sklearn error ValueError: Input contains NaN, infi

问题:

I am using sklearn and having a problem with the affinity propagation. I have built an input matrix and I keep getting the following error.

ValueError: Input contains NaN, infinity or a value too large for dtype('float64').

I have run

np.isnan(mat.any()) #and gets False
np.isfinite(mat.all()) #and gets True

I tried using

mat[np.isfinite(mat) == True] = 0

to remove the infinite values but this did not work either. What can I do to get rid of the infinite values in my matrix, so that I can use the affinity propagation algorithm?

I am using anaconda and python 2.7.9.

回答1:

This might happen inside scikit, and it depends on what you're doing. I recommend reading the documentation for the functions you're using. You might be using one which depends e.g. on your matrix being positive definite and not fulfilling that criteria.

EDIT: How could I miss that:

np.isnan(mat.any()) #and gets False
np.isfinite(mat.all()) #and gets True

is obviously wrong. Right would be:

np.any(np.isnan(mat))

and

np.all(np.isfinite(mat))

You want to check wheter any of the element is NaN, and not whether the return value of the any function is a number...

回答2:

I got the same error message when using sklearn with pandas. My solution is to reset the index of my dataframe df before running any sklearn code:

df = df.reset_index()

I encountered this issue many times when I removed some entries in my df, such as

df = df[df.label=='desired_one']

回答3:

The Dimensions of my input array were skewed, as my input csv had empty spaces.

回答4:

This is the check on which it fails:

• https://github.com/scikit-learn/scikit-learn/blob/0.17.X/sklearn/utils/validation.py#L51

Which says

def _assert_all_finite(X):
    """Like assert_all_finite, but only for ndarray."""
    X = np.asanyarray(X)
    # First try an O(n) time, O(1) space solution for the common case that
    # everything is finite; fall back to O(n) space np.isfinite to prevent
    # false positives from overflow in sum method.
    if (X.dtype.char in np.typecodes['AllFloat'] and not np.isfinite(X.sum())
            and not np.isfinite(X).all()):
        raise ValueError("Input contains NaN, infinity"
                         " or a value too large for %r." % X.dtype)

So make sure that you have non NaN values in your input. And all those values are actually float values. None of the values should be Inf either.

回答5:

This is my function (based on this) to clean the dataset of nan, Inf, and missing cells (for skewed datasets):

import pandas as pd

def clean_dataset(df):
    assert isinstance(df, pd.DataFrame), "df needs to be a pd.DataFrame"
    df.dropna(inplace=True)
    indices_to_keep = ~df.isin([np.nan, np.inf, -np.inf]).any(1)
    return df[indices_to_keep].astype(np.float64)

回答6:

I had the error after trying to select a subset of rows:

df = df.reindex(index=my_index)

Turns out that my_index contained values that were not contained in df.index, so the reindex function inserted some new rows and filled them with nan.

回答7:

I had the same error, and in my case X and y were dataframes so I had to convert them to matrices first:

X = X.as_matrix().astype(np.float)
y = y.as_matrix().astype(np.float)

回答8:

With this version of python 3:

/opt/anaconda3/bin/python --version
Python 3.6.0 :: Anaconda 4.3.0 (64-bit)

Looking at the details of the error, I found the lines of codes causing the failure:

/opt/anaconda3/lib/python3.6/site-packages/sklearn/utils/validation.py in _assert_all_finite(X)
     56             and not np.isfinite(X).all()):
     57         raise ValueError("Input contains NaN, infinity"
---> 58                          " or a value too large for %r." % X.dtype)
     59 
     60 

ValueError: Input contains NaN, infinity or a value too large for dtype('float64').

From this, I was able to extract the correct way to test what was going on with my data using the same test which fails given by the error message: np.isfinite(X)

Then with a quick and dirty loop, I was able to find that my data indeed contains nans:

print(p[:,0].shape)
index = 0
for i in p[:,0]:
    if not np.isfinite(i):
        print(index, i)
    index +=1

(367340,)
4454 nan
6940 nan
10868 nan
12753 nan
14855 nan
15678 nan
24954 nan
30251 nan
31108 nan
51455 nan
59055 nan
...

Now all I have to do is remove the values at these indexes.

回答9:

i got the same error. it worked with df.fillna(-99999, inplace=True) before doing any replacement, substitution etc

回答10:

In my case the problem was that many scikit functions return numpy arrays, which are devoid of pandas index. So there was an index mismatch when I used those numpy arrays to build new DataFrames and then I tried to mix them with the original data.

回答11:

If you can't find the problem in X, check in y