Using Scikit-Learn OneHotEncoder with a Pandas DataFrame

Question

I'm trying to replace a column within a Pandas DataFrame containing strings into a one-hot encoded equivalent using Scikit-Learn's OneHotEncoder. My code below doesn't work:

from sklearn.preprocessing import OneHotEncoder
# data is a Pandas DataFrame

jobs_encoder = OneHotEncoder()
jobs_encoder.fit(data['Profession'].unique().reshape(1, -1))
data['Profession'] = jobs_encoder.transform(data['Profession'].to_numpy().reshape(-1, 1))

It produces the following error (strings in the list are omitted):

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-91-3a1f568322f5> in <module>()
      3 jobs_encoder = OneHotEncoder()
      4 jobs_encoder.fit(data['Profession'].unique().reshape(1, -1))
----> 5 data['Profession'] = jobs_encoder.transform(data['Profession'].to_numpy().reshape(-1, 1))

/usr/local/anaconda3/envs/ml/lib/python3.6/site-packages/sklearn/preprocessing/_encoders.py in transform(self, X)
    730                                        copy=True)
    731         else:
--> 732             return self._transform_new(X)
    733 
    734     def inverse_transform(self, X):

/usr/local/anaconda3/envs/ml/lib/python3.6/site-packages/sklearn/preprocessing/_encoders.py in _transform_new(self, X)
    678         """New implementation assuming categorical input"""
    679         # validation of X happens in _check_X called by _transform
--> 680         X_int, X_mask = self._transform(X, handle_unknown=self.handle_unknown)
    681 
    682         n_samples, n_features = X_int.shape

/usr/local/anaconda3/envs/ml/lib/python3.6/site-packages/sklearn/preprocessing/_encoders.py in _transform(self, X, handle_unknown)
    120                     msg = ("Found unknown categories {0} in column {1}"
    121                            " during transform".format(diff, i))
--> 122                     raise ValueError(msg)
    123                 else:
    124                     # Set the problematic rows to an acceptable value and

ValueError: Found unknown categories ['...', ..., '...'] in column 0 during transform

Here's some sample data:

data['Profession'] =

0         unkn
1         safe
2         rece
3         unkn
4         lead
          ... 
111988    indu
111989    seni
111990    mess
111991    seni
111992    proj
Name: Profession, Length: 111993, dtype: object

What exactly am I doing wrong?

Answer 1

OneHotEncoder Encodes categorical integer features as a one-hot numeric array. Its Transform method returns a sparse matrix if sparse=True, otherwise it returns a 2-d array.

You can't cast a 2-d array (or sparse matrix) into a Pandas Series. You must create a Pandas Serie (a column in a Pandas dataFrame) for each category.

I would recommend pandas.get_dummies instead:

data = pd.get_dummies(data,prefix=['Profession'], columns = ['Profession'], drop_first=True)

EDIT:

Using Sklearn OneHotEncoder:

transformed = jobs_encoder.transform(data['Profession'].to_numpy().reshape(-1, 1))
#Create a Pandas DataFrame of the hot encoded column
ohe_df = pd.DataFrame(transformed, columns=jobs_encoder.get_feature_names())
#concat with original data
data = pd.concat([data, ohe_df], axis=1).drop(['Profession'], axis=1)

Other Options: If you are doing hyperparameter tuning with GridSearch it's recommanded to use ColumnTransformer and FeatureUnion with Pipeline or directly make_column_transformer

Answer 2

So turned out that Scikit-Learns LabelBinarizer gave me better luck in converting the data to one-hot encoded format, with help from Amnie's solution, my final code is as follows

import pandas as pd
from sklearn.preprocessing import LabelBinarizer

jobs_encoder = LabelBinarizer()
jobs_encoder.fit(data['Profession'])
transformed = jobs_encoder.transform(data['Profession'])
ohe_df = pd.DataFrame(transformed)
data = pd.concat([data, ohe_df], axis=1).drop(['Profession'], axis=1)

Answer 3

This below is an approach suggested by Kaggle Learn. Do not think there is a simpler way to do so at the moment to go from an original pandas DataFrame to a one-hot encoded DataFrame.

