Python Neural Network - running into x_test y_test fit errors

Question

I have built a neural network and it worked fine with a small dataset of around 300,000 rows with 2 categorical variables and 1 independent variable, but was running into memory errors when i increased it to 6.5 million rows. So I decided to modify the code and am getting closer but now I am running into an issue with fit errors. I have 2 categorical variables and one column for the dependent variable of 1's and 0's(suspicious or not suspicious. To start off the dataset looks like this:

DBF2
   ParentProcess                   ChildProcess               Suspicious
0  C:\Program Files (x86)\Wireless AutoSwitch\wrl...    ...            0
1  C:\Program Files (x86)\Wireless AutoSwitch\wrl...    ...            0
2  C:\Windows\System32\svchost.exe                      ...            1
3  C:\Program Files (x86)\Wireless AutoSwitch\wrl...    ...            0
4  C:\Program Files (x86)\Wireless AutoSwitch\wrl...    ...            0
5  C:\Program Files (x86)\Wireless AutoSwitch\wrl...    ...            0

My code followed/with the errors:

import pandas as pd
import numpy as np
import hashlib
import matplotlib.pyplot as plt
import timeit

X = DBF2.iloc[:, 0:2].values
y = DBF2.iloc[:, 2].values#.ravel()

from sklearn.preprocessing import LabelEncoder, OneHotEncoder
labelencoder_X_1 = LabelEncoder()
X[:, 0] = labelencoder_X_1.fit_transform(X[:, 0])
labelencoder_X_2 = LabelEncoder()
X[:, 1] = labelencoder_X_2.fit_transform(X[:, 1])

onehotencoder = OneHotEncoder(categorical_features = [0,1])
X = onehotencoder.fit_transform(X)

index_to_drop = [0, 2039]
to_keep = list(set(xrange(X.shape[1]))-set(index_to_drop))
X = X[:,to_keep]

from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size = 0.2, random_state = 0)
from sklearn.preprocessing import StandardScaler
sc = StandardScaler()
X_train = sc.fit_transform(X_train)

#ERROR
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/sklearn/base.py", line 517, in fit_transform
    return self.fit(X, **fit_params).transform(X)
  File "/usr/local/lib/python2.7/dist-packages/sklearn/preprocessing/data.py", line 590, in fit
    return self.partial_fit(X, y)
  File "/usr/local/lib/python2.7/dist-packages/sklearn/preprocessing/data.py", line 621, in partial_fit
    "Cannot center sparse matrices: pass `with_mean=False` "
ValueError: Cannot center sparse matrices: pass `with_mean=False` instead. See docstring for motivation and alternatives.

X_test = sc.transform(X_test)

#ERROR
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/sklearn/preprocessing/data.py", line 677, in transform
    check_is_fitted(self, 'scale_')
  File "/usr/local/lib/python2.7/dist-packages/sklearn/utils/validation.py", line 768, in check_is_fitted
    raise NotFittedError(msg % {'name': type(estimator).__name__})
sklearn.exceptions.NotFittedError: This StandardScaler instance is not fitted yet. Call 'fit' with appropriate arguments before using this method.

If this helps i printed the X_train and y_train:

X_train
<5621203x7043 sparse matrix of type '<type 'numpy.float64'>'
with 11242334 stored elements in Compressed Sparse Row format>

y_train
array([0, 0, 0, ..., 0, 0, 0])

Answer 1

Scikit-learn's StandardScaler does not work with sparse matrices. Either cast to a dense matrix with X.toarray() or switch from scikit-learn to another package.