Setup: This Notebook Contains All The Sample Code and Solutions To The Exercises in Chapter 3

Chapter
3 – Classification
This notebook contains all the sample code and solutions to the exercises in chapter 3.
Run in Google Colab
Setup
First, let's import a few common modules, ensure MatplotLib plots figures inline and prepare a function to save the figures. We also check
that Python 3.5 or later is installed (although Python 2.x may work, it is deprecated so we strongly recommend you use Python 3 instead), as
well as Scikit-Learn ≥0.20.
# Python ≥3.5 is required

import sys
assert sys.version_info >= (3, 5)
# Scikit-Learn ≥0.20 is required

import sklearn
assert sklearn.__version__ >= "0.20"
# 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 as mpl
import matplotlib.pyplot as plt
mpl.rc('axes', labelsize=14)
mpl.rc('xtick', labelsize=12)
mpl.rc('ytick', labelsize=12)
# Where to save the figures

PROJECT_ROOT_DIR = "."
CHAPTER_ID = "classification"
IMAGES_PATH = os.path.join(PROJECT_ROOT_DIR, "images", CHAPTER_ID)
os.makedirs(IMAGES_PATH, exist_ok=True)
def save_fig(fig_id, tight_layout=True, fig_extension="png", resolution=300):

path = os.path.join(IMAGES_PATH, fig_id + "." + fig_extension)
print("Saving figure", fig_id)
if tight_layout:
plt.tight_layout()
plt.savefig(path, format=fig_extension, dpi=resolution)
MNIST
from sklearn.datasets import fetch_openml
mnist = fetch_openml('mnist_784', version=1)
mnist.keys()
dict_keys(['data', 'target', 'frame', 'categories', 'feature_names', 'target_names', 'DESCR', 'details', 'url'])
X, y = mnist["data"], mnist["target"]
X.shape
(70000, 784)
y.shape
(70000,)
28 * 28
784
%matplotlib inline
import matplotlib as mpl
import matplotlib.pyplot as plt
some_digit = X[0]
some_digit_image = some_digit.reshape(28, 28)
plt.imshow(some_digit_image, cmap=mpl.cm.binary)
plt.axis("off")
save_fig("some_digit_plot")
plt.show()
Saving figure some_digit_plot
y[0]
'5'
y = y.astype(np.uint8)
def plot_digit(data):
image = data.reshape(28, 28)
plt.imshow(image, cmap = mpl.cm.binary,
interpolation="nearest")
plt.axis("off")
# EXTRA
def plot_digits(instances, images_per_row=10, **options):
size = 28
images_per_row = min(len(instances), images_per_row)
images = [instance.reshape(size,size) for instance in instances]
n_rows = (len(instances) - 1) // images_per_row + 1
row_images = []
n_empty = n_rows * images_per_row - len(instances)
images.append(np.zeros((size, size * n_empty)))
for row in range(n_rows):
rimages = images[row * images_per_row : (row + 1) * images_per_row]
row_images.append(np.concatenate(rimages, axis=1))
image = np.concatenate(row_images, axis=0)
plt.imshow(image, cmap = mpl.cm.binary, **options)
plt.axis("off")
plt.figure(figsize=(9,9))
example_images = X[:100]
plot_digits(example_images, images_per_row=10)
save_fig("more_digits_plot")
plt.show()
Saving figure more_digits_plot
y[0]
X_train, X_test, y_train, y_test = X[:60000], X[60000:], y[:60000], y[60000:]
Binary classifier
y_train_5 = (y_train == 5)
y_test_5 = (y_test == 5)
Note: some hyperparameters will have a different defaut value in future versions of Scikit-Learn, such as max_iter and tol . To be future-
proof, we explicitly set these hyperparameters to their future default values. For simplicity, this is not shown in the book.
from sklearn.linear_model import SGDClassifier
sgd_clf = SGDClassifier(max_iter=1000, tol=1e-3, random_state=42)

sgd_clf.fit(X_train, y_train_5)
SGDClassifier(random_state=42)
sgd_clf.predict([some_digit])
array([ True])
from sklearn.model_selection import cross_val_score

cross_val_score(sgd_clf, X_train, y_train_5, cv=3, scoring="accuracy")
array([0.95035, 0.96035, 0.9604 ])
from sklearn.model_selection import StratifiedKFold

from sklearn.base import clone
skfolds = StratifiedKFold(n_splits=3, shuffle=True, random_state=42)
for train_index, test_index in skfolds.split(X_train, y_train_5):

clone_clf = clone(sgd_clf)
X_train_folds = X_train[train_index]
y_train_folds = y_train_5[train_index]
X_test_fold = X_train[test_index]
y_test_fold = y_train_5[test_index]
clone_clf.fit(X_train_folds, y_train_folds)
y_pred = clone_clf.predict(X_test_fold)
n_correct = sum(y_pred == y_test_fold)
print(n_correct / len(y_pred))
0.9669
0.91625
0.96785
Note: shuffle=True was omitted by mistake in previous releases of the book.
from sklearn.base import BaseEstimator

class Never5Classifier(BaseEstimator):
def fit(self, X, y=None):
pass
def predict(self, X):
return np.zeros((len(X), 1), dtype=bool)
never_5_clf = Never5Classifier()
cross_val_score(never_5_clf, X_train, y_train_5, cv=3, scoring="accuracy")
array([0.91125, 0.90855, 0.90915])
Warning: this output (and many others in this notebook and other notebooks) may differ slightly from those in the book. Don't worry, that's
okay! There are several reasons for this:
first, Scikit-Learn and other libraries evolve, and algorithms get tweaked a bit, which may change the exact result you get. If you use the
latest Scikit-Learn version (and in general, you really should), you probably won't be using the exact same version I used when I wrote
the book or this notebook, hence the difference. I try to keep this notebook reasonably up to date, but I can't change the numbers on the
pages in your copy of the book.
second, many training algorithms are stochastic, meaning they rely on randomness. In principle, it's possible to get consistent outputs
from a random number generator by setting the seed from which it generates the pseudo-random numbers (which is why you will see
random_state=42 or np.random.seed(42) pretty often). However, sometimes this does not suffice due to the other factors listed
here.
third, if the training algorithm runs across multiple threads (as do some algorithms implemented in C) or across multiple processes (e.g.,
when using the n_jobs argument), then the precise order in which operations will run is not always guaranteed, and thus the exact
result may vary slightly.
lastly, other things may prevent perfect reproducibility, such as Python maps and sets whose order is not guaranteed to be stable across
sessions, or the order of files in a directory which is also not guaranteed.
from sklearn.model_selection import cross_val_predict

y_train_pred = cross_val_predict(sgd_clf, X_train, y_train_5, cv=3)
from sklearn.metrics import confusion_matrix
confusion_matrix(y_train_5, y_train_pred)
array([[53892, 687],
[ 1891, 3530]])
y_train_perfect_predictions = y_train_5 # pretend we reached perfection

confusion_matrix(y_train_5, y_train_perfect_predictions)
array([[54579, 0],
[ 0, 5421]])
from sklearn.metrics import precision_score, recall_score
precision_score(y_train_5, y_train_pred)
0.8370879772350012
cm = confusion_matrix(y_train_5, y_train_pred)
cm[1, 1] / (cm[0, 1] + cm[1, 1])
0.8370879772350012
recall_score(y_train_5, y_train_pred)
0.6511713705958311
cm[1, 1] / (cm[1, 0] + cm[1, 1])
0.6511713705958311
from sklearn.metrics import f1_score
f1_score(y_train_5, y_train_pred)
0.7325171197343846
cm[1, 1] / (cm[1, 1] + (cm[1, 0] + cm[0, 1]) / 2)
0.7325171197343847
y_scores = sgd_clf.decision_function([some_digit])
y_scores
array([2164.22030239])
threshold = 0
y_some_digit_pred = (y_scores > threshold)
y_some_digit_pred
array([ True])
threshold = 8000
threshold = 8000
y_some_digit_pred = (y_scores > threshold)
y_some_digit_pred
array([False])
y_scores = cross_val_predict(sgd_clf, X_train, y_train_5, cv=3,

