search

openjournals / joss-reviews

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

[REVIEW]: Generative DAGs as an Interface Into Probabilistic Programming with the R Package causact #4415

Closed editorialbot closed 2 years ago

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@flyaflya<!--end-author-handle-- (Adam Fleischhacker) Repository: https://github.com/flyaflya/causact/ Branch with paper.md (empty if default branch): Version: v0.4.1 Editor: !--editor-->@arfon<!--end-editor-- Reviewers: @joethorley, @ChristopherLucas Archive: 10.5281/zenodo.6949489

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/1e1eb42116078a46ded3986ab0b0e5b9"><img src="https://joss.theoj.org/papers/1e1eb42116078a46ded3986ab0b0e5b9/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/1e1eb42116078a46ded3986ab0b0e5b9/status.svg)](https://joss.theoj.org/papers/1e1eb42116078a46ded3986ab0b0e5b9)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@joethorley & @ChristopherLucas, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @terrytangyuan know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

πŸ“ Checklist for @joethorley

πŸ“ Checklist for @zhiiiyang

πŸ“ Checklist for @ChristopherLucas

editorialbot commented 2 years ago

Hello humans, 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 2 years ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1302.3 files/s, 183683.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               29            496           1142           2504
Markdown                         5            132              0            464
TeX                              1             55              0            393
Rmd                              1             76            115            169
YAML                             4             14              8             74
-------------------------------------------------------------------------------
SUM:                            40            773           1265           3604
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 2 years ago

Wordcount for paper.md is 1855

editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/0304-4076(86)90002-3 is OK
- 10.1007/978-1-4899-3242-6 is OK
- 10.18637/jss.v023.i07 is OK
- 10.1007/978-0-387-21706-2 is OK
- 10.18637/jss.v032.i10 is OK
- 10.18637/jss.v027.i08 is OK
- 10.18637/jss.v012.i03 is OK
- 10.5281/zenodo.3879620 is OK

MISSING DOIs

- 10.21236/ada208388 may be a valid DOI for title: Sampling-based approaches to calculating marginal densities
- 10.1201/b14835-11 may be a valid DOI for title: Strategies for improving MCMC
- 10.1201/9781584887218 may be a valid DOI for title: Applied Bayesian hierarchical methods
- 10.1007/978-3-642-21295-6_2 may be a valid DOI for title: Practical probabilistic programming
- 10.1016/j.jmva.2009.04.008 may be a valid DOI for title: Generating random correlation matrices based on vines and extended onion method
- 10.21105/joss.01601 may be a valid DOI for title: greta: simple and scalable statistical modelling in R
- 10.1613/jair.5371 may be a valid DOI for title: Learning discrete Bayesian networks from continuous data
- 10.3390/e19100555 may be a valid DOI for title: The prior can often only be understood in the context of the likelihood
- 10.1093/ije/dyw341 may be a valid DOI for title: Robust causal inference using directed acyclic graphs: the R package dagitty

INVALID DOIs

- None
editorialbot commented 2 years ago

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

ChristopherLucas commented 2 years ago

In Figure 1, why is there an edge from the error of the estimates?

flyaflya commented 2 years ago

Thx for the question @ChristopherLucas. Let me know if my answer below makes sense.

The edge reflects a parent-child relationship -- meaning the probability density for treatment effect $y_i$ is conditional on a given $\sigma_i$. The fact that we know $\sigma_i$ is slightly weird and it is because the famous eight-schools problem is slightly weird (at least in my eyes). The observations, $y_i$, are actually sampled means as opposed to actual student test scores. Hence, the eight observations of treatment effect, $y_i$, are assumed normally distributed around some "true" school-level effect ($\theta_i$) which will vary based on which students from school $i$ are sampled to receive the treatment. The sampling variance is assumed to be known "because the sample sizes in all eight experiments were relatively large" (Gelman et al. 2014). Thus $y_i \sim Normal(\theta_i,\sigma_i)$ where for our generative model $y_i$ and $sigma_i$ are known/observed and $\theta_i$ (i.e. a true school level effect) is the latent parameter of interest.

