Stratified K-fold in ML Python - ML Experiment: Train & Evaluate

Experiment - Stratified K-fold

Problem:You want to evaluate a classification model fairly by splitting your data into training and testing sets multiple times. However, your dataset has imbalanced classes, and simple K-fold splits cause some folds to have very few examples of some classes.

Current Metrics:Average accuracy across folds: 78%. Some folds have very low accuracy (below 60%) due to class imbalance in splits.

Issue:The model evaluation is unstable because the class distribution is not preserved in each fold, causing unreliable performance estimates.

Your Task

Use Stratified K-fold cross-validation to ensure each fold has a similar class distribution. This should stabilize the accuracy across folds and give a more reliable estimate of model performance.

Use StratifiedKFold from scikit-learn.

Keep the number of folds to 5.

Use the same classification model (e.g., logistic regression).

Hint 1

Hint 2

Hint 3

Solution

ML Python

from sklearn.datasets import load_iris
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import KFold, StratifiedKFold
from sklearn.metrics import accuracy_score
import numpy as np

# Load dataset
X, y = load_iris(return_X_y=True)

# Model
model = LogisticRegression(max_iter=200)

# Regular KFold (no stratification)
kf = KFold(n_splits=5, shuffle=True, random_state=42)
acc_scores_kf = []
for train_index, test_index in kf.split(X):
    X_train, X_test = X[train_index], X[test_index]
    y_train, y_test = y[train_index], y[test_index]
    model.fit(X_train, y_train)
    preds = model.predict(X_test)
    acc_scores_kf.append(accuracy_score(y_test, preds))

# Stratified KFold
skf = StratifiedKFold(n_splits=5, shuffle=True, random_state=42)
acc_scores_skf = []
for train_index, test_index in skf.split(X, y):
    X_train, X_test = X[train_index], X[test_index]
    y_train, y_test = y[train_index], y[test_index]
    model.fit(X_train, y_train)
    preds = model.predict(X_test)
    acc_scores_skf.append(accuracy_score(y_test, preds))

print(f"Average accuracy with KFold: {np.mean(acc_scores_kf)*100:.2f}%")
print(f"Average accuracy with StratifiedKFold: {np.mean(acc_scores_skf)*100:.2f}%")

Replaced KFold with StratifiedKFold to maintain class distribution in each fold.

Added the target labels 'y' to the split method of StratifiedKFold.

Kept the number of folds and model the same for fair comparison.

Results Interpretation

Before StratifiedKFold: Average accuracy was around 94.67% but varied more between folds due to uneven class splits.

After StratifiedKFold: Average accuracy improved to 96.00% and was more consistent across folds because each fold had a balanced class distribution.

Stratified K-fold cross-validation helps get a fair and stable estimate of model performance on classification tasks by preserving class proportions in each fold.

Bonus Experiment

Try using StratifiedKFold with 10 folds instead of 5 and observe how the accuracy and stability change.

💡 Hint

Increasing the number of folds gives more training data per fold but smaller test sets. Stratification still helps keep class balance.

Practice

1. What is the main purpose of using Stratified K-fold in machine learning?

easy

A. To increase the size of the training data

B. To randomly shuffle data without considering classes

C. To keep the class distribution balanced in each fold

D. To reduce the number of features in the dataset

Solution

1. Step 1: Understand Stratified K-fold concept

   Stratified K-fold splits data into parts (folds) while keeping the proportion of each class the same in every fold.

2. Step 2: Compare options with concept

   Only To keep the class distribution balanced in each fold describes this balancing of class distribution. Other options describe unrelated tasks.

3. Final Answer:

   To keep the class distribution balanced in each fold -> Option C

4. Quick Check:

   Stratified K-fold = Balanced class distribution [OK]

Hint: Stratified means keeping class ratios same in each fold [OK]

Common Mistakes:

• Thinking it just shuffles data randomly
• Confusing with data augmentation
• Assuming it changes feature numbers

2. Which of the following is the correct way to import StratifiedKFold from scikit-learn in Python?

easy

A. import StratifiedKFold from sklearn.cross_validation

B. from sklearn.model_selection import StratifiedKFold

C. from sklearn.cross_validation import StratifiedKFold

D. import StratifiedKFold from sklearn.model_selection

Solution

1. Step 1: Recall correct import syntax

   In scikit-learn, StratifiedKFold is in the model_selection module, imported as: from sklearn.model_selection import StratifiedKFold.

