Updated the commits for sanity checks.

linear-regression-parkinsons.py

@@ -129,7 +129,7 @@ if __name__ == "__main__":
     df.dropna(inplace=True) # remove null values
     print(f"Rows remaining after drop of the null values: {len(df)}")
 
-    # sanity checks for data validity
+    # sanity checks for data validity - realistic parkinson data range estimations
     df = df[(df['age'] >= 18) & (df['age'] <= 95)]
     df = df[(df['motor_UPDRS'] >= 0) & (df['motor_UPDRS'] <= 100)]
     df = df[(df['total_UPDRS'] >= 0) & (df['total_UPDRS'] <= 100)]

logistic-regression-wdbc.py

@@ -1,18 +1,134 @@
 import numpy as np
 import pandas as pd
 
-'''
+class LogisticRegressionGD:
-class LogisticRegression:
+    """Binary logistic regression trained with batch gradient descent."""
-    def __init__(self):
+    def __init__(self,
+                 learning_rate: float = 0.01,
+                 n_iter: int = 1000,
+                 tolerance: float = 1e-5,
+                 verbose: bool = False):
+        """
+        Parameters
+        ----------
+        learning_rate : float
+            Step size for weight updates.
+        n_iter : int
+            Maximum number of iterations.
+        tolerance : float
+            Stopping criterion: if the change in loss is < tolerance, stop.
+        verbose : bool
+            If True, prints loss at every 100 iterations.
+        """
+        self.lr = learning_rate
+        self.n_iter = n_iter
+        self.tol = tolerance
+        self.verbose = verbose
 
-    def prepare(self):
+        # placeholders that will be filled during training
+        self.w_ = None          # weights (including bias as w[0])
+        self.loss_history_ = [] # loss at each iteration
+        self.X_ = None          # feature matrix (after standardisation)
+        self.y_ = None          # target vector (0/1)
 
-    def fit(self):
+    # ------------------------------------------------------------------
+    # 2. Sigmoid helper (vectorised)
+    # ------------------------------------------------------------------
+    @staticmethod
+    def _sigmoid(z: np.ndarray) -> np.ndarray:
+        return 1.0 / (1.0 + np.exp(-z))
 
-    def predict(self):
+    # ------------------------------------------------------------------
+    # 3. Cost function (cross‑entropy)
+    # ------------------------------------------------------------------
+    @staticmethod
+    def _cost(y: np.ndarray, p: np.ndarray) -> float:
+        # avoid log(0) by clipping
+        eps = 1e-15
+        p = np.clip(p, eps, 1 - eps)
+        return -np.mean(y * np.log(p) + (1 - y) * np.log(1 - p))
+
+    # ------------------------------------------------------------------
+    # 4. Data preparation – this is where we split X / y, scale, etc.
+    # ------------------------------------------------------------------
+    def prepare(self, df: pd.DataFrame, target_col: str = 'Diagnosis') -> None:
+        """
+        Splits `df` into X and y, standardises X (mean=0, std=1),
+        and stores the result in the class attributes.
+
+        Parameters
+        ----------
+        df : pd.DataFrame
+            Cleaned data – *already* contains a numeric target in `target_col`.
+        target_col : str
+            Name of the binary target column.
+        """
+        # target must be a 0/1 array
+        self.y_ = df[target_col].values.astype(np.int64)
+
+        # X – all columns except the target
+        X_raw = df.drop(columns=[target_col]).values.astype(np.float64)
+
+        # -----------------------------------------------------------------
+        # 3.1  Feature scaling – we put the bias in the first column
+        # -----------------------------------------------------------------
+        # compute mean / std on the whole training set (no train/val split yet)
+        self.mean_ = X_raw.mean(axis=0)
+        self.std_ = X_raw.std(axis=0)
+        # avoid division by zero
+        self.std_[self.std_ == 0] = 1.0
+
+        X_scaled = (X_raw - self.mean_) / self.std_
+        # add bias column (all ones)
+        X_scaled = np.hstack([np.ones((X_scaled.shape[0], 1)), X_scaled])
+
+        self.X_ = X_scaled
+        self.w_ = np.zeros(X_scaled.shape[1])  # initialise weights
+
+    # ------------------------------------------------------------------
+    # 4. Fit – batch gradient descent
+    # ------------------------------------------------------------------
+    def fit(self) -> None:
+        """Runs batch gradient descent for `n_iter` epochs."""
+        for i in range(1, self.n_iter + 1):
+            z = np.dot(self.X_, self.w_)          # linear part
+            p = self._sigmoid(z)                   # predicted probabilities
+
+            # gradient of the log‑likelihood (including bias)
+            gradient = np.dot(self.X_.T, (p - self.y_)) / self.y_.size
+
+            # weight update
+            self.w_ -= self.lr * gradient
+
+            # record cost and check stopping criterion
+            loss = self._cost(self.y_, p)
+            self.loss_history_.append(loss)
+
+            if self.verbose and i % 100 == 0:
+                print(f"Iteration {i:4d} – loss: {loss:.6f}")
+
+            if i > 1 and abs(self.loss_history_[-2] - loss) < self.tol:
+                if self.verbose:
+                    print(f"Converged after {i} iterations.")
+                break
+
+    # ------------------------------------------------------------------
+    # 5. Predict – binary class labels
+    # ------------------------------------------------------------------
+    def predict(self, X: np.ndarray) -> np.ndarray:
+        """Return 0/1 predictions for a new X matrix (already scaled)."""
+        z = np.dot(X, self.w_)
+        probs = self._sigmoid(z)
+        return (probs >= 0.5).astype(int)
+
+    # ------------------------------------------------------------------
+    # 6. Score – accuracy on a given (X, y) pair
+    # ------------------------------------------------------------------
+    def score(self, X: np.ndarray, y: np.ndarray) -> float:
+        """Return the classification accuracy."""
+        y_pred = self.predict(X)
+        return np.mean(y_pred == y)
 
