[PRE REVIEW]: HiddenMarkovModels.jl: generic, fast and reliable state space modeling

[editorialbot]

Submitting author: @gdalle (Guillaume Dalle)
Repository: https://github.com/gdalle/HiddenMarkovModels.jl
Branch with paper.md (empty if default branch): joss
Version: v0.3.0
Editor: @jbytecode
Reviewers: @DanielRivasMD, @dmbates
Managing EiC: Arfon Smith

Status

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Author instructions

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

@gdalle 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.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (2145.6 files/s, 172655.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           44            401             31           2035
TOML                             7            376              2           1677
Markdown                        11            226              0            637
SVG                              8              0              0            562
TeX                              2             15              0            225
YAML                             6              0             10            159
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                            79           1018             43           5296
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1014

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.4454565 is OK
- 10.18637/jss.v098.i16 is OK
- 10.1137/141000671 is OK
- 10.1007/0-387-28982-8 is OK
- 10.1016/S0006-3495(00)76441-1 is OK
- 10/cswph2 is OK
- 10.5281/ZENODO.4754896 is OK

MISSING DOIs

- 10.1109/icassp43922.2022.9746824 may be a valid DOI for title: GPU-Accelerated Forward-Backward Algorithm with Application to Lattic-Free MMI

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 before considering asking the reviewers of these papers to review again for JOSS.

[editorialbot]

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

[gdalle]

Some ideas for reviewers:

• https://github.com/dmbates
• https://github.com/DanielRivasMD
• https://github.com/farnazmdi
• https://github.com/juliohm
• https://github.com/ayushpatnaikgit
• https://github.com/pitmonticone
• https://github.com/thomaspinder

[arfon]

@gdalle - 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!

[gdalle]

No worries

[arfon]

@editorialbot invite @jbytecode as editor

👋 @jbytecode, would you be willing to edit this submission for JOSS?

[editorialbot]

Invitation to edit this submission sent!

[gdalle]

Hi! Since the submission was in the backlog, I took the opportunity to revamp the package significantly, and as a result the paper and benchmarks are outdated. Can we maybe put this submission on hold? Or is it easier for your logistics if I withdraw and resubmit later?

[jbytecode]

@editorialbot assign me as editor

@arfon - of course, gladly!

[editorialbot]

Assigned! @jbytecode is now the editor

[jbytecode]

@editorialbot generate pdf

[editorialbot]

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

[jbytecode]

@gdalle - How much time do you need to reach the final version of the manuscript?

[editorialbot]

Five most similar historical JOSS papers:

CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis
Submitting author: @johncwok
Handling editor: @jbytecode (Active)
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Agents.jl: agent-based modeling framework in Julia
Submitting author: @kavir1698
Handling editor: @jedbrown (Active)
Reviewers: @Datseris, @mozhgan-kch
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MLJ: A Julia package for composable machine learning
Submitting author: @ablaom
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Reviewers: @degleris1, @henrykironde
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BoltzMM: an R package for maximum pseudolikelihood estimation of fully-visible Boltzmann machines
Submitting author: @andrewthomasjones
Handling editor: @yochannah (Retired)
Reviewers: @ja-thomas, @schalkdaniel
Similarity score: 0.8128

VBLinLogit: Variational Bayesian linear and logistic regression
Submitting author: @jdrugo
Handling editor: @usethedata (Retired)
Reviewers: @ManuelaS, @usethedata
Similarity score: 0.8108

⚠️ 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.

[gdalle]

@jbytecode I'm a bit swamped these days so I wanna play it safe and say early January

[jbytecode]

@arfon - ☝️ What to do for this issue? Set as paused or something else?

[gdalle]

I'm sorry for the inconvenience

[gdalle]

@editorialbot commands

[editorialbot]

Hello @gdalle, here are the things you can ask me to do:

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@editorialbot list editors

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@editorialbot check references

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@editorialbot check repository

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[gdalle]

@editorialbot set joss as branch

[editorialbot]

Done! branch is now joss

[jbytecode]

@gdalle - Ping me when you're ready. Thank you in advance.

