[PRE REVIEW]: LINFA: a Python library for variational inference with normalizing flow and annealing

[editorialbot]

Submitting author: !--author-handle-->@daneschi<!--end-author-handle-- (Daniele E. Schiavazzi) Repository: https://github.com/desResLab/LINFA Branch with paper.md (empty if default branch): master Version: v1.3.3 Editor: !--editor-->@lrnv<!--end-editor-- Reviewers: @robmoss, @selimfirat Managing EiC: Arfon Smith

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/adb20d3d808e8b369e827b5d9fba277b"><img src="https://joss.theoj.org/papers/adb20d3d808e8b369e827b5d9fba277b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/adb20d3d808e8b369e827b5d9fba277b/status.svg)](https://joss.theoj.org/papers/adb20d3d808e8b369e827b5d9fba277b)

Author instructions

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

@daneschi 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:

@editorialbot commands

[editorialbot]

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.07 s (970.1 files/s, 195101.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           1011            893           2939
XML                              6              0            129           1842
Jupyter Notebook                 2              0           4069            440
Markdown                         2            124              0            416
TeX                              2             45              0            379
reStructuredText                19            158            336             93
YAML                             3             14             14             63
TOML                             1              5              1             29
DOS Batch                        1              8              1             26
Bourne Shell                     2              1              0             16
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            65           1370           5450           6252
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 5049

[editorialbot]

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

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1016/b978-0-08-051581-6.50057-x may be a valid DOI for title: Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images
- 10.2172/4390578 may be a valid DOI for title: Equation of state calculations by fast computing machines
- 10.1093/oso/9780198509936.003.0015 may be a valid DOI for title: Monte Carlo sampling methods using Markov chains and their applications
- 10.21236/ada208388 may be a valid DOI for title: Sampling-based approaches to calculating marginal densities
- 10.1561/9781601981851 may be a valid DOI for title: Graphical models, exponential families, and variational inference
- 10.1109/tpami.2020.2992934 may be a valid DOI for title: Normalizing flows: An introduction and review of current methods
- 10.1016/j.jcp.2022.111454 may be a valid DOI for title: Variational inference with NoFAS: Normalizing flow with adaptive surrogate for computationally expensive models
- 10.1615/int.j.uncertaintyquantification.2022043110 may be a valid DOI for title: AdaAnn: Adaptive Annealing Scheduler for Probability Density Approximation
- 10.1016/s0951-8320(02)00229-6 may be a valid DOI for title: Theorems and examples on high dimensional model representation
- 10.1016/0041-5553(67)90144-9 may be a valid DOI for title: On the distribution of points in a cube and the approximate evaluation of integrals

INVALID DOIs

- None

[editorialbot]

Five most similar historical JOSS papers:

Linopy: Linear optimization with n-dimensional labeled variables Submitting author: @fabianhofmann Handling editor: @Fei-Tao (Active) Reviewers: @torressa, @g4brielvs Similarity score: 0.8094

dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python Submitting author: @davidtourigny Handling editor: @marcosvital (Active) Reviewers: @jdbrunner, @pstjohn, @synchon Similarity score: 0.7978

Sapsan: Framework for Supernovae Turbulence Modeling with Machine Learning Submitting author: @pikarpov-lanl Handling editor: @dfm (Active) Reviewers: @kburns, @milescranmer Similarity score: 0.7976

High-performance neural population dynamics modeling enabled by scalable computational infrastructure Submitting author: @a9p Handling editor: @emdupre (Active) Reviewers: @richford, @tachukao Similarity score: 0.7970

Capytaine: a Python-based linear potential flow solver Submitting author: @mancellin Handling editor: @leouieda (Retired) Reviewers: @mikaem, @harpolea Similarity score: 0.7961

⚠️ 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]

@daneschi - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[daneschi]

So sorry for the delay in getting back to you on this, I have missed your email. Possible reviewers are:

• Alireza Doostan, University of Colorado, Boulder ( @.***)
• Mingzhang Yin, University of Florida @.***)
• Bhattacharya Shrijita, Michigan State University @.***)
• Daniele Bigoni, Ammagamma s.r.l. @.***)
• Peng Chen, Georgia Tech @.***)
• Alessandro Veneziani, Emory University @.***)

On Sat, Dec 9, 2023 at 2:35 PM Arfon Smith @.***> wrote:

@daneschi https://github.com/daneschi - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6108#issuecomment-1848643188, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJL6EILU3T5YK2ITGUN6KLYIS4RLAVCNFSM6AAAAABADAOVQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBYGY2DGMJYHA . You are receiving this because you were mentioned.Message ID: @.***>

[daneschi]

Sorry to bother you again about this, I just wanted to know if the paper was sent for review, if I need to re-submit it or for anything else I can do on my end. Thank you very much for your Kind Assistance with this! with Best Regards, Daniele

On Sat, Dec 9, 2023 at 3:05 PM Daniele Schiavazzi < @.***> wrote:

So sorry for the delay in getting back to you on this, I have missed your email. Possible reviewers are:

• Alireza Doostan, University of Colorado, Boulder ( @.***)
• Mingzhang Yin, University of Florida @.***)
• Bhattacharya Shrijita, Michigan State University @.***)
• Daniele Bigoni, Ammagamma s.r.l. @.***)
• Peng Chen, Georgia Tech @.***)
• Alessandro Veneziani, Emory University @.***)

On Sat, Dec 9, 2023 at 2:35 PM Arfon Smith @.***> wrote:

@daneschi https://github.com/daneschi - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6108#issuecomment-1848643188, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJL6EILU3T5YK2ITGUN6KLYIS4RLAVCNFSM6AAAAABADAOVQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNBYGY2DGMJYHA . You are receiving this because you were mentioned.Message ID: @.***>

[arfon]

Nothing to do here. The submission is waitlisted until we have an editor that has capacity to handle this submission.

