[PRE REVIEW]: High-performance estimation of Higher-Order Interactions from multivariate data #7298

editorialbot · 2024-09-27T13:44:39Z

Submitting author: @EtienneCmb (Etienne Combrisson)
Repository: https://github.com/brainets/hoi
Branch with paper.md (empty if default branch): paper
Version: v0.0.1
Editor: @jbytecode
Reviewers: @pitmonticone, @ClaudMor
Managing EiC: Chris Vernon

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/cdae325c0d48fdcb8c09802b7744554f"><img src="https://joss.theoj.org/papers/cdae325c0d48fdcb8c09802b7744554f/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/cdae325c0d48fdcb8c09802b7744554f/status.svg)](https://joss.theoj.org/papers/cdae325c0d48fdcb8c09802b7744554f)

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-09-27T13:44:42Z

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:

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

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editorialbot · 2024-09-27T13:44:58Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (1521.1 files/s, 157944.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          45           1100           1853           2572
SVG                              1              0              0            729
TeX                              2             50              0            465
reStructuredText                14            187            144            207
YAML                             5             28             11            123
Markdown                         2             17              0             71
HTML                             2              6              1             48
DOS Batch                        1              8              1             26
TOML                             1              1              0             16
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            74           1401           2017           4266
-------------------------------------------------------------------------------

Commit count by author:

   139	EtienneCmb
    66	Dishie2498
    10	Pierre Robiglio
     9	Mattehub
     7	Onur Ates
     7	dependabot[bot]
     3	Matteo NERI
     2	Andrea Brovelli
     1	Christian Ferreyra
     1	Etienne Combrisson

editorialbot · 2024-09-27T13:45:02Z

Paper file info:

📄 Wordcount for paper.md is 774

✅ The paper includes a Statement of need section

editorialbot · 2024-09-27T13:45:04Z

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot · 2024-09-27T13:45:07Z

⚠️ An error happened when generating the pdf. Problem with affiliations for Christian Ferreyra, perhaps the affiliations index need quoting?.

editorialbot · 2024-09-27T13:45:48Z

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

✅ OK DOIs

- 10.1103/PhysRevE.100.032305 is OK
- 10.3390/e21090869 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Towards an extended taxonomy of information dynami...
- No DOI given, and none found for title: Nonnegative decomposition of multivariate informat...
- No DOI given, and none found for title: The physics of higher-order interactions in comple...
- No DOI given, and none found for title: A Tutorial for Information Theory in Neuroscience
- No DOI given, and none found for title: Beyond normal: On the evaluation of mutual informa...
- No DOI given, and none found for title: Neural interactions in the human frontal cortex di...
- No DOI given, and none found for title: An information-theoretic approach to hypergraph ps...
- No DOI given, and none found for title: Estimation of Shannon differential entropy: An ext...
- No DOI given, and none found for title: Information decomposition and the informational ar...

❌ MISSING DOIs

- 10.1101/2020.09.22.308981 may be a valid DOI for title: A synergistic core for human brain evolution and c...
- 10.1103/physrevresearch.5.013025 may be a valid DOI for title: Gradients of O-information: Low-order descriptors ...
- 10.4135/9781412959384.n229 may be a valid DOI for title: A mathematical theory of communication
- 10.1016/j.nbd.2022.105918 may be a valid DOI for title: Genuine high-order interactions in brain networks ...
- 10.1101/2020.03.17.995886 may be a valid DOI for title: High-order interdependencies in the aging brain
- 10.21105/joss.01081 may be a valid DOI for title: IDTxl: The Information Dynamics Toolkit xl: a Pyth...
- 10.21105/joss.00738 may be a valid DOI for title: “dit“: a Python package for discrete information t...
- 10.21105/joss.01609 may be a valid DOI for title: infotheory: A C++/Python package for multivariate ...
- 10.1371/journal.pcbi.1006343 may be a valid DOI for title: PyPhi: A toolbox for integrated information theory
- 10.1103/physrevresearch.5.013025 may be a valid DOI for title: Gradients of O-information: Low-order descriptors ...
- 10.1103/physreve.91.052802 may be a valid DOI for title: Exploration of synergistic and redundant informati...

❌ INVALID DOIs

- None

EtienneCmb · 2024-09-30T10:55:56Z

@editorialbot generate pdf

editorialbot · 2024-09-30T10:56:23Z

⚠️ An error happened when generating the pdf. Problem with affiliations for Christian Ferreyra, perhaps the affiliations index need quoting?.