method="decision_function")
from sklearn.metrics import precision_recall_curve
precisions, recalls, thresholds = precision_recall_curve(y_train_5, y_scores)
def plot_precision_recall_vs_threshold(precisions, recalls, thresholds):

plt.plot(thresholds, precisions[:-1], "b--", label="Precision", linewidth=2)
plt.plot(thresholds, recalls[:-1], "g-", label="Recall", linewidth=2)
plt.legend(loc="center right", fontsize=16) # Not shown in the book
plt.xlabel("Threshold", fontsize=16) # Not shown
plt.grid(True) # Not shown
plt.axis([-50000, 50000, 0, 1]) # Not shown
recall_90_precision = recalls[np.argmax(precisions >= 0.90)]

threshold_90_precision = thresholds[np.argmax(precisions >= 0.90)]
plt.figure(figsize=(8, 4)) # Not shown

plot_precision_recall_vs_threshold(precisions, recalls, thresholds)
plt.plot([threshold_90_precision, threshold_90_precision], [0., 0.9], "r:") # Not shown
plt.plot([-50000, threshold_90_precision], [0.9, 0.9], "r:") # Not shown
plt.plot([-50000, threshold_90_precision], [recall_90_precision, recall_90_precision], "r:")# Not shown
plt.plot([threshold_90_precision], [0.9], "ro") # Not shown
plt.plot([threshold_90_precision], [recall_90_precision], "ro") # Not shown
save_fig("precision_recall_vs_threshold_plot") # Not shown
plt.show()
Saving figure precision_recall_vs_threshold_plot
(y_train_pred == (y_scores > 0)).all()
True
def plot_precision_vs_recall(precisions, recalls):

plt.plot(recalls, precisions, "b-", linewidth=2)
plt.xlabel("Recall", fontsize=16)
plt.ylabel("Precision", fontsize=16)
plt.axis([0, 1, 0, 1])
plt.grid(True)
plt.figure(figsize=(8, 6))
plot_precision_vs_recall(precisions, recalls)
plt.plot([recall_90_precision, recall_90_precision], [0., 0.9], "r:")
plt.plot([0.0, recall_90_precision], [0.9, 0.9], "r:")
plt.plot([recall_90_precision], [0.9], "ro")
save_fig("precision_vs_recall_plot")
plt.show()
Saving figure precision_vs_recall_plot
threshold_90_precision = thresholds[np.argmax(precisions >= 0.90)]
threshold_90_precision
3370.0194991439557
y_train_pred_90 = (y_scores >= threshold_90_precision)
precision_score(y_train_5, y_train_pred_90)
0.9000345901072293
recall_score(y_train_5, y_train_pred_90)
0.4799852425751706
ROC curves
from sklearn.metrics import roc_curve
fpr, tpr, thresholds = roc_curve(y_train_5, y_scores)
def plot_roc_curve(fpr, tpr, label=None):

plt.plot(fpr, tpr, linewidth=2, label=label)
plt.plot([0, 1], [0, 1], 'k--') # dashed diagonal
plt.axis([0, 1, 0, 1]) # Not shown in the book
plt.xlabel('False Positive Rate (Fall-Out)', fontsize=16) # Not shown
plt.ylabel('True Positive Rate (Recall)', fontsize=16) # Not shown
plt.grid(True) # Not shown
plt.figure(figsize=(8, 6)) # Not shown
plot_roc_curve(fpr, tpr)
fpr_90 = fpr[np.argmax(tpr >= recall_90_precision)] # Not shown
plt.plot([fpr_90, fpr_90], [0., recall_90_precision], "r:") # Not shown
plt.plot([0.0, fpr_90], [recall_90_precision, recall_90_precision], "r:") # Not shown
plt.plot([fpr_90], [recall_90_precision], "ro") # Not shown
save_fig("roc_curve_plot") # Not shown
plt.show()
Saving figure roc_curve_plot
from sklearn.metrics import roc_auc_score
roc_auc_score(y_train_5, y_scores)
0.9604938554008616
Note: we set n_estimators=100 to be future-proof since this will be the default value in Scikit-Learn 0.22.
from sklearn.ensemble import RandomForestClassifier

forest_clf = RandomForestClassifier(n_estimators=100, random_state=42)
y_probas_forest = cross_val_predict(forest_clf, X_train, y_train_5, cv=3,
method="predict_proba")
y_scores_forest = y_probas_forest[:, 1] # score = proba of positive class

fpr_forest, tpr_forest, thresholds_forest = roc_curve(y_train_5,y_scores_forest)
recall_for_forest = tpr_forest[np.argmax(fpr_forest >= fpr_90)]
plt.plot(fpr, tpr, "b:", linewidth=2, label="SGD")
plot_roc_curve(fpr_forest, tpr_forest, "Random Forest")
plt.plot([fpr_90, fpr_90], [0., recall_90_precision], "r:")
plt.plot([0.0, fpr_90], [recall_90_precision, recall_90_precision], "r:")
plt.plot([fpr_90], [recall_90_precision], "ro")
plt.plot([fpr_90, fpr_90], [0., recall_for_forest], "r:")
plt.plot([fpr_90], [recall_for_forest], "ro")
plt.grid(True)
plt.legend(loc="lower right", fontsize=16)
save_fig("roc_curve_comparison_plot")
plt.show()
Saving figure roc_curve_comparison_plot

Saving figure roc_curve_comparison_plot
roc_auc_score(y_train_5, y_scores_forest)
0.9983436731328145
y_train_pred_forest = cross_val_predict(forest_clf, X_train, y_train_5, cv=3)

precision_score(y_train_5, y_train_pred_forest)
0.9905083315756169
recall_score(y_train_5, y_train_pred_forest)
0.8662608374838591
Multiclass classification
from sklearn.svm import SVC
svm_clf = SVC(gamma="auto", random_state=42)

svm_clf.fit(X_train[:1000], y_train[:1000]) # y_train, not y_train_5
svm_clf.predict([some_digit])
array([5], dtype=uint8)
some_digit_scores = svm_clf.decision_function([some_digit])
some_digit_scores
array([[ 2.81585438, 7.09167958, 3.82972099, 0.79365551, 5.8885703 ,

9.29718395, 1.79862509, 8.10392157, -0.228207 , 4.83753243]])
np.argmax(some_digit_scores)
svm_clf.classes_
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], dtype=uint8)

svm_clf.classes_[5]
from sklearn.multiclass import OneVsRestClassifier

ovr_clf = OneVsRestClassifier(SVC(gamma="auto", random_state=42))
ovr_clf.fit(X_train[:1000], y_train[:1000])
ovr_clf.predict([some_digit])
len(ovr_clf.estimators_)
10
sgd_clf.fit(X_train, y_train)
sgd_clf.predict([some_digit])
sgd_clf.decision_function([some_digit])
array([[-31893.03095419, -34419.69069632, -9530.63950739,

1823.73154031, -22320.14822878, -1385.80478895,
-26188.91070951, -16147.51323997, -4604.35491274,
-12050.767298 ]])
cross_val_score(sgd_clf, X_train, y_train, cv=3, scoring="accuracy")
array([0.87365, 0.85835, 0.8689 ])
from sklearn.preprocessing import StandardScaler

scaler = StandardScaler()
X_train_scaled = scaler.fit_transform(X_train.astype(np.float64))
cross_val_score(sgd_clf, X_train_scaled, y_train, cv=3, scoring="accuracy")
array([0.8983, 0.891 , 0.9018])
y_train_pred = cross_val_predict(sgd_clf, X_train_scaled, y_train, cv=3)

conf_mx = confusion_matrix(y_train, y_train_pred)
conf_mx
array([[5577, 0, 22, 5, 8, 43, 36, 6, 225, 1],

