Chapter 4 – Training Linear Models

This notebook contains all the sample code and solutions to the exercises in chapter 4.

Setup

First, let's make sure this notebook works well in both python 2 and 3, import a few common modules, ensure MatplotLib plots figures inline and prepare a function to save the figures:

# To support both python 2 and python 3
from __future__ import division, print_function, unicode_literals

# Common imports
import numpy as np
import os

# to make this notebook's output stable across runs
np.random.seed(42)

# To plot pretty figures
%matplotlib inline
import matplotlib
import matplotlib.pyplot as plt
plt.rcParams['axes.labelsize'] = 14
plt.rcParams['xtick.labelsize'] = 12
plt.rcParams['ytick.labelsize'] = 12

# Where to save the figures
PROJECT_ROOT_DIR = "."
CHAPTER_ID = "training_linear_models"

def save_fig(fig_id, tight_layout=True):
    path = os.path.join(PROJECT_ROOT_DIR, "images", CHAPTER_ID, fig_id + ".png")
    print("Saving figure", fig_id)
    if tight_layout:
        plt.tight_layout()
    plt.savefig(path, format='png', dpi=300)

# Ignore useless warnings (see SciPy issue #5998)
import warnings
warnings.filterwarnings(action="ignore", module="scipy", message="^internal gelsd")

Linear regression using the Normal Equation

import numpy as np

X = 2 * np.random.rand(100, 1)
y = 4 + 3 * X + np.random.randn(100, 1)

plt.plot(X, y, "b.")
plt.xlabel("$x_1$", fontsize=18)
plt.ylabel("$y$", rotation=0, fontsize=18)
plt.axis([0, 2, 0, 15])
save_fig("generated_data_plot")
plt.show()

Saving figure generated_data_plot

X_b = np.c_[np.ones((100, 1)), X]  # add x0 = 1 to each instance
theta_best = np.linalg.inv(X_b.T.dot(X_b)).dot(X_b.T).dot(y)

theta_best

array([[4.21509616],
       [2.77011339]])

X_new = np.array([[0], [2]])
X_new_b = np.c_[np.ones((2, 1)), X_new]  # add x0 = 1 to each instance
y_predict = X_new_b.dot(theta_best)
y_predict

array([[4.21509616],
       [9.75532293]])

plt.plot(X_new, y_predict, "r-")
plt.plot(X, y, "b.")
plt.axis([0, 2, 0, 15])
plt.show()

The figure in the book actually corresponds to the following code, with a legend and axis labels:

plt.plot(X_new, y_predict, "r-", linewidth=2, label="Predictions")
plt.plot(X, y, "b.")
plt.xlabel("$x_1$", fontsize=18)
plt.ylabel("$y$", rotation=0, fontsize=18)
plt.legend(loc="upper left", fontsize=14)
plt.axis([0, 2, 0, 15])
save_fig("linear_model_predictions")
plt.show()

Saving figure linear_model_predictions

from sklearn.linear_model import LinearRegression
lin_reg = LinearRegression()
lin_reg.fit(X, y)
lin_reg.intercept_, lin_reg.coef_

(array([4.21509616]), array([[2.77011339]]))

lin_reg.predict(X_new)

array([[4.21509616],
       [9.75532293]])

The LinearRegression class is based on the scipy.linalg.lstsq() function (the name stands for "least squares"), which you could call directly:

theta_best_svd, residuals, rank, s = np.linalg.lstsq(X_b, y, rcond=1e-6)
theta_best_svd

array([[4.21509616],
       [2.77011339]])

This function computes $\mathbf{X}^+\mathbf{y}$, where $\mathbf{X}^{+}$ is the pseudoinverse of $\mathbf{X}$ (specifically the Moore-Penrose inverse). You can use np.linalg.pinv() to compute the pseudoinverse directly:

np.linalg.pinv(X_b).dot(y)

array([[4.21509616],
       [2.77011339]])

Note: the first releases of the book implied that the LinearRegression class was based on the Normal Equation. This was an error, my apologies: as explained above, it is based on the pseudoinverse, which ultimately relies on the SVD matrix decomposition of $\mathbf{X}$ (see chapter 8 for details about the SVD decomposition). Its time complexity is $O(n^2)$ and it works even when $m < n$ or when some features are linear combinations of other features (in these cases, $\mathbf{X}^T \mathbf{X}$ is not invertible so the Normal Equation fails), see issue #184 for more details. However, this does not change the rest of the description of the LinearRegression class, in particular, it is based on an analytical solution, it does not scale well with the number of features, it scales linearly with the number of instances, all the data must fit in memory, it does not require feature scaling and the order of the instances in the training set does not matter.

Linear regression using batch gradient descent

eta = 0.1
n_iterations = 1000
m = 100
theta = np.random.randn(2,1)

for iteration in range(n_iterations):
    gradients = 2/m * X_b.T.dot(X_b.dot(theta) - y)
    theta = theta - eta * gradients

theta

array([[4.21509616],
       [2.77011339]])

X_new_b.dot(theta)

array([[4.21509616],
       [9.75532293]])

theta_path_bgd = []

def plot_gradient_descent(theta, eta, theta_path=None):
    m = len(X_b)
    plt.plot(X, y, "b.")
    n_iterations = 1000
    for iteration in range(n_iterations):
        if iteration < 10:
            y_predict = X_new_b.dot(theta)
            style = "b-" if iteration > 0 else "r--"
            plt.plot(X_new, y_predict, style)
        gradients = 2/m * X_b.T.dot(X_b.dot(theta) - y)
        theta = theta - eta * gradients
        if theta_path is not None:
            theta_path.append(theta)
    plt.xlabel("$x_1$", fontsize=18)
    plt.axis([0, 2, 0, 15])
    plt.title(r"$\eta = {}$".format(eta), fontsize=16)

np.random.seed(42)
theta = np.random.randn(2,1)  # random initialization

plt.figure(figsize=(10,4))
plt.subplot(131); plot_gradient_descent(theta, eta=0.02)
plt.ylabel("$y$", rotation=0, fontsize=18)
plt.subplot(132); plot_gradient_descent(theta, eta=0.1, theta_path=theta_path_bgd)
plt.subplot(133); plot_gradient_descent(theta, eta=0.5)

save_fig("gradient_descent_plot")
plt.show()