[gdalle]

I will, so sorry for the delay. The package will be infinitely more generic and interesting as a result 😊

[jbytecode]

@gdalle - could you please update your status?

[gdalle]

I've been making progress on the benchmarks, I'll have it ready this month

[gdalle]

I have released a new version with everything I want in it, cleaned up the benchmark set and revamped the paper, which has everything but the benchmark plots.
I only have doubts on the performance of the latest Python competitor, so I have asked its devs for feedback on my benchmark code in order to be as fair as possible. If they don't answer within a week I'll just add my current plots to the paper and submit for good.

See the issue:

• dynamax is weirdly slow in my HMM benchmark probml/dynamax#359

[gdalle]

@editorialbot generate pdf

[editorialbot]

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

[gdalle]

this article proof is still incomplete but only the benchmark section is missing

[jbytecode]

@gdalle - thank you for updating your status.

[gdalle]

@editorialbot generate pdf

[editorialbot]

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

[gdalle]

@jbytecode the paper and package are ready for review, sorry for the delay

[gdalle]

I also would like to change the title to

HiddenMarkovModels.jl: generic, fast and reliable state space modeling

if that's not a problem

[jbytecode]

@gdalle - Do you have any suggestions for potential reviewers? You can use the reviewers system link provided at the top of this page. Please don't use the @ character when you mention their GitHub account names. Thank you in advance.

[gdalle]

Some ideas for reviewers:

• https://github.com/dmbates

• https://github.com/DanielRivasMD

• https://github.com/farnazmdi

• https://github.com/juliohm

• https://github.com/ayushpatnaikgit

• https://github.com/pitmonticone

• https://github.com/thomaspinder

I had gathered a few names here

[jbytecode]

👋👋👋 Dear @dmbates, @DanielRivasMD 👋👋👋

Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)?

JOSS publishes articles about open source research software. The submission I'd like you to review is titled:

HiddenMarkovModels.jl: generic, fast and reliable state space modeling

You can find more information at the top of this Github issue (#5874).

The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know.

This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer.

Thank you in advance!

[DanielRivasMD]

Dear editor, I will be glad to assist in the review process. Best regards, Daniel Rivas

…

On 29 Feb 2024, at 10:23, Mehmet Hakan Satman ***@***.***> wrote: 👋👋👋 Dear @dmbates <https://github.com/dmbates>, @DanielRivasMD <https://github.com/DanielRivasMD> 👋👋👋 Would you be willing to assist in reviewing this submission for JOSS (Journal of Open Source Software)? JOSS publishes articles about open source research software. The submission I'd like you to review is titled: HiddenMarkovModels.jl: generic, fast and reliable state space modeling <#5874> You can find more information at the top of this Github issue (#5874 <#5874>). The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged. If you have any questions please let me know. This is the pre-review issue. After setting at least 2 reviewers we will start the review process in a separate thread. In that thread, there will be 23 check items for each single reviewer. Thank you in advance! — Reply to this email directly, view it on GitHub <#5874 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AI4RGS7WG7FIHAICX7LLH7TYV5KY3AVCNFSM6AAAAAA5GMATE6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNZRGQ4TKNZTHA>. You are receiving this because you were mentioned.

[jbytecode]

@editorialbot add @DanielRivasMD as reviewer

@DanielRivasMD - Thank you for accepting our invitation. Whenever we assign at least one more reviewers, the review will start in a separate thread. I will present the instructions there.

[editorialbot]

@DanielRivasMD added to the reviewers list!

[dmbates]

I too am happy to serve as a reviewer.

[jbytecode]

@editorialbot add @dmbates as reviewer

@dmbates - Thank you for accepting our invitation.

@dmbates, @DanielRivasMD - I am now starting the review in a separate thread. See you there!

[editorialbot]

@dmbates added to the reviewers list!

[jbytecode]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #6436.