How to convert a dataframe to sparse matrix with mixed column types?

Question

I have a data frame of following format:

df:

key   f1    f2
k1    10    a, b, c
k2    20    b, d
k3    15    NaN

The column f2 has a bag of words as values. I want to convert this data frame into a sparse matrix, as distinct words in f2 run to a few thousands. The end result I am expecting is of following format:

key    f1  f2.a  f2.b  f2.c  f2.d
k1     10   1     1     1     0
k2     20   0     1     0     1
k3     15   0     0     0     0

I could figure out how to independently create a sparse matrix just out of key and f2 field. I am first melting the column f2 so I get following dataframe:

df1:
key  f2
k1   a
k1   b
k1   c
k2   b
k2   d

Then I am encoding f2, and using the LabelEncoder from sklearn.preprocessing package to encode f2. Then I am creating a sparse matrix as follows:

df1['trainrow'] = np.arrange(df1.shape[0])
sparse.csr_matrix((np.ones(df1.shape[0], (df1.trainrow, df1.f2_encoded)))

This creates a sparse matrix by doing a one-hot encoding of field f2. But I am not sure how I can concatenate this with the numerical field f1.

Answer 1

I have figured out the optimal way I wanted to solve this, so posting it as an answer for my future reference and for the benefit of others:

Because of the enormous size of data, I had to go with sparse matrix only.

First step is to convert the bag of words to a vectorized format. I have used CountVectorizer (Thanks to @MaxU for this) as follows:

from sklearn.feature_extraction.text import CountVectorizer

vectorizer = CountVectorizer()
df2 = vectorizer.fit_transform(df['f2'].str.replace(' ',''))

I would like to ignore spaces and use comma as a forced delimiter. I couldn't figure out how to do that so I have replaced the spaces as otherwise vectorizer is splitting the words at spaces.

That has created df1 as a sparse matrix.

Then the other field f1 is converted to a different sparse matrix:

df1 = csr_matrix(df[['f1']].fillna(0))

Then used hstack to combine both these: sparseDF = hstack((df1,df2),format='csr')

Answer 2

You can use concat with str.get_dummies and add_prefix:

df = pd.concat([df[['key','f1']], df.f2.str.get_dummies(sep=', ').add_prefix('f2.')], axis=1)
print (df)
  key  f1  f2.a  f2.b  f2.c  f2.d
0  k1  10     1     1     1     0
1  k2  20     0     1     0     1
2  k3  15     0     0     0     0

In very large distinct values get_dummies is very slow, you can use custom function f:

def f(category_list):
    n_categories = len(category_list)
    return pd.Series(dict(zip(category_list, [1]*n_categories)))

#remove NaN rows and create list of values by split
df1 = df.f2.dropna().str.split(', ').apply(f).add_prefix('f2.')
df2 = pd.concat([df[['key','f1']], df1], axis=1)
#replace NaN to 0 by position from 3.column to end of df
df2.iloc[:, 2: ] = df2.iloc[:, 2: ].fillna(0).astype(int)
print (df2)
  key  f1  f2.a  f2.b  f2.c  f2.d
0  k1  10     1     1     1     0
1  k2  20     0     1     0     1
2  k3  15     0     0     0     0

Timings:

In [256]: %timeit s.str.get_dummies(sep=', ')
1 loop, best of 3: 1min 16s per loop

In [257]: %timeit (s.dropna().str.split(', ').apply(f).fillna(0).astype(int))
1 loop, best of 3: 2.95 s per loop

Code for timings:

np.random.seed(100)
s = pd.DataFrame(np.random.randint(10000, size=(1000,1000))).astype(str).apply(', '.join, axis=1)
print (s)


df2 = s.str.get_dummies(sep=', ')
print (df2)

def f(category_list):
    n_categories = len(category_list)
    return pd.Series(dict(zip(category_list, [1]*n_categories)))

print (s.dropna().str.split(', ').apply(f).fillna(0).astype(int))