8000 FIX _safe_divide should handle zero-division with numpy scalar by glemaitre · Pull Request #27312 · scikit-learn/scikit-learn · GitHub
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FIX _safe_divide should handle zero-division with numpy scalar #27312

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Merged
merged 13 commits into from
Sep 10, 2023
Merged

FIX _safe_divide should handle zero-division with numpy scalar #27312

merged 13 commits into from
Sep 10, 2023

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glemaitre
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@glemaitre glemaitre commented Sep 7, 2023 •
edited by lorentzenchr
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Fixing the main branch.

This PR should handle the case of zero-division with two numpy scalar.

ping @lorentzenchr @thomasjpfan @OmarManzoor @lesteve

Edit: The CI failure popped up after merging #26278 in the example examples/ensemble/plot_gradient_boosting_regularization.py

@glemaitre glemaitre marked this pull request as draft September 7, 2023 17:02
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github-actions bot commented Sep 7, 2023 •
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Generated for commit: ad04d77. Link to the linter CI: here

@glemaitre
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Given the failure in the example, it seems that the provided fix is not enough. We can hand up returning a very large value because the denominator is extremely small

numerator=-0.2857142857142857
denominator=3.18528276243611e-217
numerator=-8.969824879715574e+215

The next iteration, the numerator and denominator will nan.

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I am not sure what it the right fix here to handle the numerical instability: either clip in the safe division because we should not assign such a large value in raw_predictions or handle the nan values of the next iteration?

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Apparently, once we get some nan, it seems that this is too late:

Figure_1

vs. previously

image

@glemaitre
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I also see that we had potentially another strategy in the past: https://github.com/scikit-learn/scikit-learn/pull/26278/files#diff-dac0eef4868535102a7b9aeb319e1501dfbd10f1256f91d532927e12d30bfb15L732

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So this is not enough. The negative gradient vector has some nan.

In the previous loss it seems that np.nan_to_num was used. Here I tried but the algorithm is still diverging.

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I‘ll also have a look, but I need some time. Fortunately, we‘ve plenty of time to fix it.

@lorentzenchr lorentzenchr added this to the 1.4 milestone Sep 7, 2023
@glemaitre glemaitre mentioned this pull request Sep 7, 2023
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lorentzenchr commented Sep 8, 2023 •
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Which version of numpy do you use?
With numpy 1.24.1 on macos, I can't reproduce this failure. My blue curve is like the one at the bottom plot of #27312 (comment).
I was mistaken, now I see the error.

@OmarManzoor
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OmarManzoor commented Sep 8, 2023 •
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@lorentzenchr I have numpy 1.25.1 on mac M1 and I can reproduce the error when I use the main branch.

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lesteve commented Sep 8, 2023

As an aside (I don't know how much we care to be perfectly honest): code based on np.seterr + catching an exception is not going to work in Pyodide, i.e. an exception will never be raised. Floating point exceptions are not supported in WebAssembly and this is unlikely to change in the near future, see numpy/numpy#21895 (comment) for more details.

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OmarManzoor commented Sep 8, 2023 •
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@lorentzenchr @glemaitre @lesteve

scikit-learn/sklearn/ensemble/_gb.py

Lines 237 to 244 in c634b8a

for leaf in np.nonzero(tree.children_left == TREE_LEAF)[0]:
indices = np.nonzero(terminal_regions == leaf)[0] # of terminal regions
y_ = y.take(indices, axis=0)
sw = None if sample_weight is None else sample_weight[indices]
update = compute_update(y_, indices, neg_gradient, raw_prediction, k)
# TODO: Multiply here by learning rate instead of everywhere else.
tree.value[leaf, 0, 0] = update

I think we should have

indices = np.nonzero(masked_terminal_regions == leaf)[0]  # of terminal regions

if we compare with the original code.

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Plot if I use on main

indices = np.nonzero(masked_terminal_regions == leaf)[0]

Figure_1

@glemaitre
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Yep this look much what we had. It makes sense also if we where computing gradient on data that we should not have :)

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@lesteve @lorentzenchr Instead of the exception catching, we could use the previous trick that return 0.0 if smaller than smaller than a really small values. This would be OK for Pyodide?

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lesteve commented Sep 8, 2023

we could use the previous trick that return 0.0 if smaller than smaller than a really small values. This would be OK for Pyodide?

I think this would work with Pyodide.

I am not too sure to which extent we want to support Pyodide quirkiness, as I mentioned above. It feels like not getting some warnings in Pyodide would acceptable but having a gradient boosting algorithm that behave weirdly because the loss becomes NaN or inf is maybe not that great.

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So I made the fix of @OmarManzoor and change the error catching as it was previously.

@glemaitre glemaitre marked this pull request as ready for review September 8, 2023 12:57
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I also added a comment to remember why we are not using np.errstate and who knows, we could potentially change it in the future if Pyodide handles it.

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lesteve commented Sep 8, 2023 •
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I also added a comment to remember why we are not using np.errstate and who knows, we could potentially change it in the future if Pyodide handles it.

Don't hold your breath too much though, the link above says there is no plan to support it right now, so that's at least 3 years away.

glemaitre
glemaitre commented Sep 8, 2023
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LGTM just some nits.

@glemaitre @OmarManzoor @lesteve Thanks for fixing my bugs.

glemaitre and others added 3 commits September 8, 2023 23:27
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Co-authored-by: Christian Lorentzen <lorentzen.ch@gmail.com>
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LGTM. Thanks @glemaitre , @lesteve and @lorentzenchr

@OmarManzoor OmarManzoor merged commit bbc73cf into scikit-learn:main Sep 10, 2023
REDVM pushed a commit to REDVM/scikit-learn that referenced this pull request Nov 16, 2023
@glemaitre @lorentzenchr @REDVM
FIX _safe_divide should handle zero-division with numpy scalar (sciki…
3178b39 
…t-learn#27312)

Co-authored-by: Christian Lorentzen <lorentzen.ch@gmail.com>
@lorentzenchr lorentzenchr mentioned this pull request Jan 10, 2024
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