[ 0, 6400, 37, 24, 4, 44, 4, 7, 212, 10],
[ 27, 27, 5220, 92, 73, 27, 67, 36, 378, 11],
[ 22, 17, 117, 5227, 2, 203, 27, 40, 403, 73],
[ 12, 14, 41, 9, 5182, 12, 34, 27, 347, 164],
[ 27, 15, 30, 168, 53, 4444, 75, 14, 535, 60],
[ 30, 15, 42, 3, 44, 97, 5552, 3, 131, 1],
[ 21, 10, 51, 30, 49, 12, 3, 5684, 195, 210],
[ 17, 63, 48, 86, 3, 126, 25, 10, 5429, 44],
[ 25, 18, 30, 64, 118, 36, 1, 179, 371, 5107]])
# since sklearn 0.22, you can use sklearn.metrics.plot_confusion_matrix()

def plot_confusion_matrix(matrix):
"""If you prefer color and a colorbar"""
fig = plt.figure(figsize=(8,8))
ax = fig.add_subplot(111)
cax = ax.matshow(matrix)
fig.colorbar(cax)
plt.matshow(conf_mx, cmap=plt.cm.gray)
plt.matshow(conf_mx, cmap=plt.cm.gray)
save_fig("confusion_matrix_plot", tight_layout=False)
plt.show()
Saving figure confusion_matrix_plot
row_sums = conf_mx.sum(axis=1, keepdims=True)

norm_conf_mx = conf_mx / row_sums
np.fill_diagonal(norm_conf_mx, 0)
plt.matshow(norm_conf_mx, cmap=plt.cm.gray)
save_fig("confusion_matrix_errors_plot", tight_layout=False)
plt.show()
Saving figure confusion_matrix_errors_plot
cl_a, cl_b = 3, 5
X_aa = X_train[(y_train == cl_a) & (y_train_pred == cl_a)]
X_ab = X_train[(y_train == cl_a) & (y_train_pred == cl_b)]
X_ba = X_train[(y_train == cl_b) & (y_train_pred == cl_a)]
X_bb = X_train[(y_train == cl_b) & (y_train_pred == cl_b)]
plt.subplot(221); plot_digits(X_aa[:25], images_per_row=5)
plt.subplot(222); plot_digits(X_ab[:25], images_per_row=5)
plt.subplot(223); plot_digits(X_ba[:25], images_per_row=5)
plt.subplot(224); plot_digits(X_bb[:25], images_per_row=5)
save_fig("error_analysis_digits_plot")
plt.show()
Saving figure error_analysis_digits_plot

Multilabel classification
from sklearn.neighbors import KNeighborsClassifier
y_train_large = (y_train >= 7)

y_train_odd = (y_train % 2 == 1)
y_multilabel = np.c_[y_train_large, y_train_odd]
knn_clf = KNeighborsClassifier()
knn_clf.fit(X_train, y_multilabel)
KNeighborsClassifier()
knn_clf.predict([some_digit])
array([[False, True]])
Warning: the following cell may take a very long time (possibly hours depending on your hardware).
y_train_knn_pred = cross_val_predict(knn_clf, X_train, y_multilabel, cv=3)

f1_score(y_multilabel, y_train_knn_pred, average="macro")
0.976410265560605
Multioutput classification
noise = np.random.randint(0, 100, (len(X_train), 784))
X_train_mod = X_train + noise
noise = np.random.randint(0, 100, (len(X_test), 784))
X_test_mod = X_test + noise
y_train_mod = X_train
y_test_mod = X_test
some_index = 0
plt.subplot(121); plot_digit(X_test_mod[some_index])
plt.subplot(122); plot_digit(y_test_mod[some_index])
save_fig("noisy_digit_example_plot")
plt.show()
Saving figure noisy_digit_example_plot

knn_clf.fit(X_train_mod, y_train_mod)
clean_digit = knn_clf.predict([X_test_mod[some_index]])
plot_digit(clean_digit)
save_fig("cleaned_digit_example_plot")
Saving figure cleaned_digit_example_plot
Extra material
Dummy (ie. random) classifier
from sklearn.dummy import DummyClassifier

dmy_clf = DummyClassifier(strategy="prior")
y_probas_dmy = cross_val_predict(dmy_clf, X_train, y_train_5, cv=3, method="predict_proba")
y_scores_dmy = y_probas_dmy[:, 1]
fprr, tprr, thresholdsr = roc_curve(y_train_5, y_scores_dmy)

plot_roc_curve(fprr, tprr)
KNN classifier
from sklearn.neighbors import KNeighborsClassifier

knn_clf = KNeighborsClassifier(weights='distance', n_neighbors=4)
knn_clf.fit(X_train, y_train)
KNeighborsClassifier(n_neighbors=4, weights='distance')
y_knn_pred = knn_clf.predict(X_test)
from sklearn.metrics import accuracy_score

accuracy_score(y_test, y_knn_pred)
0.9714
from scipy.ndimage.interpolation import shift

def shift_digit(digit_array, dx, dy, new=0):
return shift(digit_array.reshape(28, 28), [dy, dx], cval=new).reshape(784)
plot_digit(shift_digit(some_digit, 5, 1, new=100))
X_train_expanded = [X_train]
y_train_expanded = [y_train]
for dx, dy in ((1, 0), (-1, 0), (0, 1), (0, -1)):
shifted_images = np.apply_along_axis(shift_digit, axis=1, arr=X_train, dx=dx, dy=dy)
X_train_expanded.append(shifted_images)
y_train_expanded.append(y_train)
X_train_expanded = np.concatenate(X_train_expanded)
y_train_expanded = np.concatenate(y_train_expanded)
X_train_expanded.shape, y_train_expanded.shape
((300000, 784), (300000,))
knn_clf.fit(X_train_expanded, y_train_expanded)
y_knn_expanded_pred = knn_clf.predict(X_test)
accuracy_score(y_test, y_knn_expanded_pred)
0.9763
ambiguous_digit = X_test[2589]
knn_clf.predict_proba([ambiguous_digit])
array([[0.24579675, 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0.75420325]])
plot_digit(ambiguous_digit)
Exercise solutions
1. An MNIST Classifier With Over 97% Accuracy

Warning: the next cell may take hours to run, depending on your hardware.
from sklearn.model_selection import GridSearchCV
param_grid = [{'weights': ["uniform", "distance"], 'n_neighbors': [3, 4, 5]}]
knn_clf = KNeighborsClassifier()
grid_search = GridSearchCV(knn_clf, param_grid, cv=5, verbose=3)
grid_search.fit(X_train, y_train)
Fitting 5 folds for each of 6 candidates, totalling 30 fits

[CV] n_neighbors=3, weights=uniform ..................................
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[CV] ...... n_neighbors=3, weights=uniform, score=0.972, total=11.5min
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 11.5min remaining: 0.0s
[CV] ..... n_neighbors=3, weights=uniform, score=0.971, total=720.8min
[Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 732.3min remaining: 0.0s
[CV] n_neighbors=3, weights=distance .................................
[CV] ..... n_neighbors=3, weights=distance, score=0.972, total=11.4min
[Parallel(n_jobs=1)]: Done 30 out of 30 | elapsed: 1050.5min finished
GridSearchCV(cv=5, estimator=KNeighborsClassifier(),
param_grid=[{'n_neighbors': [3, 4, 5],
'weights': ['uniform', 'distance']}],
verbose=3)
grid_search.best_params_
{'n_neighbors': 4, 'weights': 'distance'}
grid_search.best_score_
0.9716166666666666
from sklearn.metrics import accuracy_score
y_pred = grid_search.predict(X_test)
accuracy_score(y_test, y_pred)
0.9714
2. Data Augmentation
from scipy.ndimage.interpolation import shift
def shift_image(image, dx, dy):

