[PRE REVIEW]: swyft: Truncated Marginal Neural Ratio Estimation in Python

[whedon]

Submitting author: !--author-handle-->@bkmi<!--end-author-handle-- (Benjamin Miller) Repository: https://github.com/undark-lab/swyft Branch with paper.md (empty if default branch): Version: v0.3.0 Editor: !--editor-->@pdebuyl<!--end-editor-- Reviewers: @mattpitkin, @olgadoronina Managing EiC: Kyle Niemeyer

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Status

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HTML: <a href="https://joss.theoj.org/papers/2dafe33336397a6d5dd8f3c692eaab22"><img src="https://joss.theoj.org/papers/2dafe33336397a6d5dd8f3c692eaab22/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2dafe33336397a6d5dd8f3c692eaab22/status.svg)](https://joss.theoj.org/papers/2dafe33336397a6d5dd8f3c692eaab22)

Author instructions

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

The author's suggestion for the handling editor is @fabian-s.

@bkmi 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:

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.

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #4086 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.27 s (351.0 files/s, 55180.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          47           1185           1114           5290
Jupyter Notebook                14              0           4630            968
reStructuredText                22            250            310            683
YAML                             5             20             28            108
Markdown                         1             27              0             65
TeX                              2              1              0             32
DOS Batch                        1              8              1             26
make                             1              4              6             10
TOML                             1              2              0              8
-------------------------------------------------------------------------------
SUM:                            94           1497           6089           7190
-------------------------------------------------------------------------------

Statistical information for the repository 'd097089d6367bf54d7697b7c' was
gathered on 2022/01/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Adam Coogan                      2            36              7            0.05
Alex Cole                        9         15279            251           17.62
Christoph Weniger              274         13891          13242           30.78
Francesco Nattino               74          1919           1397            3.76
Meiert Grootes                   2            37             37            0.08
acole1221                        8           379            145            0.59
bkmi                           198         14898          24841           45.08
rogerkuou                       27           976            823            2.04

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
Adam Coogan                  20           55.6          7.1                0.00
Alex Cole                    14            0.1         11.5                0.00
Christoph Weniger           937            6.7          8.2               19.64
Francesco Nattino           946           49.3          4.5                6.77
bkmi                       5384           36.1          3.7                4.87
rogerkuou                   288           29.5          5.9                1.74

[kyleniemeyer]

Hi @bkmi, is your JOSS paper located in a particular branch? Our bot (and I) can't seem to find it.

[danielskatz]

@whedon generate pdf from branch joss-submission-do-not-delete

[whedon]

Attempting PDF compilation from custom branch joss-submission-do-not-delete. Reticulating splines etc...

[danielskatz]

@whedon check references from branch joss-submission-do-not-delete

[whedon]

Attempting to check references... from custom branch joss-submission-do-not-delete

[whedon]

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

[whedon]

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
- 10.21105/joss.03021 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.5281/zenodo.5712786 is OK
- 10.21105/joss.02505 is OK
- 10.21105/joss.00011 is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.1145/3093172.3093233 is OK
- 10.1051/0004-6361/201322971 is OK
- 10.1214/aos/1176346785 is OK
- 10.1093/genetics/145.2.505 is OK

MISSING DOIs

- 10.1093/mnras/stz1960 may be a valid DOI for title: Fast likelihood-free cosmology with neural density estimators and active learning
- 10.1093/mnras/sty819 may be a valid DOI for title: Massive optimal data compression and density estimation for scalable, likelihood-free inference in cosmology
- 10.1093/mnras/stz1900 may be a valid DOI for title: Nuisance hardened data compression for fast likelihood-free inference
- 10.1002/sta4.56 may be a valid DOI for title: A note on approximating ABC-MCMC using flexible classifiers
- 10.1214/20-ba1238 may be a valid DOI for title: Likelihood-free inference by ratio estimation
- 10.1007/s11222-017-9738-6 may be a valid DOI for title: Likelihood-free inference via classification
- 10.1214/06-ba127 may be a valid DOI for title: Nested sampling for general Bayesian computation
- 10.1111/j.1365-2966.2007.12353.x may be a valid DOI for title: Multimodal nested sampling: an efficient and robust alternative to Markov Chain Monte Carlo methods for astronomical data analyses
- 10.1111/j.1365-2966.2009.14548.x may be a valid DOI for title: MultiNest: an efficient and robust Bayesian inference tool for cosmology and particle physics
- 10.1093/mnras/stv1911 may be a valid DOI for title: polychord : next-generation nested sampling
- 10.1007/s11222-018-9844-0 may be a valid DOI for title: Dynamic nested sampling: an improved algorithm for parameter estimation and evidence calculation
- 10.1214/18-ss120 may be a valid DOI for title: An approximate likelihood perspective on ABC methods
- 10.1098/rsif.2008.0172 may be a valid DOI for title: Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems
- 10.1111/j.2517-6161.1984.tb01290.x may be a valid DOI for title: Monte Carlo methods of inference for implicit statistical models
- 10.1007/s11222-009-9116-0 may be a valid DOI for title: Non-linear regression models for Approximate Bayesian Computation
- 10.2172/4390578 may be a valid DOI for title: Equation of State Calculations by Fast Computing Machines
- 10.1093/biomet/57.1.97 may be a valid DOI for title: Monte Carlo sampling methods using Markov chains and their applications

