MNT Deprecate `affinity` in `AgglomerativeClustering` #23470

Micky774 · 2022-05-26T15:44:18Z

Reference Issues/PRs

Resolves #13945

What does this implement/fix? Explain your changes.

Deprecates affinity in favor of metric in AgglomerativeClustering

Any other comments?

Probably worth propagating the deprecation to linkage_tree in a follow-up PR.

thomasjpfan

I'm a bit undecided if this is worth the deprecation cycle. I think it comes down to "do we want to switch from affinity everywhere". If yes, then I think it's worth going through deprecation.

I think the questionable case is AffinityPropagation. Should affinity in AffinityPropagation by renamed to metric?

sklearn/cluster/_agglomerative.py

Micky774 · 2022-06-02T01:18:53Z

I'm a bit undecided if this is worth the deprecation cycle. I think it comes down to "do we want to switch from affinity everywhere". If yes, then I think it's worth going through deprecation.

It's definitely something that should happen in series, if at all, otherwise having only some mentions move to metric while some stay affinity would be very painful.

I think the questionable case is AffinityPropagation. Should affinity in AffinityPropagation by renamed to metric?

I think that should stay affinity. The docstring specifies that affinity="precomputed" does indeed expect a similarity matrix, and that affinity="euclidean" uses the negative squared Euclidean distances, which is a similarity.

thomasjpfan

Let's go with the deprecation.

sklearn/cluster/_agglomerative.py

Co-authored-by: Thomas J. Fan <[email protected]>

…it-learn into deprecate_affinity

sklearn/cluster/_agglomerative.py

glemaitre · 2022-06-30T08:53:06Z

I just sync with main since we introduced the parameter validation since this PR was open.

glemaitre

Looks good.

sklearn/cluster/_agglomerative.py

sklearn/cluster/tests/test_hierarchical.py

Co-authored-by: Guillaume Lemaitre <[email protected]>

thomasjpfan

Small comment otherwise LGTM!

sklearn/cluster/_agglomerative.py

…it-learn into deprecate_affinity

glemaitre · 2022-07-06T13:44:25Z

Could you modify the following example as well to avoid raising the warning:

examples/cluster/plot_agglomerative_clustering_metrics.py
examples/cluster/plot_cluster_comparison.py (I see that we might have the same inconsistency in SpectralClustering).

Micky774 · 2022-07-06T13:58:07Z

Could you modify the following example as well to avoid raising the warning:

examples/cluster/plot_agglomerative_clustering_metrics.py

examples/cluster/plot_cluster_comparison.py (I see that we might have the same inconsistency in SpectralClustering).

Fixed, good catch.

I think that SpectralClustering is fine since it genuinely builds an affinity/similarity matrix. In particular affinity="precomputed" demands an affinity/similarity matrix.

glemaitre · 2022-07-06T15:02:32Z

LGTM THanks @Micky774

…3470) Co-authored-by: Thomas J. Fan <[email protected]> Co-authored-by: Guillaume Lemaitre <[email protected]>

EwoutH · 2022-12-08T22:05:29Z

Hi! Can we change just change the keyword from affinity to metric in scikit-learn 1.2 without a change in behaviour? Any exceptions or caveats?

Micky774 · 2022-12-08T22:35:31Z

Hi! Can we change just change the keyword from affinity to metric in scikit-learn 1.2 without a change in behaviour? Any exceptions or caveats?

Yes, you should be able to replace affinity-->metric with no change in behavior!

Micky774 added 4 commits May 26, 2022 10:50

Reconciled changelog

2ca67a6

Merge branch 'main' into deprecate_affinity

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Completed initial deprecation

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Fixed deprecation

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github-actions bot added the module:cluster label May 26, 2022

Micky774 and others added 6 commits May 26, 2022 13:23

Added changelog entry

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Merge branch 'main' into deprecate_affinity

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Fixed docstring

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Corrected default param and validation

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Fixed spacing in docstring

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Merge branch 'main' into deprecate_affinity

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thomasjpfan reviewed May 31, 2022

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Micky774 added 2 commits June 1, 2022 21:19

Merge branch 'main' into deprecate_affinity

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Addressed reviewer feedback

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Merge branch 'main' into deprecate_affinity

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Update sklearn/cluster/_agglomerative.py

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Co-authored-by: Thomas J. Fan <[email protected]>

Merge branch 'deprecate_affinity' of https://github.com/Micky774/scik…

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…it-learn into deprecate_affinity

Updated test

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thomasjpfan reviewed Jun 8, 2022

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Micky774 added 2 commits June 9, 2022 12:30

Merge branch 'main' into deprecate_affinity

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Added error handling and testing for edge-case

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glemaitre self-requested a review June 30, 2022 07:45

Merge remote-tracking branch 'origin/main' into pr/Micky774/23470

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Micky774 and others added 3 commits June 30, 2022 16:30

Merge branch 'main' into deprecate_affinity

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Apply suggestions from code review

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Co-authored-by: Guillaume Lemaitre <[email protected]>

Streamlined test and renamed var

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Merge branch 'main' into deprecate_affinity

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thomasjpfan approved these changes Jul 4, 2022

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Micky774 and others added 3 commits July 4, 2022 16:41

Clarified docstring per review feedback

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Merge branch 'deprecate_affinity' of https://github.com/Micky774/scik…

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Merge branch 'main' into deprecate_affinity

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Updated affinity-->metric in plotting

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glemaitre merged commit a5d50cf into scikit-learn:main Jul 6, 2022

Micky774 deleted the deprecate_affinity branch July 6, 2022 15:03

thomasjpfan mentioned this pull request Jul 6, 2022

MNT Param validation: Constraint representing objects exposing a given interface #23791

Merged

Harsh14901 pushed a commit to Harsh14901/scikit-learn that referenced this pull request Jul 6, 2022

MNT Deprecate affinity in AgglomerativeClustering (scikit-learn#2…

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…3470) Co-authored-by: Thomas J. Fan <[email protected]> Co-authored-by: Guillaume Lemaitre <[email protected]>

ogrisel pushed a commit to ogrisel/scikit-learn that referenced this pull request Jul 11, 2022

MNT Deprecate affinity in AgglomerativeClustering (scikit-learn#2…

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…3470) Co-authored-by: Thomas J. Fan <[email protected]> Co-authored-by: Guillaume Lemaitre <[email protected]>

EwoutH mentioned this pull request Dec 8, 2022

clusterer: Update AgglomerativeClustering keyword to fix deprecation quaquel/EMAworkbench#218

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MNT Deprecate affinity in AgglomerativeClustering #23470

MNT Deprecate affinity in AgglomerativeClustering #23470

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Micky774 commented May 26, 2022

Reference Issues/PRs

What does this implement/fix? Explain your changes.

Any other comments?

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glemaitre commented Jul 6, 2022

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MNT Deprecate `affinity` in `AgglomerativeClustering` #23470

MNT Deprecate `affinity` in `AgglomerativeClustering` #23470