Saving figure gradient_descent_plot

Stochastic Gradient Descent

theta_path_sgd = []
m = len(X_b)
np.random.seed(42)

n_epochs = 50
t0, t1 = 5, 50  # learning schedule hyperparameters

def learning_schedule(t):
    return t0 / (t + t1)

theta = np.random.randn(2,1)  # random initialization

for epoch in range(n_epochs):
    for i in range(m):
        if epoch == 0 and i < 20:                    # not shown in the book
            y_predict = X_new_b.dot(theta)           # not shown
            style = "b-" if i > 0 else "r--"         # not shown
            plt.plot(X_new, y_predict, style)        # not shown
        random_index = np.random.randint(m)
        xi = X_b[random_index:random_index+1]
        yi = y[random_index:random_index+1]
        gradients = 2 * xi.T.dot(xi.dot(theta) - yi)
        eta = learning_schedule(epoch * m + i)
        theta = theta - eta * gradients
        theta_path_sgd.append(theta)                 # not shown

plt.plot(X, y, "b.")                                 # not shown
plt.xlabel("$x_1$", fontsize=18)                     # not shown
plt.ylabel("$y$", rotation=0, fontsize=18)           # not shown
plt.axis([0, 2, 0, 15])                              # not shown
save_fig("sgd_plot")                                 # not shown
plt.show()                                           # not shown

Saving figure sgd_plot

theta

array([[4.21076011],
       [2.74856079]])

from sklearn.linear_model import SGDRegressor
sgd_reg = SGDRegressor(max_iter=50, penalty=None, eta0=0.1, random_state=42)
sgd_reg.fit(X, y.ravel())

SGDRegressor(alpha=0.0001, average=False, epsilon=0.1, eta0=0.1,
       fit_intercept=True, l1_ratio=0.15, learning_rate='invscaling',
       loss='squared_loss', max_iter=50, n_iter=None, penalty=None,
       power_t=0.25, random_state=42, shuffle=True, tol=None, verbose=0,
       warm_start=False)

sgd_reg.intercept_, sgd_reg.coef_

(array([4.16782089]), array([2.72603052]))

Mini-batch gradient descent

theta_path_mgd = []

n_iterations = 50
minibatch_size = 20

np.random.seed(42)
theta = np.random.randn(2,1)  # random initialization

t0, t1 = 200, 1000
def learning_schedule(t):
    return t0 / (t + t1)

t = 0
for epoch in range(n_iterations):
    shuffled_indices = np.random.permutation(m)
    X_b_shuffled = X_b[shuffled_indices]
    y_shuffled = y[shuffled_indices]
    for i in range(0, m, minibatch_size):
        t += 1
        xi = X_b_shuffled[i:i+minibatch_size]
        yi = y_shuffled[i:i+minibatch_size]
        gradients = 2/minibatch_size * xi.T.dot(xi.dot(theta) - yi)
        eta = learning_schedule(t)
        theta = theta - eta * gradients
        theta_path_mgd.append(theta)

theta

array([[4.25214635],
       [2.7896408 ]])

theta_path_bgd = np.array(theta_path_bgd)
theta_path_sgd = np.array(theta_path_sgd)
theta_path_mgd = np.array(theta_path_mgd)

plt.figure(figsize=(7,4))
plt.plot(theta_path_sgd[:, 0], theta_path_sgd[:, 1], "r-s", linewidth=1, label="Stochastic")
plt.plot(theta_path_mgd[:, 0], theta_path_mgd[:, 1], "g-+", linewidth=2, label="Mini-batch")
plt.plot(theta_path_bgd[:, 0], theta_path_bgd[:, 1], "b-o", linewidth=3, label="Batch")
plt.legend(loc="upper left", fontsize=16)
plt.xlabel(r"$\theta_0$", fontsize=20)
plt.ylabel(r"$\theta_1$   ", fontsize=20, rotation=0)
plt.axis([2.5, 4.5, 2.3, 3.9])
save_fig("gradient_descent_paths_plot")
plt.show()

Saving figure gradient_descent_paths_plot

Polynomial regression

import numpy as np
import numpy.random as rnd

np.random.seed(42)

m = 100
X = 6 * np.random.rand(m, 1) - 3
y = 0.5 * X**2 + X + 2 + np.random.randn(m, 1)

plt.plot(X, y, "b.")
plt.xlabel("$x_1$", fontsize=18)
plt.ylabel("$y$", rotation=0, fontsize=18)
plt.axis([-3, 3, 0, 10])
save_fig("quadratic_data_plot")
plt.show()

Saving figure quadratic_data_plot

from sklearn.preprocessing import PolynomialFeatures
poly_features = PolynomialFeatures(degree=2, include_bias=False)
X_poly = poly_features.fit_transform(X)
X[0]

array([-0.75275929])

X_poly[0]

array([-0.75275929,  0.56664654])

lin_reg = LinearRegression()
lin_reg.fit(X_poly, y)
lin_reg.intercept_, lin_reg.coef_

(array([1.78134581]), array([[0.93366893, 0.56456263]]))

X_new=np.linspace(-3, 3, 100).reshape(100, 1)
X_new_poly = poly_features.transform(X_new)
y_new = lin_reg.predict(X_new_poly)
plt.plot(X, y, "b.")
plt.plot(X_new, y_new, "r-", linewidth=2, label="Predictions")
plt.xlabel("$x_1$", fontsize=18)
plt.ylabel("$y$", rotation=0, fontsize=18)
plt.legend(loc="upper left", fontsize=14)
plt.axis([-3, 3, 0, 10])
save_fig("quadratic_predictions_plot")
plt.show()

