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[PRE REVIEW]: Dynamax: A Python package for probabilistic state space modeling with JAX #7029

Closed editorialbot closed 1 month ago

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@slinderman<!--end-author-handle-- (Scott Linderman) Repository: https://github.com/probml/dynamax Branch with paper.md (empty if default branch): paper Version: v0.1.4 Editor: !--editor-->@osorensen<!--end-editor-- Reviewers: @thomaspinder, @gdalle Managing EiC: Chris Vernon

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Markdown: [![status](https://joss.theoj.org/papers/aaec4098e71833c94a74dbe1ff785d9e/status.svg)](https://joss.theoj.org/papers/aaec4098e71833c94a74dbe1ff785d9e)

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editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.18 s (668.8 files/s, 261137.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          67           3037           4303           8814
Jupyter Notebook                30              0          24675           3907
Markdown                        10             99              0            282
TeX                              1             25              0            185
reStructuredText                 2            152            208            153
YAML                             5             20              7            147
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              1              0              4
-------------------------------------------------------------------------------
SUM:                           118           3346          29201          13527
-------------------------------------------------------------------------------

Commit count by author:

   342  Scott Linderman
   178  Peter G. Chang
   135  xinglong
   131  Kevin P Murphy
    83  karalleyna
    79  gileshd
    69  Gerardo Duran-Martin
    60  petergchang
    26  Caleb Weinreb
    18  libby
    14  kostastsa
    11  slinderman
    10  Elizabeth DuPre
     8  Kevin Murphy
     6  andrewwarrington
     6  davidzoltowski
     6  patel-zeel
     4  Ravin Kumar
     3  Aleyna Kara
     2  Yixiu Zhao
     2  Zeel B Patel
     2  partev
     1  Collin Schlager
     1  Jake VanderPlas
     1  Jason Davies
     1  RaulPL
     1  Xinglong
     1  Xinglong Li
     1  xinglong-li
editorialbot commented 1 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- No DOI given, and none found for title: Computation through neural population dynamics
- No DOI given, and none found for title: Probabilistic Machine Learning: Advanced Topics
- No DOI given, and none found for title: Bayesian filtering and smoothing
- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Revisiting structured variational autoencoders
- No DOI given, and none found for title: Switching autoregressive low-rank tensor models
- No DOI given, and none found for title: Low-rank extended Kalman filtering for online lear...
- 10.1101/2023.03.16.532307 may be a valid DOI for title: Keypoint-MoSeq: parsing behavior by linking point ...
- No DOI given, and none found for title: PyHSMM: Bayesian inference in HSMMs and HMMs
- No DOI given, and none found for title: Code Companion for Bayesian Filtering and Smoothin...
- No DOI given, and none found for title: SSM: Bayesian Learning and Inference for State Spa...
- No DOI given, and none found for title: JSL: JAX State-Space models (SSM) Library
- 10.25080/majora-92bf1922-011 may be a valid DOI for title: statsmodels: Econometric and statistical modeling ...
- No DOI given, and none found for title: hmmlearn
- No DOI given, and none found for title: Biological sequence analysis: Probabilistic models...
- 10.1016/j.tree.2007.10.009 may be a valid DOI for title: State-space models of individual animal movement
- No DOI given, and none found for title: Bayesian analysis of stochastic volatility models
- No DOI given, and none found for title: A local ensemble Kalman filter for atmospheric dat...
- No DOI given, and none found for title: Parallel tridiagonal equation solvers
- 10.1109/tac.2020.2976316 may be a valid DOI for title: Temporal parallelization of Bayesian smoothers
- 10.1109/tsp.2021.3103338 may be a valid DOI for title: Temporal parallelization of inference in hidden Ma...
- No DOI given, and none found for title: Structural Time Series (STS) in JAX

INVALID DOIs

- None
editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 960

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

HiddenMarkovModels.jl: generic, fast and reliable state space modeling Submitting author: @gdalle Handling editor: @jbytecode (Active) Reviewers: @DanielRivasMD, @dmbates Similarity score: 0.7444