# Apply one-hot encoder to each column with categorical data
OH_encoder = OneHotEncoder(handle_unknown='ignore', sparse=False)
OH_cols_train = pd.DataFrame(OH_encoder.fit_transform(X_train[low_cardinality_cols]))
OH_cols_valid = pd.DataFrame(OH_encoder.transform(X_valid[low_cardinality_cols]))

# One-hot encoding removed index; put it back
OH_cols_train.index = X_train.index
OH_cols_valid.index = X_valid.index

# Remove categorical columns (will replace with one-hot encoding)
numeric_X_train = X_train.drop(low_cardinality_cols, axis=1)
numeric_X_valid = X_valid.drop(low_cardinality_cols, axis=1)

# Add one-hot encoded columns to numerical features
new_X_train = pd.concat([numeric_X_train, OH_cols_train], axis=1)
new_X_valid = pd.concat([numeric_X_valid, OH_cols_valid], axis=1)
print(new_X_train)

Answer 4

This will do the trick. Remove plotly parts if you are not interested in viz. Also change printmd to print if you don't need markdown.

def fn_cat_onehot(df):

    """Generate onehoteencoded features for all categorical columns in df"""

    printmd(f"df shape: {df.shape}")

    # NaN handing
    nan_count = df.isna().sum().sum()
    if nan_count > 0:
        printmd(f"NaN = **{nan_count}** will be categorized under feature_nan columns")

    # generation
    from sklearn.preprocessing import OneHotEncoder

    model_oh = OneHotEncoder(handle_unknown="ignore", sparse=False)
    for c in df.select_dtypes("category").columns:
        printmd(f"Encoding **{c}**")  # which column
        matrix = model_oh.fit_transform(
            df[[c]]
        )  # get a matrix of new features and values
        names = model_oh.get_feature_names_out()  # get names for these features
        df_oh = pd.DataFrame(
            data=matrix, columns=names, index=df.index
        )  # create df of these new features
        display(df_oh.plot.hist())
        df = pd.concat([df, df_oh], axis=1)  # concat with existing df
        df.drop(
            c, axis=1, inplace=True
        )  # drop categorical column so that it is all numerical for modelling

    printmd(f"#### New df shape: **{df.shape}**")
    return df

Answer 5

I capsulize @IndreshKumar's solution into a sklearn transformer:

import pandas as pd
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.preprocessing import OneHotEncoder

class CategoricalOneHot(BaseEstimator, TransformerMixin):
    def __init__(self, list_key_words=None):
        self.oh_dict = {}
        self.list_key_words = list_key_words

    def fit(self, X, y=None):
        self.list_cat_col = []
        for key_word in self.list_key_words:
            self.list_cat_col += [col for col in X.columns if key_word in col]
        for col in self.list_cat_col:
            oh = OneHotEncoder(handle_unknown="ignore", sparse=False)
            oh.fit(X[[col]])
            names = oh.get_feature_names_out()
            self.oh_dict[col] = (oh, names)
        return self

    def transform(self, X):
        _X = X.copy()
        for col in self.list_cat_col:
            oh = self.oh_dict[col][0]
            df_oh = pd.DataFrame(
                data=oh.transform(_X[[col]]),
                columns=self.oh_dict[col][1],
                index=_X.index)
            _X = pd.concat([_X, df_oh], axis=1)
            _X.drop(col, axis=1, inplace=True)
        return _X

if __name__ == "__main__":
    tex = pd.DataFrame({'city': ['a', 'a', 'e', 'b'], 'state': ['f', 'c', 'd', 'd']})
    coh = CategoricalOneHot(list_key_words=['city', 'state'])
    print(coh.fit_transform(tex))

Example: Given a data frame with two categorical columns:

  city state
0    a     f
1    a     c
2    e     d
3    b     d

the output looks like this:

   city_a  city_b  city_e  state_c  state_d  state_f
0     1.0     0.0     0.0      0.0      0.0      1.0
1     1.0     0.0     0.0      1.0      0.0      0.0
2     0.0     0.0     1.0      0.0      1.0      0.0
3     0.0     1.0     0.0      0.0      1.0      0.0

Answer 6

Thanks to the new set_output API from scikit-learn, it is now possible to get a Dataframe output after applying the OneHotEncoder.

from sklearn.preprocessing import OneHotEncoder
oh= OneHotEncoder(sparse_output=False).set_output(transform="pandas")
one_hot_encoded=oh.fit_transform(df[["Profession"]])
df = pd.concat([df,one_hot_encoded],axis=1).drop(columns=["Profession"])

Please refer to: https://scikit-learn.org/stable/auto_examples/miscellaneous/plot_set_output.html