Saving figure quadratic_predictions_plot

from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import Pipeline

for style, width, degree in (("g-", 1, 300), ("b--", 2, 2), ("r-+", 2, 1)):
    polybig_features = PolynomialFeatures(degree=degree, include_bias=False)
    std_scaler = StandardScaler()
    lin_reg = LinearRegression()
    polynomial_regression = Pipeline([
            ("poly_features", polybig_features),
            ("std_scaler", std_scaler),
            ("lin_reg", lin_reg),
        ])
    polynomial_regression.fit(X, y)
    y_newbig = polynomial_regression.predict(X_new)
    plt.plot(X_new, y_newbig, style, label=str(degree), linewidth=width)

plt.plot(X, y, "b.", linewidth=3)
plt.legend(loc="upper left")
plt.xlabel("$x_1$", fontsize=18)
plt.ylabel("$y$", rotation=0, fontsize=18)
plt.axis([-3, 3, 0, 10])
save_fig("high_degree_polynomials_plot")
plt.show()

Saving figure high_degree_polynomials_plot

from sklearn.metrics import mean_squared_error
from sklearn.model_selection import train_test_split

def plot_learning_curves(model, X, y):
    X_train, X_val, y_train, y_val = train_test_split(X, y, test_size=0.2, random_state=10)
    train_errors, val_errors = [], []
    for m in range(1, len(X_train)):
        model.fit(X_train[:m], y_train[:m])
        y_train_predict = model.predict(X_train[:m])
        y_val_predict = model.predict(X_val)
        train_errors.append(mean_squared_error(y_train[:m], y_train_predict))
        val_errors.append(mean_squared_error(y_val, y_val_predict))

    plt.plot(np.sqrt(train_errors), "r-+", linewidth=2, label="train")
    plt.plot(np.sqrt(val_errors), "b-", linewidth=3, label="val")
    plt.legend(loc="upper right", fontsize=14)   # not shown in the book
    plt.xlabel("Training set size", fontsize=14) # not shown
    plt.ylabel("RMSE", fontsize=14)              # not shown

lin_reg = LinearRegression()
plot_learning_curves(lin_reg, X, y)
plt.axis([0, 80, 0, 3])                         # not shown in the book
save_fig("underfitting_learning_curves_plot")   # not shown
plt.show()                                      # not shown

Saving figure underfitting_learning_curves_plot

from sklearn.pipeline import Pipeline

polynomial_regression = Pipeline([
        ("poly_features", PolynomialFeatures(degree=10, include_bias=False)),
        ("lin_reg", LinearRegression()),
    ])

plot_learning_curves(polynomial_regression, X, y)
plt.axis([0, 80, 0, 3])           # not shown
save_fig("learning_curves_plot")  # not shown
plt.show()                        # not shown

Saving figure learning_curves_plot

Regularized models

from sklearn.linear_model import Ridge

np.random.seed(42)
m = 20
X = 3 * np.random.rand(m, 1)
y = 1 + 0.5 * X + np.random.randn(m, 1) / 1.5
X_new = np.linspace(0, 3, 100).reshape(100, 1)

def plot_model(model_class, polynomial, alphas, **model_kargs):
    for alpha, style in zip(alphas, ("b-", "g--", "r:")):
        model = model_class(alpha, **model_kargs) if alpha > 0 else LinearRegression()
        if polynomial:
            model = Pipeline([
                    ("poly_features", PolynomialFeatures(degree=10, include_bias=False)),
                    ("std_scaler", StandardScaler()),
                    ("regul_reg", model),
                ])
        model.fit(X, y)
        y_new_regul = model.predict(X_new)
        lw = 2 if alpha > 0 else 1
        plt.plot(X_new, y_new_regul, style, linewidth=lw, label=r"$\alpha = {}$".format(alpha))
    plt.plot(X, y, "b.", linewidth=3)
    plt.legend(loc="upper left", fontsize=15)
    plt.xlabel("$x_1$", fontsize=18)
    plt.axis([0, 3, 0, 4])

plt.figure(figsize=(8,4))
plt.subplot(121)
plot_model(Ridge, polynomial=False, alphas=(0, 10, 100), random_state=42)
plt.ylabel("$y$", rotation=0, fontsize=18)
plt.subplot(122)
plot_model(Ridge, polynomial=True, alphas=(0, 10**-5, 1), random_state=42)

save_fig("ridge_regression_plot")
plt.show()

Saving figure ridge_regression_plot

from sklearn.linear_model import Ridge
ridge_reg = Ridge(alpha=1, solver="cholesky", random_state=42)
ridge_reg.fit(X, y)
ridge_reg.predict([[1.5]])

array([[1.55071465]])

sgd_reg = SGDRegressor(max_iter=5, penalty="l2", random_state=42)
sgd_reg.fit(X, y.ravel())
sgd_reg.predict([[1.5]])

array([1.13500145])

ridge_reg = Ridge(alpha=1, solver="sag", random_state=42)
ridge_reg.fit(X, y)
ridge_reg.predict([[1.5]])

array([[1.5507201]])

from sklearn.linear_model import Lasso

plt.figure(figsize=(8,4))
plt.subplot(121)
plot_model(Lasso, polynomial=False, alphas=(0, 0.1, 1), random_state=42)
plt.ylabel("$y$", rotation=0, fontsize=18)
plt.subplot(122)
plot_model(Lasso, polynomial=True, alphas=(0, 10**-7, 1), tol=1, random_state=42)

save_fig("lasso_regression_plot")
plt.show()

Saving figure lasso_regression_plot

from sklearn.linear_model import Lasso
lasso_reg = Lasso(alpha=0.1)
lasso_reg.fit(X, y)
lasso_reg.predict([[1.5]])

array([1.53788174])

from sklearn.linear_model import ElasticNet
elastic_net = ElasticNet(alpha=0.1, l1_ratio=0.5, random_state=42)
elastic_net.fit(X, y)
elastic_net.predict([[1.5]])

array([1.54333232])

np.random.seed(42)
m = 100
X = 6 * np.random.rand(m, 1) - 3
y = 2 + X + 0.5 * X**2 + np.random.randn(m, 1)

