def cross_validation_example():
""" Slightly more complex example : Perform grid search cross-validation to find optimal parameters for MinCq using
rbf kernels as voters.
"""
# We load iris dataset, We convert the labels to be -1 or 1, and we split it in two parts: train and test.
dataset = load_iris()
dataset.target[dataset.target == 0] = -1
dataset.target[dataset.target == 2] = -1
X_train, X_test, y_train, y_test = train_test_split(dataset.data, dataset.target, random_state=42)
# The learning algorithm and its parameters.
learner = MinCqLearner(mu=0.0001, voters_type='kernel', kernel='rbf', gamma=0.0)
learner_params = {'mu': [0.0001, 0.001, 0.01],
'gamma': [0.0, 0.1, 1.0, 10]}
cv_classifier = GridSearchCV(learner, learner_params, scoring=accuracy_scorer)
cv_classifier = cv_classifier.fit(X_train, y_train)
predictions_train = cv_classifier.predict(X_train)
predictions_test = cv_classifier.predict(X_test)
print_sklearn_grid_scores("Iris", "RbfMinCq", learner_params, cv_classifier.grid_scores_)
print("Best parameters: {}".format(str(cv_classifier.best_params_)))
print("Training set risk: {:.4f}".format(zero_one_loss(y_train, predictions_train)))
print("Testing set risk: {:.4f}".format(zero_one_loss(y_test, predictions_test)))
def drawLearningCurve(model, x_train, y_train, x_test, y_test, num_points = 50):
# adapted from http://sachithdhanushka.blogspot.de/2013/09/learning-curve-generator-for-learning.html
train_error = np.zeros(num_points)
crossval_error = np.zeros(num_points)
sizes = np.linspace(2, len(x_train), num=num_points).astype(int)
for i,size in enumerate(sizes):
#getting the predicted results of the model
model.fit(x_train[:size], y_train[:size])
#compute the validation error
y_pred = model.predict(x_test[:size])
crossval_error[i] = zero_one_loss(y_test[:size], y_pred, normalize=True)
#compute the training error
y_pred = model.predict(x_train[:size])
train_error[i] = zero_one_loss(y_train[:size], y_pred, normalize=True)
#draw the plot
print crossval_error
print train_error
fig,ax = plt.subplots()
ax.plot(sizes,crossval_error,lw = 2, label='cross validation error')
ax.plot(sizes,train_error, lw = 4, label='training error')
ax.set_xlabel('cross val error')
ax.set_ylabel('rms error')
ax.legend(loc = 0)
ax.set_title('Learning Curve' )
return fig
def plot_adaclassifier(classifier, n_estimators, X_train, X_test, y_train, y_test):
fig = plt.figure()
ax = fig.add_subplot(111)
#ax.plot([1, n_estimators], [dt_stump_err] * 2, 'k-',
# label='Decision Stump Error')
#ax.plot([1, n_estimators], [dt_err] * 2, 'k--',
# label='Decision Tree Error')
ada_err_test = np.zeros((n_estimators,))
for i, y_pred in enumerate(classifier.staged_predict(X_test)):
ada_err_test[i] = zero_one_loss(y_pred, y_test)
ada_err_train = np.zeros((n_estimators,))
for i, y_pred in enumerate(classifier.staged_predict(X_train)):
ada_err_train[i] = zero_one_loss(y_pred, y_train)
ax.plot(np.arange(n_estimators) + 1, ada_err_test,
label='AdaBoost Test Error',
color='red')
ax.plot(np.arange(n_estimators) + 1, ada_err_train,
label='AdaBoost Train Error',
color='blue')
ax.set_ylim((0.0, 1.0))
ax.set_xlabel('n_estimators')
ax.set_ylabel('error rate')
leg = ax.legend(loc='upper right', fancybox=True)
leg.get_frame().set_alpha(0.7)
return fig
def test_grid(features, target):
'''
Given a list of models for each genre, run the features through the models to
predict target labels, and compare the predictions to the true target labels.
'''
genre_list = ['animated', 'action', 'comedy', 'drama', 'family', 'fantasy', \
'horror', 'musical', 'mystery', 'romance', 'sci-fi', 'thriller', 'war', 'western']
ypred_mat = np.empty([target.shape[0], target.shape[1]])
for i in xrange(target.shape[1]):
filename = '../data/is_' + genre_list[i] + '.pkl'
ypred = test_prediction(filename, features, target[:,i])
for j, prob in enumerate(ypred):
ypred_mat[j,i] = prob
with open('../data/grid_pkl_500.txt','w') as f:
f.write("Model rounded by .25\n")
yrd = round_by(ypred_mat, .25)
f.write( metrics.classification_report(target, yrd) )
f.write( "Percent of misclassification: {}\n".format(metrics.zero_one_loss(target, yrd)) )
f.write("\nModel rounded by .3\n")
yrd = round_by(ypred_mat, .3)
f.write( metrics.classification_report(target, yrd) )
f.write( "Percent of misclassification: {}\n".format(metrics.zero_one_loss(target, yrd)) )
f.write("\nModel rounded by .2\n")
yrd = round_by(ypred_mat, .2)
f.write( metrics.classification_report(target, yrd) )
f.write( "Percent of misclassification: {}\n".format(metrics.zero_one_loss(target, yrd)) )
f.write("\nModel rounded by .1\n")
yrd = round_by(ypred_mat, .1)
f.write( metrics.classification_report(target, yrd) )
f.write( "Percent of misclassification: {}\n".format(metrics.zero_one_loss(target, yrd)) )
def run_gamma(x, y):
perc = 0.6
n = x.shape[0]
gamma_list = (np.power(2.0, range(-4, 12))/(n*perc)).tolist()
n_iter = 2
train_err_libsvm = np.zeros((len(gamma_list), n_iter))
test_err_libsvm = np.zeros((len(gamma_list), n_iter))
train_err_dsvm = np.zeros((len(gamma_list), n_iter))
test_err_dsvm = np.zeros((len(gamma_list), n_iter))
train_err_pegasos = np.zeros((len(gamma_list), n_iter))
test_err_pegasos = np.zeros((len(gamma_list), n_iter))
ss = cv.StratifiedShuffleSplit(y, n_iter=n_iter, test_size=1-perc, train_size=None, random_state=0)
for k, (train, test) in enumerate(ss):
ntr = len(train)
lmda = 1.0 / ntr
print "#iter: %d" % k
x_train, x_test, y_train, y_test = x[train], x[test], y[train], y[test]
mM_scale = preprocessing.MinMaxScaler(feature_range=(-1, 1))
x_train = mM_scale.fit_transform(x_train)
x_test = mM_scale.transform(x_test)
for j, gm in enumerate(gamma_list):
print "check lamda %f, gamma %f" % (lmda, gm)
clf = svm.SVC(C=lmda * ntr, kernel='rbf', gamma=gm, cache_size=600)
clf.fit(x_train, y_train)
pred = clf.predict(x_train)
train_err_libsvm[j, k] = zero_one_loss(y_train, pred)
pred = clf.predict(x_test)
test_err_libsvm[j, k] = zero_one_loss(y_test, pred)
dsvm = DualKSVM(lmda=lmda, gm=gm, kernelstr='rbf', nsweep=ntr/2, b=5, c=1)
dsvm.fit(x_train, y_train, x_test, y_test, )
train_err_dsvm[j, k] = dsvm.err_tr[-1]
test_err_dsvm[j, k] = dsvm.err_te[-1]
kpega = Pegasos(ntr, lmda, gm, nsweep=2, batchsize=2)
kpega.train_test(x_train, y_train, x_test, y_test)
train_err_pegasos[j, k] = kpega.err_tr[-1]
test_err_pegasos[j, k] = kpega.err_te[-1]
avg_train_err_libsvm = np.mean(train_err_libsvm, axis=1)
avg_test_err_libsvm = np.mean(test_err_libsvm, axis=1)
avg_train_err_dsvm = np.mean(train_err_dsvm, axis=1)
avg_test_err_dsvm = np.mean(test_err_dsvm, axis=1)
avg_train_err_pegasos = np.mean(train_err_pegasos, axis=1)
avg_test_err_pegasos = np.mean(test_err_pegasos, axis=1)
plt.figure()
# color_list = ['b', 'r', 'g', 'c', ]
# marker_list = ['o', 'x', '>', 's']
plt.loglog(gamma_list, avg_train_err_libsvm, 'bo-', label='libsvm train')
plt.loglog(gamma_list, avg_test_err_libsvm, 'ro-', label='libsvm test')
plt.loglog(gamma_list, avg_train_err_dsvm, 'gx-', label='dsvm train')
plt.loglog(gamma_list, avg_test_err_dsvm, 'cx-', label='dsvm test')
plt.loglog(gamma_list, avg_train_err_pegasos, 'mD-', label='pegasos train')
plt.loglog(gamma_list, avg_test_err_pegasos, 'kD-', label='pegasos test')
plt.legend(bbox_to_anchor=(0, 1.17, 1, .1), loc=2, ncol=2, mode="expand", borderaxespad=0)
plt.savefig('../output/usps_diff_gamma.pdf')
def build_tree(clf,type,i,X_train, X_test, y_train, y_test,attribute_names,class_names):
print("------------Run "+type+ "_"+str(i)+"----------")
clf.fit(X_train, y_train)
print("Training error =", zero_one_loss(y_train, clf.predict(X_train)))
predicted_test = clf.predict(X_test)
print("Test error =",zero_one_loss(y_test, predicted_test ) )
figure_name = type+"_"+str(i)
visualize_tree(clf,attribute_names,class_names,figure_name)
print(classification_report( y_test,predicted_test ))
print(confusion_matrix(y_test,predicted_test))
return zero_one_loss(y_test, predicted_test )
def simple_classification_example():
""" Simple example : with fixed hyperparameters, run four versions of MinCq on a single dataset.