[daneschi]

OK, Thanks for letting me know.

On Tue, Jan 9, 2024 at 2:23 PM Arfon Smith @.***> wrote:

Nothing to do here. The submission is waitlisted until we have an editor that has capacity to handle this submission.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6108#issuecomment-1883646651, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJL6ELRFR66TYPT6VGUDA3YNWKMRAVCNFSM6AAAAABADAOVQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOBTGY2DMNRVGE . You are receiving this because you were mentioned.Message ID: @.***>

[arfon]

@editorialbot invite @lrnv as editor

:wave: @lrnv – would you be willing to edit this submission for JOSS?

/ cc @vissarion for visibility.

[editorialbot]

Invitation to edit this submission sent!

[lrnv]

@assign me as editor

[lrnv]

@daneschi Hey !

Do you by chance know the github handle of the people you listed as potential reviewers ?

[daneschi]

Thank you for your message! No actually I don't.

On Sat, Jan 20, 2024, 4:01 AM Oskar Laverny @.***> wrote:

@daneschi https://github.com/daneschi Hey !

Do you by chance know the github handle of the people you listed as potential reviewers ?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6108#issuecomment-1901996847, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJL6EOXJYIAIYU4J6DJLSTYPOBWZAVCNFSM6AAAAABADAOVQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBRHE4TMOBUG4 . You are receiving this because you were mentioned.Message ID: @.***>

[arfon]

@assign me as editor

@lrnv - you need to do @editorialbot assign me as editor

[arfon]

@daneschi – it looks like GitHub might have filtered out the email addresses of the people you listed here. Perhaps you could share them directly with @lrnv ?

[arfon]

@editorialbot assign @lrnv as editor

[editorialbot]

Assigned! @lrnv is now the editor

[daneschi]

Possible reviewers are:

• Alireza Doostan, University of Colorado, Boulder ( @.***)
• Mingzhang Yin, University of Florida @.***)
• Bhattacharya Shrijita, Michigan State University @.***)
• Daniele Bigoni, Ammagamma s.r.l. @.***)
• Peng Chen, Georgia Tech @.***)
• Alessandro Veneziani, Emory University @.***) Thanks! Daniele

On Sat, Jan 20, 2024 at 9:25 AM The Open Journals editorial robot < @.***> wrote:

Assigned! @lrnv https://github.com/lrnv is now the editor

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6108#issuecomment-1902113118, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJL6EIXKBP6XWOL5SN6H2LYPPHUFAVCNFSM6AAAAABADAOVQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBSGEYTGMJRHA . You are receiving this because you were mentioned.Message ID: @.***>

[lrnv]

@arfon Thanks for helping out.

@daneschi I sent a few mails, let's wait a bit for potential responses.

[daneschi]

OK, Thank you!

On Mon, Jan 22, 2024 at 5:26 AM Oskar Laverny @.***> wrote:

@arfon https://github.com/arfon Thanks for helping out.

@daneschi https://github.com/daneschi I sent a few mails, let's wait a bit for potential responses.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6108#issuecomment-1903685765, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJL6EOV3EBAKS22NKXADPLYPY5GVAVCNFSM6AAAAABADAOVQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBTGY4DKNZWGU . You are receiving this because you were mentioned.Message ID: @.***>

[lrnv]

@daneschi no-one responded, so I am going to try to find reviewers otherwise.

[lrnv]

:wave: @fabianhofmann & @mancellin & @davidtourigny, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[FabianHofmann]

@lrnv I think I don't have the capacity to make a review in the next few months, sorry...

[mancellin]

@lrnv Thank you for the proposal, but this paper is a bit too far away from my expertise for me to provide a useful review.

[lrnv]

:wave: @Daniel-Dodd @vankesteren @robmoss, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

[vankesteren]

Sorry, have just accepted another JOSS review (just waiting on being assigned). Good luck!!

[davidtourigny]

HelloSimilarly, I don’t have much expertise in this area and so can’t review, sorry :)Best wishesDavidOn Jan 29, 2024, at 12:28 PM, Erik-Jan van Kesteren @.***> wrote: Sorry, have just accepted another JOSS review (just waiting on being assigned). Good luck!!

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

[daneschi]

Thank you for your efforts!

On Mon, Jan 29, 2024 at 4:30 AM Oskar Laverny @.***> wrote:

@daneschi https://github.com/daneschi no-one responded, so I am going to try to find reviewers otherwise.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6108#issuecomment-1914295852, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJL6EN6I6GZIRAOK2G7A2TYQ5T4ZAVCNFSM6AAAAABADAOVQGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJUGI4TKOBVGI . You are receiving this because you were mentioned.Message ID: @.***>

[lrnv]

:wave: @selimfirat, @ldliao, @atzberg, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

[robmoss]

👋 @daniel-dodd @vankesteren @robmoss, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

I have limited familiarity with variational inference, but I can review this paper. This will be my first JOSS review, so I may have some questions about the review criteria.

[selimfirat]

👋 @selimfirat, @ldliao, @atzberg, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: joss.readthedocs.io/en/latest/review_criteria.html

Thanks for the invitation. I am interested in reviewing it.

I have some background knowledge on the topic of the paper, but this will be my first time reviewing for JOSS.

[lrnv]

@robmoss, @selimfirat Do not fear the review process it is quite straightforward and correctly documented, you'll see. Thanks for your interests, let's start the' review in another thread

[lrnv]

@editorialbot add @robmoss as reviewer

[editorialbot]

@robmoss added to the reviewers list!

[lrnv]

@editorialbot add @selimfirat as reviewer

[editorialbot]

@selimfirat added to the reviewers list!

[lrnv]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6309.