X_train, X_val, y_train, y_val = train_test_split(X[:50], y[:50].ravel(), test_size=0.5, random_state=10)

poly_scaler = Pipeline([
        ("poly_features", PolynomialFeatures(degree=90, include_bias=False)),
        ("std_scaler", StandardScaler()),
    ])

X_train_poly_scaled = poly_scaler.fit_transform(X_train)
X_val_poly_scaled = poly_scaler.transform(X_val)

sgd_reg = SGDRegressor(max_iter=1,
                       penalty=None,
                       eta0=0.0005,
                       warm_start=True,
                       learning_rate="constant",
                       random_state=42)

n_epochs = 500
train_errors, val_errors = [], []
for epoch in range(n_epochs):
    sgd_reg.fit(X_train_poly_scaled, y_train)
    y_train_predict = sgd_reg.predict(X_train_poly_scaled)
    y_val_predict = sgd_reg.predict(X_val_poly_scaled)
    train_errors.append(mean_squared_error(y_train, y_train_predict))
    val_errors.append(mean_squared_error(y_val, y_val_predict))

best_epoch = np.argmin(val_errors)
best_val_rmse = np.sqrt(val_errors[best_epoch])

plt.annotate('Best model',
             xy=(best_epoch, best_val_rmse),
             xytext=(best_epoch, best_val_rmse + 1),
             ha="center",
             arrowprops=dict(facecolor='black', shrink=0.05),
             fontsize=16,
            )

best_val_rmse -= 0.03  # just to make the graph look better
plt.plot([0, n_epochs], [best_val_rmse, best_val_rmse], "k:", linewidth=2)
plt.plot(np.sqrt(val_errors), "b-", linewidth=3, label="Validation set")
plt.plot(np.sqrt(train_errors), "r--", linewidth=2, label="Training set")
plt.legend(loc="upper right", fontsize=14)
plt.xlabel("Epoch", fontsize=14)
plt.ylabel("RMSE", fontsize=14)
save_fig("early_stopping_plot")
plt.show()

Saving figure early_stopping_plot

from sklearn.base import clone
sgd_reg = SGDRegressor(max_iter=1, warm_start=True, penalty=None,
                       learning_rate="constant", eta0=0.0005, random_state=42)

minimum_val_error = float("inf")
best_epoch = None
best_model = None
for epoch in range(1000):
    sgd_reg.fit(X_train_poly_scaled, y_train)  # continues where it left off
    y_val_predict = sgd_reg.predict(X_val_poly_scaled)
    val_error = mean_squared_error(y_val, y_val_predict)
    if val_error < minimum_val_error:
        minimum_val_error = val_error
        best_epoch = epoch
        best_model = clone(sgd_reg)

best_epoch, best_model

(239, SGDRegressor(alpha=0.0001, average=False, epsilon=0.1, eta0=0.0005,
        fit_intercept=True, l1_ratio=0.15, learning_rate='constant',
        loss='squared_loss', max_iter=1, n_iter=None, penalty=None,
        power_t=0.25, random_state=42, shuffle=True, tol=None, verbose=0,
        warm_start=True))

%matplotlib inline
import matplotlib.pyplot as plt
import numpy as np

t1a, t1b, t2a, t2b = -1, 3, -1.5, 1.5

# ignoring bias term
t1s = np.linspace(t1a, t1b, 500)
t2s = np.linspace(t2a, t2b, 500)
t1, t2 = np.meshgrid(t1s, t2s)
T = np.c_[t1.ravel(), t2.ravel()]
Xr = np.array([[-1, 1], [-0.3, -1], [1, 0.1]])
yr = 2 * Xr[:, :1] + 0.5 * Xr[:, 1:]

J = (1/len(Xr) * np.sum((T.dot(Xr.T) - yr.T)**2, axis=1)).reshape(t1.shape)

N1 = np.linalg.norm(T, ord=1, axis=1).reshape(t1.shape)
N2 = np.linalg.norm(T, ord=2, axis=1).reshape(t1.shape)

t_min_idx = np.unravel_index(np.argmin(J), J.shape)
t1_min, t2_min = t1[t_min_idx], t2[t_min_idx]

t_init = np.array([[0.25], [-1]])

def bgd_path(theta, X, y, l1, l2, core = 1, eta = 0.1, n_iterations = 50):
    path = [theta]
    for iteration in range(n_iterations):
        gradients = core * 2/len(X) * X.T.dot(X.dot(theta) - y) + l1 * np.sign(theta) + 2 * l2 * theta

        theta = theta - eta * gradients
        path.append(theta)
    return np.array(path)

plt.figure(figsize=(12, 8))
for i, N, l1, l2, title in ((0, N1, 0.5, 0, "Lasso"), (1, N2, 0,  0.1, "Ridge")):
    JR = J + l1 * N1 + l2 * N2**2
    
    tr_min_idx = np.unravel_index(np.argmin(JR), JR.shape)
    t1r_min, t2r_min = t1[tr_min_idx], t2[tr_min_idx]

    levelsJ=(np.exp(np.linspace(0, 1, 20)) - 1) * (np.max(J) - np.min(J)) + np.min(J)
    levelsJR=(np.exp(np.linspace(0, 1, 20)) - 1) * (np.max(JR) - np.min(JR)) + np.min(JR)
    levelsN=np.linspace(0, np.max(N), 10)
    
    path_J = bgd_path(t_init, Xr, yr, l1=0, l2=0)
    path_JR = bgd_path(t_init, Xr, yr, l1, l2)
    path_N = bgd_path(t_init, Xr, yr, np.sign(l1)/3, np.sign(l2), core=0)

