search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
721 stars 38 forks source link

[PRE REVIEW]: sbi reloaded: a toolkit for simulation-based inference workflows #7428

Open editorialbot opened 12 hours ago

editorialbot commented 12 hours ago

Submitting author: !--author-handle-->@janfb<!--end-author-handle-- (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: Pending Reviewers: Pending Managing EiC: Chris Vernon

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2ce76f5723a6dfe80cd30fd445c4d2ce"><img src="https://joss.theoj.org/papers/2ce76f5723a6dfe80cd30fd445c4d2ce/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2ce76f5723a6dfe80cd30fd445c4d2ce/status.svg)](https://joss.theoj.org/papers/2ce76f5723a6dfe80cd30fd445c4d2ce)

Author instructions

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

@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.

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 commented 12 hours 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 12 hours ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.29 s (826.1 files/s, 196866.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         167           6632          10783          24368
Jupyter Notebook                22              0           8641           2344
Markdown                        31            575              0           1889
TeX                              1            126              0            989
YAML                            11             77             13            515
TOML                             1             12              8            126
JSON                             2              3              0             93
SVG                              2              0              1             86
JavaScript                       2             10              0             57
CSS                              1             11              7             51
Dockerfile                       1              3              3              9
-------------------------------------------------------------------------------
SUM:                           241           7449          19456          30527
-------------------------------------------------------------------------------

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 commented 12 hours ago

Paper file info:

📄 Wordcount for paper.md is 2241

✅ The paper includes a Statement of need section

editorialbot commented 12 hours ago

License info:

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

editorialbot commented 12 hours ago

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

editorialbot commented 12 hours ago 
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 commented 12 hours ago

Five most similar historical JOSS papers:

swyft: Truncated Marginal Neural Ratio Estimation in Python Submitting author: @bkmi Handling editor: @pdebuyl (Active) Reviewers: @mattpitkin, @olgadoronina Similarity score: 0.7764

BayesFlow: Amortized Bayesian Workflows With Neural Networks Submitting author: @marvinschmitt Handling editor: @osorensen (Active) Reviewers: @sandeshkatakam, @LoryPack Similarity score: 0.7711

BlackBIRDS: Black-Box Inference foR Differentiable Simulators Submitting author: @arnauqb Handling editor: @rkurchin (Active) Reviewers: @rajeshrinet, @marvinschmitt Similarity score: 0.7653

PyVBMC: Efficient Bayesian inference in Python Submitting author: @Bobby-Huggins Handling editor: @rkurchin (Active) Reviewers: @matt-graham, @isdanni Similarity score: 0.7022

Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape Submitting author: @ayush9pandey Handling editor: @csoneson (Active) Reviewers: @Farnazmdi, @Robaina Similarity score: 0.6970

⚠️ 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.