Phase 02: ML Fundamentals

Logistic Regression

Type: Build

Languages: Python

Prerequisites: Phase 2 Lesson 1-2 (What Is ML, Linear Regression)

Time: ~90 minutes

The Problem

You want to predict whether a tumor is malignant or benign given its size. You try linear regression. It outputs numbers like 0.3 or 1.7 or -0.5. What do those mean? Is 1.7 "very malignant"? Is -0.5 "very benign"? Linear regression outputs unbounded numbers. Classification needs bounded probabilities between 0 and 1, and a clear decision: yes or no.

Logistic regression solves this. It takes the same linear combination (wx + b) and passes it through the sigmoid function, which squashes any number into the range (0, 1). The output is a probability. You set a threshold (usually 0.5) and make a decision.

This is one of the most widely used algorithms in practice. Despite its name, logistic regression is a classification algorithm, not a regression algorithm. The name comes from the logistic (sigmoid) function it uses.

The Concept

Why Linear Regression Fails for Classification

Imagine predicting pass/fail (1/0) based on study hours. Linear regression fits a line through the data:

Copyhours:  1   2   3   4   5   6   7   8   9   10
actual: 0   0   0   0   1   1   1   1   1   1

A linear fit might produce predictions like -0.2 at hour 1 and 1.3 at hour 10. These values are not probabilities. They go below 0 and above 1. Worse, a single outlier (someone who studied 50 hours) would drag the entire line, changing predictions for everyone.

Classification needs a function that:

• Outputs values between 0 and 1 (probabilities)
• Creates a sharp transition (a decision boundary)
• Is not distorted by outliers far from the boundary

The Sigmoid Function

The sigmoid function does exactly this:

Properties:

• When z is large and positive, \sigma(z) approaches 1
• When z is large and negative, \sigma(z) approaches 0
• When z = 0, \sigma(z) = 0.5
• The output is always between 0 and 1
• The function is smooth and differentiable everywhere

The derivative has a convenient form: \sigma'(z) = \sigma(z) (1 - \sigma(z)). This makes gradient computation efficient.

Logistic Regression = Linear Model + Sigmoid

The model computes z = wx + b (same as linear regression), then applies sigmoid:

flowchart LR
    X[Input features x] --> L["Linear: z = wx + b"]
    L --> S["Sigmoid: p = 1/(1+e^-z)"]
    S --> D{"p >= 0.5?"}
    D -->|Yes| P[Predict 1]
    D -->|No| N[Predict 0]

The output p is interpreted as P(y=1 \mid x), the probability that the input belongs to class 1. The decision boundary is where wx + b = 0, which makes sigmoid output exactly 0.5.

Binary Cross-Entropy Loss

You cannot use MSE for logistic regression. MSE with a sigmoid creates a non-convex cost surface with many local minima. Instead, use binary cross-entropy (log loss):

Why this works:

• When y=1 and p is close to 1: \log(1) = 0, so loss is near 0 (correct, low cost)
• When y=1 and p is close to 0: \log(0) approaches negative infinity, so loss is huge (wrong, high cost)
• When y=0 and p is close to 0: \log(1) = 0, so loss is near 0 (correct, low cost)
• When y=0 and p is close to 1: \log(0) approaches negative infinity, so loss is huge (wrong, high cost)

This loss function is convex for logistic regression, guaranteeing a single global minimum.

Gradient Descent for Logistic Regression

The gradients for binary cross-entropy with sigmoid have a clean form:

These look identical to the linear regression gradients. The difference is that p = \sigma(wx + b) instead of p = wx + b. The sigmoid introduces the nonlinearity, but the gradient update rule stays the same.

flowchart TD
    A[Initialize w=0, b=0] --> B[Forward pass: z = wx+b, p = sigmoid z]
    B --> C[Compute loss: binary cross-entropy]
    C --> D["Compute gradients: dw = (1/n) * sum((p-y)*x)"]
    D --> E[Update: w = w - lr*dw, b = b - lr*db]
    E --> F{Converged?}
    F -->|No| B
    F -->|Yes| G[Model trained]

The Decision Boundary

For a 2D input (two features), the decision boundary is the line where:

Points on one side get classified as 1, points on the other side as 0. Logistic regression always produces a linear decision boundary. If you need a curved boundary, you either add polynomial features or use a nonlinear model.

Multi-Class Classification with Softmax

Binary logistic regression handles two classes. For k classes, use the softmax function:

Each class has its own weight vector. The model computes a score z_i for each class, then softmax converts scores to probabilities that sum to 1. The predicted class is the one with the highest probability.