    plt.subplot(221 + i * 2)
    plt.grid(True)
    plt.axhline(y=0, color='k')
    plt.axvline(x=0, color='k')
    plt.contourf(t1, t2, J, levels=levelsJ, alpha=0.9)
    plt.contour(t1, t2, N, levels=levelsN)
    plt.plot(path_J[:, 0], path_J[:, 1], "w-o")
    plt.plot(path_N[:, 0], path_N[:, 1], "y-^")
    plt.plot(t1_min, t2_min, "rs")
    plt.title(r"$\ell_{}$ penalty".format(i + 1), fontsize=16)
    plt.axis([t1a, t1b, t2a, t2b])
    if i == 1:
        plt.xlabel(r"$\theta_1$", fontsize=20)
    plt.ylabel(r"$\theta_2$", fontsize=20, rotation=0)

    plt.subplot(222 + i * 2)
    plt.grid(True)
    plt.axhline(y=0, color='k')
    plt.axvline(x=0, color='k')
    plt.contourf(t1, t2, JR, levels=levelsJR, alpha=0.9)
    plt.plot(path_JR[:, 0], path_JR[:, 1], "w-o")
    plt.plot(t1r_min, t2r_min, "rs")
    plt.title(title, fontsize=16)
    plt.axis([t1a, t1b, t2a, t2b])
    if i == 1:
        plt.xlabel(r"$\theta_1$", fontsize=20)

save_fig("lasso_vs_ridge_plot")
plt.show()

Saving figure lasso_vs_ridge_plot

Logistic regression

t = np.linspace(-10, 10, 100)
sig = 1 / (1 + np.exp(-t))
plt.figure(figsize=(9, 3))
plt.plot([-10, 10], [0, 0], "k-")
plt.plot([-10, 10], [0.5, 0.5], "k:")
plt.plot([-10, 10], [1, 1], "k:")
plt.plot([0, 0], [-1.1, 1.1], "k-")
plt.plot(t, sig, "b-", linewidth=2, label=r"$\sigma(t) = \frac{1}{1 + e^{-t}}$")
plt.xlabel("t")
plt.legend(loc="upper left", fontsize=20)
plt.axis([-10, 10, -0.1, 1.1])
save_fig("logistic_function_plot")
plt.show()

Saving figure logistic_function_plot

from sklearn import datasets
iris = datasets.load_iris()
list(iris.keys())

['data', 'target', 'target_names', 'DESCR', 'feature_names']

print(iris.DESCR)

Iris Plants Database
====================

Notes
-----
Data Set Characteristics:
    :Number of Instances: 150 (50 in each of three classes)
    :Number of Attributes: 4 numeric, predictive attributes and the class
    :Attribute Information:
        - sepal length in cm
        - sepal width in cm
        - petal length in cm
        - petal width in cm
        - class:
                - Iris-Setosa
                - Iris-Versicolour
                - Iris-Virginica
    :Summary Statistics:

    ============== ==== ==== ======= ===== ====================
                    Min  Max   Mean    SD   Class Correlation
    ============== ==== ==== ======= ===== ====================
    sepal length:   4.3  7.9   5.84   0.83    0.7826
    sepal width:    2.0  4.4   3.05   0.43   -0.4194
    petal length:   1.0  6.9   3.76   1.76    0.9490  (high!)
    petal width:    0.1  2.5   1.20  0.76     0.9565  (high!)
    ============== ==== ==== ======= ===== ====================

    :Missing Attribute Values: None
    :Class Distribution: 33.3% for each of 3 classes.
    :Creator: R.A. Fisher
    :Donor: Michael Marshall (MARSHALL%PLU@io.arc.nasa.gov)
    :Date: July, 1988

This is a copy of UCI ML iris datasets.
http://archive.ics.uci.edu/ml/datasets/Iris

The famous Iris database, first used by Sir R.A Fisher

This is perhaps the best known database to be found in the
pattern recognition literature.  Fisher's paper is a classic in the field and
is referenced frequently to this day.  (See Duda & Hart, for example.)  The
data set contains 3 classes of 50 instances each, where each class refers to a
type of iris plant.  One class is linearly separable from the other 2; the
latter are NOT linearly separable from each other.

References
----------
   - Fisher,R.A. "The use of multiple measurements in taxonomic problems"
     Annual Eugenics, 7, Part II, 179-188 (1936); also in "Contributions to
     Mathematical Statistics" (John Wiley, NY, 1950).
   - Duda,R.O., & Hart,P.E. (1973) Pattern Classification and Scene Analysis.
     (Q327.D83) John Wiley & Sons.  ISBN 0-471-22361-1.  See page 218.
   - Dasarathy, B.V. (1980) "Nosing Around the Neighborhood: A New System
     Structure and Classification Rule for Recognition in Partially Exposed
     Environments".  IEEE Transactions on Pattern Analysis and Machine
     Intelligence, Vol. PAMI-2, No. 1, 67-71.
   - Gates, G.W. (1972) "The Reduced Nearest Neighbor Rule".  IEEE Transactions
     on Information Theory, May 1972, 431-433.
   - See also: 1988 MLC Proceedings, 54-64.  Cheeseman et al"s AUTOCLASS II
     conceptual clustering system finds 3 classes in the data.
   - Many, many more ...