GPJax: A Gaussian Process Framework in JAX Submitting author: @thomaspinder Handling editor: @dfm (Active) Reviewers: @gpleiss, @theorashid Similarity score: 0.7331

flowMC: Normalizing flow enhanced sampling package for probabilistic inference in JAX Submitting author: @kazewong Handling editor: @rkurchin (Active) Reviewers: @matt-graham, @Daniel-Dodd Similarity score: 0.7138

pypfilt: a particle filter for Python Submitting author: @robmoss Handling editor: @diehlpk (Active) Reviewers: @tbrown122387, @Karangupta1994 Similarity score: 0.7027

RxInfer: A Julia package for reactive real-time Bayesian inference Submitting author: @bvdmitri Handling editor: @jmschrei (Active) Reviewers: @dhvalden, @alstat Similarity score: 0.6969

⚠️ 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 commented 1 month ago

:wave: @slinderman - thanks for the submission. While I get an editor set up for you, could you please add a "Statement of Need" section to the paper and address the missing DOI in the message above if they are applicable. Also, I appreciate you keeping the word count at around 1000 words - thank you!

crvernon commented 1 month ago

@editorialbot invite @osorensen as editor

Just getting your portfolio built back up @osorensen. Thanks!

editorialbot commented 1 month ago

Invitation to edit this submission sent!

slinderman commented 1 month ago

Thanks, @crvernon! I've added the missing DOIs. Please note that some online resources (e.g., GitHub repositories for related packages) do not have DOIs. I also confirmed that the paper has a "Statement of need" section.

osorensen commented 1 month ago

@editorialbot add @osorensen as editor

editorialbot commented 1 month ago

Assigned! @osorensen is now the editor

osorensen commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

HiddenMarkovModels.jl: generic, fast and reliable state space modeling Submitting author: @gdalle Handling editor: @jbytecode (Active) Reviewers: @DanielRivasMD, @dmbates Similarity score: 0.7350

GPJax: A Gaussian Process Framework in JAX Submitting author: @thomaspinder Handling editor: @dfm (Active) Reviewers: @gpleiss, @theorashid Similarity score: 0.7315

flowMC: Normalizing flow enhanced sampling package for probabilistic inference in JAX Submitting author: @kazewong Handling editor: @rkurchin (Active) Reviewers: @matt-graham, @Daniel-Dodd Similarity score: 0.7072

PyNumDiff: A Python package for numerical differentiation of noisy time-series data Submitting author: @florisvb Handling editor: @christinahedges (Retired) Reviewers: @pmli, @billtubbs Similarity score: 0.6858

RxInfer: A Julia package for reactive real-time Bayesian inference Submitting author: @bvdmitri Handling editor: @jmschrei (Active) Reviewers: @dhvalden, @alstat Similarity score: 0.6854

⚠️ 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.

osorensen commented 1 month ago

👋 @Saran-nns, @GarrettMerz, @edeno, @thomaspinder, 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

thomaspinder commented 1 month ago

I can review

osorensen commented 1 month ago

@editorialbot add @thomaspinder as reviewer

editorialbot commented 1 month ago

@thomaspinder added to the reviewers list!

osorensen commented 1 month ago

👋 @gdalle, @florisvb, @bvdmitri, 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

gdalle commented 1 month ago

Yeah I can definitely review this one! Although I coded the Julia counterpart so there is a slight competition here 😉

osorensen commented 1 month ago

@editorialbot add @gdalle as reviewer

editorialbot commented 1 month ago

@gdalle added to the reviewers list!

osorensen commented 1 month ago

@editorialbot start review

editorialbot commented 1 month ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7069.

florisvb commented 3 weeks ago

Sorry I was out of town the last 2 weeks, but it looks like you have enough reviewers for this now?

On Sat, Aug 3, 2024 at 2:22 AM Øystein Sørensen @.***> wrote:

👋 @gdalle https://github.com/gdalle, @florisvb https://github.com/florisvb, @bvdmitri https://github.com/bvdmitri, 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

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7029#issuecomment-2266651588, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAB4EPAXFPD2YQPISOYFGM3ZPSOO3AVCNFSM6AAAAABLMO57NSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRWGY2TCNJYHA . You are receiving this because you were mentioned.Message ID: @.***>

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osorensen commented 3 weeks ago

Indeed @florisvb, we have enough reviewers, but thanks anyway