image = image.reshape((28, 28))
shifted_image = shift(image, [dy, dx], cval=0, mode="constant")
return shifted_image.reshape([-1])
image = X_train[1000]
shifted_image_down = shift_image(image, 0, 5)
shifted_image_left = shift_image(image, -5, 0)
plt.subplot(131)
plt.title("Original", fontsize=14)
plt.imshow(image.reshape(28, 28), interpolation="nearest", cmap="Greys")
plt.subplot(132)
plt.title("Shifted down", fontsize=14)
plt.imshow(shifted_image_down.reshape(28, 28), interpolation="nearest", cmap="Greys")
plt.subplot(133)
plt.title("Shifted left", fontsize=14)
plt.imshow(shifted_image_left.reshape(28, 28), interpolation="nearest", cmap="Greys")
plt.show()
X_train_augmented = [image for image in X_train]

y_train_augmented = [label for label in y_train]
for dx, dy in ((1, 0), (-1, 0), (0, 1), (0, -1)):
for image, label in zip(X_train, y_train):
X_train_augmented.append(shift_image(image, dx, dy))
y_train_augmented.append(label)
X_train_augmented = np.array(X_train_augmented)
y_train_augmented = np.array(y_train_augmented)
shuffle_idx = np.random.permutation(len(X_train_augmented))
X_train_augmented = X_train_augmented[shuffle_idx]
y_train_augmented = y_train_augmented[shuffle_idx]
knn_clf = KNeighborsClassifier(**grid_search.best_params_)
knn_clf.fit(X_train_augmented, y_train_augmented)
y_pred = knn_clf.predict(X_test)
accuracy_score(y_test, y_pred)
0.9763
By simply augmenting the data, we got a 0.5% accuracy boost. :)
3. Tackle the Titanic dataset

The goal is to predict whether or not a passenger survived based on attributes such as their age, sex, passenger class, where they embarked
and so on.
First, login to Kaggle and go to the Titanic challenge to download train.csv and test.csv . Save them to the datasets/titanic
directory.
Next, let's load the data:
import os
TITANIC_PATH = os.path.join("datasets", "titanic")
import pandas as pd
def load_titanic_data(filename, titanic_path=TITANIC_PATH):

csv_path = os.path.join(titanic_path, filename)
return pd.read_csv(csv_path)
train_data = load_titanic_data("train.csv")
test_data = load_titanic_data("test.csv")
The data is already split into a training set and a test set. However, the test data does not contain the labels: your goal is to train the best
model you can using the training data, then make your predictions on the test data and upload them to Kaggle to see your final score.
Let's take a peek at the top few rows of the training set:
train_data.head()
PassengerId Survived Pclass Name Sex Age SibSp Parch Ticket Fare Cabin Embarked
0 1 0 3 Braund, Mr. Owen Harris male 22.0 1 0 A/5 21171 7.2500 NaN S
Cumings, Mrs. John Bradley (Florence

1 2 1 1 female 38.0 1 0 PC 17599 71.2833 C85 C
Briggs Th...
STON/O2.
2 3 1 3 Heikkinen, Miss. Laina female 26.0 0 0 7.9250 NaN S
3101282
Futrelle, Mrs. Jacques Heath (Lily May

3 4 1 1 female 35.0 1 0 113803 53.1000 C123 S
Peel)
4 5 0 3 Allen, Mr. William Henry male 35.0 0 0 373450 8.0500 NaN S
The attributes have the following meaning:
Survived: that's the target, 0 means the passenger did not survive, while 1 means he/she survived.
Pclass: passenger class.
Name, Sex, Age: self-explanatory
SibSp: how many siblings & spouses of the passenger aboard the Titanic.
Parch: how many children & parents of the passenger aboard the Titanic.
Ticket: ticket id
Fare: price paid (in pounds)
Cabin: passenger's cabin number
Embarked: where the passenger embarked the Titanic
Let's get more info to see how much data is missing:
train_data.info()
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 891 entries, 0 to 890
Data columns (total 12 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 PassengerId 891 non-null int64
1 Survived 891 non-null int64
2 Pclass 891 non-null int64
3 Name 891 non-null object
4 Sex 891 non-null object
5 Age 714 non-null float64
6 SibSp 891 non-null int64
7 Parch 891 non-null int64
8 Ticket 891 non-null object
9 Fare 891 non-null float64
10 Cabin 204 non-null object
11 Embarked 889 non-null object
dtypes: float64(2), int64(5), object(5)
memory usage: 83.7+ KB
Okay, the Age, Cabin and Embarked attributes are sometimes null (less than 891 non-null), especially the Cabin (77% are null). We will
ignore the Cabin for now and focus on the rest. The Age attribute has about 19% null values, so we will need to decide what to do with them.
Replacing null values with the median age seems reasonable.
The Name and Ticket attributes may have some value, but they will be a bit tricky to convert into useful numbers that a model can consume.
So for now, we will ignore them.
Let's take a look at the numerical attributes:
train_data.describe()
PassengerId Survived Pclass Age SibSp Parch Fare
count 891.000000 891.000000 891.000000 714.000000 891.000000 891.000000 891.000000
mean 446.000000 0.383838 2.308642 29.699118 0.523008 0.381594 32.204208
std 257.353842 0.486592 0.836071 14.526497 1.102743 0.806057 49.693429
min 1.000000 0.000000 1.000000 0.420000 0.000000 0.000000 0.000000
25% 223.500000 0.000000 2.000000 20.125000 0.000000 0.000000 7.910400
50% 446.000000 0.000000 3.000000 28.000000 0.000000 0.000000 14.454200
75% 668.500000 1.000000 3.000000 38.000000 1.000000 0.000000 31.000000
max 891.000000 1.000000 3.000000 80.000000 8.000000 6.000000 512.329200
Yikes, only 38% Survived. :( That's close enough to 40%, so accuracy will be a reasonable metric to evaluate our model.
The mean Fare was £32.20, which does not seem so expensive (but it was probably a lot of money back then).
The mean Age was less than 30 years old.
Let's check that the target is indeed 0 or 1:
train_data["Survived"].value_counts()
0 549
1 342
Name: Survived, dtype: int64
Now let's take a quick look at all the categorical attributes:
train_data["Pclass"].value_counts()
3 491
1 216
2 184
Name: Pclass, dtype: int64
train_data["Sex"].value_counts()
male 577
female 314
Name: Sex, dtype: int64
train_data["Embarked"].value_counts()
S 644
C 168
Q 77
Name: Embarked, dtype: int64
The Embarked attribute tells us where the passenger embarked: C=Cherbourg, Q=Queenstown, S=Southampton.
Note: the code below uses a mix of Pipeline , FeatureUnion and a custom DataFrameSelector to preprocess some columns
differently. Since Scikit-Learn 0.20, it is preferable to use a ColumnTransformer , like in the previous chapter.
Now let's build our preprocessing pipelines. We will reuse the DataframeSelector we built in the previous chapter to select specific
attributes from the DataFrame :
from sklearn.base import BaseEstimator, TransformerMixin
class DataFrameSelector(BaseEstimator, TransformerMixin):

def __init__(self, attribute_names):
self.attribute_names = attribute_names
return self
def transform(self, X):
return X[self.attribute_names]
Let's build the pipeline for the numerical attributes:

Let's build the pipeline for the numerical attributes:
from sklearn.pipeline import Pipeline

from sklearn.impute import SimpleImputer
num_pipeline = Pipeline([
("select_numeric", DataFrameSelector(["Age", "SibSp", "Parch", "Fare"])),
("imputer", SimpleImputer(strategy="median")),
])
num_pipeline.fit_transform(train_data)
array([[22. , 1. , 0. , 7.25 ],
[38. , 1. , 0. , 71.2833],
[26. , 0. , 0. , 7.925 ],
...,
[28. , 1. , 2. , 23.45 ],
[26. , 0. , 0. , 30. ],
[32. , 0. , 0. , 7.75 ]])
We will also need an imputer for the string categorical columns (the regular SimpleImputer does not work on those):
# Inspired from stackoverflow.com/questions/25239958

class MostFrequentImputer(BaseEstimator, TransformerMixin):
self.most_frequent_ = pd.Series([X[c].value_counts().index[0] for c in X],
index=X.columns)
return self
def transform(self, X, y=None):
return X.fillna(self.most_frequent_)
from sklearn.preprocessing import OneHotEncoder
Now we can build the pipeline for the categorical attributes:
cat_pipeline = Pipeline([
("select_cat", DataFrameSelector(["Pclass", "Sex", "Embarked"])),
("imputer", MostFrequentImputer()),
("cat_encoder", OneHotEncoder(sparse=False)),
])
cat_pipeline.fit_transform(train_data)
array([[0., 0., 1., ..., 0., 0., 1.],

