[PRE REVIEW]: sbi reloaded: a toolkit for simulation-based inference workflows

[editorialbot]

Submitting author: @janfb (Jan Boelts)
Repository: https://github.com/sbi-dev/sbi
Branch with paper.md (empty if default branch): joss-submission-2024
Version: v0.23.2
Editor: @boisgera
Reviewers: @arnauqb, @francois-rozet
Managing EiC: Chris Vernon

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Software report:

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SUM:                           241           7449          19456          30527
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Commit count by author:

   303	janfb
   182	Michael Deistler
   125	Alvaro Tejero-Cantero
    92	Jan
    72	Jan Boelts
    68	michaeldeistler
    66	michael
    65	jan-matthis
    56	michael.deistler
    28	Jan-Matthis
    21	meteore
    18	manuelgloeckler
    17	Fabio Muratore
    15	Guy Moss
    12	Peter Steinbach
     9	pedro goncalves
     7	tomMoral
     6	Sebastian Bischoff
     6	coschroeder
     6	jnsbck
     5	Julia Linhart
     5	LouisRouillard
     5	zinaStef
     4	Benjamin Kurt Miller
     4	Thomas Moreau
     4	jsvetter
     3	Imahn
     3	Matthijs Pals
     3	Yves Bernaerts
     3	augustes
     3	danielmk
     3	dgreenberg
     2	Conor Durkan
     2	Gilles Louppe
     2	Maternus
     2	Pedro L. C. Rodrigues
     2	Pedro Rodrigues
     2	milagorecki
     2	rdgao
     1	A. Ziaeemehr
     1	Abdul Samad
     1	Abdul Samad Siddiqui
     1	Abolfazl Ziaeemehr
     1	Alexandre Gramfort
     1	Ankush Checkervarty
     1	Arnaud Delaunoy
     1	Cornelius
     1	David Greenberg
     1	Eslam Khaled
     1	Felix Pei
     1	Harry Fu Yu
     1	Imahn Shekhzadeh
     1	JBeckUniTb
     1	JH Macke
     1	Janne Lappalainen
     1	Kristof Schröder
     1	Miles Cranmer
     1	Narendra Mukherjee
     1	Nastya Krouglova
     1	Nathan Musoke
     1	Nick Tolley
     1	Pietro Monticone
     1	Pizza GitHub
     1	Richard Gao
     1	Seth Axen
     1	Thomas Gessey-Jones
     1	Victor Buendía
     1	Yoav Ram
     1	bkmi
     1	felixp8
     1	max-dax
     1	tbmiller-astro
     1	theo
     1	theogruner
     1	Álvaro Tejero-Cantero

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2241

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[editorialbot]

