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How to classify and substitute NaN with a pipeline

I have the following data frame:
import pandas as pd
d = {'hrs': [1, "NaN", 2], 'Department': ["ResearchDevelopment", "NaN", "ResearchDevelopment"]}
df = pd.DataFrame(data=d)
df
And I want to use a pipeline in order to classify it as categorical or numerical and predict NaN values as the median in the case of numerical and ignore in the case of categorical.
I have done the following:
from sklearn.compose import ColumnTransformer
from sklearn.datasets import fetch_openml
from sklearn.pipeline import Pipeline
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import StandardScaler, OneHotEncoder
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import train_test_split, GridSearchCV
from sklearn import pipeline
numeric_features = ["hrs"]
numeric_transformer = Pipeline(
steps=[("imputer", SimpleImputer(strategy="median")), ("scaler", StandardScaler())]
)
categorical_features = ["Department"]
categorical_transformer = Pipeline(
steps=[("imputer", SimpleImputer(strategy="most_frequent")),("OneHotEncoder", OneHotEncoder(handle_unknown="ignore"))]
)
preprocessor = ColumnTransformer(
transformers=[
("num", numeric_transformer, numeric_features),
("cat", categorical_transformer, categorical_features),
]
)
But I do not know where is the error, and if I have to call the data frame or not.
No error happens, but the pipeline is not changing anything.

Sklearn pipeline transform specific columns - ValueError: too many values to unpack (expected 2)

i am trying make pipeline with scaler, onhotencoder, polynomialfeature, and finally linear regression model
from sklearn.pipeline import Pipeline
pipeline = Pipeline([
('scaler', StandardScaler(), num_cols),
('polynom', PolynomialFeatures(3), num_cols),
('encoder', OneHotEncoder(), cat_cols),
('linear_regression', LinearRegression() )
])
but when i fit the pipeline i have ValueError: too many values to unpack (expected 2)
pipeline.fit(x_train,y_train)
pipeline.score(x_test, y_test)

If I understand correctly, you want to apply some steps of the pipeline to specific columns. Instead of doing it by adding the column names ad the end of the pipeline stage (which is incorrect and causes the error), you have to use a ColumnTransformer. Here you can find another similar example.
In your case, you could do something like this:
import pandas as pd
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.preprocessing import PolynomialFeatures
from sklearn.preprocessing import OneHotEncoder
from sklearn.linear_model import LinearRegression
from sklearn.compose import ColumnTransformer
# Fake data.
train_data = pd.DataFrame({'n1': range(10), 'n2': range(10)})
train_data['c1'] = 0
train_data['c1'][5:] = 1
y_train = [0]*10
y_train[5:] = [1]*5
# Here I assumed you are using a DataFrame. If not, use integer indices instead of column names.
num_cols = ['n1', 'n2']
cat_cols = ['c1']
# Pipeline to transform the numerical features.
numerical_transformer = Pipeline([('scaler', StandardScaler()),
('polynom', PolynomialFeatures(3))
])
# Apply the numerical transformer only on the numerical columns.
# Spearately, apply the OneHotEncoder.
ct = ColumnTransformer([('num_transformer', numerical_transformer, num_cols),
('encoder', OneHotEncoder(), cat_cols)])
# Main pipeline for fitting.
pipeline = Pipeline([
('column_transformer', ct),
('linear_regression', LinearRegression() )
])
pipeline.fit(train_data, y_train)
Schematically, the layout of your pipeline would be like this:

