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MaxwellLZH · 2021-03-31T09:17:09Z

Reference Issues/PRs

This is an implementation for #19744.

What does this implement/fix? Explain your changes.

The implementation added a radius argument to Isomap class.

When n_neighbors argument is provided, we continue using kneighbors_graph to build the underlying graph as we did before, so it's backward compatible. When n_neighbors is None, we use radius_neighbors_graph instead to build the graph.

Corresponding test cases are also added.

ogrisel · 2021-03-31T13:04:41Z

I had a quick look at the diff and it looks good. Please document the change under doc/whats_new.rst/v1.0.rst.

I am trying to think of a case where radius based isomap would make a qualitative difference. Have you tried it on "real" datasets?

Is there an existing example (under the examples/ folder) that could be extended to illustrate the impact of the new functionality?

MaxwellLZH · 2021-06-15T11:35:50Z

Hi @TomDLT, sorry for the late action. I've made the suggested changes.

TomDLT · 2021-06-15T18:19:00Z

Thanks ! It seems like you have an git issue on this branch, many commits do not belong here.
Could you clean this up? Not sure what the easiest fix is, I would suggest creating a new branch from main and cherry-pick your 7 commits. Then I would rename the old branch for backup, rename the new branch to the old name, and force push.

Move radius to the last argument Co-authored-by: Tom Dupré la Tour <[email protected]>

update isomap tests Co-authored-by: Tom Dupré la Tour <[email protected]>

MaxwellLZH · 2021-06-16T02:15:33Z

Apology for the git mess, should be fixed now :)

Co-authored-by: Olivier Grisel <[email protected]>

ogrisel · 2021-06-16T08:14:24Z

 path_methods = ['auto', 'FW', 'D']

+N_per_side = 5
+Npts = N_per_side ** 2


Since we change those line, let's name those variable more explicitly use either lower case or all upper case to respect scikit-learn conventions:

N_GRID_TICKS_PER_SIDE = 5 N_GRID_POINTS = N_GRID_TICKS_PER_SIDE ** 2

ogrisel

Another round of comments:

Co-authored-by: Olivier Grisel <[email protected]>

Co-authored-by: Tom Dupré la Tour <[email protected]>

MaxwellLZH · 2021-06-17T11:47:42Z

Hi @ogrisel @TomDLT , I've added the test case and UserWarning as suggested :)

TomDLT

We should add a test that a warning is raised, using with pytest.warns.

Co-authored-by: Tom Dupré la Tour <[email protected]>

jjerphan · 2022-01-28T15:32:41Z

@MaxwellLZH: I've corrected the status of this branch, merging main in.

Part of this PR changes (e.g https://github.com/scikit-learn/scikit-learn/pull/19794/files#diff-6f9bfaa7a4978e0d1aa64c5f613eb7a4bd988fb1b7227b170f825657693c056aR243-R247) might need some adaptation due to some change made by @TomDLT in #20531 in the meantime.

thomasjpfan

Thanks for the PR @MaxwellLZH !

I left a comment for reviewers regarding the behavior when both n_neighbors and radius are set.

thomasjpfan · 2022-02-14T21:13:11Z

+                "Radius is ignored when both n_neighbors and radius "
+                "are provided, n_neighbors should be set to None "
+                "explicitly when radius is passed."


If we are not raising an error, then I think n_neighbors should be the one that gets ignored when both parameters are not None. The default for n_neighbors is 5. Lets say one writes Isomap(radius=0.8), then radius is ignored and n_neighbors is set to 5. That feels very counter initiative.

For the record, I do prefer raising an error here instead of raising a warning.

Good catch, I agree this is counter intuitive and we should ignore n_neighbors.

I am also ok raising an error instead (see #19794 (comment)), but then the same problem would arise, because Isomap(radius=0.8) would raise an error. To solve this issue, we could have both parameters default to None, and if none are provided use n_neighbors=5. WDYT ?

If we error, I was thinking of letting Isomap(radius=0.8) error and recommending Isomap(radius=0.8, n_neighbors=None).

To solve this issue, we could have both parameters default to None, and if none are provided use n_neighbors=5. WDYT ?

