# 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)
from sklearn.datasets import fetch_openml
mnist = fetch_openml('mnist_784', version=1)
mnist.keys()
X, y = mnist["data"], mnist["target"]
X.shape
y.shape
28 * 28
%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]
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:]
y_train_5 = (y_train == 5) # True for all 5s, False for all other digits
y_test_5 = (y_test == 5)
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)
sgd_clf.predict([some_digit])
from sklearn.model_selection import cross_val_score
cross_val_score(sgd_clf, X_train, y_train_5, cv=3, scoring="accuracy")
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
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")
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)
y_train_perfect_predictions = y_train_5 # pretend we reached perfection
confusion_matrix(y_train_5, y_train_perfect_predictions)
from sklearn.metrics import precision_score, recall_score
precision_score(y_train_5, y_train_pred)
cm = confusion_matrix(y_train_5, y_train_pred)
cm[1, 1] / (cm[0, 1] + cm[1, 1])
recall_score(y_train_5, y_train_pred)
cm[1, 1] / (cm[1, 0] + cm[1, 1])
from sklearn.metrics import f1_score
f1_score(y_train_5, y_train_pred)
cm[1, 1] / (cm[1, 1] + (cm[1, 0] + cm[0, 1]) / 2)
y_scores = sgd_clf.decision_function([some_digit])
y_scores
threshold = 0
y_some_digit_pred = (y_scores > threshold)
y_some_digit_pred
threshold = 8000
y_some_digit_pred = (y_scores > threshold)
y_some_digit_pred
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()
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
y_train_pred_90 = (y_scores >= threshold_90_precision)
precision_score(y_train_5, y_train_pred_90)
recall_score(y_train_5, y_train_pred_90)
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)
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.figure(figsize=(8, 6))
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
roc_auc_score(y_train_5, y_scores_forest)
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)
recall_score(y_train_5, y_train_pred_forest)
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])
some_digit_scores = svm_clf.decision_function([some_digit])
some_digit_scores
np.argmax(some_digit_scores)
svm_clf.classes_
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_)
sgd_clf.fit(X_train, y_train)
sgd_clf.predict([some_digit])
sgd_clf.decision_function([some_digit])
cross_val_score(sgd_clf, X_train, y_train, cv=3, scoring="accuracy")
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")
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
# 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)
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.figure(figsize=(8,8))
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
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)
knn_clf.predict([some_digit])
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")
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