ColumnTransformer(s) in various parts of a pipeline do not play well

I am using sklearn and mlxtend.regressor.StackingRegressor to build a stacked regression model.
For example, say I want the following small pipeline:
A Stacking Regressor with two regressors:
A pipeline which:
Performs data imputation
1-hot encodes categorical features
Performs linear regression
A pipeline which:
Performs data imputation
Performs regression using a Decision Tree
Unfortunately this is not possible, because StackingRegressor doesn't accept NaN in its input data.
This is even if its regressors know how to handle NaN, as it would be in my case where the regressors are actually pipelines which perform data imputation.
However, this is not a problem: I can just move data imputation outside the stacked regressor.
Now my pipeline looks like this:
Perform data imputation
Apply a Stacking Regressor with two regressors:
A pipeline which:
1-hot encodes categorical features
Standardises numerical features
Performs linear regression
An sklearn.tree.DecisionTreeRegressor.
One might try to implement it as follows (the entire minimal working example in this gist, with comments):
sr_linear = Pipeline(steps=[
('preprocessing', ColumnTransformer(transformers=[
('categorical',
make_pipeline(OneHotEncoder(), StandardScaler()),
make_column_selector(dtype_include='category')),
('numerical',
StandardScaler(),
make_column_selector(dtype_include=np.number))
])),
('model', LinearRegression())
])
sr_tree = DecisionTreeRegressor()
ct_imputation = ColumnTransformer(transformers=[
('categorical',
SimpleImputer(strategy='constant', fill_value='None'),
make_column_selector(dtype_include='category')),
('numerical',
SimpleImputer(strategy='median'),
make_column_selector(dtype_include=np.number))
])
stacked_regressor = Pipeline(steps=[
('imputation', ct_imputation),
('back_to_pandas', FunctionTransformer(
func=lambda values: pd.DataFrame(values, columns=ct_imputation.get_feature_names_out())
)),
('model', StackingRegressor(
regressors=[sr_linear, sr_tree],
meta_regressor=DecisionTreeRegressor(),
use_features_in_secondary=True
))
])
Note that the "outer" ColumnTransformer (in stacked_regressor) returns a numpy matrix.
But the "inner" ColumnTransformer (in sr_linear) expects a pandas.DataFrame, so I had to convert the matrix back to a data frame using step back_to_pandas.
(To use get_feature_names_out I had to use the nightly version of sklearn, because the current stable 1.0.2 version does not support it yet. Fortunately it can be installed with one simple command.)
The above code fails when calling stacked_regressor.fit(), with the following error (the entire stacktrace is again in the gist):
ValueError: make_column_selector can only be applied to pandas dataframes
However, because I added the back_to_pandas step to my outer pipeline, the inner pipelines should be getting a pandas data frame!
In fact, if I only fit_transform() my ct_imputation object, I clearly obtain a pandas data frame.
I cannot understand where and when exactly the data which gets passed around ceases to be a data frame.
Why is my code failing?

Imo the issue has to be ascribed to StackingRegressor. Actually, I am not an expert on its usage and still I have not explored its source code, but I've found this sklearn issue - #16473 which seems implying that << the concatenation [of regressors and meta_regressors] does not preserve dataframe >> (though this is referred to sklearn StackingRegressor instance, rather than on mlxtend one).
Indeed, have a look at what happens once you replace it with your sr_linear pipeline:
from sklearn.datasets import fetch_openml
from sklearn.pipeline import Pipeline, make_pipeline
from sklearn.compose import ColumnTransformer, make_column_selector
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import StandardScaler, OneHotEncoder, FunctionTransformer
from sklearn.linear_model import LinearRegression
from sklearn.tree import DecisionTreeRegressor
from sklearn.model_selection import train_test_split
from mlxtend.regressor import StackingRegressor
import numpy as np
import pandas as pd
# We use the Ames house prices dataset for this example
d = fetch_openml('house_prices', as_frame=True).frame
# Small data preprocessing:
for column in d.columns:
if d[column].dtype == object or column == 'MSSubClass':
d[column] = pd.Categorical(d[column])
d.drop(columns='Id', inplace=True)
# Prepare the data for training
label = 'SalePrice'
features = [col for col in d.columns if col != label]
X, y = d[features], d[label]
# Train the stacked regressor
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, shuffle=True)
sr_linear = Pipeline(steps=[
('preprocessing', ColumnTransformer(transformers=[
('categorical',
make_pipeline(OneHotEncoder(), StandardScaler(with_mean=False)),
make_column_selector(dtype_include='category')),
('numerical',
StandardScaler(),
make_column_selector(dtype_include=np.number))
])),
('model', LinearRegression())
])
ct_imputation = ColumnTransformer(transformers=[
('categorical',
SimpleImputer(missing_values=np.nan, strategy='constant', fill_value='None'),
make_column_selector(dtype_include='category')),
('numerical',
SimpleImputer(strategy='median'),
make_column_selector(dtype_include=np.number))
])
stacked_regressor = Pipeline(steps=[
('imputation', ct_imputation),
('back_to_pandas', FunctionTransformer(
func=lambda values: pd.DataFrame(values, columns=ct_imputation.get_feature_names_out()).astype(types)
)),
('mdl', sr_linear)
])
stacked_regressor.fit(X_train, y_train)
Observe that I had to slightly modify the 'back_to_pandas' step because for some reason pd.DataFrame was changing the dtypes of the columns to 'object' only (from 'category' and 'float64'), therefore clashing with the imputation performed in sr_linear. For this reason, I've applied .astype(types) to the pd.DataFrame constructor, where types is defined as follows (based on the implementation of .get_feature_names_out() method of the SimpleImputer from the dev version of sklearn):
types = {}
for col in d.columns[:-1]:
if d[col].dtype == 'category':
types['categorical__' + col] = str(d[col].dtype)
else:
types['numerical__' + col] = str(d[col].dtype)

The correct thing to do was:
Move from mlxtend's to sklearn's StackingRegressor. I believe the former was creater when sklearn still didn't have a stacking regressor. Now there is no need to use more 'obscure' solutions. sklearn's stacking regressor works pretty well.
Move the 1-hot-encoding step to the outer pipeline, because (surprisingly!) sklearn's DecisionTreeRegressor cannot handle categorical data among the features.
A working version of the code is given below:
from sklearn.datasets import fetch_openml
from sklearn.pipeline import Pipeline, make_pipeline
from sklearn.compose import ColumnTransformer, make_column_selector
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import StandardScaler, OneHotEncoder
from sklearn.linear_model import LinearRegression
from sklearn.tree import DecisionTreeRegressor
from sklearn.model_selection import train_test_split
from sklearn.ensemble import StackingRegressor
import numpy as np
import pandas as pd
def set_correct_categories(df: pd.DataFrame) -> pd.DataFrame:
for column in df.columns:
if df[column].dtype == object or 'MSSubClass' in column:
df[column] = pd.Categorical(df[column])
return df
d = fetch_openml('house_prices', as_frame=True).frame
d = set_correct_categories(d).drop(columns='Id')
sr_linear = Pipeline(steps=[
('preprocessing', StandardScaler()),
('model', LinearRegression())
])
ct_preprocessing = ColumnTransformer(transformers=[
('categorical',
make_pipeline(
SimpleImputer(strategy='constant', fill_value='None'),
OneHotEncoder(sparse=False, handle_unknown='ignore')
),
make_column_selector(dtype_include='category')),
('numerical',
SimpleImputer(strategy='median'),
make_column_selector(dtype_include=np.number))
])
stacking_regressor = Pipeline(steps=[
('preprocessing', ct_preprocessing),
('model', StackingRegressor(
estimators=[('linear_regression', sr_linear), ('regression_tree', DecisionTreeRegressor())],
final_estimator=DecisionTreeRegressor(),
passthrough=True
))
])
label = 'SalePrice'
features = [col for col in d.columns if col != label]
X, y = d[features], d[label]
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, shuffle=True)
stacking_regressor.fit(X_train, y_train)
Thanks to user amiola for his answer putting me on the right track.

How to solve 'Input contains NaN, infinity or a value too large for dtype('float64')' after already preprocessing using Pipeline?

There are many posts containing this error, but I couldn't find the solution for this problem. I'm using this dataset. This is what I've done, a preprocessing, with SimpleImputer for categorical and numerical features:
import pandas as pd
import numpy as np
%load_ext nb_black
from sklearn.preprocessing import StandardScaler, OrdinalEncoder
from sklearn.impute import SimpleImputer
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
from category_encoders import CatBoostEncoder
from sklearn.model_selection import train_test_split
housing = pd.read_csv("housing.csv")
housing.head()
X = housing.drop(["longitude", "latitude", "median_house_value"], axis=1)
y = housing["median_house_value"]
X_train, X_test, y_train, y_test = train_test_split(
X, y, test_size=0.3, random_state=42
)
numeric_transformer = Pipeline(
steps=[("imputer", SimpleImputer(strategy="median")), ("scaler", StandardScaler())]
)
categorical_transformer = Pipeline(
steps=[
("imputer", SimpleImputer(strategy="constant")),
("encoder", CatBoostEncoder()),
]
)
numeric_features = [
"housing_median_age",
"total_rooms",
"total_bedrooms",
"population",
"households",
"median_income",
]
categorical_features = ["ocean_proximity"]
preprocessor = ColumnTransformer(
transformers=[
("numeric", numeric_transformer, numeric_features),
("categorical", categorical_transformer, categorical_features),
]
)
from sklearn.linear_model import LinearRegression
pipeline = Pipeline(
steps=[("preprocessor", preprocessor), ("regressor", LinearRegression())]
)
lr_model = pipeline.fit(X_train, y_train)
But I got this error:
ValueError: Input contains NaN, infinity or a value too large for dtype('float64').
Any idea of what's happening in here?

It seems that the CatBoostEncoder is returning several nan values when fitted to the training set, which is why the LinearRegression throws an error.
import pandas as pd
import numpy as np
from sklearn.preprocessing import StandardScaler
from sklearn.impute import SimpleImputer
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
from sklearn.model_selection import train_test_split
from sklearn.linear_model import LinearRegression
from category_encoders import CatBoostEncoder
housing = pd.read_csv("housing.csv")
X = housing.drop(["longitude", "latitude", "median_house_value"], axis=1)
y = housing["median_house_value"]
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3, random_state=42)
numeric_transformer = Pipeline(steps=[
("imputer", SimpleImputer(strategy="median")),
("scaler", StandardScaler())
])
categorical_transformer = Pipeline(steps=[
("imputer", SimpleImputer(strategy="constant")),
("encoder", CatBoostEncoder())
])
numeric_features = ["housing_median_age", "total_rooms", "total_bedrooms", "population", "households", "median_income"]
categorical_features = ["ocean_proximity"]
preprocessor = ColumnTransformer(transformers=[
("numeric", numeric_transformer, numeric_features),
("categorical", categorical_transformer, categorical_features),
])
X_new = preprocessor.fit_transform(X_train, y_train)
print(np.isnan(X_new).sum(axis=0))
# array([ 0, 0, 0, 0, 0, 0, 4315])

How to access ColumnTransformer elements in GridSearchCV

I wanted to find out the correct naming convention when referring to individual preprocessor included in ColumnTransformer (which is part of a pipeline) in param_grid for grid_search.
Environment & sample data:
import seaborn as sns
from sklearn.model_selection import train_test_split, GridSearchCV
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import OneHotEncoder, KBinsDiscretizer, MinMaxScaler
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
from sklearn.linear_model import LogisticRegression
df = sns.load_dataset('titanic')[['survived', 'age', 'embarked']]
X_train, X_test, y_train, y_test = train_test_split(df.drop(columns='survived'), df['survived'], test_size=0.2,
random_state=123)
Pipeline:
num = ['age']
cat = ['embarked']
num_transformer = Pipeline(steps=[('imputer', SimpleImputer()),
('discritiser', KBinsDiscretizer(encode='ordinal', strategy='uniform')),
('scaler', MinMaxScaler())])
cat_transformer = Pipeline(steps=[('imputer', SimpleImputer(strategy='constant', fill_value='missing')),
('onehot', OneHotEncoder(handle_unknown='ignore'))])
preprocessor = ColumnTransformer(transformers=[('num', num_transformer, num),
('cat', cat_transformer, cat)])
pipe = Pipeline(steps=[('preprocessor', preprocessor),
('classiffier', LogisticRegression(random_state=1, max_iter=10000))])
param_grid = dict([SOMETHING]imputer__strategy = ['mean', 'median'],
[SOMETHING]discritiser__nbins = range(5,10),
classiffier__C = [0.1, 10, 100],
classiffier__solver = ['liblinear', 'saga'])
grid_search = GridSearchCV(pipe, param_grid=param_grid, cv=10)
grid_search.fit(X_train, y_train)
Basically, what should I write instead of [SOMETHING] in my code?
I have looked at this answer which answered the question for make_pipeline - so using the similar idea, I tried 'preprocessor__num__', 'preprocessor__num_', 'pipeline__num__', 'pipeline__num_' - no luck so far.
Thank you