[1., 0., 0., ..., 1., 0., 0.],
[0., 0., 1., ..., 0., 0., 1.],
...,
[0., 0., 1., ..., 0., 0., 1.],
[1., 0., 0., ..., 1., 0., 0.],
[0., 0., 1., ..., 0., 1., 0.]])
Finally, let's join the numerical and categorical pipelines:
from sklearn.pipeline import FeatureUnion

preprocess_pipeline = FeatureUnion(transformer_list=[
("num_pipeline", num_pipeline),
("cat_pipeline", cat_pipeline),
])
Cool! Now we have a nice preprocessing pipeline that takes the raw data and outputs numerical input features that we can feed to any
Machine Learning model we want.
X_train = preprocess_pipeline.fit_transform(train_data)
X_train
array([[22., 1., 0., ..., 0., 0., 1.],

[38., 1., 0., ..., 1., 0., 0.],
[26., 0., 0., ..., 0., 0., 1.],
...,
[28., 1., 2., ..., 0., 0., 1.],
[26., 0., 0., ..., 1., 0., 0.],
[32., 0., 0., ..., 0., 1., 0.]])
Let's not forget to get the labels:
y_train = train_data["Survived"]
We are now ready to train a classifier. Let's start with an SVC :
from sklearn.svm import SVC
svm_clf = SVC(gamma="auto")
svm_clf.fit(X_train, y_train)
SVC(gamma='auto')
Great, our model is trained, let's use it to make predictions on the test set:
X_test = preprocess_pipeline.transform(test_data)
y_pred = svm_clf.predict(X_test)
And now we could just build a CSV file with these predictions (respecting the format excepted by Kaggle), then upload it and hope for the
best. But wait! We can do better than hope. Why don't we use cross-validation to have an idea of how good our model is?
svm_scores = cross_val_score(svm_clf, X_train, y_train, cv=10)

svm_scores.mean()
0.7329588014981274
Okay, over 73% accuracy, clearly better than random chance, but it's not a great score. Looking at the leaderboard for the Titanic
competition on Kaggle, you can see that you need to reach above 80% accuracy to be within the top 10% Kagglers. Some reached 100%,
but since you can easily find the list of victims of the Titanic, it seems likely that there was little Machine Learning involved in their
performance! ;-) So let's try to build a model that reaches 80% accuracy.
Let's try a RandomForestClassifier :
from sklearn.ensemble import RandomForestClassifier
forest_clf = RandomForestClassifier(n_estimators=100, random_state=42)

forest_scores = cross_val_score(forest_clf, X_train, y_train, cv=10)
forest_scores.mean()
0.8126466916354558
That's much better!
Instead of just looking at the mean accuracy across the 10 cross-validation folds, let's plot all 10 scores for each model, along with a box plot
highlighting the lower and upper quartiles, and "whiskers" showing the extent of the scores (thanks to Nevin Yilmaz for suggesting this
visualization). Note that the boxplot() function detects outliers (called "fliers") and does not include them within the whiskers. Specifically,
if the lower quartile is Q 1 and the upper quartile is Q 3, then the interquartile range IQR = Q 3 − Q 1 (this is the box's height), and any score
lower than Q 1 − 1.5 × IQR is a flier, and so is any score greater than Q3 + 1.5 × IQR.
plt.plot([1]*10, svm_scores, ".")
plt.plot([2]*10, forest_scores, ".")
plt.boxplot([svm_scores, forest_scores], labels=("SVM","Random Forest"))
plt.ylabel("Accuracy", fontsize=14)
plt.show()
To improve this result further, you could:
Compare many more models and tune hyperparameters using cross validation and grid search,
Do more feature engineering, for example:
replace SibSp and Parch with their sum,
try to identify parts of names that correlate well with the Survived attribute (e.g. if the name contains "Countess", then survival
seems more likely),
try to convert numerical attributes to categorical attributes: for example, different age groups had very different survival rates (see below),
so it may help to create an age bucket category and use it instead of the age. Similarly, it may be useful to have a special category for
people traveling alone since only 30% of them survived (see below).
train_data["AgeBucket"] = train_data["Age"] // 15 * 15
train_data[["AgeBucket", "Survived"]].groupby(['AgeBucket']).mean()
Survived
AgeBucket
0.0 0.576923
15.0 0.362745
30.0 0.423256
45.0 0.404494
60.0 0.240000
75.0 1.000000
train_data["RelativesOnboard"] = train_data["SibSp"] + train_data["Parch"]

train_data[["RelativesOnboard", "Survived"]].groupby(['RelativesOnboard']).mean()
Survived
RelativesOnboard
0 0.303538
1 0.552795
2 0.578431
3 0.724138
4 0.200000
5 0.136364
6 0.333333
7 0.000000
10 0.000000
4. Spam classifier
First, let's fetch the data:
import os
import tarfile
import urllib
DOWNLOAD_ROOT = "http://spamassassin.apache.org/old/publiccorpus/"
HAM_URL = DOWNLOAD_ROOT + "20030228_easy_ham.tar.bz2"
SPAM_URL = DOWNLOAD_ROOT + "20030228_spam.tar.bz2"
SPAM_PATH = os.path.join("datasets", "spam")
def fetch_spam_data(spam_url=SPAM_URL, spam_path=SPAM_PATH):

if not os.path.isdir(spam_path):
os.makedirs(spam_path)
for filename, url in (("ham.tar.bz2", HAM_URL), ("spam.tar.bz2", SPAM_URL)):
path = os.path.join(spam_path, filename)
if not os.path.isfile(path):
urllib.request.urlretrieve(url, path)
tar_bz2_file = tarfile.open(path)
tar_bz2_file.extractall(path=SPAM_PATH)
tar_bz2_file.close()
fetch_spam_data()
Next, let's load all the emails:
HAM_DIR = os.path.join(SPAM_PATH, "easy_ham")

SPAM_DIR = os.path.join(SPAM_PATH, "spam")
ham_filenames = [name for name in sorted(os.listdir(HAM_DIR)) if len(name) > 20]
spam_filenames = [name for name in sorted(os.listdir(SPAM_DIR)) if len(name) > 20]
len(ham_filenames)
2500
len(spam_filenames)
500
We can use Python's email module to parse these emails (this handles headers, encoding, and so on):
import email
import email.policy
def load_email(is_spam, filename, spam_path=SPAM_PATH):

directory = "spam" if is_spam else "easy_ham"
with open(os.path.join(spam_path, directory, filename), "rb") as f:
return email.parser.BytesParser(policy=email.policy.default).parse(f)
ham_emails = [load_email(is_spam=False, filename=name) for name in ham_filenames]

spam_emails = [load_email(is_spam=True, filename=name) for name in spam_filenames]
Let's look at one example of ham and one example of spam, to get a feel of what the data looks like:
print(ham_emails[1].get_content().strip())
Martin A posted:
Tassos Papadopoulos, the Greek sculptor behind the plan, judged that the
limestone of Mount Kerdylio, 70 miles east of Salonika and not far from the
Mount Athos monastic community, was ideal for the patriotic sculpture.