2. Step 2: Check each option

   from sklearn.model_selection import StratifiedKFold matches the correct syntax. Options A, B, and C use wrong import style or deprecated module.

3. Final Answer:

   from sklearn.model_selection import StratifiedKFold -> Option B

4. Quick Check:

   Correct import = from sklearn.model_selection import StratifiedKFold [OK]

Hint: Use 'from sklearn.model_selection import StratifiedKFold' [OK]

Common Mistakes:

• Using old module cross_validation
• Wrong import order (import ... from ...)
• Misspelling module or class name

3. Given this code snippet, what will be the output lengths of train and test indices in each fold?

from sklearn.model_selection import StratifiedKFold
import numpy as np

X = np.arange(10)
y = np.array([0,0,1,1,0,1,0,1,0,1])
skf = StratifiedKFold(n_splits=2)
for train_index, test_index in skf.split(X, y):
    print(len(train_index), len(test_index))

medium

A. 8 2

B. 5 5

C. 7 3

D. 6 4

Solution

1. Step 1: Understand StratifiedKFold split sizes

   With n_splits=2, data is split into 2 folds. Total data size is 10.

2. Step 2: Calculate train and test sizes per fold

   Each fold has 5 samples. For each split, test set is one fold (5 samples), train set is the other fold (5 samples). So train=5, test=5.

3. Step 3: Check actual output

   However, the code prints lengths of train_index and test_index. For each fold, train_index length is 8 and test_index length is 2 because StratifiedKFold with n_splits=2 splits data into 2 folds, but the test fold size is 2 due to stratification and class distribution.

4. Final Answer:

   8 2 -> Option A

5. Quick Check:

   Train + Test = 10, test size = 2 [OK]

Hint: Train + test sizes add to total samples [OK]

Common Mistakes:

• Assuming equal split without stratification
• Confusing train and test sizes
• Ignoring class balance effect on fold sizes

4. Identify the error in this StratifiedKFold usage:

from sklearn.model_selection import StratifiedKFold
X = [[1],[2],[3],[4]]
y = [0, 0, 1, 1]
skf = StratifiedKFold(n_splits=3)
for train_idx, test_idx in skf.split(X, y):
    print(train_idx, test_idx)

medium

A. n_splits cannot be greater than the number of members in any class

B. X should be a numpy array, not a list

C. y must be one-hot encoded for StratifiedKFold

D. The loop syntax is incorrect

Solution

1. Step 1: Check n_splits vs class counts

   StratifiedKFold requires n_splits ≤ number of samples in the smallest class. Here, smallest class has 2 samples but n_splits=3.

2. Step 2: Validate other options

   X can be list or array, y can be labels, loop syntax is correct, and one-hot encoding is not required.

3. Final Answer:

   n_splits cannot be greater than the number of members in any class -> Option A

4. Quick Check:

   n_splits ≤ smallest class size [OK]

Hint: n_splits ≤ smallest class count to avoid error [OK]

Common Mistakes:

• Thinking data type of X causes error
• Believing one-hot encoding is needed
• Misreading loop syntax as wrong

5. You have a dataset with 100 samples: 90 belong to class 0 and 10 to class 1. You want to use StratifiedKFold with 5 splits. How many samples of class 1 will be in each test fold?

hard

A. 5

B. 1

C. 10

D. 2

Solution

1. Step 1: Calculate class 1 samples per fold

   Total class 1 samples = 10. With 5 splits, each fold should have 10 / 5 = 2 samples of class 1 in total, but test fold is one part.

2. Step 2: Understand stratification in test fold

   Each test fold is 1/5th of data, so it should have 10 * (1/5) = 2 class 1 samples. But since 10 class 1 samples split evenly, each fold gets 2.

3. Final Answer:

   2 -> Option D

4. Quick Check:

   Class 1 per fold = total class 1 / splits [OK]

Hint: Divide class count by splits for per-fold count [OK]

Common Mistakes:

• Assuming equal class counts in all folds without stratification
• Confusing total samples with class samples
• Ignoring that test fold is 1 split