"""
# MinCq parameters, fixed to a given value as this is a simple example.
mu = 0.001
# We load iris dataset, We convert the labels to be -1 or 1, and we split it in two parts: train and test.
dataset = load_iris()
dataset.target[dataset.target == 0] = -1
dataset.target[dataset.target == 2] = -1
X_train, X_test, y_train, y_test = train_test_split(dataset.data, dataset.target, random_state=42)
# We train MinCq using decision stumps as voters, on the training set.
learner = MinCqLearner(mu, voters_type='stumps')
learner.fit(X_train, y_train)
# We predict the train and test labels and print the risk.
predictions_train = learner.predict(X_train)
predictions_test = learner.predict(X_test)
print("\nStumpsMinCq")
print("-----------")
print("Training set risk: {:.4f}".format(zero_one_loss(y_train, predictions_train)))
print("Testing set risk: {:.4f}\n".format(zero_one_loss(y_test, predictions_test)))
# We do the same again, now with a linear kernel.
learner = MinCqLearner(mu, voters_type='kernel', kernel='linear')
learner.fit(X_train, y_train)
predictions_train = learner.predict(X_train)
predictions_test = learner.predict(X_test)
print("\nLinearMinCq")
print("-----------")
print("Training set risk: {:.4f}".format(zero_one_loss(y_train, predictions_train)))
print("Testing set risk: {:.4f}\n".format(zero_one_loss(y_test, predictions_test)))
# We do the same again, now with a polynomial kernel.
learner = MinCqLearner(mu, voters_type='kernel', kernel='poly')
learner.fit(X_train, y_train)
predictions_train = learner.predict(X_train)
predictions_test = learner.predict(X_test)
print("\nPolyMinCq")
print("-----------")
print("Training set risk: {:.4f}".format(zero_one_loss(y_train, predictions_train)))
print("Testing set risk: {:.4f}\n".format(zero_one_loss(y_test, predictions_test)))
# We do the same again, now with an RBF kernel.
learner = MinCqLearner(mu, voters_type='kernel', kernel='rbf', gamma=0.0)
learner.fit(X_train, y_train)
predictions_train = learner.predict(X_train)
predictions_test = learner.predict(X_test)
print("\nRbfMinCq")
print("--------")
print("Training set risk: {:.4f}".format(zero_one_loss(y_train, predictions_train)))
print("Testing set risk: {:.4f}\n".format(zero_one_loss(y_test, predictions_test)))
def test_losses():
"""Test loss functions"""
y_true, y_pred, _ = make_prediction(binary=True)
n_samples = y_true.shape[0]
n_classes = np.size(unique_labels(y_true))
# Classification
# --------------
with warnings.catch_warnings(record=True):
# Throw deprecated warning
assert_equal(zero_one(y_true, y_pred), 11)
assert_almost_equal(zero_one_loss(y_true, y_pred),
11 / float(n_samples), 2)
assert_equal(zero_one_loss(y_true, y_pred, normalize=False), 11)
assert_almost_equal(zero_one_loss(y_true, y_true), 0.0, 2)
assert_almost_equal(hamming_loss(y_true, y_pred),
2 * 11. / (n_samples * n_classes), 2)
assert_equal(accuracy_score(y_true, y_pred),
1 - zero_one_loss(y_true, y_pred))
with warnings.catch_warnings(True):
# Throw deprecated warning
assert_equal(zero_one_score(y_true, y_pred),
1 - zero_one_loss(y_true, y_pred))
# Regression
# ----------
assert_almost_equal(mean_squared_error(y_true, y_pred),
10.999 / n_samples, 2)
assert_almost_equal(mean_squared_error(y_true, y_true),
0.00, 2)
# mean_absolute_error and mean_squared_error are equal because
# it is a binary problem.
assert_almost_equal(mean_absolute_error(y_true, y_pred),
10.999 / n_samples, 2)
assert_almost_equal(mean_absolute_error(y_true, y_true), 0.00, 2)
assert_almost_equal(explained_variance_score(y_true, y_pred), 0.16, 2)
assert_almost_equal(explained_variance_score(y_true, y_true), 1.00, 2)
assert_equal(explained_variance_score([0, 0, 0], [0, 1, 1]), 0.0)
assert_almost_equal(r2_score(y_true, y_pred), 0.12, 2)
assert_almost_equal(r2_score(y_true, y_true), 1.00, 2)
assert_equal(r2_score([0, 0, 0], [0, 0, 0]), 1.0)
assert_equal(r2_score([0, 0, 0], [0, 1, 1]), 0.0)
def lr(X_train, y_train, X_test, y_test):
# Tune the hyperparameter
maxScore = float("-inf")
maxC = 0
for c in np.arange(0.1, 1, 0.1):
clf = LogisticRegression(penalty="l2", C=c).fit(X_train, y_train)
scores = cross_val_score(clf, X_train, y_train, cv=5)
mean = np.mean(scores)
print("C: %f and Score: %f" % (c, mean))
if mean > maxScore:
maxScore = mean
maxC = c
# Train the model
print("MaxC: %f" % maxC)
print("MaxScore: %f" % maxScore)
clf = LogisticRegression(penalty="l2", C=maxC).fit(X_train, y_train)
# Predict labels for the test data
pred = clf.predict(X_test)
pred_prob = clf.predict_proba(X_test)
# Calculate the misclassification rate
mc_rate = zero_one_loss(y_test, pred)
print("MC rate: %f" % mc_rate)
# Calculate the ROC curve
prob = pred_prob[:, 1:]
roc_score = roc_auc_score(y_test, prob)
print("ROC score: %f" % roc_score)
return (mc_rate, roc_score)
def train(min_samples_leaf, max_depth, dataset):
mlflow.log_param("min_samples_leaf", min_samples_leaf)
mlflow.log_param("max_depth", max_depth)
clf = DecisionTreeClassifier(min_samples_leaf=min_samples_leaf, max_depth=max_depth)
print("Classifier:",clf)
clf.fit(dataset.data, dataset.target)
expected = dataset.target
predicted = clf.predict(dataset.data)
mlflow.sklearn.log_model(clf, "model")
write_artifact('confusion_matrix.txt',str(metrics.confusion_matrix(expected, predicted)))
write_artifact('classification_report.txt',metrics.classification_report(expected, predicted))
auc = metrics.auc(expected, predicted)
accuracy_score = metrics.accuracy_score(expected, predicted)
zero_one_loss = metrics.zero_one_loss(expected, predicted)
mlflow.log_metric("auc", auc)
mlflow.log_metric("accuracy_score", accuracy_score)
mlflow.log_metric("zero_one_loss", zero_one_loss)
print("Params: min_samples_leaf={} max_depth={}".format(min_samples_leaf,max_depth))
print("Metrics: auc={} accuracy_score={} zero_one_loss={}".format(auc,accuracy_score,zero_one_loss))
def experiment_neighbors_k_nearest_neighbors():
avgError = []
x_learners = []
for k_neighbors in range(1, 20, 1):
k = 10
skf = StratifiedKFold(labels,n_folds=k)
averageError = 0.0
for train_index, test_index in skf:
X_train, X_test = mfcc[:,train_index], mfcc[:,test_index]
y_train, y_test = labels[train_index], labels[test_index]
knc = KNeighborsClassifier(n_neighbors=k_neighbors, weights='distance')
knc.fit(X_train.T,y_train)
y_pred = knc.predict(X_test.T)