As well as Alexander's granite features, 240 ft high and 170 ft wide, a
museum, a restored amphitheatre and car park for admiring crowds are
planned
---------------------
So is this mountain limestone or granite?
If it's limestone, it'll weather pretty fast.
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To unsubscribe from this group, send an email to:
[email protected]
Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/
print(spam_emails[6].get_content().strip())
Help wanted. We are a 14 year old fortune 500 company, that is

growing at a tremendous rate. We are looking for individuals who
want to work from home.
This is an opportunity to make an excellent income. No experience

is required. We will train you.
So if you are looking to be employed from home with a career that has
vast opportunities, then go:
http://www.basetel.com/wealthnow
We are looking for energetic and self motivated people. If that is you
than click on the link and fill out the form, and one of our
employement specialist will contact you.
To be removed from our link simple go to:
http://www.basetel.com/remove.html
4139vOLW7-758DoDY1425FRhM1-764SMFc8513fCsLl40
Some emails are actually multipart, with images and attachments (which can have their own attachments). Let's look at the various types of
structures we have:
def get_email_structure(email):
if isinstance(email, str):
return email
payload = email.get_payload()
if isinstance(payload, list):
return "multipart({})".format(", ".join([
get_email_structure(sub_email)
for sub_email in payload
]))
else:
return email.get_content_type()
from collections import Counter
def structures_counter(emails):
structures = Counter()
for email in emails:
structure = get_email_structure(email)
structures[structure] += 1
return structures
structures_counter(ham_emails).most_common()
[('text/plain', 2408),
('multipart(text/plain, application/pgp-signature)', 66),
('multipart(text/plain, text/html)', 8),
('multipart(text/plain, text/plain)', 4),
('multipart(text/plain)', 3),
('multipart(text/plain, application/octet-stream)', 2),
('multipart(text/plain, text/enriched)', 1),
('multipart(text/plain, application/ms-tnef, text/plain)', 1),
('multipart(multipart(text/plain, text/plain, text/plain), application/pgp-signature)',
1),
('multipart(text/plain, video/mng)', 1),
('multipart(text/plain, multipart(text/plain))', 1),
('multipart(text/plain, application/x-pkcs7-signature)', 1),
('multipart(text/plain, multipart(text/plain, text/plain), text/rfc822-headers)',
1),
('multipart(text/plain, multipart(text/plain, text/plain), multipart(multipart(text/plain, application/x-pkcs7-s
ignature)))',
1),
('multipart(text/plain, application/x-java-applet)', 1)]
structures_counter(spam_emails).most_common()
[('text/plain', 218),
('text/html', 183),
('multipart(text/plain, text/html)', 45),
('multipart(text/html)', 20),
('multipart(text/plain)', 19),
('multipart(multipart(text/html))', 5),
('multipart(text/plain, image/jpeg)', 3),
('multipart(text/html, application/octet-stream)', 2),
('multipart(text/plain, application/octet-stream)', 1),
('multipart(text/html, text/plain)', 1),
('multipart(multipart(text/html), application/octet-stream, image/jpeg)', 1),
('multipart(multipart(text/plain, text/html), image/gif)', 1),
('multipart/alternative', 1)]
It seems that the ham emails are more often plain text, while spam has quite a lot of HTML. Moreover, quite a few ham emails are signed
using PGP, while no spam is. In short, it seems that the email structure is useful information to have.
Now let's take a look at the email headers:
for header, value in spam_emails[0].items():

print(header,":",value)
Return-Path : <[email protected]>
Delivered-To : [email protected]
Received : from localhost (localhost [127.0.0.1]) by phobos.labs.spamassassin.taint.org (Postfix) with ESMTP id 1
36B943C32 for <zzzz@localhost>; Thu, 22 Aug 2002 08:17:21 -0400 (EDT)
Received : from mail.webnote.net [193.120.211.219] by localhost with POP3 (fetchmail-5.9.0) for zzzz@localhost (s
ingle-drop); Thu, 22 Aug 2002 13:17:21 +0100 (IST)
Received : from dd_it7 ([210.97.77.167]) by webnote.net (8.9.3/8.9.3) with ESMTP id NAA04623 for <zzzz@spamassass
in.taint.org>; Thu, 22 Aug 2002 13:09:41 +0100
From : [email protected]
Received : from r-smtp.korea.com - 203.122.2.197 by dd_it7 with Microsoft SMTPSVC(5.5.1775.675.6); Sat, 24 Aug
2002 09:42:10 +0900
To : [email protected]
Subject : Life Insurance - Why Pay More?
Date : Wed, 21 Aug 2002 20:31:57 -1600
MIME-Version : 1.0
Message-ID : <0103c1042001882DD_IT7@dd_it7>
Content-Type : text/html; charset="iso-8859-1"
Content-Transfer-Encoding : quoted-printable
There's probably a lot of useful information in there, such as the sender's email address ([email protected] looks fishy), but we will just
focus on the Subject header:
spam_emails[0]["Subject"]
'Life Insurance - Why Pay More?'
Okay, before we learn too much about the data, let's not forget to split it into a training set and a test set:
import numpy as np
from sklearn.model_selection import train_test_split
X = np.array(ham_emails + spam_emails, dtype=object)

y = np.array([0] * len(ham_emails) + [1] * len(spam_emails))
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)
Okay, let's start writing the preprocessing functions. First, we will need a function to convert HTML to plain text. Arguably the best way to do
this would be to use the great BeautifulSoup library, but I would like to avoid adding another dependency to this project, so let's hack a quick
& dirty solution using regular expressions (at the risk of un̨ho͞ly radiańcé destro҉ying all enli̍̈́̂ghtenment). The following function first
drops the <head> section, then converts all <a> tags to the word HYPERLINK, then it gets rid of all HTML tags, leaving only the plain text.
For readability, it also replaces multiple newlines with single newlines, and finally it unescapes html entities (such as > or ):
import re
from html import unescape
def html_to_plain_text(html):
text = re.sub('<head.*?>.*?</head>', '', html, flags=re.M | re.S | re.I)
text = re.sub('<a\s.*?>', ' HYPERLINK ', text, flags=re.M | re.S | re.I)
text = re.sub('<.*?>', '', text, flags=re.M | re.S)
text = re.sub(r'(\s*\n)+', '\n', text, flags=re.M | re.S)
return unescape(text)
Let's see if it works. This is HTML spam:
html_spam_emails = [email for email in X_train[y_train==1]

if get_email_structure(email) == "text/html"]
sample_html_spam = html_spam_emails[7]
print(sample_html_spam.get_content().strip()[:1000], "...")
<HTML><HEAD><TITLE></TITLE><META http-equiv="Content-Type" content="text/html; charset=windows-1252"><STYLE>A:lin