X = iris["data"][:, 3:]  # petal width
y = (iris["target"] == 2).astype(np.int)  # 1 if Iris-Virginica, else 0

from sklearn.linear_model import LogisticRegression
log_reg = LogisticRegression(random_state=42)
log_reg.fit(X, y)

LogisticRegression(C=1.0, class_weight=None, dual=False, fit_intercept=True,
          intercept_scaling=1, max_iter=100, multi_class='ovr', n_jobs=1,
          penalty='l2', random_state=42, solver='liblinear', tol=0.0001,
          verbose=0, warm_start=False)

X_new = np.linspace(0, 3, 1000).reshape(-1, 1)
y_proba = log_reg.predict_proba(X_new)

plt.plot(X_new, y_proba[:, 1], "g-", linewidth=2, label="Iris-Virginica")
plt.plot(X_new, y_proba[:, 0], "b--", linewidth=2, label="Not Iris-Virginica")

[<matplotlib.lines.Line2D at 0x10fc0a5c0>]

The figure in the book actually is actually a bit fancier:

X_new = np.linspace(0, 3, 1000).reshape(-1, 1)
y_proba = log_reg.predict_proba(X_new)
decision_boundary = X_new[y_proba[:, 1] >= 0.5][0]

plt.figure(figsize=(8, 3))
plt.plot(X[y==0], y[y==0], "bs")
plt.plot(X[y==1], y[y==1], "g^")
plt.plot([decision_boundary, decision_boundary], [-1, 2], "k:", linewidth=2)
plt.plot(X_new, y_proba[:, 1], "g-", linewidth=2, label="Iris-Virginica")
plt.plot(X_new, y_proba[:, 0], "b--", linewidth=2, label="Not Iris-Virginica")
plt.text(decision_boundary+0.02, 0.15, "Decision  boundary", fontsize=14, color="k", ha="center")
plt.arrow(decision_boundary, 0.08, -0.3, 0, head_width=0.05, head_length=0.1, fc='b', ec='b')
plt.arrow(decision_boundary, 0.92, 0.3, 0, head_width=0.05, head_length=0.1, fc='g', ec='g')
plt.xlabel("Petal width (cm)", fontsize=14)
plt.ylabel("Probability", fontsize=14)
plt.legend(loc="center left", fontsize=14)
plt.axis([0, 3, -0.02, 1.02])
save_fig("logistic_regression_plot")
plt.show()

Saving figure logistic_regression_plot

decision_boundary

array([1.61561562])

log_reg.predict([[1.7], [1.5]])

array([1, 0])

from sklearn.linear_model import LogisticRegression

X = iris["data"][:, (2, 3)]  # petal length, petal width
y = (iris["target"] == 2).astype(np.int)

log_reg = LogisticRegression(C=10**10, random_state=42)
log_reg.fit(X, y)

x0, x1 = np.meshgrid(
        np.linspace(2.9, 7, 500).reshape(-1, 1),
        np.linspace(0.8, 2.7, 200).reshape(-1, 1),
    )
X_new = np.c_[x0.ravel(), x1.ravel()]

y_proba = log_reg.predict_proba(X_new)

plt.figure(figsize=(10, 4))
plt.plot(X[y==0, 0], X[y==0, 1], "bs")
plt.plot(X[y==1, 0], X[y==1, 1], "g^")

zz = y_proba[:, 1].reshape(x0.shape)
contour = plt.contour(x0, x1, zz, cmap=plt.cm.brg)


left_right = np.array([2.9, 7])
boundary = -(log_reg.coef_[0][0] * left_right + log_reg.intercept_[0]) / log_reg.coef_[0][1]

plt.clabel(contour, inline=1, fontsize=12)
plt.plot(left_right, boundary, "k--", linewidth=3)
plt.text(3.5, 1.5, "Not Iris-Virginica", fontsize=14, color="b", ha="center")
plt.text(6.5, 2.3, "Iris-Virginica", fontsize=14, color="g", ha="center")
plt.xlabel("Petal length", fontsize=14)
plt.ylabel("Petal width", fontsize=14)
plt.axis([2.9, 7, 0.8, 2.7])
save_fig("logistic_regression_contour_plot")
plt.show()

Saving figure logistic_regression_contour_plot

X = iris["data"][:, (2, 3)]  # petal length, petal width
y = iris["target"]

softmax_reg = LogisticRegression(multi_class="multinomial",solver="lbfgs", C=10, random_state=42)
softmax_reg.fit(X, y)

LogisticRegression(C=10, class_weight=None, dual=False, fit_intercept=True,
          intercept_scaling=1, max_iter=100, multi_class='multinomial',
          n_jobs=1, penalty='l2', random_state=42, solver='lbfgs',
          tol=0.0001, verbose=0, warm_start=False)

x0, x1 = np.meshgrid(
        np.linspace(0, 8, 500).reshape(-1, 1),
        np.linspace(0, 3.5, 200).reshape(-1, 1),
    )
X_new = np.c_[x0.ravel(), x1.ravel()]


y_proba = softmax_reg.predict_proba(X_new)
y_predict = softmax_reg.predict(X_new)

zz1 = y_proba[:, 1].reshape(x0.shape)
zz = y_predict.reshape(x0.shape)

plt.figure(figsize=(10, 4))
plt.plot(X[y==2, 0], X[y==2, 1], "g^", label="Iris-Virginica")
plt.plot(X[y==1, 0], X[y==1, 1], "bs", label="Iris-Versicolor")
plt.plot(X[y==0, 0], X[y==0, 1], "yo", label="Iris-Setosa")

from matplotlib.colors import ListedColormap
custom_cmap = ListedColormap(['#fafab0','#9898ff','#a0faa0'])

plt.contourf(x0, x1, zz, cmap=custom_cmap)
contour = plt.contour(x0, x1, zz1, cmap=plt.cm.brg)
plt.clabel(contour, inline=1, fontsize=12)
plt.xlabel("Petal length", fontsize=14)
plt.ylabel("Petal width", fontsize=14)
plt.legend(loc="center left", fontsize=14)
plt.axis([0, 7, 0, 3.5])
save_fig("softmax_regression_contour_plot")
plt.show()

Saving figure softmax_regression_contour_plot

softmax_reg.predict([[5, 2]])

array([2])

softmax_reg.predict_proba([[5, 2]])

array([[6.33134077e-07, 5.75276067e-02, 9.42471760e-01]])

Exercise solutions

1. to 11.

See appendix A.

12. Batch Gradient Descent with early stopping for Softmax Regression

(without using Scikit-Learn)

Let's start by loading the data. We will just reuse the Iris dataset we loaded earlier.