You were close, the correct way to declare it is like this:
param_grid = {'preprocessor__num__imputer__strategy' : ['mean', 'median'],
'preprocessor__num__discritiser__n_bins' : range(5,10),
'classiffier__C' : [0.1, 10, 100],
'classiffier__solver' : ['liblinear', 'saga']}
Here is the full code:
import seaborn as sns
from sklearn.model_selection import train_test_split, GridSearchCV
from sklearn.impute import SimpleImputer
from sklearn.preprocessing import OneHotEncoder, KBinsDiscretizer, MinMaxScaler
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
from sklearn.linear_model import LogisticRegression
df = sns.load_dataset('titanic')[['survived', 'age', 'embarked']]
X_train, X_test, y_train, y_test = train_test_split(df.drop(columns='survived'), df['survived'], test_size=0.2,
random_state=123)
num = ['age']
cat = ['embarked']
num_transformer = Pipeline(steps=[('imputer', SimpleImputer()),
('discritiser', KBinsDiscretizer(encode='ordinal', strategy='uniform')),
('scaler', MinMaxScaler())])
cat_transformer = Pipeline(steps=[('imputer', SimpleImputer(strategy='constant', fill_value='missing')),
('onehot', OneHotEncoder(handle_unknown='ignore'))])
preprocessor = ColumnTransformer(transformers=[('num', num_transformer, num),
('cat', cat_transformer, cat)])
pipe = Pipeline(steps=[('preprocessor', preprocessor),
('classiffier', LogisticRegression(random_state=1, max_iter=10000))])
param_grid = {'preprocessor__num__imputer__strategy' : ['mean', 'median'],
'preprocessor__num__discritiser__n_bins' : range(5,10),
'classiffier__C' : [0.1, 10, 100],
'classiffier__solver' : ['liblinear', 'saga']}
grid_search = GridSearchCV(pipe, param_grid=param_grid, cv=10)
grid_search.fit(X_train, y_train)
One simply way to check the available parameter names is like this:
print(pipe.get_params().keys())
This will print out the list of all the available parameters which you can copy directly into your params dictionary.
I have written a utility function which you can use to check if a parameter exist in a pipeline/classifier by simply passing in a keyword.
def check_params_exist(esitmator, params_keyword):
all_params = esitmator.get_params().keys()
available_params = [x for x in all_params if params_keyword in x]
if len(available_params)==0:
return "No matching params found!"
else:
return available_params
Now if you are unsure of the exact name, just pass imputer as the keyword
print(check_params_exist(pipe, 'imputer'))
This will print the following list:
['preprocessor__num__imputer',
'preprocessor__num__imputer__add_indicator',
'preprocessor__num__imputer__copy',
'preprocessor__num__imputer__fill_value',
'preprocessor__num__imputer__missing_values',
'preprocessor__num__imputer__strategy',
'preprocessor__num__imputer__verbose',
'preprocessor__cat__imputer',
'preprocessor__cat__imputer__add_indicator',
'preprocessor__cat__imputer__copy',
'preprocessor__cat__imputer__fill_value',
'preprocessor__cat__imputer__missing_values',
'preprocessor__cat__imputer__strategy',
'preprocessor__cat__imputer__verbose']