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Merged
merged 85 commits into from
Mar 1, 2019
Merged

[MRG+2] DOC examples added to the rest of sklearn/covariance classes #11732

merged 85 commits into from
Mar 1, 2019

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adrinjalali
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See #3846

Examples added to GraphicalLasso and GraphicalLassoCV in sklearn/covariance/graph_lasso_.py

@adrinjalali adrinjalali mentioned this pull request Aug 3, 2018
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@adrinjalali adrinjalali changed the title DOC added graphicallasso and graphicallassocv examples [WIP] DOC added graphicallasso and graphicallassocv examples Aug 3, 2018
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adrinjalali commented Aug 4, 2018 •
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So apparently the results depend on something other than the random seed.

The output is deterministic, as long as we don't change the setup. But my personal computer, a server I used to test, and the setup travis uses, do not agree with each other and each give a different output.

In this PR the values are the ones reported by travis, and that's why the travis tests pass. But users may get slightly different results based on their setup.

I suspect it may depend on lower lever libraries used (blas, lapack, etc), but not sure.

@adrinjalali adrinjalali force-pushed the examples/graphlasso branch from 4099adb to a2fede3 Compare August 4, 2018 09:27
@adrinjalali adrinjalali changed the title [WIP] DOC added graphicallasso and graphicallassocv examples [MRG] DOC added graphicallasso and graphicallassocv examples Aug 4, 2018
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jnothman commented Aug 6, 2018

What kind of differences are we talking about?

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the estimated negative log likelihood: 26.1847 vs 26.1927
the real negative log likelihood: 27.8393 vs 27.7033

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jnothman commented Aug 6, 2018 via email

@adrinjalali adrinjalali changed the title [MRG] DOC added graphicallasso and graphicallassocv examples [WIP] DOC added graphicallasso and graphicallassocv examples Aug 7, 2018
This was referenced Sep 20, 2018
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@adrinjalali adrinjalali changed the title [WIP] DOC added graphicallasso and graphicallassocv examples DOC examples added to the rest of sklearn/covariance classes Sep 25, 2018
jnothman
jnothman reviewed Sep 26, 2018
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sklearn/covariance/graph_lasso_.py Outdated
... largest_coef=.7,
... random_state=0)
>>> cov = linalg.inv(prec)
>>> d = np.sqrt(np.diag(cov))
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I think this normalisation deserves a comment, and ideally would be g performed with some existing scipy function

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I found other mistakes in the example. They'd make the example kinda too long, and our docs already show this example. So changed it to be more like the other covariance examples we have, with a manually set sparse covariance matrix, if that's okay.

@adrinjalali adrinjalali mentioned this pull request Sep 27, 2018
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@adrinjalali adrinjalali changed the title DOC examples added to the rest of sklearn/covariance classes [MRG] DOC examples added to the rest of sklearn/covariance classes Oct 5, 2018
adrinjalali and others added 15 commits January 7, 2019 11:34
@adrinjalali
BLD circle-ci should only run/build plot_* files (scikit-learn#12797)
5b74898
@albertcthomas @adrinjalali
DOC add sentence about line length of rst files (scikit-learn#12883)
22956f8
@amueller @adrinjalali
DOC link to dev docs instead of contributing docs in the menu (scikit…
370fd03 
…-learn#12885)
@NicolasHug @adrinjalali
DOC Added tips for reading the code base (scikit-learn#12874)
c010069 
* Added tips for reading the code base

* Put it in contributing.rst

* Added bullet point about inheritance
@qinhanmin2014 @adrinjalali
TST Manually scramble the indices in svm tests (scikit-learn#12890)
3463b4d 
* [scipy-dev] manually scramble the indices

* [scipy-dev] review comment
@elsander @adrinjalali
FIX predict method for multiclass multioutput ensemble models (scikit…
e7f6d4f 
…-learn#12834)
@pakallis @adrinjalali
DOC Fix typo in glossary.rst (scikit-learn#12913)
0f277f2
@amueller @adrinjalali
MRG Drop legacy python / remove six dependencies (scikit-learn#12639)
14621e8
@rth @adrinjalali
MNT Use scipy.special.xlogy to avoid indefinite limit in 0 for x*log(…
3e10ea7 
…y) (scikit-learn#12915)
@ZaydH @adrinjalali
FIX Use scipy.special.expit in calibration (scikit-learn#12909)
2b7ca5f
@qinhanmin2014 @adrinjalali
FIX learning_rate default value in update_terminal_regions (scikit-le…
4fe3d1b 
…arn#12925)
@BoboTiG @adrinjalali
EXA Fix several DeprecationWarning: invalid escape sequence in exampl…
8d1ac41 
…es (scikit-learn#12924)
@GaelVaroquaux @adrinjalali
DOC How to deal with stalled PR (scikit-learn#12894)
f13605d
@rth @adrinjalali
MAINT Use set litterals when possible (scikit-learn#12667)
1264247
@adrinjalali
(review reminder) Merge remote-tracking branch 'upstream/master' into…
6ccdd03 
… examples/graphlasso
jnothman
jnothman approved these changes Feb 28, 2019
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Pending real_ -> true_

ogrisel
ogrisel approved these changes Feb 28, 2019
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Let's merge.

@agramfort agramfort changed the title [MRG] DOC examples added to the rest of sklearn/covariance classes [MRG+2] DOC examples added to the rest of sklearn/covariance classes Feb 28, 2019
@jnothman jnothman merged commit 8755fa7 into scikit-learn:master Mar 1, 2019
@adrinjalali adrinjalali deleted the examples/graphlasso branch March 1, 2019 10:37
xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019
@adrinjalali
DOC examples added to the rest of sklearn/covariance classes (scikit-…
be36a44 
…learn#11732)
xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019
Revert "DOC examples added to the rest of sklearn/covariance classes (s…
86d2b22 
…cikit-learn#11732)"

This reverts commit be36a44.
xhluca pushed a commit to xhluca/scikit-learn that referenced this pull request Apr 28, 2019
Revert "DOC examples added to the rest of sklearn/covariance classes (s…
4b5738a 
…cikit-learn#11732)"

This reverts commit be36a44.
koenvandevelde pushed a commit to koenvandevelde/scikit-learn that referenced this pull request Jul 12, 2019
@adrinjalali @koenvandevelde
DOC examples added to the rest of sklearn/covariance classes (scikit-…
76aa830 
…learn#11732)
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@jnothman jnothman jnothman approved these changes

@ogrisel ogrisel ogrisel approved these changes

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