For the above quote and more description, see Gelman et al. (2014) p. 119-120 (available here: http://www.stat.columbia.edu/~gelman/book/BDA3.pdf) and relevant paragraph shown below:

image

terrytangyuan commented 2 years ago

@editorialbot add @zhiiiyang as reviewer

editorialbot commented 2 years ago

@zhiiiyang added to the reviewers list!

zhiiiyang commented 2 years ago

Review checklist for @zhiiiyang

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Reviews (Not finalized yet)

  1. https://github.com/flyaflya/causact/issues/43
  2. Has the 2nd author contributed to any of the package writing? What is his or her contribution to the paper?
joethorley commented 2 years ago

Review checklist for @joethorley

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

joethorley commented 2 years ago

@flyaflya - this is a great piece of work. Congratulations. Comments to follow:

R code in paper should be edited so it can be copied and pasted as is see https://github.com/flyaflya/causact/issues/45

joethorley commented 2 years ago

@terrytangyuan and @flyaflya - I think the paper is ready for acceptance conditional on the issues I have opened being addressed to my satisfaction (see above)

Congratulations again on a great package.

flyaflya commented 2 years ago

@zhiiiyang . Thx for agreeing to review and I am working on your checklist. Below, I want to address your question about the second author's contribution.

The second author is my PhD advisee who has been working on this project alongside me since 2019. She authored the first draft of our submitted paper and has contributed to the development and thought process behind the causact package by developing a parallel backend using Julia instead of Tensorflow/Python. Her main code contributions have not been merged as I am not ready to support the Julia backend quite yet (just supporting the greta backend for now). You can see evidence of her extensive coding efforts here: https://github.com/flyaflya/causact/compare/master...Rosenguyen0411:master.

flyaflya commented 2 years ago

@joethorley - Thanks a million for all the helpful suggestions. I think I have addressed your concerns and I went ahead and closed all the issues with comments regarding the commits that fix the raised issues. Please have a look to make sure they are all okay. I can reopen any issues that were not resolved properly or need further improvement (and my apologies if I should not have closed them ... not sure of the protocol for whether I close them when I think they are complete or when you say they are resolved satisfactorily).

ChristopherLucas commented 2 years ago

It is possible I'm misunderstanding the example or the DAG, and maybe @joethorley or @zhiiiyang can weigh in, but I don't understand why there's an edge from the estimated SE. E.G., the treatment effect is not dependent on my estimates of parameters of the sampling distribution of the estimator.

Again, it's possible I'm just misunderstanding the example, but presumably others might as well.

ChristopherLucas commented 2 years ago

Review checklist for @ChristopherLucas

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

zhiiiyang commented 2 years ago

@flyaflya, thank you for addressing my comments. I have encountered a fatal crash when using greta and the maintainers of greta are trying to help me debug https://github.com/greta-dev/greta/issues/526#issuecomment-1144470814. I will return the complete review reports once we figure it out.

joethorley commented 2 years ago

@flyaflya - thanks for resolving and closing my issues.

joethorley commented 2 years ago

I'm am happy with it being published.

joethorley commented 2 years ago

@ChristopherLucas My understanding is that the edge is there because the values of the treatment effect depends on the expected treatment effect and the standard deviation of the variation in the treatment effect.

flyaflya commented 2 years ago

@ChristopherLucas A nearly equivalent representation of the eight-schools problem can be shown like this: image (variable() represents a flat prior). This picture above exactly matches the description in Gelman et al. (2014) p. 119-120 (available here: http://www.stat.columbia.edu/~gelman/book/BDA3.pdf). If this representation seems more helpful, I can use it in place of the one that is there already?

I am with you that typically the "the treatment effect (y)" should not be "dependent on my estimates of parameters (i.e. sigma) of the sampling distribution of the estimator." The only reason the eight-schools problem looks like this is due to this key assumption articulated in Gelman: "the sampling variances [i.e. the std error of effect] are known, for all practical purposes." Thus, the measured treatment effect is dependent on the assumed-to-be-known parameters of the sampling distribution of the estimator.

