rewrite radon notebook using ArviZ and xarray #3963

OriolAbril · 2020-06-14T03:00:27Z

I am in the process of rewriting the notebook to exploit all ArviZ and xarray goodness. Comments are very welcome and I hope it is useful as a way to showcase xarray mostly and ArviZ capabilities inherited from xarray. Part of #3959

Depending on what your PR does, here are a few things you might want to address in the description:

important background, or details about the implementation
- Doing this I have encountered a couple bugs in ArviZ so this notebook won't even run on ArviZ master, only on PR branch. I am not sure about the timeline of the doc sprint but it will end up either running on ArviZ master or on next release (there may be a release coming in the coming weeks 🤔). Depends on fix io_pymc3 bug when model not passed explicitly arviz-devs/arviz#1240 and [WIP] fix hdi false positive warning arviz-devs/arviz#1241 All PRs have been merged and ArviZ 0.9.0 has been released!
- I have checked doc generation locally to make sure xarray html repr is rendered properly
right before it's ready to merge, mention the PR in the RELEASE-NOTES.md

review-notebook-app · 2020-06-14T03:00:33Z

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review-notebook-app · 2020-06-14T03:11:16Z

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OriolAbril commented on 2020-06-14T03:11:15Z
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I am not sure if I am using xarray explicitly or not, I think not, but I am relying heavily on it so even if there are no xr.func calls I would add it manually to the watermark

review-notebook-app · 2020-06-14T03:11:16Z

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OriolAbril commented on 2020-06-14T03:11:16Z
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I just want to highlight this couple of lines that apply hdi to xarray groupby objects

review-notebook-app · 2020-06-14T03:11:17Z

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OriolAbril commented on 2020-06-14T03:11:17Z
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Note to self: I forgot to sort here and half of the plot is inverted: basement to the right, floor to the left

OriolAbril · 2020-06-15T21:52:19Z

I think that the part that has already been updated is ready for review, I hope all xarray tricks are clear and do not seem too obfuscating. Please comment on explanations being too little (or too much) detailed, names used (variables, coordinates, dimensions...), all comments will be welcome

AlexAndorra · 2020-06-16T20:23:42Z

Just did a quick skim and this is looking really nice @OriolAbril 👌 A first quick comment: you can use pm.sample(return_inferencedata=True) in several places. Will do a complete review later this week.
This NB is definitely gonna enter our hall of fame 😉

review-notebook-app · 2020-06-17T02:20:21Z

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ColCarroll commented on 2020-06-17T02:20:20Z
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can get rid of some white space here

OriolAbril commented on 2020-06-17T17:13:10Z
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There is only one line between model context and plotting, the rest are reviewNB artifacts

review-notebook-app · 2020-06-17T02:20:22Z

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ColCarroll commented on 2020-06-17T02:20:21Z
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"Radon" is lower case twice, plus missing a period at the end of the paragraph)

review-notebook-app · 2020-06-17T02:20:23Z

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ColCarroll commented on 2020-06-17T02:20:22Z
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this is funny that the previous run had only 3 cores! also, in the paragraph below here, would you mind lowercasing "Flash" to "flash"?

AlexAndorra commented on 2020-06-17T09:51:01Z
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This is a nerdy reference to "The Flash", so no lowercase required ;)

OriolAbril commented on 2020-06-17T17:14:42Z
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Maybe I should upercase "The" then?

review-notebook-app · 2020-06-17T02:20:23Z

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ColCarroll commented on 2020-06-17T02:20:23Z
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I can't tell if this white space in the cell is just from reviewnb or not... also in the cell below

AlexAndorra commented on 2020-06-17T09:51:42Z
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Yeah, the white space is from ReviewNB. I think they do that do that to ease comparison within cells, but I find it's not yet optimal

review-notebook-app · 2020-06-17T02:20:25Z

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ColCarroll commented on 2020-06-17T02:20:24Z
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lowercase Radon -> radon again

review-notebook-app · 2020-06-17T02:20:25Z

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ColCarroll commented on 2020-06-17T02:20:25Z
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I wonder what happened to make this take 5 seconds instead of 93 seconds!

ColCarroll · 2020-06-17T02:26:47Z

this looks awesome oriol! i'm also excited about alex's change, with the return_inferencedata=True.

