

⚠️ 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.

arfon commented 9 months ago

In addition to refactoring the original code, we have adopted algebraic programming more thoroughly, greatly improving scalability, and making it easy to any iterative simulation. It has a natural way to implement the multi-population genetic algorithms (even multi-multi-population), since we make use of the similar algebraic structures of the two. We have implemented a variety of intelligent algorithms, including quantum GA, PSO, DE; designed specialized chromosomes for special variables such as probability distributions and permutations; designed a caching system to accelerate computation; and initially implemented parallel computing, although currently limited to parallel computation of fitness. Combined with machine learning models, we provide scikit-learn-style APIs, such as the GAMLPRegressor with the same APIs of MLPRegressor, which implements the evoluationary neural network.

OK, thanks for the additional information @Freakwill. Have all of these changes been made since the earlier paper was published?

Freakwill commented 9 months ago

In addition to refactoring the original code, we have adopted algebraic programming more thoroughly, greatly improving scalability, and making it easy to any iterative simulation. It has a natural way to implement the multi-population genetic algorithms (even multi-multi-population), since we make use of the similar algebraic structures of the two. We have implemented a variety of intelligent algorithms, including quantum GA, PSO, DE; designed specialized chromosomes for special variables such as probability distributions and permutations; designed a caching system to accelerate computation; and initially implemented parallel computing, although currently limited to parallel computation of fitness. Combined with machine learning models, we provide scikit-learn-style APIs, such as the GAMLPRegressor with the same APIs of MLPRegressor, which implements the evoluationary neural network.

OK, thanks for the additional information @Freakwill. Have all of these changes been made since the earlier paper was published?

Sure. GitHub records all commits.