I could use a different dataset/model to showcase causact, but this dataset was used because it commonly appears in the computational Bayesian inference literature and the graphical illustration of the model helps to initiate conversations about assumptions like the conversation we are having here. Examples of eight schools used as demo model:

PS: The justification for the simplifiying asumption that the estimated sigma from the data is assumed to be equivalent to the "true" sigma of the sampling distribution is because the treatment effect (y) is actually an observed mean treatment effect over many (>30) individual student performances at each school. Presumably, if you run the experiment with a different set of students, the sampling distribution of their mean treatment effect $y \sim Normal(theta,sigma)$.

zhiiiyang commented 2 years ago

@terrytangyuan, I just found out that I can't use this package since it depends on greta failing to run on an M1 Mac。:(. This has been confirmed by the maintainer. Could you remove me from the reviewer list? Sorry about the inconveniences. https://github.com/greta-dev/greta/issues/526#issuecomment-1151903419

joethorley commented 2 years ago

@zhiiiyang - that is good to know - is there any sense of when this might be fixed?

terrytangyuan commented 2 years ago

@editorialbot remove @zhiiiyang from reviewers

editorialbot commented 2 years ago

@zhiiiyang removed from the reviewers list!

zhiiiyang commented 2 years ago

@joethorley the greta maintainer asked me to follow this issue https://github.com/greta-dev/greta/issues/458

flyaflya commented 2 years ago

@terrytangyuan Even though @zhiiiyang is no longer an official reviewer, her comments/suggestions were much appreciated and there is a new CRAN release of causact as of today to support adding a vignette. You can see more details about my response to @zhiiiyang 's review here: https://github.com/flyaflya/causact/issues/43#issuecomment-1155419729

flyaflya commented 2 years ago

Hi all - just wanted to gently check on the progress of this review. @ChristopherLucas does https://github.com/openjournals/joss-reviews/issues/4415#issuecomment-1147543764 help ease your concerns about the presented model in the paper? @terrytangyuan is there any additional outstanding comments/issues that I can help address?

Thanks to all for the help!

arfon commented 2 years ago

@editorialbot assign @arfon as editor

:wave: folks. As @terrytangyuan is stepping down from the JOSS editorial team (thanks for all of your help over the years Yuan!) I'm going to be taking over this review.

Based on my reading of the review thread thus far, it looks like there has been some feedback from @flyaflya in response to @ChristopherLucas' feedback. @ChristopherLucas – could you take another look and see if you're able to complete your review at this stage?

Many thanks!

editorialbot commented 2 years ago

Assigned! @arfon is now the editor

ChristopherLucas commented 2 years ago

@ChristopherLucas A nearly equivalent representation of the eight-schools problem can be shown like this: image (variable() represents a flat prior). This picture above exactly matches the description in Gelman et al. (2014) p. 119-120 (available here: http://www.stat.columbia.edu/~gelman/book/BDA3.pdf). If this representation seems more helpful, I can use it in place of the one that is there already?

I am with you that typically the "the treatment effect (y)" should not be "dependent on my estimates of parameters (i.e. sigma) of the sampling distribution of the estimator." The only reason the eight-schools problem looks like this is due to this key assumption articulated in Gelman: "the sampling variances [i.e. the std error of effect] are known, for all practical purposes." Thus, the measured treatment effect is dependent on the assumed-to-be-known parameters of the sampling distribution of the estimator.

I could use a different dataset/model to showcase causact, but this dataset was used because it commonly appears in the computational Bayesian inference literature and the graphical illustration of the model helps to initiate conversations about assumptions like the conversation we are having here. Examples of eight schools used as demo model:

* Sturtz, S., Ligges, U., & Gelman, A. (2005). R2WinBUGS: a package for running WinBUGS from R. Journal of Statistical software, 12, 1-16 (https://www.jstatsoft.org/index.php/jss/article/view/v012i03/33).

* `rstan` Vignette:  https://cran.r-project.org/web/packages/rstan/vignettes/rstan.html

PS: The justification for the simplifiying asumption that the estimated sigma from the data is assumed to be equivalent to the "true" sigma of the sampling distribution is because the treatment effect (y) is actually an observed mean treatment effect over many (>30) individual student performances at each school. Presumably, if you run the experiment with a different set of students, the sampling distribution of their mean treatment effect y∼Normal(theta,sigma).