error = zero_one_loss(y_pred,y_test)
print error
averageError += (1./k) * error
print "Average error: %4.2f%s" % (100 * averageError,'%')
avgError.append(averageError)
x_learners.append(k_neighbors)
plt.plot(x_learners, avgError)
plt.ylabel('Average Error (k=10)')
plt.xlabel('Number of Neighbors')
plt.title('Error as a function of the number of neighbors taken into consideration')
plt.show()
def experiment_pca_n_components_random_forest():
pca = decomposition.PCA()
rf = RandomForestClassifier(n_estimators=maxLearners, max_depth = maxDepth, warm_start = False)
pipe = Pipeline(steps=[('pca', pca), ('rf', rf)])
avgError = []
x_learners = []
for k_components in range(10, 100, 10):
k = 10
skf = StratifiedKFold(labels,n_folds=k)
averageError = 0.0
for train_index, test_index in skf:
X_train, X_test = mfcc[:,train_index], mfcc[:,test_index]
y_train, y_test = labels[train_index], labels[test_index]
estimator = GridSearchCV(pipe, dict(pca__n_components=[k_components]))
estimator.fit(X_train.T,y_train)
y_pred = estimator.predict(X_test.T)
error = zero_one_loss(y_pred,y_test)
print error
averageError += (1./k) * error
print "Average error: %4.2f%s" % (100 * averageError,'%')
avgError.append(averageError)
x_learners.append(k_components)
plt.plot(x_learners, avgError)
plt.ylabel('Average Error (k=10)')
plt.xlabel('Number of Components')
plt.title('Error as a function of the number of components')
plt.show()
def classify_by_KNeighbors(train_x, train_Y, test_x, test_Y, colors, category):
classifier = KNeighborsClassifier(n_neighbors=3, n_jobs=-1)
classifier.fit(train_x, train_Y)
pred_y = classifier.predict(test_x)
results = confusion_matrix(test_Y, pred_y)
error = zero_one_loss(test_Y, pred_y)
accuracy = metrics.accuracy_score(test_Y, pred_y)
classification = metrics.classification_report(test_Y, pred_y)
pca = PCA(n_components=2)
train_x_pca_cont = pca.fit_transform(test_x)
plt.figure(figsize=(15, 10))
for color, cat in zip(colors, category.keys()):
plt.scatter(train_x_pca_cont[pred_y == cat, 0],
train_x_pca_cont[pred_y == cat, 1],
color=color,
alpha=.8,
lw=2,
label=cat)
plt.legend(loc='best', shadow=False, scatterpoints=1)
plt.title(" KNeibors result visualization")
plt.show()
plt.figure(figsize=(10, 7))
sn.heatmap(results, annot=True, fmt='d')
plt.title("KNeighbors confusion matrix: \n")
print("KNeighbors confusion matrix: ", results)
print("Error: ", error * 100, '%')
print("Accuracy: ", accuracy * 100, "%")
print("Classification report:" "\n", classification)
return pred_y
def experiment_estimators_AdaBoostRandomForest():
avgError = []
x_learners = []
rf = RandomForestClassifier(n_estimators=maxLearners, max_depth = maxDepth, warm_start = False)
for lr in frange(0.01, 1., 0.25):
k = 10
skf = StratifiedKFold(labels,n_folds=k)
averageError = 0.0
for train_index, test_index in skf:
X_train, X_test = mfcc[:,train_index], mfcc[:,test_index]
y_train, y_test = labels[train_index], labels[test_index]
adb = AdaBoostClassifier(base_estimator=rf, n_estimators=100, learning_rate=lr)
adb.fit(X_train.T,y_train)
y_pred = adb.predict(X_test.T)
error = zero_one_loss(y_pred,y_test)
print error
averageError += (1./k) * error
print "Average error: %4.2f%s" % (100 * averageError,'%')
avgError.append(averageError)
x_learners.append(lr)
# graph the errors now.
plt.plot(x_learners, avgError)
plt.ylabel('Average Error (k=10)')
plt.xlabel('Learning Rate')
plt.title('Error as a function of the learning rate')
plt.show()
def evaluate_naivebayes(classifier, test_reviews):
# For computing metrics
ref_set = collections.defaultdict(set)
test_set = collections.defaultdict(set)
ref_set_arr = []
test_set_arr = []
# Create gold standard and predicted labels
for i, (feat, label) in enumerate(test_reviews):
# Predict
observed = classifier.classify(feat)
ref_set[label].add(i)
test_set[observed].add(i)
label = 0 if label == "neg" else 1
observed = 0 if observed == "neg" else 1
ref_set_arr.append(label)
test_set_arr.append(observed)
print('pos precision:', precision(ref_set['pos'], test_set['pos']))
print('pos recall:', recall(ref_set['pos'], test_set['pos']))
print('neg precision:', precision(ref_set['neg'], test_set['neg']))
print('neg recall:', recall(ref_set['neg'], test_set['neg']))
print('misclassification rate', zero_one_loss(ref_set_arr, test_set_arr))
print('most informative features',
classifier.show_most_informative_features(10))
def experiment_learners_random_forest():
avgError = []
x_learners = []
for maxLearners in range(10, 150, 20):
k = 10
skf = StratifiedKFold(labels,n_folds=k)
averageError = 0.0
for train_index, test_index in skf:
X_train, X_test = mfcc[:,train_index], mfcc[:,test_index]
y_train, y_test = labels[train_index], labels[test_index]
rf = RandomForestClassifier(n_estimators=maxLearners, max_depth = maxDepth, warm_start = False)
rf.fit(X_train.T,y_train)
y_pred = rf.predict(X_test.T)
error = zero_one_loss(y_pred,y_test)
print error
averageError += (1./k) * error
print "Average error: %4.2f%s" % (100 * averageError,'%')
avgError.append(averageError)
x_learners.append(maxLearners)
plt.plot(x_learners, avgError)
plt.ylabel('Average Error (k=10)')
plt.xlabel('Max Learners')
plt.title('Error as a function of the number of learners')
plt.show()
def perceptron_v0(max_iters, pred_every, X_train, X_test, Y_train, Y_test):
acc = []
w = np.zeros([num_digits, X_train.shape[1]])
iters = 0
while iters < max_iters:
# Train
for i in range(len(Y_train)):
iters += 1
for int_class in range(num_digits):
Y_mult = 1 if Y_train[i] == int_class else -1
if Y_mult * np.dot(w[int_class], X_train[i]) <= 0:
w[int_class] += Y_mult * X_train[i]
if iters % pred_every == 0:
# Predict
Y_pred = np.zeros(Y_test.shape)
for k in range(len(Y_test)):
preds = np.zeros(num_digits)
for int_class in range(num_digits):
preds[int_class] = np.dot(w[int_class], X_test[k])
Y_pred[k] = np.argmax(preds)
# Test
acc.append(zero_one_loss(Y_test, Y_pred))
return acc
def train(self, train_data, tr_lab=None):
"""
Method that performs training. It compares the clustering labels on training set
(i.e., A(X) computed by :class:`reval.relative_validation.RelativeValidation.clust_method`) against
the labels obtained from the classification algorithm
(i.e., f(X), computed by :class:`reval.relative_validation.RelativeValidation.class_method`).
It returns the misclassification error, the supervised model fitted to the data,
and both clustering and classification labels.
:param train_data: training dataset.
:type train_data: ndarray, (n_samples, n_features)
:param tr_lab: cluster labels found during CV for clustering methods with no `n_clusters` parameter.
If not None the clustering method is not performed on the whole test set. Default None.
:type tr_lab: list
:return: misclassification error, fitted supervised model object, clustering and classification labels.
:rtype: float, object, ndarray (n_samples,)
"""
if tr_lab is None:
clustlab_tr = self.clust_method.fit_predict(train_data) # A_k(X)
else:
clustlab_tr = tr_lab
if len([cl for cl in clustlab_tr if cl >= 0]) == 0:
logging.info(
f"No clusters found during training with {self.clust_method}.")
return None
fitclass_tr = self.class_method.fit(train_data, clustlab_tr)
classlab_tr = fitclass_tr.predict(train_data)
misclass = zero_one_loss(clustlab_tr, classlab_tr)
return misclass, fitclass_tr, clustlab_tr
def inline(inputfile, outputfile):
# data = np.loadtxt(sys.stdin)
data = np.loadtxt(inputfile, delimiter=',')
if np.ndim(data) == 1:
data = np.array([data])
train_x = data[:, 1:]
train_y = data[:, 0]
candidate_size = 1000
evaluation_size = 1000
x, y = make_classification(n_samples=candidate_size + evaluation_size,
n_features=2,
n_informative=1,
n_redundant=1,
n_clusters_per_class=1,
random_state=37)
eval_x = x[candidate_size:]
eval_y = y[candidate_size:]
learner = KNeighborsClassifier(n_neighbors=1)
learner = learner.fit(train_x, train_y)
pred_y = learner.predict(eval_x)
with open(outputfile, 'w') as f:
l = zero_one_loss(eval_y, pred_y)
f.write(str(l))
def __train_with_cross_validation(self):
"""
This method enables sk-learn algorithms to perform KFold-cross-validation.
The method also initiates the cnvrg experiment with all its metrics.
"""
scores = cross_validate(estimator=self.__model,
X=self.__x_train.values,
y=self.__y_train.values,
cv=self.__cross_val_folds,
return_train_score=True,
scoring=['neg_mean_squared_error', 'accuracy'],
return_estimator=True)
train_acc_cv = scores['train_accuracy']
train_err_cv = (-1) * scores['train_neg_mean_squared_error']
val_acc_cv = scores['test_accuracy']
val_err_cv = (-1) * scores['test_neg_mean_squared_error']
self.__model = scores['estimator'][-1]
y_pred = self.__model.predict(self.__x_test.values)
test_acc = accuracy_score(self.__y_test.values, y_pred)
test_loss = zero_one_loss(self.__y_test.values, y_pred)
self.__metrics.update({
'train_acc': train_acc_cv,
'train_loss': train_err_cv,
'train_loss_type': 'MSE',
'validation_acc': val_acc_cv,
'validation_loss': val_err_cv,
'validation_loss_type': 'MSE',
'test_acc': test_acc,
'test_loss': test_loss,
'test_loss_type': 'zero_one_loss'
})
self.__plot_all(y_pred)
def test(self, test_data, fit_model):
"""
Method that compares test set clustering labels (i.e., A(X'), computed by
:class:`reval.relative_validation.RelativeValidation.clust_method`) against
the (permuted) labels obtained through the classification algorithm fitted to the training set
(i.e., f(X'), computed by
:class:`reval.relative_validation.RelativeValidation.class_method`).
It returns the misclassification error, together with
both clustering and classification labels.
:param test_data: test dataset.
:type test_data: ndarray, (n_samples, n_features)
:param fit_model: fitted supervised model.
:type fit_model: class
:return: misclassification error, clustering and classification labels.
:rtype: float, dictionary of ndarrays (n_samples,)
"""
clustlab_ts = self.clust_method.fit_predict(test_data) # A_k(X')
if len([cl for cl in clustlab_ts if cl >= 0]) == 0:
logging.info(
f"No clusters found during testing with {self.clust_method}")
return None
classlab_ts = fit_model.predict(test_data)
bestperm = kuhn_munkres_algorithm(classlab_ts,
clustlab_ts) # array of integers
misclass = zero_one_loss(classlab_ts, bestperm)
return misclass, bestperm
def nb(X_train, y_train, X_test, y_test):
# Tune the hyperparameter
maxScore = float("-inf")
maxA = 0
for a in np.arange(0.1, 1, 0.1):
clf = MultinomialNB(alpha=a).fit(X_train, y_train)
scores = cross_val_score(clf, X_train, y_train, cv=5)
mean = np.mean(scores)
print("A: %f and Score: %f" % (a, mean))
if mean > maxScore:
maxScore = mean
maxA = a
# Train the model
print("MaxA: %f" % maxA)
print("MaxScore: %f" % maxScore)
clf = MultinomialNB(alpha=maxA).fit(X_train, y_train)
# Predict labels for the test data
pred = clf.predict(X_test)
pred_prob = clf.predict_proba(X_test)
# Calculate the misclassification rate
mc_rate = zero_one_loss(y_test, pred)
print("MC rate: %f" % mc_rate)
# Calculate the ROC curve
prob = pred_prob[:, 1:]
roc_score = roc_auc_score(y_test, prob)
print("ROC score: %f" % roc_score)
return (mc_rate, roc_score)
def rf(X_train, y_train, X_test, y_test):
# Tune the hyperparameter
maxScore = float("-inf")
maxN = 0
for n in np.arange(100, 600, 100):
clf = RandomForestClassifier(n_estimators=n).fit(X_train, y_train)
scores = cross_val_score(clf, X_train, y_train, cv=5)
mean = np.mean(scores)
print("N: %f and Score: %f" % (n, mean))
if mean > maxScore:
maxScore = mean
maxN = n
# Train the model
print("MaxN: %f" % maxN)
print("MaxScore: %f" % maxScore)
clf = RandomForestClassifier(n_estimators=maxN).fit(X_train, y_train)
# Predict labels for the test data
pred = clf.predict(X_test)
pred_prob = clf.predict_proba(X_test)
# Calculate the misclassification rate
mc_rate = zero_one_loss(y_test, pred)
print("MC rate: %f" % mc_rate)
# Calculate the ROC curve
prob = pred_prob[:, 1:]
roc_score = roc_auc_score(y_test, prob)
curve = roc_curve(y_test, prob)
print("ROC score: %f" % roc_score)
return (mc_rate, roc_score, curve)
def cross_valid(h, y, ratio_list):
"""
cross validation to tune the best cap probability for soft-margin boosting
"""
print " find optimal ratio"
n_samples = h.shape[0]
n_folds = 4
ntr = n_samples/n_folds
ratio_list = ratio_list[ratio_list >= 1.0/ntr]
kf = cv.KFold(n=n_samples, n_folds=n_folds)
err_tr = np.zeros((n_folds, len(ratio_list)))
err_te = np.zeros((n_folds, len(ratio_list)))
k = 0
for tr_ind, te_ind in kf:
print "nfold: %d" % (k)
xtr, ytr, xte, yte = h[tr_ind, :], y[tr_ind], h[te_ind, :], y[te_ind]
for i, r in enumerate(ratio_list):
pd = ParaBoost(epsi=0.005, has_dcap=True, ratio=r)
pd.train(xtr, ytr)
pred = pd.test_h(xte)
err_te[k, i] = zero_one_loss(y_true=yte, y_pred=pred)
err_tr[k, i] = pd.err_tr[-1]
k += 1
err_te_avg = np.mean(err_te, axis=0)
err_tr_avg = np.mean(err_tr, axis=0)
arg = np.argmin(err_te_avg)
best_ratio = ratio_list[arg]
err = err_te_avg[arg]
return best_ratio
def clf_bias_var(clf, X, y, n_replicas):
roc_auc_scorer = get_scorer("roc_auc")
# roc_auc_scorer(clf, X_test, y_test)
auc_scores = []
error_scores = []
counts = np.zeros(X.shape[0], dtype = np.float64)
sum_preds = np.zeros(X.shape[0], dtype = np.float64)
for it in xrange(n_replicas):
# generate train sets and test sets
train_indices = np.random.randint(X.shape[0], size = X.shape[0])
# get test sets
in_train = np.unique(train_indices)
mask = np.ones(X.shape[0], dtype = np.bool)
mask[in_train] = False
test_indices = np.arange(X.shape[0])[mask]
clf.fit(X[train_indices], y[train_indices])
auc_scores.append(roc_auc_scorer(clf, X[test_indices], y[test_indices]))
error_scores.append(zero_one_loss(y[test_indices], clf.predict(X[test_indices])))
preds = clf.predict(X)
for index in test_indices:
counts[index] += 1
sum_preds[index] += preds[index]
test_mask = (counts > 0) # indices of samples that have been tested
# print('counts mean: {}'.format(np.mean(counts)))
# print('counts standard derivation: {}'.format(np.std(counts)))
bias, var = bias_var(y[test_mask], sum_preds[test_mask], counts[test_mask], n_replicas)
return auc_scores, error_scores, bias, var
def exercise_1():
X, y = make_blobs(n_samples=1000,centers=50, n_features=2, random_state=0)
n_samples = len(X)
kf = cross_validation.KFold(n_samples, n_folds=10, shuffle=False, random_state=None)
# kf = cross_validation.ShuffleSplit(1000,n_iter=25, test_size=0.1, train_size=0.9, random_state=None)
error_total = np.zeros([49, 1], dtype=float)
for k in range(1,50):
error = []
clf = KNeighborsClassifier(n_neighbors=k)
for train_index, test_index in kf:
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
clf.fit(X_train, y_train)
error.append( zero_one_loss(y_test, clf.predict(X_test)) )
# error.append(clf.predict(X_test))
# error.append( 1. - clf.score(X_test, y_test) ) #, accuracy_score(y_test, clf.predict(X_test))
# error.append(mean_squared_error(y_test, clf.predict(X_test)))
# error.append()
# print error
error_total[k-1, 0] = np.array(error).mean()
# print error_total
x = np.arange(1,50, dtype=int)
plt.style.use('ggplot')
plt.plot(x, error_total[:, 0], '#009999', marker='o')
# plt.errorbar(x, accuracy_lst[:, 0], accuracy_lst[:, 1], linestyle='None', marker='^')
plt.xticks(x, x)
plt.margins(0.02)
plt.xlabel('K values')
plt.ylabel('Missclasification Error')
plt.show()
def exercise_2():
#connect to openml api
apikey = 'ca2397ea8a2cdd9707ef39d76576e786'
connector = APIConnector(apikey=apikey)
dataset = connector.download_dataset(44)
X, y, attribute_names = dataset.get_dataset(target=dataset.default_target_attribute, return_attribute_names=True)
kf = cross_validation.KFold(len(X), n_folds=10, shuffle=False, random_state=0)
error = []
error_mean = []
lst = [int(math.pow(2, i)) for i in range(0, 8)]
clf = RandomForestClassifier(oob_score=True,
max_features="auto",
random_state=0)
for i in lst:
error_mean = []
for train_index, test_index in kf:
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
clf.set_params(n_estimators=i)
clf.fit(X_train, y_train)
error_mean.append( zero_one_loss(y_test, clf.predict(X_test)) )
error.append( np.array(error_mean).mean() )
#plot
plt.style.use('ggplot')
plt.plot(lst, error, '#009999', marker='o')
plt.xticks(lst)
plt.show()
def test_sample_order_invariance():
y_true, y_pred, _ = make_prediction(binary=True)
y_true_shuffle, y_pred_shuffle = shuffle(y_true, y_pred,
random_state=0)
for metric in [accuracy_score,
hamming_loss,
zero_one_loss,
lambda y1, y2: zero_one_loss(y1, y2, normalize=False),
precision_score,
recall_score,
f1_score,
lambda y1, y2: fbeta_score(y1, y2, beta=2),
lambda y1, y2: fbeta_score(y1, y2, beta=0.5),
matthews_corrcoef,
mean_absolute_error,
mean_squared_error,
explained_variance_score,
r2_score]:
assert_almost_equal(metric(y_true, y_pred),
metric(y_true_shuffle, y_pred_shuffle),
err_msg="%s is not sample order invariant"
% metric)
def fit(self, data, target): no_of_stages = self.no_of_stages decision_stump = DecisionTreeClassifier(criterion='gini', splitter='best', max_depth=1, max_features=1) #No. of samples m = data.shape[0] weight = numpy.ones(m) weight = numpy.float32(weight)/m Alpha = numpy.zeros(no_of_stages) classifiers = [] for i in range(no_of_stages): decision_stump = decision_stump.fit(data, target, sample_weight = weight) classifiers.append(decision_stump) pred = decision_stump.predict(data) error = zero_one_loss(target, pred, normalize=True, sample_weight = weight) if error > 0.5: print 'error value is greater than 0.5!' beta = error/(1-error) if beta != 0: weight[pred == target] = weight[pred==target]*beta weight = weight / weight.sum() print weight # beta_mat = (pred==target)*beta # beta_mat[beta_mat==0] = 1 # weight = numpy.multiply(weight, beta_mat) if beta > 0: alpha = math.log(1/beta) else: alpha = 10000 # make alpha extremly large if decision stump is totally correct. Alpha[i] = alpha self.Alpha = Alpha self.classifiers = classifiers
def run_ordinal_regression(X_train, y_train, X_test, y_test, ordinal_regression_model):
print("Running ordinal regression with multiclass labels...")
ordinal_regression_clf = ordinal_regression_model(alpha=ALPHA, max_iter=MAX_ITER)
ordinal_regression_clf.fit(X_train, y_train)
y_pred = ordinal_regression_clf.predict(X_train)
training_err = metrics.zero_one_loss(y_train, y_pred, normalize=False)
print("%.4f = Training accuracy for ordinal regression with multiclass labels" %
(float(len(y_train) - training_err) / len(y_train)))
y_pred = ordinal_regression_clf.predict(X_test)
test_err = metrics.zero_one_loss(y_test, y_pred, normalize=False)
print("%.4f = Test accuracy for ordinal regression with multiclass labels" %
(float(len(y_test) - test_err) / len(y_test)))
return float(len(y_test) - test_err) / len(y_test)
def apply_dbn(files, main_driver=1):
"""
Applies DBN for identifying trips which are not from the driver of interest
"""
(X_train, Y_train, weight, X, driver_trip_arr) = \
get_train_data(files, main_driver)
a = np.empty(shape=[0, 2])
net = DBN([len(COL), 10, 2],
learn_rates=0.3,
learn_rate_decays=0.9,
epochs=10,
verbose=0)
net.fit(X_train, Y_train)
Y_dbn = net.predict(X_train)
print main_driver, ':', 1 - zero_one_loss(Y_train, Y_dbn)
# print "Classification report:"
# print classification_report(Y_train, preds)
i = 0
Y = net.predict(X)
for y in Y:
driver_trip = driver_trip_arr[i][0]
prob = str(int(Y[i]))
a = np.append(a, np.array([[driver_trip, prob]]), axis=0)
i = i + 1
print main_driver, ': ', sum([1 for p in a if p[1] == '1'])
return a
def compare_manual_vs_model():
with open(DATA_FOLDER + "labels_int.p", "r") as f:
y_dict = pickle.load(f)
print "Loading test data"
X_test, y_test, filenames_test = dataset.load_test()
y_pred = joblib.load("../models/pred_ml_improved.pkl")
relevant = []
for pred, correct, filename in zip(y_pred, y_test, filenames_test):
if filename in FILES:
relevant.append((pred, correct, filename, CLASSIFICATIONS[filename]))
model_predictions, correct, filename, manual_predictions = zip(*relevant)
manual_predictions = learn.multilabel_binary_y(manual_predictions)
model_predictions = np.array(model_predictions)
correct = learn.multilabel_binary_y(correct)
rules = infer_topology.infer_topology_rules()
improved_manual = infer_topology.apply_topology_rules(rules, manual_predictions)
prediction_names = ["MODEL", "MANUAL", "IMPROVED_MANUAL"]
predictions = [model_predictions, manual_predictions, improved_manual]
for name, pred in zip(prediction_names, predictions):
print "\n{}\n--".format(name)
print "Zero-one classification loss", zero_one_loss(correct, pred)
print "Hamming loss", hamming_loss(correct, pred)
print "Precision:", precision_score(correct, pred, average="weighted", labels=label_list)
print "Recall :", recall_score(correct, pred, average="weighted", labels=label_list)
print "F1 score :", f1_score(correct, pred, average="weighted", labels=label_list)
def classify(self, model, test_y, test_x):
pred = model.predict(test_x)
if not self.multi:
rec, spec, acc = self.score(pred, test_y)
return rec, spec, acc
else:
return 1 - zero_one_loss(test_y, pred)
def use_sklearn_ml_knn():
"""
:return:
"""
base_path = os.getcwd()
# train_x = np.load(os.path.join(base_path, 'dataset/train_x.npy'), allow_pickle=True)
# train_y = np.load(os.path.join(base_path, 'dataset/train_y.npy'), allow_pickle=True)
train_x = np.load(os.path.join(base_path, 'my_dataset/train_x.npy'),
allow_pickle=True)
train_y = np.load(os.path.join(base_path, 'my_dataset/train_y.npy'),
allow_pickle=True)
new_train_y = []
for tup in train_y:
tmp = []
for label in tup:
if label == 0:
tmp.append(0)
else:
tmp.append(1)
new_train_y.append(tmp)
# test_x = np.load('dataset/test_x.npy', allow_pickle=True)
# test_y = np.load('dataset/test_y.npy', allow_pickle=True)
test_x = np.load('my_dataset/test_x.npy', allow_pickle=True)
test_y = np.load('my_dataset/test_y.npy', allow_pickle=True)
new_test_y = []
for tup in test_y:
tmp = []
for label in tup:
if label == 0:
tmp.append(0)
else:
tmp.append(1)
new_test_y.append(tmp)
new_test_y = np.array(new_test_y)
classifier = MLkNN2(train_x, np.array(new_train_y), k=10)
# classifier.fit(train_x, np.array(new_train_y))
classifier.fit()
predictions = classifier.predict(test_x)
predictions = convert_prediction(predictions)
# hamming_loss = HammingLoss(new_test_y, predictions)
h_loss = hamming_loss(new_test_y, predictions)
z = zero_one_loss(new_test_y, predictions)
c = coverage_error(new_test_y, predictions)
r = label_ranking_loss(new_test_y, predictions)
a = average_precision_score(new_test_y, predictions)
print('hamming_loss = ', h_loss)
print('0-1_loss = ', z)
print('cover_loss = ', c)
print('rank_loss = ', r)
print('average_loss = ', a)
def modelevaluation(self, y_test, y_pred, features, ml):
'''
confusion = metrics.confusion_matrix(y_test, y_pred)
print("Confussion matrix: \n", confusion)
TP = confusion[1, 1]
TN = confusion[0, 0]
FP = confusion[0, 1]
FN = confusion[1, 0]
'''
data = {}
data[features] = []
print('----------REPORT-----------')
print("Accuracy: ", metrics.accuracy_score(y_test, y_pred))
print("Balanced Accuracy: ",
metrics.balanced_accuracy_score(
y_test, y_pred,
sample_weight=None)) #Average of label accuracies
print("Precision: ", metrics.precision_score(y_test, y_pred))
print("Recall: ", metrics.recall_score(y_test, y_pred))
print("F1 score macro: ",
metrics.f1_score(y_test, y_pred, average='macro'))
print("F1 score micro: ",
metrics.f1_score(y_test, y_pred, average='micro'))
print("F-Beta score: ", metrics.fbeta_score(y_test, y_pred, beta=10))
print("AUC Score: ", metrics.roc_auc_score(y_test, y_pred))
print("Zero_one_loss", metrics.zero_one_loss(y_test, y_pred))
print(
"Matthews_corrcoef", metrics.matthews_corrcoef(y_test, y_pred)
) #Gives equal weight to all TP, TN, FP, FN (Better than F1-score)
print(
"Brier score: ", metrics.brier_score_loss(y_test, y_pred)
) #The Brier score is calculated as the mean squared error between the expected probabilities for the positive class (e.g. 1.0) and the predicted probabilities. (Better than log_loss)
print(
"Cohen keppa score: ", metrics.cohen_kappa_score(y_test, y_pred)
) #It basically tells you how much better your classifier is performing over the performance of a classifier that simply guesses at random according to the frequency of each class.
print("Classification_report\n",
metrics.classification_report(y_test, y_pred, output_dict=True))
print('----------REPORT-----------')
with open('evaluations/model_evaluation.json', 'r+') as opened_file:
current_json = json.load(opened_file)
current_json[features] = {
'model':
'' + ml,
'accuracy':
metrics.accuracy_score(y_test, y_pred),
'fraud_precision':
metrics.classification_report(
y_test, y_pred, output_dict=True)['1']['precision'],
'fraud_recall':
metrics.classification_report(y_test, y_pred,
output_dict=True)['1']['recall'],
'fraud_f1_score':
metrics.classification_report(
y_test, y_pred, output_dict=True)['1']['f1-score']
}
opened_file.seek(0)
opened_file.truncate(0)
json.dump(current_json, opened_file)
def main():
test_label = [1]*100 + [2]*100 + [3]*100 + [4]*100 + [5]*100 + \
[6]*100 + [7]*100 + [8]*100
filename = sys.argv[1]
with open(filename, 'rU') as f:
pred = [rec for rec in csv.reader(f, delimiter=',')]
pred = sum(pred, [])
pred = [int(x) for x in pred]
print zero_one_loss(pred, test_label)
cm = confusion_matrix(test_label, pred, labels=[1, 2, 3, 4, 5, 6, 7, 8])
np.set_printoptions(precision=2)
fig = plt.figure()
fig.patch.set_facecolor('white')
plot_confusion_matrix(cm)
plt.show()
def compute_evaluation(true_matrix, predict_matrix):
h = hamming_loss(true_matrix, predict_matrix)
z = zero_one_loss(true_matrix, predict_matrix)
c = coverage_error(true_matrix, predict_matrix)
result = [h, z, c]
return result
def test_logitboost_hastie_fitting():
c = LogitBoostClassifier(base_estimator=DecisionTreeRegressor(max_depth=1),
n_estimators=30,
learning_rate=1.0)
data = Hastie_10_2()
c.fit(data.data, np.sign(data.labels))
assert_array_less(c.estimator_errors_, 0.5)
assert zero_one_loss(np.sign(data.labels), c.predict(data.data)) < 0.2
def sklearnSvm():
svc = SVC()
score = make_scorer(zero_one_loss,greater_is_better=False)
clf = GridSearchCV(svc, tuned_parameters, scoring = score,cv = 5)
clf.fit(data_Train_feature,data_Train_label)
test_true, test_predict = data_Test_label, clf.predict(data_Test_feature)
train_ture, train_predict = data_Train_label, clf.predict(data_Train_feature)
err_Train = zero_one_loss(train_ture, train_predict)
err_Test = zero_one_loss(test_true, test_predict)
print(clf.best_params_)
print(classification_report(test_true, test_predict))
print(err_Train)
print(err_Test)
def kNN(pickle_file):
fin = open(pickle_file, "rb")
train, test = pickle.load(fin)
X_tr, y_tr = train
X_te, y_te = test
n = [1,3,5,7,9]
figure = plt.figure()
for spot in range(len(n)):
knc = KNeighborsClassifier(n_neighbors = n[spot])
knc.fit(X_tr, y_tr)
predicted_tr = (knc.predict(X_tr))
predicted_te = (knc.predict(X_te))
axis = figure.add_subplot(1,5,spot+1)
xtr_1 = []
xtr_2 = []
for pair in X_tr:
xtr_1.append(pair[0])
xtr_2.append(pair[1])
xte_1 = []
xte_2 = []
for pair in X_te:
xte_1.append(pair[0])
xte_2.append(pair[1])
colors = ListedColormap(['#FF0000', '#0000FF'])
axis.scatter(xtr_1,xtr_2, c = y_tr, cmap = colors, edgecolors = 'k')
axis.scatter(xte_1,xte_2, marker="*", c = y_te, cmap = colors, edgecolors = 'k')
x1min, x1max, x2min, x2max = helpers.get_bounds(X_tr)
helpers.plot_decision_boundary(axis, knc, x1min, x1max, x2min, x2max)
axis.set_title("n_neighbors = " + str(n[spot]))
tr_loss = round(zero_one_loss(y_tr,predicted_tr),2)
te_loss = round(zero_one_loss(y_te,predicted_te),2)
axis.set_xlabel("Tr loss: " + str(tr_loss)+"\n Te loss: " + str(te_loss))
plt.show()
def drawLearningCurve(model, x_train, y_train, x_test, y_test, num_points = 50):
# adapted from http://sachithdhanushka.blogspot.de/2013/09/learning-curve-generator-for-learning.html
train_error = np.zeros(num_points)
crossval_error = np.zeros(num_points)
#Fix a based array that has an entry from both classes
baseitem0 = list(y_train).index(0)
xbase = x_train[baseitem0,:]
ybase = [y_train[baseitem0]]
baseitem1 = list(y_train).index(1)
xbase = np.vstack((xbase, x_train[baseitem1,:]))
ybase = np.append(ybase,y_train[baseitem1])
#ybase = np.vstack((ybase, y_train[baseitem1]))
x_train = np.delete(x_train, (baseitem0), axis=0)
x_train = np.delete(x_train, (baseitem1), axis=0)
y_train = np.delete(y_train, (baseitem0), axis=0)
y_train = np.delete(y_train, (baseitem1), axis=0)
sizes = np.linspace(1, len(x_train), num=num_points).astype(int)
for i,size in enumerate(sizes):
#getting the predicted results of the model
xvals = np.vstack((xbase, x_train[:size,:]))
yvals = np.append(ybase,y_train[:size])
model.fit(xvals, yvals)
#compute the validation error
y_pred = model.predict(x_test[:size])
crossval_error[i] = zero_one_loss(y_test[:size], y_pred, normalize=True)
#compute the training error
y_pred = model.predict(x_train[:size])
train_error[i] = zero_one_loss(y_train[:size], y_pred, normalize=True)
#draw the plot
print crossval_error
print train_error
fig,ax = plt.subplots()
ax.plot(sizes+1,crossval_error,lw = 2, label='cross validation error')
ax.plot(sizes+1,train_error, lw = 4, label='training error')
ax.set_xlabel('cross val error')
ax.set_ylabel('rms error')
ax.legend(loc = 0)
ax.set_title('Learning Curve' )
return fig
def train_svm(kernels=None, labels=None):
if kernels is None:
trn_k, trn_y = load_svmlight_file(
'dns_data_kernel/trn_kernel_mat.svmlight')
val_k, val_y = load_svmlight_file(
'dns_data_kernel/val_kernel_mat.svmlight')
tst_k, tst_y = load_svmlight_file(
'dns_data_kernel/tst_kernel_mat.svmlight')
trn_k = trn_k.todense()
val_k = val_k.todense()
tst_k = tst_k.todense()
else:
trn_k, trn_y = kernels[0], labels[0]
val_k, val_y = kernels[1], labels[1]
tst_k, tst_y = kernels[2], labels[2]
pred = dict()
C = [0.01, 0.1, 1, 10, 100]
val_errs = []
for c in C:
m = svm.SVC(kernel='precomputed', C=c)
m.fit(trn_k, trn_y)
trn_label = m.predict(trn_k)
val_label = m.predict(val_k)
trn_err = zero_one_loss(trn_label, trn_y)
val_err = zero_one_loss(val_label, val_y)
pred[c] = [trn_err, val_err, sum(m.n_support_)]
val_errs.append(val_err)
opt_c = C[val_errs.index(min(val_errs))]
m = svm.SVC(kernel='precomputed', C=opt_c)
m.fit(trn_k, trn_y)
tst_label = m.predict(tst_k)
tst_err = zero_one_loss(tst_label, tst_y)
print("Test Error: {0:.2%}".format(tst_err))
return pred
def runTests(X_train, X_test, y_train, y_test):
zeroSums = np.zeros((13))
count = 0
#Knn
neighborList = [1, 3, 5, 7, 9]
for value in neighborList:
kNeighbors = KNeighborsClassifier(n_neighbors=value)
kNeighbors.fit(X_train, y_train)
predTest = kNeighbors.predict(X_test)
zeroSums[count] = zero_one_loss(y_test, predTest)
count += 1
#dTree
depthList = [1, 2, 3, 4, None]
for depth in depthList:
dTree = DecisionTreeClassifier(max_depth=depth)
dTree.fit(X_train, y_train)
predTest = dTree.predict(X_test)
zeroSums[count] = zero_one_loss(y_test, predTest)
count += 1
#svms
linSVM = SVC(kernel='linear')
linSVM.fit(X_train, y_train)
predTest = linSVM.predict(X_test)
zeroSums[count] = zero_one_loss(y_test, predTest)
count += 1
rbfSVM = SVC(kernel='rbf')
rbfSVM.fit(X_train, y_train)
predTest = rbfSVM.predict(X_test)
zeroSums[count] = zero_one_loss(y_test, predTest)
count += 1
polySVM = SVC(kernel='poly', degree=3)
polySVM.fit(X_train, y_train)
predTest = polySVM.predict(X_test)
zeroSums[count] = zero_one_loss(y_test, predTest)
count += 1
#print(zeroSums)
return zeroSums
def benchmark(clf):
t0 = time()
clf.fit(X_train, y_train)
train_time = time() - t0
t0 = time()
pred = clf.predict(X_test)
test_time = time() - t0
err = metrics.zero_one_loss(y_test, pred, normalize=True)
return err, train_time, test_time
def test_group_zero_one_loss_unnormalized():
result = metrics.group_zero_one_loss(Y_true,
Y_pred,
groups,
normalize=False)
expected_overall = skm.zero_one_loss(Y_true, Y_pred, False)
assert result.overall == expected_overall
def basic(scheduler_address, backends):
ESTIMATORS = {
'RandomForest': RandomForestClassifier(n_estimators=100),
'ExtraTreesClassifier': ExtraTreesClassifier(n_estimators=100)
}
X_train, X_test, y_train, y_test = load_data()
print_data(X_train, y_train, X_test, y_test)
BACKENDS = build_backends(backends, scheduler_address, X_train, y_train)
print("Training Classifiers")
print("====================")
error, train_time, test_time = {}, {}, {}
for est_name, estimator in sorted(ESTIMATORS.items()):
for backend, backend_kwargs in BACKENDS:
print("Training %s with %s backend... " % (est_name, backend),
end="")
estimator_params = estimator.get_params()
estimator.set_params(
**{
p: RANDOM_STATE
for p in estimator_params if p.endswith("random_state")
})
if "n_jobs" in estimator_params:
estimator.set_params(n_jobs=-1)
# Key for the results
name = '%s, %s' % (est_name, backend)
with parallel_backend(backend, **backend_kwargs):
time_start = time()
estimator.fit(X_train, y_train)
train_time[name] = time() - time_start
time_start = time()
y_pred = estimator.predict(X_test)
test_time[name] = time() - time_start
error[name] = zero_one_loss(y_test, y_pred)
print("done")
print()
print("Classification performance:")
print("===========================")
print("%s %s %s %s" %
("Classifier ", "train-time", "test-time", "error-rate"))
print("-" * 44)
for name in sorted(error, key=error.get):
print("%s %s %s %s" % (name, ("%.4fs" % train_time[name]),
("%.4fs" % test_time[name]),
("%.4f" % error[name])))
print()
def test_prediction(filename, features, target):
'''
Given the filename of a pickled estimator, unpickle the estimator, run the
features through it, compare the results with the target, and return the
results.
