Using FunctionTransformer to select columns

Shows how to use a function transformer in a pipeline. If you know your dataset’s first principle component is irrelevant for a classification task, you can use the FunctionTransformer to select all but the first column of the PCA transformed data.

Python source code: plot_function_transformer.py

import matplotlib.pyplot as plt
import numpy as np

from sklearn.cross_validation import train_test_split
from sklearn.decomposition import PCA
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import FunctionTransformer


def _generate_vector(shift=0.5, noise=15):
    return np.arange(1000) + (np.random.rand(1000) - shift) * noise


def generate_dataset():
    """
    This dataset is two lines with a slope ~ 1, where one has
    a y offset of ~100
    """
    return np.vstack((
        np.vstack((
            _generate_vector(),
            _generate_vector() + 100,
        )).T,
        np.vstack((
            _generate_vector(),
            _generate_vector(),
        )).T,
    )), np.hstack((np.zeros(1000), np.ones(1000)))


def all_but_first_column(X):
    return X[:, 1:]


def drop_first_component(X, y):
    """
    Create a pipeline with PCA and the column selector and use it to
    transform the dataset.
    """
    pipeline = make_pipeline(
        PCA(), FunctionTransformer(all_but_first_column),
    )
    X_train, X_test, y_train, y_test = train_test_split(X, y)
    pipeline.fit(X_train, y_train)
    return pipeline.transform(X_test), y_test


if __name__ == '__main__':
    X, y = generate_dataset()
    plt.scatter(X[:, 0], X[:, 1], c=y, s=50)
    plt.show()
    X_transformed, y_transformed = drop_first_component(*generate_dataset())
    plt.scatter(
        X_transformed[:, 0],
        np.zeros(len(X_transformed)),
        c=y_transformed,
        s=50,
    )
    plt.show()

Total running time of the example: 0.00 seconds ( 0 minutes 0.00 seconds)