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

✅ OK DOIs

- 10.1093/biomet/asp052 is OK
- 10.1201/9781315117195 is OK
- 10.1098/rsif.2008.0172 is OK
- 10.12751/nncn.bc2018.0222 is OK
- 10.1186/s12868-017-0370-3 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: ABCpy
- No DOI given, and none found for title: pydelfi: Density Estimation Likelihood-Free Infere...
- No DOI given, and none found for title: nflows:  Normalizing flows in PyTorch
- No DOI given, and none found for title: Zuko - Normalizing flows in PyTorch
- No DOI given, and none found for title: Pyro: Deep Universal Probabilistic Programming
- No DOI given, and none found for title: DELFI: Density Estimation Likelihood-Free Inferenc...
- No DOI given, and none found for title: joblib
- No DOI given, and none found for title: Neural spline flows
- No DOI given, and none found for title: ELFI: engine for likelihood-free inference
- No DOI given, and none found for title: PyTorch: An Imperative Style, High-Performance Dee...
- No DOI given, and none found for title: Sequential monte carlo without likelihoods
- No DOI given, and none found for title: Python 3 Reference Manual
- No DOI given, and none found for title: Flexible statistical inference for mechanistic mod...
- No DOI given, and none found for title: Neural Approximate Sufficient Statistics for Impli...
- No DOI given, and none found for title: Fast \varepsilon-free inference of simulation mode...
- No DOI given, and none found for title: Normalizing flows for probabilistic modeling and i...
- No DOI given, and none found for title: Sequential neural likelihood: Fast likelihood-free...
- No DOI given, and none found for title: Masked autoregressive flow for density estimation
- No DOI given, and none found for title: Neural spline flows
- No DOI given, and none found for title: Automatic posterior transformation for likelihood-...
- No DOI given, and none found for title: Benchmarking simulation-based inference
- No DOI given, and none found for title: Likelihood-free inference with emulator networks
- No DOI given, and none found for title: Truncated marginal neural ratio estimation
- No DOI given, and none found for title: Variational methods for simulation-based inference
- No DOI given, and none found for title: Training deep neural density estimators to identif...
- No DOI given, and none found for title: Efficient bayesian experimental design for implici...
- No DOI given, and none found for title: Bayesian inference for biophysical neuron models e...
- No DOI given, and none found for title: The frontier of simulation-based inference
- No DOI given, and none found for title: Variational inference with normalizing flows
- No DOI given, and none found for title: Inference Compilation and Universal Probabilistic ...
- No DOI given, and none found for title: Likelihood-free mcmc with amortized approximate ra...
- No DOI given, and none found for title: Sequential neural methods for likelihood-free infe...
- No DOI given, and none found for title: Amortised inference for mechanistic models of neur...
- No DOI given, and none found for title: Adam: A Method for Stochastic Optimization
- No DOI given, and none found for title: Bayesian optimization for likelihood-free inferenc...
- No DOI given, and none found for title: Mixture density networks
- No DOI given, and none found for title: Sequential monte carlo without likelihoods
- No DOI given, and none found for title: Adaptive approximate Bayesian computation
- No DOI given, and none found for title: On contrastive learning for likelihood-free infere...
- No DOI given, and none found for title: Group equivariant neural posterior estimation
- No DOI given, and none found for title: A Crisis In Simulation-Based Inference? Beware, Yo...
- No DOI given, and none found for title: Validating Bayesian inference algorithms with simu...
- No DOI given, and none found for title: Flexible and efficient simulation-based inference ...
- No DOI given, and none found for title: Auto-Encoding Variational Bayes
- No DOI given, and none found for title: Robust Neural Posterior Estimation and Statistical...
- No DOI given, and none found for title: Differentiable likelihoods for fast inversion of’l...
- No DOI given, and none found for title: Truncated proposals for scalable and hassle-free s...
- No DOI given, and none found for title: Optimal simulation-based Bayesian decisions
- No DOI given, and none found for title: Contrastive neural ratio estimation
- No DOI given, and none found for title: Compositional score modeling for simulation-based ...
- No DOI given, and none found for title: Jana: Jointly amortized neural approximation of co...
- No DOI given, and none found for title: Simulation-based Inference with the Generalized Ku...
- No DOI given, and none found for title: Sensitivity-Aware Amortized Bayesian Inference
- No DOI given, and none found for title: Neural Score Estimation: Likelihood-Free Inference...
- No DOI given, and none found for title: Inference compilation and universal probabilistic ...
- No DOI given, and none found for title: MADE: Masked Autoencoder for Distribution Estimati...
- No DOI given, and none found for title: Flow Matching for Scalable Simulation-Based Infere...
- No DOI given, and none found for title: Generalized Bayesian inference for scientific simu...
- No DOI given, and none found for title: Amortized Bayesian Decision Making for simulation-...
- No DOI given, and none found for title: A crisis in simulation-based inference? beware, yo...
- No DOI given, and none found for title: Embryo-uterine interaction coordinates mouse embry...
- No DOI given, and none found for title: Meta-learning families of plasticity rules in recu...
- No DOI given, and none found for title: Neural networks enable efficient and accurate simu...
- No DOI given, and none found for title: Variational methods for simulation-based inference
- No DOI given, and none found for title: Neural simulation-based inference approach for cha...
- No DOI given, and none found for title: Black-box Bayesian inference for economic agent-ba...
- No DOI given, and none found for title: Investigating the impact of model misspecification...
- No DOI given, and none found for title: Neural posterior domain randomization
- No DOI given, and none found for title: Skewed distribution of spines is independent of pr...
- No DOI given, and none found for title: Adversarial robustness of amortized Bayesian infer...
- No DOI given, and none found for title: Calibrating Agent-based Models to Microdata with G...
- No DOI given, and none found for title: Sequential neural posterior and likelihood approxi...
- No DOI given, and none found for title: Bayesian model comparison for simulation-based inf...
- No DOI given, and none found for title: Simulation-based inference using surjective sequen...
- No DOI given, and none found for title: L-c2st: Local diagnostics for posterior approximat...
- No DOI given, and none found for title: Sampling-based accuracy testing of posterior estim...
- No DOI given, and none found for title: Score-Based Generative Modeling through Stochastic...
- No DOI given, and none found for title: All-in-one simulation-based inference
- No DOI given, and none found for title: Flow Matching for Generative Modeling
- No DOI given, and none found for title: sbijax: Simulation-based inference in JAX
- No DOI given, and none found for title: LAMPE: Likelihood-free AMortized Posterior Estimat...
- No DOI given, and none found for title: Swyft: A system for scientific simulation-based in...
- No DOI given, and none found for title: Simulation-based inference with the Python Package...
- No DOI given, and none found for title: Generalized Bayesian inference for scientific simu...

❌ MISSING DOIs

- 10.7717/peerj-cs.1516 may be a valid DOI for title: PyMC: a modern, and comprehensive probabilistic pr...
- 10.1038/nature09319 may be a valid DOI for title: Statistical inference for noisy nonlinear ecologic...
- 10.1093/genetics/162.4.2025 may be a valid DOI for title: Approximate Bayesian computation in population gen...
- 10.21105/joss.02505 may be a valid DOI for title: sbi: A toolkit for simulation-based inference
- 10.1080/01621459.2013.864178 may be a valid DOI for title: Expectation propagation for likelihood-free infere...
- 10.1101/669218 may be a valid DOI for title: Approximate Bayesian Inference for a Mechanistic M...
- 10.5705/ss.202015.0340 may be a valid DOI for title: Learning summary statistic for approximate Bayesia...
- 10.1093/genetics/162.4.2025 may be a valid DOI for title: Approximate Bayesian computation in population gen...
- 10.1007/s11222-009-9116-0 may be a valid DOI for title: Non-linear regression models for Approximate Bayes...
- 10.1214/20-ba1238 may be a valid DOI for title: Likelihood-free inference by ratio estimation
- 10.1214/18-ba1121 may be a valid DOI for title: Efficient acquisition rules for model-based approx...
- 10.1073/pnas.2207632119 may be a valid DOI for title: Energy-efficient network activity from disparate c...
- 10.1109/hpec49654.2021.9622796 may be a valid DOI for title: A comparison of automatic differentiation and cont...
- 10.1109/tnnls.2020.3042395 may be a valid DOI for title: BayesFlow: Learning complex stochastic models with...
- 10.1109/cvpr.2016.90 may be a valid DOI for title: Deep residual learning for image recognition
- 10.1101/2024.08.21.608979 may be a valid DOI for title: Differentiable simulation enables large-scale trai...
- 10.1002/9781119585640.ch2 may be a valid DOI for title: Deep learning in population genetics
- 10.1038/s41586-022-04428-3 may be a valid DOI for title: A biophysical account of multiplication by a singl...
- 10.1016/j.neuron.2023.11.006 may be a valid DOI for title: Disinhibition by VIP interneurons is orthogonal to...
- 10.1016/j.celrep.2023.112906 may be a valid DOI for title: Theta and gamma rhythmic coding through two spike ...
- 10.3847/1538-4357/ac7b84 may be a valid DOI for title: Accelerated Bayesian SED modeling using amortized ...
- 10.1103/physrevd.109.083536 may be a valid DOI for title: Field-level simulation-based inference of galaxy c...
- 10.1016/j.neuroimage.2023.120278 may be a valid DOI for title: Bayesian inference of a spectral graph model for b...
- 10.1101/2023.01.31.526269 may be a valid DOI for title: Simulation-based inference for efficient identific...
- 10.1093/bioinformatics/bty361 may be a valid DOI for title: pyABC: distributed, likelihood-free inference
- 10.21105/joss.01143 may be a valid DOI for title: ArviZ a unified library for exploratory analysis o...
- 10.21105/joss.05702 may be a valid DOI for title: BayesFlow: Amortized Bayesian workflows with neura...
- 10.1101/2024.08.21.608969 may be a valid DOI for title: Deep inverse modeling reveals dynamic-dependent in...
- 10.1101/2023.03.02.530774 may be a valid DOI for title: Combined statistical-mechanistic modeling links io...
- 10.2139/ssrn.4982890 may be a valid DOI for title: A Comprehensive Guide to Simulation-based Inferenc...
- 10.1016/j.bpj.2022.11.920 may be a valid DOI for title: Simulation-based inference of single-molecule forc...
- 10.1016/j.neunet.2023.03.040 may be a valid DOI for title: Amortized Bayesian inference on generative dynamic...