-    def score(self):
-'''
 
 if __name__ == "__main__":
     columns = [
@@ -43,7 +159,7 @@ if __name__ == "__main__":
     for col in num_cols:
         df = df[df[col] >= 0]
 
-    # sanity checks for data validity
+    # sanity checks for data validity - max tumor sizes possible
     df = df[(df['radius_mean'] > 0) & (df['radius_mean'] <= 30)]
     df = df[(df['radius_worst'] > 0) & (df['radius_worst'] <= 30)]
     df = df[(df['texture_mean'] >= 0) & (df['texture_mean'] <= 100)]
@@ -57,4 +173,32 @@ if __name__ == "__main__":
     assert df.isna().sum().sum() == 0, "There are still some null values."
 
     df['Diagnosis'] = df['Diagnosis'].map({'M': 1, 'B': 0})  # making diagnosis numeric
-    df['Diagnosis'] = df['Diagnosis'].astype('category')
+    df['Diagnosis'] = df['Diagnosis'].astype('category')
+
+    # ---- 7.2  Instantiate and train ------------------------------------
+    model = LogisticRegressionGD(learning_rate=0.05,
+                                 n_iter=5000,
+                                 tolerance=1e-6,
+                                 verbose=True)
+
+    # we need to split X / y here
+    X = df.drop(columns=['Diagnosis'])
+    y = df['Diagnosis'].cat.codes.values   # 0/1 array
+
+    # Standardise X inside the model for us – we’ll do it in `prepare`
+    model.X_ = (X - X.mean()) / X.std()          # bias‑column will be added later
+    model.X_ = np.hstack([np.ones((model.X_.shape[0], 1)), model.X_])  # add bias
+    model.y_ = y
+
+    # Fit the model
+    model.fit()
+
+    # -------------------------------------------------
+    # 8. Evaluate on the same data (you could split)
+    # -------------------------------------------------
+    acc = model.score(model.X_, model.y_)
+    print(f"Training accuracy (on the whole cleaned set): {acc:.4f}")
+
+    # Example: predict on the first 10 samples
+    y_hat = model.predict(model.X_[:10])
+    print("First 10 predictions:", y_hat)

mini-batch-sgd-linear-regression-parkinsons.py

@@ -135,7 +135,7 @@ if __name__ == "__main__":
     df.dropna(inplace=True) # remove null values
     print(f"Rows remaining after drop of the null values: {len(df)}")
 
-    # sanity checks for data validity
+    # sanity checks for data validity - realistic parkinson data range estimations
     df = df[(df['age'] >= 18) & (df['age'] <= 95)]
     df = df[(df['motor_UPDRS'] >= 0) & (df['motor_UPDRS'] <= 100)]
     df = df[(df['total_UPDRS'] >= 0) & (df['total_UPDRS'] <= 100)]

mini-batch-sgd-logistic-regression-wdbc.py

@@ -43,7 +43,7 @@ if __name__ == "__main__":
     for col in num_cols:
         df = df[df[col] >= 0]
 
-    # sanity checks for data validity
+    # sanity checks for data validity - max tumor sizes possible
     df = df[(df['radius_mean'] > 0) & (df['radius_mean'] <= 30)]
     df = df[(df['radius_worst'] > 0) & (df['radius_worst'] <= 30)]
     df = df[(df['texture_mean'] >= 0) & (df['texture_mean'] <= 100)]