k {TEX-DECORATION: none}A:active {TEXT-DECORATION: none}A:visited {TEXT-DECORATION: none}A:hover {COLOR: #0033ff;
TEXT-DECORATION: underline}</STYLE><META content="MSHTML 6.00.2713.1100" name="GENERATOR"></HEAD>
<BODY text="#000000" vLink="#0033ff" link="#0033ff" bgColor="#CCCC99"><TABLE borderColor="#660000" cellSpacing="0
" cellPadding="0" border="0" width="100%"><TR><TD bgColor="#CCCC99" valign="top" colspan="2" height="27">
<font size="6" face="Arial, Helvetica, sans-serif" color="#660000">
<b>OTC</b></font></TD></TR><TR><TD height="2" bgcolor="#6a694f">
<font size="5" face="Times New Roman, Times, serif" color="#FFFFFF">
<b> Newsletter</b></font></TD><TD height="2" bgcolor="#6a694f"><div align="right"><font color="#FFFFFF">
<b>Discover Tomorrow's Winners </b></font></div></TD></TR><TR><TD height="25" colspan="2" bgcolor="#CCCC99">
<table width="100%" border="0" ...
And this is the resulting plain text:
print(html_to_plain_text(sample_html_spam.get_content())[:1000], "...")
OTC
Newsletter
Discover Tomorrow's Winners
For Immediate Release
Cal-Bay (Stock Symbol: CBYI)
Watch for analyst "Strong Buy Recommendations" and several advisory newsletters picking CBYI. CBYI has filed to
be traded on the OTCBB, share prices historically INCREASE when companies get listed on this larger trading excha
nge. CBYI is trading around 25 cents and should skyrocket to $2.66 - $3.25 a share in the near future.
Put CBYI on your watch list, acquire a position TODAY.
REASONS TO INVEST IN CBYI
A profitable company and is on track to beat ALL earnings estimates!
One of the FASTEST growing distributors in environmental & safety equipment instruments.
Excellent management team, several EXCLUSIVE contracts. IMPRESSIVE client list including the U.S. Air Force, Anh
euser-Busch, Chevron Refining and Mitsubishi Heavy Industries, GE-Energy & Environmental Research.
RAPIDLY GROWING INDUSTRY
Industry revenues exceed $900 million, estimates indicate that there could be as much as $25 billi ...
Great! Now let's write a function that takes an email as input and returns its content as plain text, whatever its format is:
def email_to_text(email):
html = None
for part in email.walk():
ctype = part.get_content_type()
if not ctype in ("text/plain", "text/html"):
continue
try:
content = part.get_content()
except: # in case of encoding issues
content = str(part.get_payload())
if ctype == "text/plain":
return content
else:
html = content
if html:
return html_to_plain_text(html)
print(email_to_text(sample_html_spam)[:100], "...")
OTC
Newsletter
Discover Tomorrow's Winners
For Immediate Release
Cal-Bay (Stock Symbol: CBYI)
Wat ...
Let's throw in some stemming! For this to work, you need to install the Natural Language Toolkit (NLTK). It's as simple as running the
following command (don't forget to activate your virtualenv first; if you don't have one, you will likely need administrator rights, or use the --
user option):
$ pip3 install nltk
try:
import nltk
stemmer = nltk.PorterStemmer()
for word in ("Computations", "Computation", "Computing", "Computed", "Compute", "Compulsive"):
print(word, "=>", stemmer.stem(word))
except ImportError:
print("Error: stemming requires the NLTK module.")
stemmer = None
Computations => comput

Computation => comput
Computing => comput
Computed => comput
Compute => comput
Compulsive => compuls
We will also need a way to replace URLs with the word "URL". For this, we could use hard core regular expressions but we will just use the
urlextract library. You can install it with the following command (don't forget to activate your virtualenv first; if you don't have one, you will
likely need administrator rights, or use the --user option):
$ pip3 install urlextract
# if running this notebook on Colab, we just pip install urlextract

try:
import google.colab
!pip install -q -U urlextract
except ImportError:
pass # not running on Colab
try:
import urlextract # may require an Internet connection to download root domain names

url_extractor = urlextract.URLExtract()
print(url_extractor.find_urls("Will it detect github.com and https://youtu.be/7Pq-S557XQU?t=3m32s"))
except ImportError:
print("Error: replacing URLs requires the urlextract module.")
url_extractor = None
['github.com', 'https://youtu.be/7Pq-S557XQU?t=3m32s']
We are ready to put all this together into a transformer that we will use to convert emails to word counters. Note that we split sentences into
words using Python's split() method, which uses whitespaces for word boundaries. This works for many written languages, but not all.
For example, Chinese and Japanese scripts generally don't use spaces between words, and Vietnamese often uses spaces even between
syllables. It's okay in this exercise, because the dataset is (mostly) in English.
from sklearn.base import BaseEstimator, TransformerMixin

class EmailToWordCounterTransformer(BaseEstimator, TransformerMixin):
def __init__(self, strip_headers=True, lower_case=True, remove_punctuation=True,
replace_urls=True, replace_numbers=True, stemming=True):
self.strip_headers = strip_headers
self.lower_case = lower_case
self.remove_punctuation = remove_punctuation
self.replace_urls = replace_urls
self.replace_numbers = replace_numbers
self.stemming = stemming
return self
X_transformed = []
for email in X:
text = email_to_text(email) or ""
if self.lower_case:
text = text.lower()
if self.replace_urls and url_extractor is not None:
urls = list(set(url_extractor.find_urls(text)))
urls.sort(key=lambda url: len(url), reverse=True)
for url in urls:
text = text.replace(url, " URL ")
if self.replace_numbers:
text = re.sub(r'\d+(?:\.\d*(?:[eE]\d+))?', 'NUMBER', text)
if self.remove_punctuation:
text = re.sub(r'\W+', ' ', text, flags=re.M)
word_counts = Counter(text.split())
if self.stemming and stemmer is not None:
stemmed_word_counts = Counter()
for word, count in word_counts.items():
stemmed_word = stemmer.stem(word)
stemmed_word_counts[stemmed_word] += count
word_counts = stemmed_word_counts
X_transformed.append(word_counts)
return np.array(X_transformed)
Let's try this transformer on a few emails:
X_few = X_train[:3]
X_few_wordcounts = EmailToWordCounterTransformer().fit_transform(X_few)
X_few_wordcounts
array([Counter({'chuck': 1, 'murcko': 1, 'wrote': 1, 'stuff': 1, 'yawn': 1, 'r': 1}),

Counter({'the': 11, 'of': 9, 'and': 8, 'all': 3, 'christian': 3, 'to': 3, 'by': 3, 'jefferson': 2, 'i': 2,
'have': 2, 'superstit': 2, 'one': 2, 'on': 2, 'been': 2, 'ha': 2, 'half': 2, 'rogueri': 2, 'teach': 2, 'jesu': 2,
'some': 1, 'interest': 1, 'quot': 1, 'url': 1, 'thoma': 1, 'examin': 1, 'known': 1, 'word': 1, 'do': 1, 'not': 1,
'find': 1, 'in': 1, 'our': 1, 'particular': 1, 'redeem': 1, 'featur': 1, 'they': 1, 'are': 1, 'alik': 1, 'found':
1, 'fabl': 1, 'mytholog': 1, 'million': 1, 'innoc': 1, 'men': 1, 'women': 1, 'children': 1, 'sinc': 1, 'introduct
': 1, 'burnt': 1, 'tortur': 1, 'fine': 1, 'imprison': 1, 'what': 1, 'effect': 1, 'thi': 1, 'coercion': 1, 'make':
1, 'world': 1, 'fool': 1, 'other': 1, 'hypocrit': 1, 'support': 1, 'error': 1, 'over': 1, 'earth': 1, 'six': 1, '
histor': 1, 'american': 1, 'john': 1, 'e': 1, 'remsburg': 1, 'letter': 1, 'william': 1, 'short': 1, 'again': 1, '
becom': 1, 'most': 1, 'pervert': 1, 'system': 1, 'that': 1, 'ever': 1, 'shone': 1, 'man': 1, 'absurd': 1, 'untrut
h': 1, 'were': 1, 'perpetr': 1, 'upon': 1, 'a': 1, 'larg': 1, 'band': 1, 'dupe': 1, 'import': 1, 'led': 1, 'paul'
: 1, 'first': 1, 'great': 1, 'corrupt': 1}),
Counter({'url': 4, 's': 3, 'group': 3, 'to': 3, 'in': 2, 'forteana': 2, 'martin': 2, 'an': 2, 'and': 2, 'w
e': 2, 'is': 2, 'yahoo': 2, 'unsubscrib': 2, 'y': 1, 'adamson': 1, 'wrote': 1, 'for': 1, 'altern': 1, 'rather': 1
, 'more': 1, 'factual': 1, 'base': 1, 'rundown': 1, 'on': 1, 'hamza': 1, 'career': 1, 'includ': 1, 'hi': 1, 'beli
ef': 1, 'that': 1, 'all': 1, 'non': 1, 'muslim': 1, 'yemen': 1, 'should': 1, 'be': 1, 'murder': 1, 'outright': 1,
'know': 1, 'how': 1, 'unbias': 1, 'memri': 1, 'don': 1, 't': 1, 'html': 1, 'rob': 1, 'sponsor': 1, 'number': 1, '
dvd': 1, 'free': 1, 'p': 1, 'join': 1, 'now': 1, 'from': 1, 'thi': 1, 'send': 1, 'email': 1, 'egroup': 1, 'com':
1, 'your': 1, 'use': 1, 'of': 1, 'subject': 1})],
dtype=object)
This looks about right!
Now we have the word counts, and we need to convert them to vectors. For this, we will build another transformer whose fit() method will
build the vocabulary (an ordered list of the most common words) and whose transform() method will use the vocabulary to convert word
counts to vectors. The output is a sparse matrix.
from scipy.sparse import csr_matrix
class WordCounterToVectorTransformer(BaseEstimator, TransformerMixin):

