Feature Scaling in Machine Learning

Introduction

Feature scaling is an important preprocessing step for many machine learning algorithms. It involves rescaling each feature such that it has a standard deviation of 1 and a mean of 0. In this lab, we will explore the importance of feature scaling and its effect on machine learning models using the scikit-learn library in Python.

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Load and Prepare Data

We will load the wine dataset from scikit-learn and split it into training and testing sets. We will also scale the features in the training set using the StandardScaler from the scikit-learn preprocessing module.

from sklearn.datasets import load_wine
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler

X, y = load_wine(return_X_y=True, as_frame=True)
scaler = StandardScaler().set_output(transform="pandas")

X_train, X_test, y_train, y_test = train_test_split(
    X, y, test_size=0.30, random_state=42
)
scaled_X_train = scaler.fit_transform(X_train)

Effect of Rescaling on a k-neighbors Model

We will use a subset of two features from the wine dataset to train a K-nearest neighbors classifier. We will visualize the decision boundary of the classifier using unscaled and scaled data.

import matplotlib.pyplot as plt
from sklearn.inspection import DecisionBoundaryDisplay
from sklearn.neighbors import KNeighborsClassifier

X_plot = X[["proline", "hue"]]
X_plot_scaled = scaler.fit_transform(X_plot)
clf = KNeighborsClassifier(n_neighbors=20)

def fit_and_plot_model(X_plot, y, clf, ax):
    clf.fit(X_plot, y)
    disp = DecisionBoundaryDisplay.from_estimator(
        clf,
        X_plot,
        response_method="predict",
        alpha=0.5,
        ax=ax,
    )
    disp.ax_.scatter(X_plot["proline"], X_plot["hue"], c=y, s=20, edgecolor="k")
    disp.ax_.set_xlim((X_plot["proline"].min(), X_plot["proline"].max()))
    disp.ax_.set_ylim((X_plot["hue"].min(), X_plot["hue"].max()))
    return disp.ax_

fig, (ax1, ax2) = plt.subplots(ncols=2, figsize=(12, 6))

fit_and_plot_model(X_plot, y, clf, ax1)
ax1.set_title("KNN without scaling")

fit_and_plot_model(X_plot_scaled, y, clf, ax2)
ax2.set_xlabel("scaled proline")
ax2.set_ylabel("scaled hue")
_ = ax2.set_title("KNN with scaling")

Effect of Rescaling on a PCA Dimensional Reduction

We will use Principal Component Analysis (PCA) to reduce the dimensionality of the wine dataset. We will compare the principal components found using PCA on unscaled data with those obtained when using a StandardScaler to scale data first.

import pandas as pd
from sklearn.decomposition import PCA

pca = PCA(n_components=2).fit(X_train)
scaled_pca = PCA(n_components=2).fit(scaled_X_train)
X_train_transformed = pca.transform(X_train)
X_train_std_transformed = scaled_pca.transform(scaled_X_train)

first_pca_component = pd.DataFrame(
    pca.components_[0], index=X.columns, columns=["without scaling"]
)
first_pca_component["with scaling"] = scaled_pca.components_[0]
first_pca_component.plot.bar(
    title="Weights of the first principal component", figsize=(6, 8)
)

_ = plt.tight_layout()

fig, (ax1, ax2) = plt.subplots(nrows=1, ncols=2, figsize=(10, 5))

target_classes = range(0, 3)
colors = ("blue", "red", "green")
markers = ("^", "s", "o")

for target_class, color, marker in zip(target_classes, colors, markers):
    ax1.scatter(
        x=X_train_transformed[y_train == target_class, 0],
        y=X_train_transformed[y_train == target_class, 1],
        color=color,
        label=f"class {target_class}",
        alpha=0.5,
        marker=marker,
    )

    ax2.scatter(
        x=X_train_std_transformed[y_train == target_class, 0],
        y=X_train_std_transformed[y_train == target_class, 1],
        color=color,
        label=f"class {target_class}",
        alpha=0.5,
        marker=marker,
    )

ax1.set_title("Unscaled training dataset after PCA")
ax2.set_title("Standardized training dataset after PCA")

for ax in (ax1, ax2):
    ax.set_xlabel("1st principal component")
    ax.set_ylabel("2nd principal component")
    ax.legend(loc="upper right")
    ax.grid()

_ = plt.tight_layout()

Effect of Rescaling on Model's Performance

We will train a logistic regression model with PCA-reduced data to evaluate the effect of feature scaling on model performance. We will compare the performance of the model with unscaled and scaled features.

import numpy as np
from sklearn.pipeline import make_pipeline
from sklearn.linear_model import LogisticRegressionCV
from sklearn.metrics import accuracy_score
from sklearn.metrics import log_loss

Cs = np.logspace(-5, 5, 20)

unscaled_clf = make_pipeline(pca, LogisticRegressionCV(Cs=Cs))
unscaled_clf.fit(X_train, y_train)

scaled_clf = make_pipeline(scaler, pca, LogisticRegressionCV(Cs=Cs))
scaled_clf.fit(X_train, y_train)

y_pred = unscaled_clf.predict(X_test)
y_pred_scaled = scaled_clf.predict(X_test)
y_proba = unscaled_clf.predict_proba(X_test)
y_proba_scaled = scaled_clf.predict_proba(X_test)

print("Test accuracy for the unscaled PCA")
print(f"{accuracy_score(y_test, y_pred):.2%}\n")
print("Test accuracy for the standardized data with PCA")
print(f"{accuracy_score(y_test, y_pred_scaled):.2%}\n")
print("Log-loss for the unscaled PCA")
print(f"{log_loss(y_test, y_proba):.3}\n")
print("Log-loss for the standardized data with PCA")
print(f"{log_loss(y_test, y_proba_scaled):.3}")

Summary

In this lab, we learned about the importance of feature scaling in machine learning and its effect on model performance. We explored the effect of feature scaling on a K-nearest neighbors model and PCA dimensional reduction. We also trained a logistic regression model with PCA-reduced data to evaluate the effect of feature scaling on model performance. We found that scaling the features before reducing the dimensionality results in components with the same order of magnitude and improves the separability of the classes, leading to better model performance.