EtienneCmb · 2024-09-30T11:06:20Z

@editorialbot generate pdf

editorialbot · 2024-09-30T11:07:37Z

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

editorialbot · 2024-09-30T11:08:20Z

Five most similar historical JOSS papers:

IDTxl: The Information Dynamics Toolkit xl: a Python package for the efficient analysis of multivariate information dynamics in networks
Submitting author: @pwollstadt
Handling editor: @cMadan (Retired)
Reviewers: @danielemarinazzo, @Autoplectic
Similarity score: 0.7443

infotheory: A C++/Python package for multivariate information theoretic analysis
Submitting author: @madvn
Handling editor: @poulson (Retired)
Reviewers: @ajgates42, @artemyk
Similarity score: 0.7314

Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU
Submitting author: @edeno
Handling editor: @emdupre (Active)
Reviewers: @AJQuinn, @sappelhoff, @EtienneCmb
Similarity score: 0.7099

XGI: A Python package for higher-order interaction networks
Submitting author: @nwlandry
Handling editor: @vissarion (Active)
Reviewers: @arashbm, @MridulS
Similarity score: 0.7045

Openseize: A digital signal processing package for large EEG datasets in Python
Submitting author: @mscaudill
Handling editor: @samhforbes (Active)
Reviewers: @szorowi1, @AJQuinn
Similarity score: 0.6959

⚠️ 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.

EtienneCmb · 2024-09-30T11:20:18Z

Suggested reviewers :

EtienneCmb · 2024-09-30T11:37:54Z

@editorialbot generate pdf

editorialbot · 2024-09-30T11:39:12Z

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

editorialbot · 2024-09-30T11:39:53Z

Five most similar historical JOSS papers:

IDTxl: The Information Dynamics Toolkit xl: a Python package for the efficient analysis of multivariate information dynamics in networks
Submitting author: @pwollstadt
Handling editor: @cMadan (Retired)
Reviewers: @danielemarinazzo, @Autoplectic
Similarity score: 0.7430

infotheory: A C++/Python package for multivariate information theoretic analysis
Submitting author: @madvn
Handling editor: @poulson (Retired)
Reviewers: @ajgates42, @artemyk
Similarity score: 0.7351

XGI: A Python package for higher-order interaction networks
Submitting author: @nwlandry
Handling editor: @vissarion (Active)
Reviewers: @arashbm, @MridulS
Similarity score: 0.7075

Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU
Submitting author: @edeno
Handling editor: @emdupre (Active)
Reviewers: @AJQuinn, @sappelhoff, @EtienneCmb
Similarity score: 0.7074

Openseize: A digital signal processing package for large EEG datasets in Python
Submitting author: @mscaudill
Handling editor: @samhforbes (Active)
Reviewers: @szorowi1, @AJQuinn
Similarity score: 0.7056

⚠️ 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 · 2024-10-08T01:52:05Z

@editorialbot invite @jbytecode as editor

👋 @jbytecode are you available to take this one on as editor?

editorialbot · 2024-10-08T01:52:08Z

Invitation to edit this submission sent!

jbytecode · 2024-10-08T06:32:10Z

@crvernon - sure, gladly!

jbytecode · 2024-10-08T06:32:26Z

@editorialbot assign me as editor

editorialbot · 2024-10-08T06:32:29Z

Assigned! @jbytecode is now the editor

jbytecode · 2024-10-08T06:34:09Z

@editorialbot check references

editorialbot · 2024-10-08T06:34:41Z

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

✅ OK DOIs

- 10.1103/PhysRevE.100.032305 is OK
- 10.1038/s41593-022-01070-0 is OK
- 10.3390/e21090869 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1038/s41567-021-01371-4 is OK
- 10.1523/ENEURO.0052-18.2018 is OK
- 10.1016/j.nbd.2022.105918 is OK
- 10.1089/brain.2020.0982 is OK
- 10.7554/eLife.92938 is OK
- 10.21105/joss.01081 is OK
- 10.21105/joss.00738 is OK
- 10.21105/joss.01609 is OK
- 10.1371/journal.pcbi.1006343 is OK
- 10.1016/j.tics.2023.11.005 is OK
- 10.1103/PhysRevResearch.5.013025 is OK
- 10.1103/PhysRevE.91.052802 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Towards an extended taxonomy of information dynami...
- No DOI given, and none found for title: Nonnegative decomposition of multivariate informat...
- No DOI given, and none found for title: Beyond normal: On the evaluation of mutual informa...
- No DOI given, and none found for title: An information-theoretic approach to hypergraph ps...
- No DOI given, and none found for title: Estimation of Shannon differential entropy: An ext...

