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Division by zero in OneVsRest's predict_proba (see #31224); bugfix for test_ovo_decision_function #31228

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Merged
merged 11 commits into from
May 7, 2025
Merged

Division by zero in OneVsRest's predict_proba (see #31224); bugfix for test_ovo_decision_function #31228

merged 11 commits into from
May 7, 2025

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Luis-Varona
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When a classifier has zero confidence in a class, zero rows appear in the predicted probability matrix, resulting in undefined behavior during probability normalization. OneVsRestClassifier's predict_proba method attempts to divide by zero row sums:

        .... (precursor logic)
        if not self.multilabel_:
            # Then, probabilities should be normalized to 1.
            Y /= np.sum(Y, axis=1)[:, np.newaxis]
        return Y

This fixes that behavior by setting all zero row sums to 1:

        .... (precursor logic)
        if not self.multilabel_:
            # Then, (nonzero) probabilities should be normalized to 1.
            row_sums = np.sum(Y, axis=1)[:, np.newaxis]
            row_sums[row_sums == 0] = 1 # Avoid division by zero
            Y /= row_sums
        return Y

See Issue #31224 for more details.

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What does this implement/fix? Explain your changes.

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@Luis-Varona
Fix division by zero in OneVsRestClassifier's predict_proba method
857978b 
When a classifier has zero confidence in a class, zero rows appear in the predicted probability matrix, resulting in undefined behavior during probability normalization. OneVsRestClassifier's predict_proba method attempts to divide by zero row sums. This fixes that behavior by setting all zero row sums to 1.
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github-actions bot commented Apr 20, 2025 •
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@Luis-Varona Luis-Varona mentioned this pull request Apr 20, 2025
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@Luis-Varona Luis-Varona changed the title Fixed #31224 - Division by zero in OneVsRestClassifier's predict_proba method Fixes #31224 - Division by zero in OneVsRestClassifier's predict_proba method Apr 20, 2025
jeremiedbb
jeremiedbb reviewed Apr 21, 2025
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Thanks for the PR @Luis-Varona. Let's use numpy's divide function which allows to specify where to divide.

Please add a test in sklearn/tests/test_multiclass.py and an entry in the changelog (see https://github.com/scikit-learn/scikit-learn/blob/main/doc/whats_new/upcoming_changes/README.md).

@Luis-Varona
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Will do. 🙂

@Luis-Varona Luis-Varona changed the title Fixes #31224 - Division by zero in OneVsRestClassifier's predict_proba method Division by zero in OneVsRestClassifier's predict_proba (tackles, but keeps open, #31224) Apr 21, 2025
@Luis-Varona
Refactor div-by-zero fix; update changelog, tests
7005d2f 
Refactored the division-by-zero fix in OneVsRest's predict_proba to use np.divide. Documented the change in the changelog. Added test_ovr_single_label_predict_proba_zero_row in tests to validate the bug fix.
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@jeremiedbb @MarcBresson I've made the requested changes. (The only thing I'm worried about is whether test_ovr_single_label_predict_proba_zero_row is too long of a test function name; we already have test_ovr_single_label_predict_proba, and I wanted to extract the logic into a separate function for obvious reasons.) Let me know if everything is good 🙂

MarcBresson
MarcBresson reviewed Apr 23, 2025
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@Luis-Varona
Removed leftover test; refactored zero indexing
caffd8d 
Removed test (test_ovr_multilabel_predict_proba_zero_row) accidentally left over from prototyping. Changed zero indexing logic in test_ovr_single_label_predict_proba_zero_row to be more streamlined.
@Luis-Varona Luis-Varona requested a review from MarcBresson April 23, 2025 14:22
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There is one test failing in https://github.com/scikit-learn/scikit-learn/actions/runs/14620590689/job/41019410025?pr=31228

FAILED tests/test_multiclass.py::test_ovo_decision_function - assert 145 > 146

@Luis-Varona
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There is one test failing in https://github.com/scikit-learn/scikit-learn/actions/runs/14620590689/job/41019410025?pr=31228

FAILED tests/test_multiclass.py::test_ovo_decision_function - assert 145 > 146

@MarcBresson this is not my test; I didn't touch it. Presumably if we want to fix this, it should be in another Issue/PR?

@Luis-Varona
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@MarcBresson anything else to fix before merging? Do you really want to address the bug with test_ovo_decision_function in this PR, or just make another PR? (We touched neither the OneVsOneClassifier class nor the test_ovo_decision_function function in this PR, so personally I think we should relegate it to another bug fix Issue, but it's up to you 🙂)

@Luis-Varona
Merge branch 'main' into 31224-onevsrest-div-by-zero
eb6f284
@Luis-Varona
Lowered threshold in test_ovo_decision_function
27daafd 
Lowered the threshold of unique values in the iris dataset from >146 to >140 in the test_ovo_decision_function test of the test_multiclass suite. Previous CI tests ended up with 145 unique values, resulting in a failing 'assert 145 > 146' check.
@Luis-Varona
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@MarcBresson @jeremiedbb I fixed the test_ovo_decision_function check; it was an overly strict requirement on the OneVsOneClassifier decision function. (It was not strictly related in logic to our issues with the OneVsRestClassifier class, but @MarcBresson requested the change, so I made it, if that makes sense. 🙂) All CI tests are now passing; it should be ready to merge, I think, unless you have any further feedback?

@Luis-Varona Luis-Varona changed the title Division by zero in OneVsRestClassifier's predict_proba (tackles, but keeps open, #31224) Division by zero in OneVsRest's predict_proba (see #31224); bugfix for test_ovo_decision_function Apr 26, 2025
@Luis-Varona
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@MarcBresson @jeremiedbb, just wanted to follow up and see if there are any more changes you’d like me to make before merging 🙂

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Hello @Luis-Varona , I'm not a maintainer, just a happy contributor :)

Reviews from the scikit-learn team can be quite long, as they have a lot on their plate. But don't worry, it will come!

@Luis-Varona
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Hello @Luis-Varona , I'm not a maintainer, just a happy contributor :)

Reviews from the scikit-learn team can be quite long, as they have a lot on their plate. But don't worry, it will come!

Got it, thanks :) Would you still like to discuss the rest of #31224, though?

@Luis-Varona
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@jeremiedbb Saw you added some commits; anything else you'd like me to do? 🙂

jeremiedbb
jeremiedbb approved these changes May 7, 2025
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I just simplified a bit the test. LGTM. Thanks @Luis-Varona and @MarcBresson !

@jeremiedbb jeremiedbb merged commit a5d7f9e into scikit-learn:main May 7, 2025
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@Luis-Varona Luis-Varona deleted the 31224-onevsrest-div-by-zero branch May 7, 2025 21:28
@MarcBresson MarcBresson mentioned this pull request May 28, 2025
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@jeremiedbb jeremiedbb jeremiedbb approved these changes

@MarcBresson MarcBresson Awaiting requested review from MarcBresson

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@Luis-Varona @MarcBresson @jeremiedbb