❌ INVALID DOIs

- None

[editorialbot]

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⚠️ 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.

[crvernon]

@janfb - could you clarify here what parts of this new version are novel when compared to your last published version? Thank you.

[janfb]

Hi @crvernon , thanks a lot for starting this process. Yes of course. There are lots of new features and general changes to the package. We implemented several new SBI algorithms, new validation methods and more plotting tools, and provided access to the widely-used sampling libraries for posterior sampling and visualization (pyro, pymc, arviz). We also added many more tutorials, revised the entire documentation website, and improved the package maintenance pipelines.

In the paper, we added a figure to give an overview of the new features:

In lines 71-78 in the draft PDF, we also give a summary of what changed compared to the last published version.

Please let me know, if you need further clarification.
Thanks,
Jan

[janfb]

@janfb 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.

List of potential reviewers:

• Kyle Cranmer (reviewed the last published version)
• Francois Lanusse (reviewed the last published version)
• François Rozet
• Virgile Andreani
• Patrick Gray
• Aneesh Naik
• Simon Mutch
• Erik-Jan van Kesteren
• Griffin Daniel Chure

[crvernon]

Thank you @janfb

[crvernon]

@editorialbot invite @boisgera as editor

👋 @boisgera can you take this one on as editor? Thanks!

[editorialbot]

Invitation to edit this submission sent!

[boisgera]

@editorialbot assign @boisgera as editor

[editorialbot]

Assigned! @boisgera is now the editor

[boisgera]

For the record, I have contacted a few researchers of my University that could review this project. I'll give them ~1 week to tell me if they can do it and if needed I'll reach out for another set of potential reviewers. See you soon!

[boisgera]

Hi @janfb,

I wish you a happy new year!

I am sorry for the delay here, I have been far too busy to handle JOSS matters properly at the end of 2024.

Let me tell you where we stand: I have received a majority of "no" and a few "maybe but later" to my first batch of proposals to review your project (nothing suprising unfortunately, and not connected at all with the quality of your submission!).

I am contacting again the "maybes" and opening the proposal to a few other potential reviewers. I hope that we'll be ready to start the review soon!

Best regards,

Sébastien

[janfb]

Hi @boisgera ,

thanks for the update here! And thanks for your efforts for finding reviewers.

Best,
Jan

[boisgera]

@editorialbot add @arnauqb as reviewer

[editorialbot]

@arnauqb added to the reviewers list!

[boisgera]

@editorialbot add @francois-rozet as reviewer

[editorialbot]

@francois-rozet added to the reviewers list!

[boisgera]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7754.