[PRE REVIEW]: pymdp: A Python library for active inference in discrete state spaces

[whedon]

Submitting author: @conorheins (Conor Heins) Repository: https://github.com/infer-actively/pymdp Version: v0.0.4 Editor: @emdupre Reviewers: @seankmartin, @patrickmineault Managing EiC: Daniel S. Katz

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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Author instructions

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

@conorheins if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

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For a list of things I can do to help you, just type:

@whedon commands

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.13 s (484.3 files/s, 174779.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          30           1995           1963           4615
Jupyter Notebook                11              0           9723           1496
MATLAB                           9            558            790           1406
Markdown                         2             94              0            234
YAML                             2             10             10             42
reStructuredText                 8             29             40             36
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            64           2698          12534           7864
-------------------------------------------------------------------------------

Statistical information for the repository '7cedfe214e7c8c9994a0c05b' was
gathered on 2022/01/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Alexander Kiefer                 2             5              3            0.01
Beren                            4           193             54            0.32
Brennan Klein                    1             1              1            0.00
Conor Heins                     87          8074           2193           13.16
alec-tschantz                   55          8626           6334           19.18
arun                             3            88             73            0.21
conorheins                     237         26192          26172           67.13

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Alexander Kiefer              5          100.0          6.5                0.00
Beren                        13            6.7         20.0               15.38
alec-tschantz              1245           14.4         18.4               12.21
arun                         13           14.8         11.6                0.00
conorheins                 7297           27.9          7.3                9.09

[whedon]

PDF failed to compile for issue #4067 with the following error:

 Can't find any papers to compile :-(

[danielskatz]

@whedon check references from branch paper_branch

[whedon]

Attempting to check references... from custom branch paper_branch

[danielskatz]

@whedon generate pdf from branch paper_branch

[whedon]

Attempting PDF compilation from custom branch paper_branch. Reticulating splines etc...

[whedon]

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

OK DOIs

- 10.1371/journal.pone.0006421 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1162/neco_a_01354 is OK
- 10.1080/17588928.2015.1020053 is OK
- 10.1038/s41598-018-38246-3 is OK
- 10.1561/2200000001 is OK
- 10.1167/jov.20.4.12 is OK
- 10.1038/ncomms14218 is OK
- 10.3390/e22050552 is OK
- 10.1162/neco.1992.4.3.415 is OK
- 10.1016/j.neuroimage.2004.07.041 is OK
- 10.1080/01621459.2017.1285773 is OK
- 10.1126/science.1238406 is OK
- 10.1007/s00422-012-0512-8 is OK
- 10.1016/j.tics.2011.11.018 is OK
- 10.1162/neco_a_01357 is OK
- 10.1109/IJCNN48605.2020.9207382 is OK
- 10.1016/0166-2236(83)90190-X is OK
- 10.1523/JNEUROSCI.11-03-00641.1991 is OK
- 10.1162/NECO_a_00912 is OK
- 10.3390/e21030257 is OK
- 10.3389/frobt.2019.00020 is OK
- 10.1007/s00422-018-0785-7 is OK
- 10.1371/journal.pcbi.1007805 is OK
- 10.1109/ICASSP40776.2020.9054364 is OK
- 10.1016/B978-0-12-372560-8.X5000-1 is OK
- 10.1038/nrn2787 is OK
- 10.1016/j.jmp.2020.102447 is OK
- 10.1016/S0004-3702(98)00023-X is OK
- 10.1162/neco_a_01351 is OK
- 10.1093/cercor/bhu159 is OK
- 10.1016/j.drugalcdep.2020.108208 is OK
- 10.1503/jpn.200032 is OK
- 10.31234/osf.io/b4jm6 is OK
- 10.1016/j.neuroimage.2008.02.054 is OK
- 10.1016/j.jmp.2020.102348 is OK
- 10.1007/978-3-030-64919-7_1 is OK
- 10.1016/j.neubiorev.2016.06.022 is OK
- 10.1162/neco.1995.7.5.889 is OK
- 10.1037/13536-000 is OK
- 10.1016/j.neunet.2021.05.010 is OK
- 10.1109/LRA.2021.3090015 is OK
- 10.1016/B978-0-323-88506-5.50066-8 is OK
- 10.1007/s00422-019-00805-w is OK
- 10.3390/e23020198 is OK
- 10.1080/10407413.2021.1965480 is OK
- 10.1098/rsif.2013.0475 is OK
- 10.7554/eLife.41703 is OK
- 10.1162/neco_a_00999 is OK

MISSING DOIs

- 10.1162/neco_a_01427 may be a valid DOI for title: Chance-Constrained Active Inference
- 10.1017/s0140525x19001353 may be a valid DOI for title: Generative models as parsimonious descriptions of sensorimotor loops
- 10.7551/mitpress/7111.003.0009 may be a valid DOI for title: Perceptions as hypotheses
- 10.31234/osf.io/2rzu5 may be a valid DOI for title: Active inference, selective attention, and the cocktail party problem
- 10.1016/j.schres.2021.07.032 may be a valid DOI for title: Everything is connected: Inference and attractors in delusions
- 10.31234/osf.io/bsuh8 may be a valid DOI for title: Long-term stability of computational parameters during approach-avoidance conflict in a transdiagnostic psychiatric patient sample

INVALID DOIs

- None

[whedon]

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

[danielskatz]

👋 @emdupre - are you able to edit this JOSS submission?

[danielskatz]

@whedon invite @emdupre as editor

[whedon]

@emdupre has been invited to edit this submission.

[emdupre]

Yes, happy to take this ! Thanks @danielskatz

[emdupre]

@whedon assign @emdupre as editor

[whedon]

OK, the editor is @emdupre

[emdupre]

:wave: Hi @conorheins, and thank you for your submission to JOSS !

If you have any suggestions for potential reviewers, please let me know by listing their names or GitHub handles (without the @, so they don't receive a notification) here.

You can suggest reviewers from any relevant project, though we often recommend starting with this list of people as they have already agreed to review for JOSS (please start at the bottom of the list).

[conorheins]

Hi @emdupre, thanks for agreeing to review our submission!

I leave some the github handles of some suggested reviewers below (some from the list, some not):

From the list: woolfeh seankmartin olgadoronina franziskaaah bramvandijk88 richrobe

not on the list: ucbtns kaiu85 semihakbayrak ivan-bocharov rssmith33 cjwhyte micahgallen

[emdupre]

:wave: Hi @seankmartin, @richrobe, @semihakbayrak, @patrickmineault !

Would you be willing to review pymdp: A Python library for active inference in discrete state spaces for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.04067/joss.04067/10.21105.joss.04067.pdf

If you're available to review this work, please let me know and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you !

[richrobe]

Hi @emdupre, sorry, I can't do a review right now :/ Hopefully next time!

Best, Robert

[seankmartin]

Hi @emdupre

Sure, I'm good to review pymdp!

[semihakbayrak]

Hi @emdupre! Unfortunately I am not available. Bests!

[patrickmineault]

@emdupre I can do it

[emdupre]

Hi everyone, thanks for your quick responses !

I'll go ahead and add @seankmartin and @patrickmineault as reviewers for this submission and start the review process :rocket:

[emdupre]

@whedon add @seankmartin as reviewer

[whedon]

OK, @seankmartin is now a reviewer

[emdupre]

@whedon add @patrickmineault as reviewer

[whedon]

OK, @patrickmineault is now a reviewer

[emdupre]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4098.