python – invalid value encountered in log

Question

I have the following expression:
log = np.sum(np.nan_to_num(-y*np.log(a+ 1e-7)-(1-y)*np.log(1-a+ 1e-7)))

it is giving me the following warning:

RuntimeWarning: invalid value encountered in log
  log = np.sum(np.nan_to_num(-y*np.log(a+ 1e-7)-(1-y)*np.log(1-a+ 1e-7)))

I don’t understand what might be the invalid value or why am I getting it. Any and every help is appreciated.

NOTE: This is a cross-entropy cost function where I added 1e-7 to avoid having zeros inside log. y & a are numpy arrays and numpy is imported as np.

Asked By: helix

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Source

Answer 1

You probably still have negative values inside the log, which gives nan with real numbers.

a and y should represent probability between 0 to 1, So you need to check why do you have smaller/larger values there. Adding 1e-7 shows there is something fishy, because np.log(0) gives -inf, which I think is the value you want.

Answered By: Elad Joseph

Answer 2

You can use math.log() replacing numpy.log(), which could raise error

>>> import numpy
>>> numpy.log(0)
-inf
>>> numpy.__version__
'1.3.0'
>>> import math
>>> math.log(0)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ValueError: math domain error

Answered By: WANG.Zhongzhi

Answer 3

log(x) where x<=0 edge cases

np.log(0)

RuntimeWarning: divide by zero encountered in log

-inf

np.log(-1)

RuntimeWarning: invalid value encountered in log

nan

Answered By: Kermit

python – invalid value encountered in log

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