X = iris["data"][:, (2, 3)]  # petal length, petal width
y = iris["target"]

We need to add the bias term for every instance ($x_0 = 1$):

X_with_bias = np.c_[np.ones([len(X), 1]), X]

And let's set the random seed so the output of this exercise solution is reproducible:

np.random.seed(2042)

The easiest option to split the dataset into a training set, a validation set and a test set would be to use Scikit-Learn's train_test_split() function, but the point of this exercise is to try understand the algorithms by implementing them manually. So here is one possible implementation:

test_ratio = 0.2
validation_ratio = 0.2
total_size = len(X_with_bias)

test_size = int(total_size * test_ratio)
validation_size = int(total_size * validation_ratio)
train_size = total_size - test_size - validation_size

rnd_indices = np.random.permutation(total_size)

X_train = X_with_bias[rnd_indices[:train_size]]
y_train = y[rnd_indices[:train_size]]
X_valid = X_with_bias[rnd_indices[train_size:-test_size]]
y_valid = y[rnd_indices[train_size:-test_size]]
X_test = X_with_bias[rnd_indices[-test_size:]]
y_test = y[rnd_indices[-test_size:]]

The targets are currently class indices (0, 1 or 2), but we need target class probabilities to train the Softmax Regression model. Each instance will have target class probabilities equal to 0.0 for all classes except for the target class which will have a probability of 1.0 (in other words, the vector of class probabilities for ay given instance is a one-hot vector). Let's write a small function to convert the vector of class indices into a matrix containing a one-hot vector for each instance:

def to_one_hot(y):
    n_classes = y.max() + 1
    m = len(y)
    Y_one_hot = np.zeros((m, n_classes))
    Y_one_hot[np.arange(m), y] = 1
    return Y_one_hot

Let's test this function on the first 10 instances:

y_train[:10]

array([0, 1, 2, 1, 1, 0, 1, 1, 1, 0])

to_one_hot(y_train[:10])

array([[1., 0., 0.],
       [0., 1., 0.],
       [0., 0., 1.],
       [0., 1., 0.],
       [0., 1., 0.],
       [1., 0., 0.],
       [0., 1., 0.],
       [0., 1., 0.],
       [0., 1., 0.],
       [1., 0., 0.]])

Looks good, so let's create the target class probabilities matrix for the training set and the test set:

Y_train_one_hot = to_one_hot(y_train)
Y_valid_one_hot = to_one_hot(y_valid)
Y_test_one_hot = to_one_hot(y_test)

Now let's implement the Softmax function. Recall that it is defined by the following equation:

$\sigma\left(\mathbf{s}(\mathbf{x})\right)_k = \dfrac{\exp\left(s_k(\mathbf{x})\right)}{\sum\limits_{j=1}^{K}{\exp\left(s_j(\mathbf{x})\right)}}$

def softmax(logits):
    exps = np.exp(logits)
    exp_sums = np.sum(exps, axis=1, keepdims=True)
    return exps / exp_sums

We are almost ready to start training. Let's define the number of inputs and outputs:

n_inputs = X_train.shape[1] # == 3 (2 features plus the bias term)
n_outputs = len(np.unique(y_train))   # == 3 (3 iris classes)

Now here comes the hardest part: training! Theoretically, it's simple: it's just a matter of translating the math equations into Python code. But in practice, it can be quite tricky: in particular, it's easy to mix up the order of the terms, or the indices. You can even end up with code that looks like it's working but is actually not computing exactly the right thing. When unsure, you should write down the shape of each term in the equation and make sure the corresponding terms in your code match closely. It can also help to evaluate each term independently and print them out. The good news it that you won't have to do this everyday, since all this is well implemented by Scikit-Learn, but it will help you understand what's going on under the hood.

So the equations we will need are the cost function:

$J(\mathbf{\Theta}) =

• \dfrac{1}{m}\sum\limits{i=1}^{m}\sum\limits{k=1}^{K}{y_k^{(i)}\log\left(\hat{p}_k^{(i)}\right)}$

And the equation for the gradients:

$\nabla_{\mathbf{\theta}^{(k)}} \, J(\mathbf{\Theta}) = \dfrac{1}{m} \sum\limits_{i=1}^{m}{ \left ( \hat{p}^{(i)}_k - y_k^{(i)} \right ) \mathbf{x}^{(i)}}$

Note that $\log\left(\hat{p}_k^{(i)}\right)$ may not be computable if $\hat{p}_k^{(i)} = 0$. So we will add a tiny value $\epsilon$ to $\log\left(\hat{p}_k^{(i)}\right)$ to avoid getting nan values.

eta = 0.01
n_iterations = 5001
m = len(X_train)
epsilon = 1e-7

Theta = np.random.randn(n_inputs, n_outputs)

for iteration in range(n_iterations):
    logits = X_train.dot(Theta)
    Y_proba = softmax(logits)
    loss = -np.mean(np.sum(Y_train_one_hot * np.log(Y_proba + epsilon), axis=1))
    error = Y_proba - Y_train_one_hot
    if iteration % 500 == 0:
        print(iteration, loss)
    gradients = 1/m * X_train.T.dot(error)
    Theta = Theta - eta * gradients

0 5.446183864821945
500 0.8351003035768683
1000 0.6876961554414912
1500 0.6010299835452122
2000 0.5442782811959167
2500 0.5037262742244605
3000 0.4728357293908468
3500 0.4481872508179334
4000 0.4278347262806174
4500 0.4105891022823527
5000 0.39568032574889406

And that's it! The Softmax model is trained. Let's look at the model parameters:

Theta

array([[ 3.3172417 , -0.6476445 , -2.99855999],
       [-1.16505434,  0.11283387,  0.10251113],
       [-0.72087779, -0.083875  ,  1.48587045]])

Let's make predictions for the validation set and check the accuracy score:

logits = X_valid.dot(Theta)
Y_proba = softmax(logits)
y_predict = np.argmax(Y_proba, axis=1)

accuracy_score = np.mean(y_predict == y_valid)
accuracy_score

0.9666666666666667

Well, this model looks pretty good. For the sake of the exercise, let's add a bit of $\ell_2$ regularization. The following training code is similar to the one above, but the loss now has an additional $\ell_2$ penalty, and the gradients have the proper additional term (note that we don't regularize the first element of Theta since this corresponds to the bias term). Also, let's try increasing the learning rate eta.