def __init__(self, vocabulary_size=1000):
self.vocabulary_size = vocabulary_size
total_count = Counter()
for word_count in X:
for word, count in word_count.items():
total_count[word] += min(count, 10)
most_common = total_count.most_common()[:self.vocabulary_size]
self.most_common_ = most_common
self.vocabulary_ = {word: index + 1 for index, (word, count) in enumerate(most_common)}
return self
rows = []
cols = []
data = []
for row, word_count in enumerate(X):
for word, count in word_count.items():
rows.append(row)
cols.append(self.vocabulary_.get(word, 0))
data.append(count)
return csr_matrix((data, (rows, cols)), shape=(len(X), self.vocabulary_size + 1))
vocab_transformer = WordCounterToVectorTransformer(vocabulary_size=10)
X_few_vectors = vocab_transformer.fit_transform(X_few_wordcounts)
X_few_vectors
<3x11 sparse matrix of type '<class 'numpy.longlong'>'

with 20 stored elements in Compressed Sparse Row format>
X_few_vectors.toarray()
array([[ 6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[99, 11, 9, 8, 3, 1, 3, 1, 3, 2, 3],
[67, 0, 1, 2, 3, 4, 1, 2, 0, 1, 0]], dtype=int64)
What does this matrix mean? Well, the 99 in the second row, first column, means that the second email contains 99 words that are not part of
the vocabulary. The 11 next to it means that the first word in the vocabulary is present 11 times in this email. The 9 next to it means that the
second word is present 9 times, and so on. You can look at the vocabulary to know which words we are talking about. The first word is "the",
the second word is "of", etc.
vocab_transformer.vocabulary_
{'the': 1,
'of': 2,
'and': 3,
'to': 4,
'url': 5,
'all': 6,
'in': 7,
'christian': 8,
'on': 9,
'by': 10}
We are now ready to train our first spam classifier! Let's transform the whole dataset:
from sklearn.pipeline import Pipeline
preprocess_pipeline = Pipeline([
("email_to_wordcount", EmailToWordCounterTransformer()),
("wordcount_to_vector", WordCounterToVectorTransformer()),
])
X_train_transformed = preprocess_pipeline.fit_transform(X_train)
Note: to be future-proof, we set solver="lbfgs" since this will be the default value in Scikit-Learn 0.22.
from sklearn.linear_model import LogisticRegression

log_clf = LogisticRegression(solver="lbfgs", max_iter=1000, random_state=42)

score = cross_val_score(log_clf, X_train_transformed, y_train, cv=3, verbose=3)
score.mean()
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.

[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 0.1s remaining: 0.0s
[CV] ................................................................
[CV] .................................... , score=0.981, total= 0.1s
[CV] ................................................................
[CV] .................................... , score=0.985, total= 0.2s
[CV] ................................................................
[Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 0.3s remaining: 0.0s
[CV] .................................... , score=0.991, total= 0.2s

[Parallel(n_jobs=1)]: Done 3 out of 3 | elapsed: 0.5s finished
0.9858333333333333
Over 98.5%, not bad for a first try! :) However, remember that we are using the "easy" dataset. You can try with the harder datasets, the
results won't be so amazing. You would have to try multiple models, select the best ones and fine-tune them using cross-validation, and so
on.
But you get the picture, so let's stop now, and just print out the precision/recall we get on the test set:
from sklearn.metrics import precision_score, recall_score
X_test_transformed = preprocess_pipeline.transform(X_test)
log_clf = LogisticRegression(solver="lbfgs", max_iter=1000, random_state=42)

log_clf.fit(X_train_transformed, y_train)
y_pred = log_clf.predict(X_test_transformed)
print("Precision: {:.2f}%".format(100 * precision_score(y_test, y_pred)))

print("Recall: {:.2f}%".format(100 * recall_score(y_test, y_pred)))
Precision: 95.88%
Recall: 97.89%

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Setup: This Notebook Contains All The Sample Code and Solutions To The Exercises in Chapter 3

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Chapter

Run in Google Colab

# Python ≥3.5 is required

# Scikit-Learn ≥0.20 is required

# to make this notebook's output stable across runs

# To plot pretty figures

# Where to save the figures

def save_fig(fig_id, tight_layout=True, fig_extension="png", resolution=300):

dict_keys(['data', 'target', 'frame', 'categories', 'feature_names', 'target_names', 'DESCR', 'details', 'url'])

Saving figure some_digit_plot

Saving figure more_digits_plot

X_train, X_test, y_train, y_test = X[:60000], X[60000:], y[:60000], y[60000:]

from sklearn.linear_model import SGDClassifier

sgd_clf = SGDClassifier(max_iter=1000, tol=1e-3, random_state=42)

from sklearn.model_selection import cross_val_score

array([0.95035, 0.96035, 0.9604 ])

from sklearn.model_selection import StratifiedKFold

skfolds = StratifiedKFold(n_splits=3, shuffle=True, random_state=42)

for train_index, test_index in skfolds.split(X_train, y_train_5):

Note: shuffle=True was omitted by mistake in previous releases of the book.

from sklearn.base import BaseEstimator

array([0.91125, 0.90855, 0.90915])

from sklearn.model_selection import cross_val_predict

from sklearn.metrics import confusion_matrix

y_train_perfect_predictions = y_train_5 # pretend we reached perfection

from sklearn.metrics import precision_score, recall_score

cm[1, 1] / (cm[1, 0] + cm[1, 1])

from sklearn.metrics import f1_score

cm[1, 1] / (cm[1, 1] + (cm[1, 0] + cm[0, 1]) / 2)

y_scores = cross_val_predict(sgd_clf, X_train, y_train_5, cv=3,

from sklearn.metrics import precision_recall_curve

precisions, recalls, thresholds = precision_recall_curve(y_train_5, y_scores)

def plot_precision_recall_vs_threshold(precisions, recalls, thresholds):

recall_90_precision = recalls[np.argmax(precisions >= 0.90)]

plt.figure(figsize=(8, 4)) # Not shown

Saving figure precision_recall_vs_threshold_plot

(y_train_pred == (y_scores > 0)).all()

def plot_precision_vs_recall(precisions, recalls):

Saving figure precision_vs_recall_plot

threshold_90_precision = thresholds[np.argmax(precisions >= 0.90)]

y_train_pred_90 = (y_scores >= threshold_90_precision)

fpr, tpr, thresholds = roc_curve(y_train_5, y_scores)

def plot_roc_curve(fpr, tpr, label=None):

Saving figure roc_curve_plot

from sklearn.metrics import roc_auc_score

from sklearn.ensemble import RandomForestClassifier

y_scores_forest = y_probas_forest[:, 1] # score = proba of positive class

recall_for_forest = tpr_forest[np.argmax(fpr_forest >= fpr_90)]

Saving figure roc_curve_comparison_plot

y_train_pred_forest = cross_val_predict(forest_clf, X_train, y_train_5, cv=3)

svm_clf = SVC(gamma="auto", random_state=42)

array([[ 2.81585438, 7.09167958, 3.82972099, 0.79365551, 5.8885703 ,

array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], dtype=uint8)

from sklearn.multiclass import OneVsRestClassifier

array([[-31893.03095419, -34419.69069632, -9530.63950739,

cross_val_score(sgd_clf, X_train, y_train, cv=3, scoring="accuracy")

array([0.87365, 0.85835, 0.8689 ])

from sklearn.preprocessing import StandardScaler

array([0.8983, 0.891 , 0.9018])