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Custom Transformers

Reference for scikit-learn-pipeline-builder · 91 lines

AI & Machine Learning / Classical Machine Learningv1.0.0Updated OCT 25 20265 references2 scripts

The estimator contract

  1. __init__ stores each parameter as an attribute with the same name, unchanged; no validation, no computation. clone(), get_params() and set_params() depend on this.
  2. fit(X, y=None) learns state into attributes ending in _ and returns self.
  3. transform(X) uses only fitted state; never refits.
  4. Set n_features_in_ (and feature_names_in_ for DataFrames) in fit.
  5. Provide get_feature_names_out (or inherit OneToOneFeatureMixin / ClassNamePrefixFeaturesOutMixin).

Mixin order: mixins first, BaseEstimator last: class T(OneToOneFeatureMixin, TransformerMixin, BaseEstimator).

Stateful example: clipping + log

python
import numpy as np
from sklearn.base import BaseEstimator, OneToOneFeatureMixin, TransformerMixin
from sklearn.utils.validation import check_is_fitted, validate_data   # validate_data: sklearn >= 1.6

class Log1pClip(OneToOneFeatureMixin, TransformerMixin, BaseEstimator):
    def __init__(self, upper_quantile=0.99):
        self.upper_quantile = upper_quantile

    def fit(self, X, y=None):
        X = validate_data(self, X, ensure_all_finite="allow-nan")
        self.upper_ = np.nanquantile(X, self.upper_quantile, axis=0)
        return self

    def transform(self, X):
        check_is_fitted(self)
        X = validate_data(self, X, ensure_all_finite="allow-nan", reset=False)
        return np.log1p(np.clip(X, 0, self.upper_))

    def __sklearn_tags__(self):                 # declare NaN support so check_estimator and pipelines know
        tags = super().__sklearn_tags__()
        tags.input_tags.allow_nan = True
        return tags

On scikit-learn < 1.6 use self._validate_data(...) (method), force_all_finite= and _more_tags() returning {"allow_nan": True} instead. This class passes check_estimator on scikit-learn 1.9.

Column-aware example: ratio features from a DataFrame

python
class RatioFeatures(TransformerMixin, BaseEstimator):
    def __init__(self, pairs=(("total_charges", "tenure_months"),)):
        self.pairs = pairs

    def fit(self, X, y=None):
        self.feature_names_in_ = np.asarray(X.columns, dtype=object)
        self.n_features_in_ = X.shape[1]
        return self

    def transform(self, X):
        out = {f"{a}_per_{b}": X[a] / X[b].replace(0, np.nan) for a, b in self.pairs}
        return pd.DataFrame(out, index=X.index)

    def get_feature_names_out(self, input_features=None):
        return np.array([f"{a}_per_{b}" for a, b in self.pairs], dtype=object)

Use with a ColumnTransformer column list that contains every referenced column.

Stateless vs stateful

KindExamplePlacement
Statelessdate parts, ratios, log1panywhere; FunctionTransformer is enough
Stateful (learns from X)clipping bounds, frequency maps, vocabulariesmust be a fitted transformer in the Pipeline
Supervised (learns from y)target encoding, supervised binning, selectionin the Pipeline; cross-fitted if it encodes rows used for training

Testing

python
from sklearn.utils.estimator_checks import check_estimator
check_estimator(Log1pClip())          # runs the full API compliance suite (strict; aim for library code)

Unit-test behaviour too: fit on one frame, transform another with unseen values, NaN, and different column order; assert shapes and names.

Common bugs

BugSymptom
Modifying parameters in __init__ (self.cols = list(cols))clone warnings, searches ignore settings
Learning state in transformCV leakage, different results per call
Returning a new object from fitpipelines break
Mutating the input DataFramecaller's data changes; use X = X.copy()
No get_feature_names_outdownstream get_feature_names_out fails
Lambdas stored as parameterspickling fails
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