The loss function becomes categorical cross-entropy:

where y_k is 1 for the true class and 0 for all others (one-hot encoding).

Evaluation Metrics

Accuracy alone is not enough. For a dataset with 95% negative and 5% positive, a model that always predicts negative gets 95% accuracy but is useless.

Confusion Matrix:

Precision: Of all predicted positives, how many are actually positive?

Recall (Sensitivity): Of all actual positives, how many did we catch?

F1 Score: Harmonic mean of precision and recall. Balances both metrics.

When to prioritize:

• Precision: when false positives are costly (spam filter, you do not want to block legitimate email)
• Recall: when false negatives are costly (cancer screening, you do not want to miss a tumor)
• F1: when you need a single balanced metric

Build It

Step 1: Sigmoid function and data generation

pythonCopyimport random
import math

def sigmoid(z):
    z = max(-500, min(500, z))
    return 1.0 / (1.0 + math.exp(-z))


random.seed(42)
N = 200
X = []
y = []

for _ in range(N // 2):
    X.append([random.gauss(2, 1), random.gauss(2, 1)])
    y.append(0)

for _ in range(N // 2):
    X.append([random.gauss(5, 1), random.gauss(5, 1)])
    y.append(1)

combined = list(zip(X, y))
random.shuffle(combined)
X, y = zip(*combined)
X = list(X)
y = list(y)

print(f"Generated {N} samples (2 classes, 2 features)")
print(f"Class 0 center: (2, 2), Class 1 center: (5, 5)")
print(f"First 5 samples:")
for i in range(5):
    print(f"  Features: [{X[i][0]:.2f}, {X[i][1]:.2f}], Label: {y[i]}")

Step 2: Logistic regression from scratch

pythonCopyclass LogisticRegression:
    def __init__(self, n_features, learning_rate=0.01):
        self.weights = [0.0] * n_features
        self.bias = 0.0
        self.lr = learning_rate
        self.loss_history = []

    def predict_proba(self, x):
        z = sum(w * xi for w, xi in zip(self.weights, x)) + self.bias
        return sigmoid(z)

    def predict(self, x, threshold=0.5):
        return 1 if self.predict_proba(x) >= threshold else 0

    def compute_loss(self, X, y):
        n = len(y)
        total = 0.0
        for i in range(n):
            p = self.predict_proba(X[i])
            p = max(1e-15, min(1 - 1e-15, p))
            total += y[i] * math.log(p) + (1 - y[i]) * math.log(1 - p)
        return -total / n

    def fit(self, X, y, epochs=1000, print_every=200):
        n = len(y)
        n_features = len(X[0])
        for epoch in range(epochs):
            dw = [0.0] * n_features
            db = 0.0
            for i in range(n):
                p = self.predict_proba(X[i])
                error = p - y[i]
                for j in range(n_features):
                    dw[j] += error * X[i][j]
                db += error
            for j in range(n_features):
                self.weights[j] -= self.lr * (dw[j] / n)
            self.bias -= self.lr * (db / n)
            loss = self.compute_loss(X, y)
            self.loss_history.append(loss)
            if epoch % print_every == 0:
                print(f"  Epoch {epoch:4d} | Loss: {loss:.4f} | w: [{self.weights[0]:.3f}, {self.weights[1]:.3f}] | b: {self.bias:.3f}")
        return self

    def accuracy(self, X, y):
        correct = sum(1 for i in range(len(y)) if self.predict(X[i]) == y[i])
        return correct / len(y)


split = int(0.8 * N)
X_train, X_test = X[:split], X[split:]
y_train, y_test = y[:split], y[split:]

print("\n=== Training Logistic Regression ===")
model = LogisticRegression(n_features=2, learning_rate=0.1)
model.fit(X_train, y_train, epochs=1000, print_every=200)

print(f"\nTrain accuracy: {model.accuracy(X_train, y_train):.4f}")
print(f"Test accuracy:  {model.accuracy(X_test, y_test):.4f}")
print(f"Weights: [{model.weights[0]:.4f}, {model.weights[1]:.4f}]")
print(f"Bias: {model.bias:.4f}")