eta = 0.1
n_iterations = 5001
m = len(X_train)
epsilon = 1e-7
alpha = 0.1  # regularization hyperparameter

Theta = np.random.randn(n_inputs, n_outputs)

for iteration in range(n_iterations):
    logits = X_train.dot(Theta)
    Y_proba = softmax(logits)
    xentropy_loss = -np.mean(np.sum(Y_train_one_hot * np.log(Y_proba + epsilon), axis=1))
    l2_loss = 1/2 * np.sum(np.square(Theta[1:]))
    loss = xentropy_loss + alpha * l2_loss
    error = Y_proba - Y_train_one_hot
    if iteration % 500 == 0:
        print(iteration, loss)
    gradients = 1/m * X_train.T.dot(error) + np.r_[np.zeros([1, n_outputs]), alpha * Theta[1:]]
    Theta = Theta - eta * gradients

0 6.629574947908294
500 0.5341631554372782
1000 0.5037712748637474
1500 0.4948056455575166
2000 0.49140819484111964
2500 0.4900085074445459
3000 0.48940742896132616
3500 0.4891431024691195
4000 0.48902516549065855
4500 0.48897205809605315
5000 0.4889480004791563

Because of the additional $\ell_2$ penalty, the loss seems greater than earlier, but perhaps this model will perform better? Let's find out:

logits = X_valid.dot(Theta)
Y_proba = softmax(logits)
y_predict = np.argmax(Y_proba, axis=1)

accuracy_score = np.mean(y_predict == y_valid)
accuracy_score

1.0

Cool, perfect accuracy! We probably just got lucky with this validation set, but still, it's pleasant.

Now let's add early stopping. For this we just need to measure the loss on the validation set at every iteration and stop when the error starts growing.

eta = 0.1 
n_iterations = 5001
m = len(X_train)
epsilon = 1e-7
alpha = 0.1  # regularization hyperparameter
best_loss = np.infty

Theta = np.random.randn(n_inputs, n_outputs)

for iteration in range(n_iterations):
    logits = X_train.dot(Theta)
    Y_proba = softmax(logits)
    xentropy_loss = -np.mean(np.sum(Y_train_one_hot * np.log(Y_proba + epsilon), axis=1))
    l2_loss = 1/2 * np.sum(np.square(Theta[1:]))
    loss = xentropy_loss + alpha * l2_loss
    error = Y_proba - Y_train_one_hot
    gradients = 1/m * X_train.T.dot(error) + np.r_[np.zeros([1, n_outputs]), alpha * Theta[1:]]
    Theta = Theta - eta * gradients

    logits = X_valid.dot(Theta)
    Y_proba = softmax(logits)
    xentropy_loss = -np.mean(np.sum(Y_valid_one_hot * np.log(Y_proba + epsilon), axis=1))
    l2_loss = 1/2 * np.sum(np.square(Theta[1:]))
    loss = xentropy_loss + alpha * l2_loss
    if iteration % 500 == 0:
        print(iteration, loss)
    if loss < best_loss:
        best_loss = loss
    else:
        print(iteration - 1, best_loss)
        print(iteration, loss, "early stopping!")
        break

0 4.70940845273367
500 0.5740996073458012
1000 0.5436382813658034
1500 0.535638768431427
2000 0.5332563789170385
2500 0.5326544271776569
2765 0.5326058224570446
2766 0.5326058230506047 early stopping!

logits = X_valid.dot(Theta)
Y_proba = softmax(logits)
y_predict = np.argmax(Y_proba, axis=1)

accuracy_score = np.mean(y_predict == y_valid)
accuracy_score

1.0

Still perfect, but faster.

Now let's plot the model's predictions on the whole dataset:

x0, x1 = np.meshgrid(
        np.linspace(0, 8, 500).reshape(-1, 1),
        np.linspace(0, 3.5, 200).reshape(-1, 1),
    )
X_new = np.c_[x0.ravel(), x1.ravel()]
X_new_with_bias = np.c_[np.ones([len(X_new), 1]), X_new]

logits = X_new_with_bias.dot(Theta)
Y_proba = softmax(logits)
y_predict = np.argmax(Y_proba, axis=1)

zz1 = Y_proba[:, 1].reshape(x0.shape)
zz = y_predict.reshape(x0.shape)

plt.figure(figsize=(10, 4))
plt.plot(X[y==2, 0], X[y==2, 1], "g^", label="Iris-Virginica")
plt.plot(X[y==1, 0], X[y==1, 1], "bs", label="Iris-Versicolor")
plt.plot(X[y==0, 0], X[y==0, 1], "yo", label="Iris-Setosa")

from matplotlib.colors import ListedColormap
custom_cmap = ListedColormap(['#fafab0','#9898ff','#a0faa0'])

plt.contourf(x0, x1, zz, cmap=custom_cmap)
contour = plt.contour(x0, x1, zz1, cmap=plt.cm.brg)
plt.clabel(contour, inline=1, fontsize=12)
plt.xlabel("Petal length", fontsize=14)
plt.ylabel("Petal width", fontsize=14)
plt.legend(loc="upper left", fontsize=14)
plt.axis([0, 7, 0, 3.5])
plt.show()

And now let's measure the final model's accuracy on the test set:

logits = X_test.dot(Theta)
Y_proba = softmax(logits)
y_predict = np.argmax(Y_proba, axis=1)

accuracy_score = np.mean(y_predict == y_test)
accuracy_score

0.9333333333333333

Our perfect model turns out to have slight imperfections. This variability is likely due to the very small size of the dataset: depending on how you sample the training set, validation set and the test set, you can get quite different results. Try changing the random seed and running the code again a few times, you will see that the results will vary.