ML assignment Lab Module 2

# 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()

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()

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))

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()

(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()

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()

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()

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()

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()

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()

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()

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")