A note I don't feel strongly about, but can make the cells a little cleaner: if you np.random.set_seed(42) at the start of the notebook, it should be reproducible, so long as you are using the same number of chains at each step and you run the notebook in order. This can lower the clutter of passing a RANDOM_SEED at every sample call.

AlexAndorra

Ok, did a complete review! Lots of good stuff in there. I had some comments and questions that you'll find below but that shouldn't be too much work 😉 Tell me if anything is unclear!

review-notebook-app · 2020-06-17T09:48:07Z

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AlexAndorra commented on 2020-06-17T09:48:07Z
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~~ArviZ integration~~

You may be wondering why we are using the pm.Data container above, even though the variable floor_idx is not an observed variable nor a parameter of the model. As you'll see, this will make our lives much easier when we'll plot and diagnose our model. In short, this will tell ArviZ that floor_idx is information used by the model to index variables. ArviZ will thus include floor_idx as a variable in theconstant_data group of the resulting InferenceData object.

review-notebook-app · 2020-06-17T09:48:08Z

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AlexAndorra commented on 2020-06-17T09:48:08Z
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I don't think you need to pass the model kwarg to from_pymc3 since we're inside the model context

OriolAbril commented on 2020-06-17T21:28:03Z
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used to (due to bug in ArviZ), I am updating this so I'll mark as resolved :)

review-notebook-app · 2020-06-17T09:48:09Z

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AlexAndorra commented on 2020-06-17T09:48:09Z
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~~xarray~~

ArviZ InferenceData uses xarray.Datasets under the hood, which give access to several common plotting functions with plot...

This is nice ;)

review-notebook-app · 2020-06-17T09:48:11Z

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AlexAndorra commented on 2020-06-17T09:48:10Z
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Let's use pooled_idata = pm.sample(return_inferencedata=True, random_seed=RANDOM_SEED), now that 3.9.1 is out ;) I think you can do that in most of the models in this NB.

OriolAbril commented on 2020-06-17T21:12:46Z
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yep, I was waiting until merging the fix for automagical coords (otherwise I would have had to update the code to use return inferencedata and inferencedata kwargs and then again to remove the kwargs)

review-notebook-app · 2020-06-17T09:48:12Z

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AlexAndorra commented on 2020-06-17T09:48:11Z
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No need for model kwarg inside model context

review-notebook-app · 2020-06-17T09:48:13Z

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AlexAndorra commented on 2020-06-17T09:48:12Z
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"... workflow into a single object. This will also make the rendering of plots and diagnostics faster -- otherwise ArviZ will need to convert your trace to InferenceData each time you call it."

review-notebook-app · 2020-06-17T09:48:14Z

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AlexAndorra commented on 2020-06-17T09:48:13Z
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Not sure the last paragraph needs all the details of the difference between xarray and ArviZ. I would just explain why you need input_core_dims below

OriolAbril commented on 2020-06-17T21:36:22Z
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I think this will give more context into xarray which will ease the application of these techniques to different (but still somewhat similar) analylsis. I would not oppose to removing it though.

AlexAndorra commented on 2020-06-18T07:59:44Z
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It's your call honestly. If you keep everything though, maybe emphasize the input_core_dims stuff, and talk about the rest as context?

review-notebook-app · 2020-06-17T09:48:15Z

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AlexAndorra commented on 2020-06-17T09:48:14Z
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Very cool stuff ;)

review-notebook-app · 2020-06-17T09:48:16Z

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AlexAndorra commented on 2020-06-17T09:48:15Z
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pooled_idata.observed_data = pooled_idata.observed_data.assign_coords(
   {"Level": pooled_idata.posterior.Level[pooled_idata.constant_data.floor_idx]}
).sortby("Level")
pooled_idata.observed_data.plot.scatter(x="Level", y="y", label="Observations", alpha=0.4)

This is quite complicated compared to the previous implementation:

plt.scatter(floor, log_radon, label="Observations", alpha=0.4)

If you want to keep for educational purposes of xarray usage, I would briefly explain what this is doing.

OriolAbril commented on 2020-06-17T22:02:45Z
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I want to leave this for 2 motives:

albeit conceptually more convoluted, this is only 1 line more of code (labels are automatic this this and therefore there is not need to set xticklables nor xlabel anymore)
I do want to encourage it. This is adding a coordinate to the observed_data group -- which can then be used at any time! It is not the case here, but if we had 4 plots instead of 1 we could remove manual setting of xticklabels and xlabel for all 4 of them.

I am moving it to its own cell above to explain what is happening and why.

AlexAndorra commented on 2020-06-18T08:01:40Z
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I agree it's a good educational opportunity. Moving it to its own cell above to explain what is happening and why is the right thing to do IMO

review-notebook-app · 2020-06-17T09:48:16Z

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AlexAndorra commented on 2020-06-17T09:48:16Z
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This is nice!

I would change the xticklabels as "titled" and not as capitalized. That way they'll take less place and maybe you'll be able to put more of them. Also, making the figure bigger vertically would give more space to the plots.

review-notebook-app · 2020-06-17T09:48:18Z

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AlexAndorra commented on 2020-06-17T09:48:17Z
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Return Inf Data directly and no need for model kwarg

review-notebook-app · 2020-06-17T09:48:18Z

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AlexAndorra commented on 2020-06-17T09:48:18Z
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Return Inf Data directly and no need for model kwarg

review-notebook-app · 2020-06-17T09:48:19Z

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AlexAndorra commented on 2020-06-17T09:48:19Z
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use constrained_layout ?

AlexAndorra · 2020-06-17T09:51:01Z

This is a nerdy reference to "The Flash", so no lowercase required ;)

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AlexAndorra · 2020-06-17T09:51:43Z

Yeah, the white space is from ReviewNB. I think they do that do that to ease comparison within cells, but I find it's not yet optimal

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review-notebook-app · 2020-06-18T08:36:48Z

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AlexAndorra commented on 2020-06-18T08:36:48Z
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"We will multiply b with an xvals DataArray to introduce..."

review-notebook-app · 2020-06-18T08:36:49Z

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AlexAndorra commented on 2020-06-18T08:36:49Z
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"However, we don't have that much of a problem to sample..."

review-notebook-app · 2020-06-18T08:36:50Z

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AlexAndorra commented on 2020-06-18T08:36:50Z
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What is chain_prop useful for?

OriolAbril commented on 2020-06-18T10:34:03Z
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It governs how the chain number affects the plotted lines. The default for compact is chain_prop=("ls", ("-", "--", ":", "-.")) which makes each line have a different linestyle.

AlexAndorra commented on 2020-06-18T10:41:22Z
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Ah nice, didn't know about that!

OriolAbril · 2020-06-18T10:34:04Z

It governs how the chain number affects the plotted lines. The default for compact is chain_prop=("ls", ("-", "--", ":", "-.")) which makes each line have a different linestyle.

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AlexAndorra · 2020-06-18T10:41:23Z

Ah nice, didn't know about that!

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OriolAbril · 2020-06-18T11:38:17Z

I am having some issues with reviewNB so I'll comment here:

This plot is the one with most differences between previous version and current implementation -- I strived to make all plots look exactly the same as the original. That is because the implementation is actually different:

Original nb: average a, a_county, b... and then ~~add~~ operate (edited, there are also products involved which is the problem)
Current version: ~~add~~ operate a, a_county, b and then average

Not sure if this is worth mentioning in the notebook, i.e. something along the lines of how seamless it is to average the desired dimensions after all calculations have been done now that we don't have to care about broadcasting rules.

AlexAndorra · 2020-06-18T13:14:01Z

Do you mean that the results are different, or the code to get them is? In the first case that'd be a problem because it would mean weren't computing the same quantity. In the case, it's fine and well worth highlighting that we don't have to care about broadcasting and shape handling with xarrays 👌

OriolAbril · 2020-06-18T14:08:06Z

results are different! Sorry I was not clear enough and I can't get reviewNB to show the same cell side by side so it is difficult to see the differences.

As I was saying above, the original approach was to average first, operate afterwards. This therefore assumes that the expected value of an operation is the operation applied to the expected values of the operands. This is true for sums (and therefore correct for covariation_intercept_slope as we are only adding a+a_county or b+b_county) but does not always hold for products (and therefore does not hold for varying_intercept_slope as a + za_county * sigma_a does not take into account the covariance between za_county and sigma_a). If you pay a lot of attention to the 2 plots you'll see that the black dots are at the same positions but the blue ones are not.

TL;DR: yes, results are different because they should be due to an averaging mistake in the previous version.

AlexAndorra · 2020-06-18T16:30:46Z

Very clear, thanks 👌 And I realize I wasn't very clear either 😅
In short, I agree that we should totally operate first and aggregate second

kyleabeauchamp · 2020-06-21T16:23:41Z

Looks like there's a lot of verbosity in the cells displaying the xarray objects, might want to suppress those outputs for brevity.

OriolAbril · 2020-06-21T21:06:39Z

Looks like there's a lot of verbosity in the cells displaying the xarray objects, might want to suppress those outputs for brevity.

@kyleabeauchamp I guess you are talking about the html repr which is not rendered by github, the raw text is really long, but it is hidden and can be shown interactively, here is a proper render: https://nbviewer.jupyter.org/github/OriolAbril/pymc3/blob/radon_nb/docs/source/notebooks/multilevel_modeling.ipynb

Roughly half notebook has been updated

OriolAbril · 2020-06-28T23:35:07Z

I think I have addressed all comments so far, do not hesitate to complain if I missed some comment. I have reexecuted the nb on pymc 3.9.2 and ArviZ 0.9.0 so I think everything is ready to merge now unless there are still more reviews coming which will always be very welcome

AlexAndorra · 2020-06-29T08:55:04Z

Ha ha I have one last nitpick comment: I think import seaborn as sns can be removed now, as it's no longer used in the NB

OriolAbril · 2020-06-29T15:45:42Z

Should this be added to release notes?

AlexAndorra · 2020-06-29T15:58:59Z

I think so, it's a pretty big revamp, so it's good to publicize it 😉
Will merge once tests pass 👌

AlexAndorra

Thanks a lot @OriolAbril, all looks awesome now 🎉 I'm in love with this notebook 💘

* Update GP NBs to use standard notebook style (pymc-devs#3978) * update gp-latent nb to use arviz * rerun, run black * rerun after fixes from comments * rerun black * rewrite radon notebook using ArviZ and xarray (pymc-devs#3963) * rewrite radon notebook using ArviZ and xarray Roughly half notebook has been updated * add comments on xarray usage * rewrite 2n half of notebook * minor fix * rerun notebook and minor changes * rerun notebook on pymc3.9.2 and ArviZ 0.9.0 * remove unused import * add change to release notes * SMC: refactor, speed-up and run multiple chains in parallel for diagnostics (pymc-devs#3981) * first attempt to vectorize smc kernel * add ess, remove multiprocessing * run multiple chains * remove unused imports * add more info to report * minor fix * test log * fix type_num error * remove unused imports update BF notebook * update notebook with diagnostics * update notebooks * update notebook * update notebook * Honor discard_tuned_samples during KeyboardInterrupt (pymc-devs#3785) * Honor discard_tuned_samples during KeyboardInterrupt * Do not compute convergence checks without samples * Add time values as sampler stats for NUTS (pymc-devs#3986) * Add time values as sampler stats for NUTS * Use float time counters for nuts stats * Add timing sampler stats to release notes * Improve doc of time related sampler stats Co-authored-by: Alexandre ANDORRA <[email protected]> Co-authored-by: Alexandre ANDORRA <[email protected]> * Drop support for py3.6 (pymc-devs#3992) * Drop support for py3.6 * Update RELEASE-NOTES.md Co-authored-by: Colin <[email protected]> Co-authored-by: Colin <[email protected]> * Fix Mixture distribution mode computation and logp dimensions Closes pymc-devs#3994. * Add more info to divergence warnings (pymc-devs#3990) * Add more info to divergence warnings * Add dataclasses as requirement for py3.6 * Fix tests for extra divergence info * Remove py3.6 requirements * follow-up of py36 drop (pymc-devs#3998) * Revert "Drop support for py3.6 (pymc-devs#3992)" This reverts commit 1bf867e. * Update README.rst * Update setup.py * Update requirements.txt * Update requirements.txt Co-authored-by: Adrian Seyboldt <[email protected]> * Show pickling issues in notebook on windows (pymc-devs#3991) * Merge close remote connection * Manually pickle step method in multiprocess sampling * Fix tests for extra divergence info * Add test for remote process crash * Better formatting in test_parallel_sampling Co-authored-by: Junpeng Lao <[email protected]> * Use mp_ctx forkserver on MacOS * Add test for pickle with dill Co-authored-by: Junpeng Lao <[email protected]> * Fix keep_size for arviz structures. (pymc-devs#4006) * Fix posterior pred. sampling keep_size w/ arviz input. Previously posterior predictive sampling functions did not properly handle the `keep_size` keyword argument when getting an xarray Dataset as parameter. Also extended these functions to accept InferenceData object as input. * Reformatting. * Check type errors. Make errors consistent across sample_posterior_predictive and fast_sample_posterior_predictive, and add 2 tests. * Add changelog entry. Co-authored-by: Robert P. Goldman <[email protected]> * SMC-ABC add distance, refactor and update notebook (pymc-devs#3996) * update notebook * move dist functions out of simulator class * fix docstring * add warning and test for automatic selection of sort sum_stat when using wassertein and energy distances * update release notes * fix typo * add sim_data test * update and add tests * update and add tests * add docs for interpretation of length scales in periodic kernel (pymc-devs#3989) * fix the expression of periodic kernel * revert change and add doc * FIXUP: add suggested doc string * FIXUP: revertchanges in .gitignore * Fix Matplotlib type error for tests (pymc-devs#4023) * Fix for issue 4022. Check for support for `warn` argument in `matplotlib.use()` call. Drop it if it causes an error. * Alternative fix. * Switch from pm.DensityDist to pm.Potential to describe the likelihood in MLDA notebooks and script examples. This is done because of the bug described in arviz-devs/arviz#1279. The commit also changes a few parameters in the MLDA .py example to match the ones in the equivalent notebook. * Remove Dirichlet distribution type restrictions (pymc-devs#4000) * Remove Dirichlet distribution type restrictions Closes pymc-devs#3999. * Add missing Dirichlet shape parameters to tests * Remove Dirichlet positive concentration parameter constructor tests This test can't be performed in the constructor if we're allowing Theano-type distribution parameters. * Add a hack to statically infer Dirichlet argument shapes Co-authored-by: Brandon T. Willard <[email protected]> Co-authored-by: Bill Engels <[email protected]> Co-authored-by: Oriol Abril-Pla <[email protected]> Co-authored-by: Osvaldo Martin <[email protected]> Co-authored-by: Adrian Seyboldt <[email protected]> Co-authored-by: Alexandre ANDORRA <[email protected]> Co-authored-by: Colin <[email protected]> Co-authored-by: Brandon T. Willard <[email protected]> Co-authored-by: Junpeng Lao <[email protected]> Co-authored-by: rpgoldman <[email protected]> Co-authored-by: Robert P. Goldman <[email protected]> Co-authored-by: Tirth Patel <[email protected]> Co-authored-by: Brandon T. Willard <[email protected]>

AlexAndorra self-requested a review June 14, 2020 15:40

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OriolAbril mentioned this pull request Jun 21, 2020

Improve documentation on InferenceData.map arviz-devs/arviz#1252

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OriolAbril added 6 commits June 29, 2020 00:58

rewrite radon notebook using ArviZ and xarray

f2d6a78

Roughly half notebook has been updated

add comments on xarray usage

fb5b2b9

rewrite 2n half of notebook

7b06f18

minor fix

76e3e28

rerun notebook and minor changes

47050b8

rerun notebook on pymc3.9.2 and ArviZ 0.9.0

74f2b5f

OriolAbril force-pushed the radon_nb branch from 7c21e8d to 74f2b5f Compare June 28, 2020 23:30

remove unused import

dcf2fe8

add change to release notes

e1edf1f

AlexAndorra approved these changes Jun 29, 2020

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AlexAndorra merged commit facbdf1 into pymc-devs:master Jun 29, 2020

OriolAbril deleted the radon_nb branch June 29, 2020 17:55

kyleabeauchamp added this to the 3.9.3 milestone Jul 28, 2020

rewrite radon notebook using ArviZ and xarray #3963

rewrite radon notebook using ArviZ and xarray #3963

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