Sklearn Pipelines

Posted on Jan 8, 2019

Pipeline of transforms with a final estimator.


Whether you’re using sklearn transformations already or implementing data wrangling from scratch, there are interesting aspects to squeezing those into an sklearn pipeline. Most notably, this will:

It would be possible to do all such processing without a pipeline object: once on the whole dataset. Yet, this is only legitimate for data-independent [0] transformations. For data-dependent transformations, such as imputation by mean, you would cause data leakage [1]. In order to avoid that, we can express how training and validation set should be processed individually, per cross validation split.

This distinction is manifested through fit and transform methods in sklearn. For data-dependent operations, fit is supposed to capture said dependence. fit is therefore only applied to training data while transform is applied to both training and validation data. Moreover it follows that fit for data-dependent operations is stateful.

Pipeline building blocks

A pipeline of n steps constitutes of n-1 transforms and a final estimator.

Transform steps

In order to define a transform step, fit and transform have to be implemented. Conventionally, this is achieved by inherting from sklearn’s TransformerMixin.

Given that the pipeline is fed a pandas dataframe, the following are examples of sequential transform step classes:

  1. Data-indepdent imputation.
class DateImputer(TransformerMixin):

    def transform(self, df):
        # Observations don't always exist. Hence impute by lower/upper bound.
        df = df.fillna({'date_first_observation': df['date_creation'],
                        'date_last_observation': df['date_deletion']})
        return df

    def fit(self, df, labels=None):
        return self
  1. Data-independent creation of feature.
class RelativeWeightCreator(TransformerMixin):

    def transform(self, df):
        for column_name in ['weight_a', 'weight_b', 'weight_c']:
            df.loc[:, "rel" + column_name] = df[column_name] / df['total_weight']
        return df

    def fit(self, df, labels=None):
        return self
  1. Data-dependent creation of feature.
class AggregateCreator(TransformerMixin):

    def __init__(self):
        self.asset_mean_dict = {}

    def fit(self, df, labels=None):
        outcome = 'profit'
        mask = df[outcome] > 0
        df = df.loc[mask, :]
        asset_aggregates = df.groupby('asset_type')[outcome]
        self.asset_mean_dict = asset_aggregates.mean().to_dict()
        return self

    def transform(self, df):
        asset_types = df['asset_types']
        asset_means =

        # For validation data, some asset_type values might not have been
        # encountered in training data.
        asset_means = asset_means.fillna(-1)

        df.loc[:, 'asset_mean'] = asset_means
        return df
  1. Data-independent dropping of columns.
class ColumnDropper(TransformerMixin):

    def __init__(self, column_names):
        self.column_names = column_names

    def transform(self, df):
        df = df.drop(self.column_names, axis=1)
        return df

    def fit(self, df, labels=None):
        return self

Many more use cases exist.

Meta information step

Steps in a pipeline don’t have to actually process or estimate. See an example of a pipeline step which prints some stats about the data before it’s being handed to the regressor. In addition, it stores column name information, which would not be obtainable by default. This is arguably hacky.

class MetaInformer(TransformerMixin):

    def __init__(self):
        self.column_names = []

    def transform(self, df):
        print('#columns: %d' % df.shape[1])
        column_nullity = df.isnull().any()
        if column_nullity.any():
            print('Contain nulls:')
            print(column_nullity[lambda x: x].keys())
        column_redundancy = df.apply(lambda c: c.min() == c.max(), axis=0)
        if column_redundancy.any():
            print('Has redundant columns:')
            print(column_redundancy[lambda x: x].keys())
        return df

    def fit(self, df, labels=None):
        self.column_names = df.columns
        return self

    def get_column_names(self):
        return self.column_names

Estimation step

We can simply use an out-of-the-box estimator from sklearn, such as RandomForestRegressor. If you intend to either eliminate rows (requiring access to the target dataframe) or want to still operate on predictions, it is possible to wrap a conventional estimator inside of a custom one. The latter case might, for instance, be relevant if you have a strong belief on how a target variable is constructed off of intermediate target variables.

Assuming you happen to know that profit/square meters is ’easier’ to infer than profits, you could manually build an interaction term multiplying the inferred profits per surface area by surface area. If you want this type of post-inference-processing to work with GridSearchCV, you need to implement the set_params method.

Applying a logarithm to the predictions is not inherent to the approach of building the interaction term. It is an independent design choice that can be conveniently placed at this stage of the pipeline.

class InteractionRegressor(BaseEstimator):

    def __init__(self, use_lb, use_log_on_savings):
        self.regressor = RandomForestRegressor()
        self.intermediate_target_column = 'profit_per_sqm'
        self.max_depth = None
        self.n_estimators = None

    def fit(self, df_wo_pseudo_target, df_pseudo_target):
        df = df_wo_pseudo_target
        # Split target from samples.
        intermediate_target = df[self.intermediate_target_column]
        df_wo_intermediate_target = df.drop(self.intermediate_target_column,

        intermediate_target_log = np.log(intermediate_target), intermediate_target_log)

    def predict(self, df):
        df_wo_intermediate_target = df.drop(self.intermediate_target_column,
        surface_areas = df['surface_area']
        intermediate_target_log = self.regressor.predict(
        # log of product is sum of logs.
        return intermediate_target_log + np.log(surface_areas)

    def get_rf_params(self):
        return {'max_depth': self.max_depth,
                'n_estimators': self.n_estimators}

    def set_params(self, **params):

Instantiating a pipeline

# from sklearn.ensemble import RandomForestRegressor
# from sklearn.pipeline import Pipeline
weight_columns = ['weight_a', 'weight_b', 'weight_c']
redundant_columns = ['useless', 'noise', 'garbage']
target_columns = ['revenue', 'profit']

pipeline = Pipeline([
  ('date_imputer', DateImputer()),
  ('relative_weight_creator', RelativeWeightCreator()),
  ('aggregate_creator', AggregateCreator()),
  ('weight_column_dropper', ColumnDropper(weight_columns)),
  ('redundant_column_dropper', ColumnDropper(redundant_columns)),
  ('target_column_dropper', ColumnDropper(target_columns)),
  ('meta_informer', MetaInformer())
  ('rf_regressor', RandomForestRegressor())

Using a pipeline

Process, obtain meta information and predict

Note that in order for the feature importance information to be meaningful, we first need to retrieve the column names, stored in the 'meta_informer' step of the pipeline., df_target)
column_names = pipeline.named_steps['meta_informer'].get_column_names()
feature_importances = pipeline.named_steps['rf_regressor'].feature_importances_
name_importance_tuples = sorted(
  [(column_names[i], x) for i, x in enumerate(feature_importances) if x > 0],
  key=lambda p: p[1],
predictions = pipeline.predict(df_target)

Cross validation

# from sklearn.model_selection import cross_val_score
cv_scores = cross_val_score(pipeline, df_data, df_target, cv=10,
avg_rmse = np.mean(np.sqrt(-cv_scores))

Grid search

In order to associate a hyperparameter to a certain step, you need to prefix the hyperparameter attribute by the name of the pipeline step. The postfix of the hyperparameter attribute is the parameter said step of the pipeline expects, as used in set_params. Both parts are joined via a double underscore.

# from sklearn.model_selection import GridSearchCV
hyperparameters = [{'rf_regressor__max_depth': [5, 10, 15, 25],
                    'rf_regressor__n_estimators': [100, 200, 300]}]
grid_search = GridSearchCV(pipeline, hyperparameters), df_target)

[0] Data-dependent: If f is applied to sample xi out of all n samples, the outcome is independent of all other n-1 samples.