Step 3: Confusion matrix and metrics from scratch

pythonCopyclass ClassificationMetrics:
    def __init__(self, y_true, y_pred):
        self.tp = sum(1 for t, p in zip(y_true, y_pred) if t == 1 and p == 1)
        self.tn = sum(1 for t, p in zip(y_true, y_pred) if t == 0 and p == 0)
        self.fp = sum(1 for t, p in zip(y_true, y_pred) if t == 0 and p == 1)
        self.fn = sum(1 for t, p in zip(y_true, y_pred) if t == 1 and p == 0)

    def accuracy(self):
        total = self.tp + self.tn + self.fp + self.fn
        return (self.tp + self.tn) / total if total > 0 else 0

    def precision(self):
        denom = self.tp + self.fp
        return self.tp / denom if denom > 0 else 0

    def recall(self):
        denom = self.tp + self.fn
        return self.tp / denom if denom > 0 else 0

    def f1(self):
        p = self.precision()
        r = self.recall()
        return 2 * p * r / (p + r) if (p + r) > 0 else 0

    def print_confusion_matrix(self):
        print(f"\n  Confusion Matrix:")
        print(f"                  Predicted")
        print(f"                  Pos   Neg")
        print(f"  Actual Pos     {self.tp:4d}  {self.fn:4d}")
        print(f"  Actual Neg     {self.fp:4d}  {self.tn:4d}")

    def print_report(self):
        self.print_confusion_matrix()
        print(f"\n  Accuracy:  {self.accuracy():.4f}")
        print(f"  Precision: {self.precision():.4f}")
        print(f"  Recall:    {self.recall():.4f}")
        print(f"  F1 Score:  {self.f1():.4f}")


y_pred_test = [model.predict(x) for x in X_test]
print("\n=== Classification Report (Test Set) ===")
metrics = ClassificationMetrics(y_test, y_pred_test)
metrics.print_report()

Step 4: Decision boundary analysis

pythonCopyprint("\n=== Decision Boundary ===")
w1, w2 = model.weights
b = model.bias
print(f"Decision boundary: {w1:.4f}*x1 + {w2:.4f}*x2 + {b:.4f} = 0")
if abs(w2) > 1e-10:
    print(f"Solved for x2:     x2 = {-w1/w2:.4f}*x1 + {-b/w2:.4f}")

print("\nSample predictions near the boundary:")
test_points = [
    [3.0, 3.0],
    [3.5, 3.5],
    [4.0, 4.0],
    [2.5, 2.5],
    [5.0, 5.0],
]
for point in test_points:
    prob = model.predict_proba(point)
    pred = model.predict(point)
    print(f"  [{point[0]}, {point[1]}] -> prob={prob:.4f}, class={pred}")

Step 5: Multi-class with softmax

pythonCopyclass SoftmaxRegression:
    def __init__(self, n_features, n_classes, learning_rate=0.01):
        self.n_features = n_features
        self.n_classes = n_classes
        self.lr = learning_rate
        self.weights = [[0.0] * n_features for _ in range(n_classes)]
        self.biases = [0.0] * n_classes

    def softmax(self, scores):
        max_score = max(scores)
        exp_scores = [math.exp(s - max_score) for s in scores]
        total = sum(exp_scores)
        return [e / total for e in exp_scores]

    def predict_proba(self, x):
        scores = [
            sum(self.weights[k][j] * x[j] for j in range(self.n_features)) + self.biases[k]
            for k in range(self.n_classes)
        ]
        return self.softmax(scores)

    def predict(self, x):
        probs = self.predict_proba(x)
        return probs.index(max(probs))

    def fit(self, X, y, epochs=1000, print_every=200):
        n = len(y)
        for epoch in range(epochs):
            grad_w = [[0.0] * self.n_features for _ in range(self.n_classes)]
            grad_b = [0.0] * self.n_classes
            total_loss = 0.0
            for i in range(n):
                probs = self.predict_proba(X[i])
                for k in range(self.n_classes):
                    target = 1.0 if y[i] == k else 0.0
                    error = probs[k] - target
                    for j in range(self.n_features):
                        grad_w[k][j] += error * X[i][j]
                    grad_b[k] += error
                true_prob = max(probs[y[i]], 1e-15)
                total_loss -= math.log(true_prob)
            for k in range(self.n_classes):
                for j in range(self.n_features):
                    self.weights[k][j] -= self.lr * (grad_w[k][j] / n)
                self.biases[k] -= self.lr * (grad_b[k] / n)
            if epoch % print_every == 0:
                print(f"  Epoch {epoch:4d} | Loss: {total_loss / n:.4f}")
        return self

    def accuracy(self, X, y):
        correct = sum(1 for i in range(len(y)) if self.predict(X[i]) == y[i])
        return correct / len(y)


random.seed(42)
X_3class = []
y_3class = []

centers = [(1, 1), (5, 1), (3, 5)]
for label, (cx, cy) in enumerate(centers):
    for _ in range(50):
        X_3class.append([random.gauss(cx, 0.8), random.gauss(cy, 0.8)])
        y_3class.append(label)

