2

I'm not really sure whether this is a numpy or a scikit-learn issue... or a windows issue? When calculating the matthews_corrcoef using scikit learn on the code below, i get an overflow warning. it is coming from the den = np.sqrt((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn)) line in sklearn\metrics\metrics.py. The result is an MCC well outside of it's defined bounds [-1 1]

As far as I can tell, the issue comes about because the default int type for a numpy array in windows is 32bit. On my ubuntu install this problem doesn't occur because the default int type is 64bit.

So my question is, what is the best way to work around this? Can i specify somewhere that ints should default to 64bit for numpy under windows (is this possible?)... or should scikit handle this internally. I'm currently a little scared about what other stuff might be overflowing that i'm not picking up when doing a bit of machine learning under windows.

Any help is much appreciated. And sorry for all the 1s and 0s below.

Cheers chris

from sklearn.metrics import matthews_corrcoef
import numpy as np

y_true = np.array([1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 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y_pred = np.array([0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 0, 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1, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1])

print matthews_corrcoef(y_true, y_pred)
Rohan Nadagouda
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cdiddy
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  • I don't think it will solve your problem, but you can easily make these arrays use int64 by creating them as `y_true = np.array([1, 1, 0, ..., 1, 0, 0], dtype='int64')`. Or if the arrays already exist, you can just call the function like `matthews_corrcoef(y_true.astype('int64'), y_pred.astype('int64'))`. – askewchan Nov 29 '13 at 02:35
  • I get no overflow on win64. Is the Python X86-64? Which Numpy? – cyborg Nov 29 '13 at 03:35
  • I don't get an int overflow in 64bit OSX either: the output of the script it 0.219716904793 in my case. – ogrisel Nov 29 '13 at 16:10
  • @cyborg I think/hope both my python and numpy install are 64bit. I am using Anaconda 1.8 with the x86_64 installer for windows. Using the test from [link](http://stackoverflow.com/questions/1842544/how-do-i-detect-if-python-is-running-as-a-64-bit-application) I can confirm that my python install is rnning 64bit. Not sure how to check numpy specifically. Any ideas? – cdiddy Dec 01 '13 at 22:23
  • You should show us the actual warning. Report numpy bugs in https://github.com/numpy/numpy/issues . – cyborg Dec 01 '13 at 23:01
  • The warning is 'RuntimeWarning: overflow encountered in long_scalars den = np.sqrt((tp + fp) * (tp + fn) * (tn + fp) * (tn + fn))' I'm not entirely sure if this is an issue with numpy, or if sklearn should be handling the case of calculating this when ints are 32bit... any thoughts? – cdiddy Dec 01 '13 at 23:27
  • or is it an issue with the anaconda install? Sorry, I'm a bit lost under windows here. i miss my ubuntu setup ;-) – cdiddy Dec 01 '13 at 23:28
  • Did askewchan's advice work? You can download Numpy and other packages from other places. – cyborg Dec 02 '13 at 19:15
  • @cyborg, askewchan's advice unfortunately doesn't work for me because the array is created internally in sklearn. so without hacking the sklearn code to force the dtype i can't stope the error. I might try installing one of the precompiled numpy binaries for 64bit and see if that helps – cdiddy Dec 03 '13 at 00:39

0 Answers0