❌ MISSING DOIs

- 10.4135/9781412959384.n229 may be a valid DOI for title: A mathematical theory of communication

❌ INVALID DOIs

- None

jbytecode · 2024-10-08T06:36:36Z

@editorialbot generate pdf

editorialbot · 2024-10-08T06:37:56Z

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

editorialbot · 2024-10-08T06:38:40Z

Five most similar historical JOSS papers:

IDTxl: The Information Dynamics Toolkit xl: a Python package for the efficient analysis of multivariate information dynamics in networks
Submitting author: @pwollstadt
Handling editor: @cMadan (Retired)
Reviewers: @danielemarinazzo, @Autoplectic
Similarity score: 0.7530

infotheory: A C++/Python package for multivariate information theoretic analysis
Submitting author: @madvn
Handling editor: @poulson (Retired)
Reviewers: @ajgates42, @artemyk
Similarity score: 0.7462

Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU
Submitting author: @edeno
Handling editor: @emdupre (Active)
Reviewers: @AJQuinn, @sappelhoff, @EtienneCmb
Similarity score: 0.7143

XGI: A Python package for higher-order interaction networks
Submitting author: @nwlandry
Handling editor: @vissarion (Active)
Reviewers: @arashbm, @MridulS
Similarity score: 0.7103

Openseize: A digital signal processing package for large EEG datasets in Python
Submitting author: @mscaudill
Handling editor: @samhforbes (Active)
Reviewers: @szorowi1, @AJQuinn
Similarity score: 0.7042

⚠️ 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.

jbytecode · 2024-10-08T17:00:17Z

👋👋👋 Dear @jkbren and @ajgates42 👋👋👋

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:

High-performance estimation of Higher-Order Interactions from multivariate data

You can find more information at the top of this Github issue (#7298).

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 about 25 check items for each single reviewer.

Thank you in advance!

jbytecode · 2024-10-11T18:29:29Z

👋👋👋 Dear @Saran-nns and @pitmonticone 👋👋👋

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:

High-performance estimation of Higher-Order Interactions from multivariate data

You can find more information at the top of this Github issue (#7298).

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 about 25 check items for each single reviewer.

Thank you in advance!

pitmonticone · 2024-10-11T19:07:25Z

Dear @jbytecode,

Thank you for considering me for the review. I am happy to confirm that I am available to assist in reviewing this submission.

Additionally, I would like to suggest @ClaudMor to join the review process if available.

jbytecode · 2024-10-11T19:09:46Z

@editorialbot add @pitmonticone as reviewer

@pitmonticone - Thank you for the quick response

editorialbot · 2024-10-11T19:09:49Z

@pitmonticone added to the reviewers list!

ClaudMor · 2024-10-11T19:26:05Z

Hi @pitmonticone and @jbytecode!

I confirm I would be available for this review.

jbytecode · 2024-10-15T17:00:08Z

@editorialbot add @ClaudMor as reviewer

editorialbot · 2024-10-15T17:00:11Z

@ClaudMor added to the reviewers list!

jbytecode · 2024-10-15T17:00:30Z

@editorialbot start review

jbytecode · 2024-10-15T17:03:06Z

@editorialbot start review

jbytecode · 2024-10-15T17:05:54Z

Sorry, there is a system issue and I am waiting it to be fixed. The review thread will start soon.

jbytecode · 2024-10-16T05:57:01Z

@editorialbot start review

editorialbot · 2024-10-16T05:57:05Z

OK, I've started the review over in #7360.

editorialbot added pre-review Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels Sep 27, 2024

editorialbot added Python TeX labels Sep 27, 2024

editorialbot assigned jbytecode Oct 8, 2024

editorialbot assigned pitmonticone Oct 11, 2024

editorialbot assigned ClaudMor Oct 15, 2024

editorialbot closed this as completed Oct 16, 2024

[PRE REVIEW]: High-performance estimation of Higher-Order Interactions from multivariate data #7298

[PRE REVIEW]: High-performance estimation of Higher-Order Interactions from multivariate data #7298

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