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Locally Linear Embedding manifold doesn't work with integer inputs #6033

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Jezzamonn opened this issue Dec 15, 2015 · 4 comments
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Locally Linear Embedding manifold doesn't work with integer inputs #6033

Jezzamonn opened this issue Dec 15, 2015 · 4 comments

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@Jezzamonn
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An error occurs when you try to use manifold.LocallyLinearEmbedding with an integer array as the input if you have certain values of the method parameter. I'm running the latest version of scikit-learn (I got this error, updated through conda, and the error still occurs).

Traceback (most recent call last):
  File "C:/Users/jswanson/Downloads/plot_compare_methods.py", line 63, in <module>
    method=method).fit_transform(X)
  File "C:\Users\jswanson\AppData\Local\Continuum\Anaconda3\lib\site-packages\sklearn\manifold\locally_linear.py", line 652, in fit_transform
    self._fit_transform(X)
  File "C:\Users\jswanson\AppData\Local\Continuum\Anaconda3\lib\site-packages\sklearn\manifold\locally_linear.py", line 623, in _fit_transform
    random_state=random_state, reg=self.reg)
  File "C:\Users\jswanson\AppData\Local\Continuum\Anaconda3\lib\site-packages\sklearn\manifold\locally_linear.py", line 476, in locally_linear_embedding
    Xi -= Xi.mean(0)
TypeError: Cannot cast ufunc subtract output from dtype('float64') to dtype('int64') with casting rule 'same_kind'

For some code that demonstrates the error, you can run the example here http://scikit-learn.org/stable/auto_examples/manifold/plot_compare_methods.html, but cast the data to int64 first. You can do this by inserting the following line below line 38

X = (1000 * X).astype('int64')

By glancing through similar issues, I think this is caused by an update to numpy.

I'll just work around the issue by casting my data to floats, but I thought I should still bring it up.
@soupault
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soupault commented Feb 4, 2016

I confirm. Error is raised for both method='ltsa' (see @Jezzamonn log) and method='hessian' (see log below). Everything else works fine.

Traceback (most recent call last):
  File "test.py", line 46, in <module>
    method=method).fit_transform(X)
  File "/usr/lib/python3.5/site-packages/sklearn/manifold/locally_linear.py", line 652, in fit_transform
    self._fit_transform(X)
  File "/usr/lib/python3.5/site-packages/sklearn/manifold/locally_linear.py", line 623, in _fit_transform
    random_state=random_state, reg=self.reg)
  File "/usr/lib/python3.5/site-packages/sklearn/manifold/locally_linear.py", line 327, in locally_linear_embedding
    Gi -= Gi.mean(0)
TypeError: Cannot cast ufunc subtract output from dtype('float64') to dtype('int64') with casting rule 'same_kind'

jakevdp added a commit to jakevdp/scikit-learn that referenced this issue Feb 4, 2016
@jakevdp
BUG: handle integer inputs in LLE (fixes scikit-learn#6033)
83483ca
@jakevdp
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jakevdp commented Feb 4, 2016

I added a fix in #6282

@soupault
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soupault commented Feb 5, 2016

@jakevdp thanks a lot!

@amueller
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amueller commented Oct 7, 2016

Fixed in #6282

@amueller amueller closed this as completed Oct 7, 2016
amueller pushed a commit that referenced this issue Oct 7, 2016
@jakevdp @amueller
BUG: handle integer inputs in LLE (fixes #6033) (#6282)
c948319
amueller pushed a commit to amueller/scikit-learn that referenced this issue Oct 14, 2016
@jakevdp @amueller
BUG: handle integer inputs in LLE (fixes scikit-learn#6033) (scikit-l…
84e480f 
…earn#6282)
Sundrique pushed a commit to Sundrique/scikit-learn that referenced this issue Jun 14, 2017
@jakevdp @Sundrique
BUG: handle integer inputs in LLE (fixes scikit-learn#6033) (scikit-l…
6754578 
…earn#6282)
paulha pushed a commit to paulha/scikit-learn that referenced this issue Aug 19, 2017
@jakevdp @paulha
BUG: handle integer inputs in LLE (fixes scikit-learn#6033) (scikit-l…
896bcfd 
…earn#6282)
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4 participants
@amueller @jakevdp @soupault @Jezzamonn