I am +0.75 with this. It is the only solution we have to make Isomap(radius=0.8) work. The downside is that one needs to read the docstring to get the default value. Explaining the behavior in the docstring is slightly move involved:

n_neighbors : If `None` and `radius` is `None`, then the default is 5. radius : Can be set only when `n_neighbors` is None.

Recommending Isomap(radius=0.8, n_neighbors=None) is a bit heavier, but I agree it is simpler to explain/understand, and more explicit than a default hidden in the docstring. Let's do that.

I've updated the code to raise a ValueError when both arguments are set, might need some help with the phrasing of the error message

thomasjpfan

Thanks for the update!

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

thomasjpfan

Thanks for the update!

thomasjpfan

Minor nits, otherwise LGTM

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

jjerphan

LGTM. Thank you, @MaxwellLZH.

Co-authored-by: Tom Dupré la Tour <[email protected]> Co-authored-by: Olivier Grisel <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]> Co-authored-by: Julien Jerphanion <[email protected]>

github-actions Bot added the module:manifold label Mar 31, 2021

TomDLT reviewed Apr 5, 2021

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github-actions Bot added the cython label Jun 15, 2021

MaxwellLZH and others added 7 commits June 16, 2021 10:04

FIX isomap supports radius-based neighbors

d80715d

update whats_new

2193c0b

Update sklearn/manifold/_isomap.py

59daf69

Move radius to the last argument Co-authored-by: Tom Dupré la Tour <[email protected]>

Update sklearn/manifold/tests/test_isomap.py

c4247a2

update isomap tests Co-authored-by: Tom Dupré la Tour <[email protected]>

Move radius to last argument

8e881d4

Add comment to move radius parameter

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Move radius argument

c76836d

MaxwellLZH force-pushed the fet/isomap branch from 7541c4c to c76836d Compare June 16, 2021 02:12

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Update sklearn/manifold/_isomap.py

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MaxwellLZH and others added 5 commits June 17, 2021 09:53

Update sklearn/manifold/_isomap.py

a5045ed

Co-authored-by: Tom Dupré la Tour <[email protected]>

Update sklearn/manifold/_isomap.py

59459b2

Co-authored-by: Tom Dupré la Tour <[email protected]>

Update sklearn/manifold/_isomap.py

4396509

Co-authored-by: Tom Dupré la Tour <[email protected]>

Add test case and warnings

1319515

fix typo

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Update sklearn/manifold/_isomap.py

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jjerphan force-pushed the fet/isomap branch from 864ea3e to 24be7f4 Compare January 28, 2022 15:28

update test cases to use data which connect_components=1

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thomasjpfan reviewed Feb 15, 2022

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change default behaviour for n_neighbors and radius & add test case

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MaxwellLZH force-pushed the fet/isomap branch from 1edb983 to d7508b3 Compare February 15, 2022 08:55

MaxwellLZH added 2 commits February 15, 2022 22:55

merge main

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black formatting

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doc formatting

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

doc formatting

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

add versionadded for radius argument

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MaxwellLZH added 3 commits February 17, 2022 16:49

move n_pts to function argument

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use functions from sklearn.utils._testing

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Merge branch 'main' into fet/isomap

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thomasjpfan changed the title ~~Isomap supports radius-based neighbors~~ ENH Isomap supports radius-based neighbors Feb 17, 2022

MaxwellLZH and others added 5 commits February 18, 2022 10:07

set n_pts to 25 explicitely

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set n_pts to 25 explicitely

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move test comment to function docstring

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fix whatsnew

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Merge branch 'main' into fet/isomap

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CLN Address comments

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thomasjpfan merged commit 7165684 into scikit-learn:main Feb 28, 2022

adrinjalali mentioned this pull request Apr 19, 2024

ENH Isomap: adding choice option for neighborhood function (plus some code cleaning) #6992

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MaxwellLZH commented Mar 31, 2021

Reference Issues/PRs

What does this implement/fix? Explain your changes.

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ogrisel commented Mar 31, 2021

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MaxwellLZH commented Jun 15, 2021

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TomDLT commented Jun 15, 2021

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