INVALID DOIs

- None

[kyleniemeyer]

@danielskatz 😂 thanks, somehow I missed that branch...

[kyleniemeyer]

@bkmi you can disregard my above message! As we are getting started, though, please take a look at those missing DOI messages for your article.

[kyleniemeyer]

@whedon invite @fabian-s as editor

👋 @fabian-s can you edit this submission?

[whedon]

@fabian-s has been invited to edit this submission.

[bkmi]

Just saw this thread, sorry for the slow reply. I will certainly look at those missing DOIs ASAP, probably tomorrow morning!

[fabian-s]

Sorry for the late reply -- I'd rather not, since I don't know Python and the problem this package solves is outside my area of expertise.

[bkmi]

@whedon check references from branch joss-submission-do-not-delete

[whedon]

Attempting to check references... from custom branch joss-submission-do-not-delete

[whedon]

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
- 10.21105/joss.03021 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.3509134 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.5281/zenodo.5712786 is OK
- 10.21105/joss.02505 is OK
- 10.21105/joss.00011 is OK
- 10.1093/bioinformatics/bty361 is OK
- 10.1145/3093172.3093233 is OK
- 10.1093/mnras/stz1960 is OK
- 10.1093/mnras/sty819 is OK
- 10.1093/mnras/stz1900 is OK
- 10.1002/sta4.56 is OK
- 10.1214/20-ba1238 is OK
- 10.1007/s11222-017-9738-6 is OK
- 10.1214/06-ba127 is OK
- 10.1111/j.1365-2966.2007.12353.x is OK
- 10.1111/j.1365-2966.2009.14548.x is OK
- 10.1093/mnras/stv1911 is OK
- 10.1051/0004-6361/201322971 is OK
- 10.1007/s11222-018-9844-0 is OK
- 10.1214/18-ss120 is OK
- 10.1098/rsif.2008.0172 is OK
- 10.1111/j.2517-6161.1984.tb01290.x is OK
- 10.1214/aos/1176346785 is OK
- 10.1093/genetics/145.2.505 is OK
- 10.1007/s11222-009-9116-0 is OK
- 10.2172/4390578 is OK
- 10.1093/biomet/57.1.97 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[bkmi]

May I suggest @dfm as editor? If he's willing, of course.

• Although generally applicable to simulation-based inference, our software is utilized in astrophysics papers.
• Dan mentioned in his profile that he reviews python.
• Dan also reviewed sbi, an important simulation-based inference package in python.

[arfon]

@whedon invite @pdebuyl as editor

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

[whedon]

@pdebuyl has been invited to edit this submission.

[pdebuyl]

@whedon assign me as editor

[whedon]

OK, the editor is @pdebuyl

[bkmi]

Thanks for editing @pdebuyl!

[pdebuyl]

@whedon assign @mattpitkin as reviewer

[whedon]

OK, @mattpitkin is now a reviewer

[bkmi]

Thanks for reviewing @mattpitkin!

[pdebuyl]

@bkmi I am still looking out for a second reviewer, which is necessary to start the review. I contact reviewers by email most of the time, as many people do not read GitHub's notifications. I'll update you here of course when there is progress!

[pdebuyl]

@editorialbot add @olgadoronina as reviewer

[editorialbot]

@olgadoronina added to the reviewers list!

[pdebuyl]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4205.