This all makes sense to me. I still worry that researchers regularly working with DAGs will find it confusing to mix the causal structure with assumptions about the estimator for estimands denoted by that structure. I think the authors know precisely what they mean by the example, and that they mean something sensible, but I do think it will be unclear to many researchers who regularly work with DAGs but not with Bayesian models. I'd probably use a simpler example and perhaps invoke the 8-schools problem elsewhere in the docs, where there is more space to clarify what's going on. E.G., if I were to set up an example of the eight-schools problem, I'd write the estimand in potential outcomes notation, then denote a DAG (or several DAGs) under which a particular estimator returns an estimate of that estimand with some characterizable properties wrt bias/variance. That's probably a bit outside the bounds of a software submission, so I don't think it necessary here, but I do worry that as written many interested readers will be unnecessarily confused.

flyaflya commented 2 years ago

Roger that @ChristopherLucas. I will switch to a more straight forward example. I too experience some discomfort with 8-schools and I think you are right that more readers will benefit from a different example. I'll revise the manuscript accordingly. Thanks for pushing on this!

ChristopherLucas commented 2 years ago

Congrats, again, on a great package. I spent some time looking through the docs yesterday - awesome materials, some of which I'll probably use in one of my grad courses.

flyaflya commented 2 years ago

Thanks @ChristopherLucas for the encouragement. I switched the example model to use another well known dataset without the weird modelling of standard errors. This time I am using a medium complexity version of the chimpanzee example from McElreath's Statistical Rethinking. Experiment discussed here: https://youtu.be/n2aJYtuGu54?t=513

The updated paper is an artifact from the last action and can be downloaded here:
https://github.com/flyaflya/causact/suites/7535235027/artifacts/310574849

ChristopherLucas commented 2 years ago

This looks great to me. Congrats on the package and paper!

flyaflya commented 2 years ago

Fixed a few minor typos and the most recent manuscript can be found as the artifact here: https://github.com/flyaflya/causact/actions/runs/2743355474

@arfon, thanks for taking over as editor. I believe the review process is nearing its conclusion (checklists complete and all issues have been addressed), so please let me know what I else I can do to help shepherd things along. Thanks again!

arfon commented 2 years ago

@arfon, thanks for taking over as editor. I believe the review process is nearing its conclusion (checklists complete and all issues have been addressed), so please let me know what I else I can do to help shepherd things along. Thanks again!

I think we're in good shape here. At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

I can then move forward with accepting the submission.

flyaflya commented 2 years ago

This is great news. Thanks to all!!

@arfon the archived DOI is: 10.5281/zenodo.6949489

A link to the Zenodo archive is here: https://zenodo.org/record/6949489#.Yuf-THbMKUk

arfon commented 2 years ago

@editorialbot set 10.5281/zenodo.6949489 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6949489

arfon commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.5281/zenodo.3879620 is OK
- 10.18637/jss.v012.i03 is OK

MISSING DOIs

- 10.1201/9781584887218 may be a valid DOI for title: Applied Bayesian hierarchical methods
- 10.21236/ada208388 may be a valid DOI for title: Sampling-based approaches to calculating marginal densities
- 10.1201/b14835-11 may be a valid DOI for title: Strategies for improving MCMC
- 10.21105/joss.01601 may be a valid DOI for title: greta: simple and scalable statistical modelling in R
- 10.1007/978-3-642-21295-6_2 may be a valid DOI for title: Practical probabilistic programming
- 10.1093/ije/dyw341 may be a valid DOI for title: Robust causal inference using directed acyclic graphs: the R package β€˜dagitty’

INVALID DOIs

- None
editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3425, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 2 years ago

🐦🐦🐦 πŸ‘‰ Tweet for this paper πŸ‘ˆ 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3426
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04415
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! πŸŽ‰πŸŒˆπŸ¦„πŸ’ƒπŸ‘»πŸ€˜

Any issues? Notify your editorial technical team...

arfon commented 2 years ago

@joethorley, @ChristopherLucas, @zhiiiyang – many thanks for your reviews here and to @terrytangyuan for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@flyaflya – your paper is now accepted and published in JOSS :zap::rocket::boom: