Allow for batched `alpha` in `StickBreakingWeights` #6042

purna135 · 2022-08-09T19:55:12Z

What is this PR about?
Addressing #5383
This enables StickBreakingWeight's alpha to accept batched data (>2D), make the infer_shape work with batched data, and fix the rng_fn by broadcasting alpha to K.

Checklist

Explain important implementation details 👆
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Link relevant issues (preferably in nice commit messages)
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Fill out the short summary sections 👇

Major / Breaking Changes

...

Bugfixes / New features

StickBreakingWeights now supports batched alpha parameters

Docs / Maintenance

...

pymc/tests/test_distributions_random.py

codecov · 2022-08-09T20:14:39Z

Codecov Report

Merging #6042 (2a5df64) into main (ad16bf4) will decrease coverage by 1.82%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #6042      +/-   ##
==========================================
- Coverage   89.27%   87.44%   -1.83%     
==========================================
  Files          72       72              
  Lines       12890    12946      +56     
==========================================
- Hits        11507    11321     -186     
- Misses       1383     1625     +242

Impacted Files	Coverage Δ
pymc/distributions/multivariate.py	`91.25% <100.00%> (-0.75%)`	⬇️
pymc/distributions/timeseries.py	`43.36% <0.00%> (-35.28%)`	⬇️
pymc/model_graph.py	`65.66% <0.00%> (-29.80%)`	⬇️
pymc/model.py	`76.14% <0.00%> (-12.06%)`	⬇️
pymc/step_methods/hmc/quadpotential.py	`73.76% <0.00%> (-6.94%)`	⬇️
pymc/util.py	`75.29% <0.00%> (-2.36%)`	⬇️
pymc/distributions/discrete.py	`97.65% <0.00%> (-1.57%)`	⬇️
pymc/step_methods/hmc/base_hmc.py	`89.76% <0.00%> (-0.79%)`	⬇️
pymc/gp/gp.py	`92.73% <0.00%> (-0.45%)`	⬇️
... and 9 more

Co-authored-by: Sayam Kumar <sayamkumar049@gmail.com>

ricardoV94

Good start. I found some issues about the interpretation of size in conjugation with batched alphas

pymc/distributions/multivariate.py

pymc/tests/test_distributions.py

pymc/distributions/multivariate.py

pymc/tests/test_distributions.py

pymc/distributions/multivariate.py

pymc/tests/test_distributions_random.py

pymc/tests/test_distributions.py

larryshamalama

Great work @purna135! :)

pymc/distributions/multivariate.py

larryshamalama · 2022-08-16T17:54:24Z

Would the moment and logp methods in the distribution class need appropriate broadcasting for vector-valued alphas? I am just reading over this PR and might have missed previous discussions

ricardoV94 · 2022-08-16T19:47:19Z

Would the moment and logp methods in the distribution class need appropriate broadcasting for vector-valued alphas? I am just reading over this PR and might have missed previous discussions

We have tests for batched alpha, but not moment (we should)

purna135 · 2022-08-18T09:54:48Z

pymc/tests/test_distributions.py

-    def test_stickbreakingweights_logp(self, value, alpha, K, logp):
-        with Model() as model:
+    def test_stickbreakingweights_logp(self, alpha, K, _compile_stickbreakingweights_logpdf):


Is it acceptable to combine test_stickbreakingweights_logp and test_stickbreakingweights_vectorized in a single test?

If test_stickbreakingweights_vectorized fails, it would point to shapes not being handled properly to form batches. So, lets keep them separate to have better isolation of tests.

Now I separate the test for batched alpha

purna135 · 2022-08-18T10:31:21Z

We have tests for batched alpha, but not moment (we should)

I need some assistance calculating expected in test_stickbreakingweights_moment.

pymc/tests/test_distributions.py

ricardoV94 · 2022-08-25T09:50:04Z

Left a comment above about the fixture. Also don't forget @larryshamalama remark above that we should test the moment function works for batched alpha as well. The existing tests are in here:

pymc/pymc/tests/test_distributions_moments.py

Lines 1171 to 1174 in 7af102d

    
           def test_stickbreakingweights_moment(alpha, K, size, expected): 
        
               with Model() as model: 
        
                   StickBreakingWeights("x", alpha=alpha, K=K, size=size) 
        
               assert_moment_is_expected(model, expected)

Should be enough to test with a vector of two alphas, maybe one of those that is already tested for single alpha (reusing the same k) and the other being an extreme value like alpha=1 or alpha=0 (if that's valid), which might have a very simple moment.

purna135 · 2022-08-25T10:05:13Z

Yes, I got the test for moment but I am not sure how the expected is calculated here.
Is there any equation to determine the expected?

pymc/pymc/tests/test_distributions_moments.py

Lines 1147 to 1151 in 7af102d

    
           @pytest.mark.parametrize( 
        
               "alpha, K, size, expected", 
        
               [ 
        
                   (3, 11, None, np.append((3 / 4) ** np.arange(11) * 1 / 4, (3 / 4) ** 11)), 
        
                   (5, 19, None, np.append((5 / 6) ** np.arange(19) * 1 / 6, (5 / 6) ** 19)),

ricardoV94 · 2022-08-25T10:27:41Z

Yes, I got the test for moment but I am not sure how the expected is calculated here. Is there any equation to determine the expected?

pymc/pymc/tests/test_distributions_moments.py

Lines 1147 to 1151 in 7af102d

@pytest.mark.parametrize(

"alpha, K, size, expected",

[

(3, 11, None, np.append((3 / 4) ** np.arange(11) * 1 / 4, (3 / 4) ** 11)),

(5, 19, None, np.append((5 / 6) ** np.arange(19) * 1 / 6, (5 / 6) ** 19)),

You can check what the moment is for two distinct single alphas, and it should be the same for a batched alpha that has those two values.

purna135 · 2022-08-25T10:35:47Z

Ok got it now, do I need to create a separate test for batched alpha as we did in TestStickBreakingWeights_1D_alpha ?

ricardoV94 · 2022-08-25T11:02:35Z

Ok got it now, do I need to create a separate test for batched alpha as we did in TestStickBreakingWeights_1D_alpha ?

Nope, you can just add it as an extra condition in the existing tests. Moments is less sensitive than logp so we can keep it bundled together

ricardoV94 · 2022-08-29T10:28:56Z

Looks complete to me. The failing test is unrelated. Just asked if @larryshamalama could leave a review as well.

larryshamalama

Looks great @purna135! Just one question for myself 😅

larryshamalama · 2022-08-30T21:20:11Z

pymc/tests/test_distributions.py

+            (np.arange(1, 7, dtype="float64").reshape(2, 3), 5),
+        ],
+    )
+    def test_stickbreakingweights_vectorized(self, alpha, K, stickbreakingweights_logpdf):


Is stickbreakingweights_logpdf passed as an argument here via the fixture sharing decorator of the function?

Yes, that's how fixtures work

purna135 commented Aug 9, 2022

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allow alpha to take batched data for StickBreakingWeights

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Co-authored-by: Sayam Kumar <sayamkumar049@gmail.com>

purna135 force-pushed the generalize_StickBreaking branch from ab3d6e2 to 7fde39a Compare August 9, 2022 20:22

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ricardoV94 changed the title ~~allow alpha to take batched data for StickBreakingWeights~~ Allow for batched alpha in StickBreakingWeights Aug 10, 2022

add supp_shape_from_params() and fix shape

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fixed shape and added test for batched alpha

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ricardoV94 requested a review from larryshamalama August 16, 2022 15:53

refactored tests

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made pytest fixture and added test for batched alpha

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purna135 commented Aug 18, 2022

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test logp for batched alpha

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added test for moment

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ricardoV94 approved these changes Aug 29, 2022

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ricardoV94 requested a review from larryshamalama August 29, 2022 10:28

ricardoV94 mentioned this pull request Aug 30, 2022

Increase support for batched multivariate distributions #5383

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ricardoV94 merged commit 0b191ad into pymc-devs:main Aug 31, 2022

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Allow for batched `alpha` in `StickBreakingWeights` #6042

Allow for batched `alpha` in `StickBreakingWeights` #6042

purna135 commented Aug 9, 2022 •

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Allow for batched alpha in StickBreakingWeights #6042

Allow for batched alpha in StickBreakingWeights #6042

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Allow for batched `alpha` in `StickBreakingWeights` #6042

Allow for batched `alpha` in `StickBreakingWeights` #6042

purna135 commented Aug 9, 2022 •

edited by ricardoV94

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