combined = list(zip(X_3class, y_3class))
random.shuffle(combined)
X_3class, y_3class = zip(*combined)
X_3class = list(X_3class)
y_3class = list(y_3class)

split_3 = int(0.8 * len(X_3class))
X_train_3 = X_3class[:split_3]
y_train_3 = y_3class[:split_3]
X_test_3 = X_3class[split_3:]
y_test_3 = y_3class[split_3:]

print("\n=== Multi-class Softmax Regression (3 classes) ===")
softmax_model = SoftmaxRegression(n_features=2, n_classes=3, learning_rate=0.1)
softmax_model.fit(X_train_3, y_train_3, epochs=1000, print_every=200)
print(f"\nTrain accuracy: {softmax_model.accuracy(X_train_3, y_train_3):.4f}")
print(f"Test accuracy:  {softmax_model.accuracy(X_test_3, y_test_3):.4f}")

print("\nSample predictions:")
for i in range(5):
    probs = softmax_model.predict_proba(X_test_3[i])
    pred = softmax_model.predict(X_test_3[i])
    print(f"  True: {y_test_3[i]}, Predicted: {pred}, Probs: [{', '.join(f'{p:.3f}' for p in probs)}]")

Step 6: Threshold tuning

pythonCopyprint("\n=== Threshold Tuning ===")
print("Default threshold: 0.5. Adjusting the threshold trades precision for recall.\n")

thresholds = [0.3, 0.4, 0.5, 0.6, 0.7]
print(f"{'Threshold':>10} {'Accuracy':>10} {'Precision':>10} {'Recall':>10} {'F1':>10}")
print("-" * 52)

for t in thresholds:
    y_pred_t = [1 if model.predict_proba(x) >= t else 0 for x in X_test]
    m = ClassificationMetrics(y_test, y_pred_t)
    print(f"{t:>10.1f} {m.accuracy():>10.4f} {m.precision():>10.4f} {m.recall():>10.4f} {m.f1():>10.4f}")

Use It

Now the same thing with scikit-learn.

pythonCopyfrom sklearn.linear_model import LogisticRegression as SklearnLR
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score
from sklearn.metrics import confusion_matrix, classification_report
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
import numpy as np

np.random.seed(42)
X_0 = np.random.randn(100, 2) + [2, 2]
X_1 = np.random.randn(100, 2) + [5, 5]
X_sk = np.vstack([X_0, X_1])
y_sk = np.array([0] * 100 + [1] * 100)

X_tr, X_te, y_tr, y_te = train_test_split(X_sk, y_sk, test_size=0.2, random_state=42)

scaler = StandardScaler()
X_tr_sc = scaler.fit_transform(X_tr)
X_te_sc = scaler.transform(X_te)

lr = SklearnLR()
lr.fit(X_tr_sc, y_tr)
y_pred = lr.predict(X_te_sc)

print("=== Scikit-learn Logistic Regression ===")
print(f"Accuracy:  {accuracy_score(y_te, y_pred):.4f}")
print(f"Precision: {precision_score(y_te, y_pred):.4f}")
print(f"Recall:    {recall_score(y_te, y_pred):.4f}")
print(f"F1:        {f1_score(y_te, y_pred):.4f}")
print(f"\nConfusion Matrix:\n{confusion_matrix(y_te, y_pred)}")
print(f"\nClassification Report:\n{classification_report(y_te, y_pred)}")

Your from-scratch implementation produces the same decision boundary and metrics. Scikit-learn adds solver options (liblinear, lbfgs, saga), automatic regularization, multi-class strategies (one-vs-rest, multinomial), and numerical stability optimizations.

Ship It

This lesson produces:

• code/logistic_regression.py - logistic regression from scratch with metrics

Exercises

1. Generate a dataset that is NOT linearly separable (e.g., two concentric circles). Train logistic regression and observe its failure. Then add polynomial features (x_1^2, x_2^2, x_1 x_2) and train again. Show that the accuracy improves.
2. Implement a multi-class confusion matrix for the 3-class softmax model. Compute per-class precision and recall. Which class is hardest to classify?
3. Build an ROC curve from scratch. For 100 threshold values from 0 to 1, compute the true positive rate and false positive rate. Calculate the AUC (area under the curve) using the trapezoidal rule.

Key Terms

This free lesson is part of the AI Engineering from Scratch curriculum. Read the full explanation, run the lesson code, and verify the result in the interactive reader or from the repository source.

Browse the complete course catalog or open this lesson on GitHub.