'''
estimator = pickle.load( open( filename, "rb" ) )
res = estimator.predict_proba(features)[:,0]
print "\nResults for {0}: \n".format(filename)
print "\nRounded by .25\n"
yrd = round_by(res, .25)
print metrics.classification_report(target, yrd)
print "Percent of misclassification: {}\n".format(metrics.zero_one_loss(target, yrd))
print "\nRounded by .1\n"
yrd = round_by(res, .1)
print metrics.classification_report(target, yrd)
print "Percent of misclassification: {}\n".format(metrics.zero_one_loss(target, yrd))
return res
def votingClassifier():
print(colored("------Voting Classification-------", 'red'))
# models
random_forest = RandomForestClassifier(criterion='entropy',
max_depth=30,
n_estimators=48,
random_state=0)
clf_lr = LogisticRegression()
clf_knn = KNeighborsClassifier(n_neighbors=7)
# build classifier
model = VotingClassifier(estimators=[('rf', random_forest),
('knn', clf_knn)],
voting='soft',
n_jobs=-1,
weights=[2, 1])
print("Training the Voting classification.......")
# start timer
starttime = timeit.default_timer() # start timer
cnn = CondensedNearestNeighbour(random_state=42) # doctest: +SKIP
# train
model.fit(train_x, train_Y)
print("The time difference is :", timeit.default_timer() - starttime)
print("Predicting test data.......")
# predict
y_pred = model.predict(test_x)
# results
c_matrix = confusion_matrix(test_Y, y_pred)
error = zero_one_loss(test_Y, y_pred)
score = accuracy_score(test_Y, y_pred)
# display results
print('Confusion Matrix\n---------------------------\n', c_matrix)
print('---------------------------')
print("Error: {:.4f}%".format(error * 100))
print("Accuracy Score: {:.4f}%".format(score * 100))
print(classification_report(test_Y, y_pred))
print('accuracy: ', c_matrix.diagonal() / c_matrix.sum(axis=1))
# Plot non-normalized confusion matrix
disp = plot_confusion_matrix(model,
test_x,
test_Y,
cmap=plt.cm.Greens,
values_format='.0f',
xticks_rotation='horizontal')
plt.title("Confusion Matrix for Voting Classifier")
plt.show()
def benchmark(clf):
t0 = time()
clf.fit(X_train, y_train)
train_time = time() - t0
t0 = time()
pred = clf.predict(X_test)
test_time = time() - t0
err = metrics.zero_one_loss(y_test, pred) / float(pred.shape[0])
return err, train_time, test_time
def benchmark(clf):
t0 = time()
clf.fit(X_train, y_train)
train_time = time() - t0
t0 = time()
pred = clf.predict(X_test)
test_time = time() - t0
err = metrics.zero_one_loss(y_test, pred) / float(pred.shape[0])
return err, train_time, test_time
def compute_error(targets, predictions, binary):
mse = mean_squared_error(targets, predictions)
loss = 0
# fraction of misclassifications
if binary:
predictions = np.where(predictions >= 0, 1, -1)
loss = zero_one_loss(targets, predictions, normalize=True)
return loss, mse
def compute_evaluation(true_matrix, predict_matrix):
h = hamming_loss(true_matrix, predict_matrix)
z = zero_one_loss(true_matrix, predict_matrix)
c = coverage_error(true_matrix, predict_matrix) - 1
r = label_ranking_loss(true_matrix, predict_matrix)
a = average_precision_score(true_matrix, predict_matrix)
result = [h, z, c, r, a]
return result
def benchmark(clf):
t0 = time()
clf.fit(X_train, y_train)
train_time = time() - t0
t0 = time()
pred = clf.predict(X_test)
test_time = time() - t0
err = metrics.zero_one_loss(y_test, pred, normalize=True)
return err, train_time, test_time
def vde(y_true, y_pred):
"""
Voicing Decision Error
----------------------
Proportion of frames for which an incorrect voiced/unvoiced decision is
made.
"""
return zero_one_loss(y_true, y_pred)
def NB(trainvector, trainlabels, testvector, testlabels):
from sklearn.naive_bayes import GaussianNB
Multi = GaussianNB()
Multi.fit(trainvector, trainlabels)
error = zero_one_loss(trainlabels,
Multi.predict(trainvector),
normalize=False)
errorrate = zero_one_loss(trainlabels, Multi.predict(trainvector))
accuracy = accuracy_score(testlabels, Multi.predict(testvector))
#print('No of errors = %d and error rate= %f of the training data' % (error, errorrate))
errort = zero_one_loss(testlabels,
Multi.predict(testvector),
normalize=False)
errorratet = zero_one_loss(testlabels, Multi.predict(testvector))
#print('No of errors = %d and error rate= %f of the testing data' % (error, errorrate))
return error, errorrate, errort, errorratet, accuracy
def question2(Wp, Wnp):
tssSet = [100, 250, 500, 1000, 2000]
kMeanAvg = np.array([])
kMeanSD = np.array([])
sKMeanAvg = np.array([])
sKMeanSD = np.array([])
for skm in range(2):
sphericalKMeans = bool(skm)
title = "Spherical KMeans NBC Analysis" if sphericalKMeans else "KMeans NBC Analysis"
Tp = KMeans(n_clusters=50, n_init=10)
Tnp = KMeans(n_clusters=50, n_init=10)
if sphericalKMeans:
Tp = SphericalKMeans(n_clusters=50, n_init=10)
Tnp = SphericalKMeans(n_clusters=50, n_init=10)
print "TP"
Tp.fit(Wp)
print "TNP"
Tnp.fit(Wnp)
TList = TopicList(Wp, Tp, Wnp, Tnp)
data = np.transpose(TList.X)
classifiers = np.append(np.ones(len(data)/2,dtype=int), np.zeros(len(data)/2, dtype=int))
clf = GaussianNB()
for tss in tssSet:
print tss
kf = KFold(len(data), n_folds=10, shuffle=True)
zeroOneLoss = np.array([])
for train, test_indeces in kf:
train_indeces = np.random.permutation(train)[:tss]
test_set = data[test_indeces]
train_set = data[train_indeces]
clf.fit(train_set, classifiers[train_indeces])
y_pred = clf.predict(test_set)# y_pred = [1, 2, 3, 4]
y_true = classifiers[test_indeces]# y_true = [2, 2, 3, 4]
zeroOneLoss = np.append(zeroOneLoss, zero_one_loss(y_true, y_pred))#.25 <-returns zero one loss percentage
if sphericalKMeans:
sKMeanAvg = np.append(sKMeanAvg, np.average(zeroOneLoss))
sKMeanSD = np.append(sKMeanSD, np.std(zeroOneLoss) / np.sqrt(10))
else:
kMeanAvg = np.append(kMeanAvg, np.average(zeroOneLoss))
kMeanSD = np.append(kMeanSD, np.std(zeroOneLoss) / np.sqrt(10))
np.savetxt(title + '.csv',np.row_stack((tssSet,kMeanAvg, kMeanSD,sKMeanAvg,sKMeanSD)),delimiter=',')
fig = plt.figure()
fig.suptitle(title, fontsize=14, fontweight='bold')
ax = fig.add_subplot(111)
ax.set_xlabel('training set sizes')
ax.set_ylabel('Zero-One Loss')
ax.plot(tssSet, kMeanAvg, 'r-', tssSet, sKMeanAvg, 'b-')
ax.errorbar(tssSet, kMeanAvg, yerr=kMeanSD, fmt='ro')
ax.errorbar(tssSet, sKMeanAvg, yerr=sKMeanSD, fmt='bo')
ax.axis([50, 2050, 0, 1])
plt.savefig(title)
plt.show()
def test_logitboost_musk_fitting():
c = LogitBoostClassifier(
base_estimator=DecisionTreeRegressor(max_depth=1),
n_estimators=30,
learning_rate=1.0
)
data = MUSK1()
c.fit(data.data, np.sign(data.labels))
assert_array_less(c.estimator_errors_, 0.6)
assert zero_one_loss(np.sign(data.labels), c.predict(data.data)) < 0.05
def test_gentleboost_hastie_fitting():
c = GentleBoostClassifier(
base_estimator=DecisionTreeRegressor(max_depth=1),
n_estimators=30,
learning_rate=1.0
)
data = Hastie_10_2()
c.fit(data.data, np.sign(data.labels))
assert_array_less(c.estimator_errors_, 0.5)
assert zero_one_loss(np.sign(data.labels), c.predict(data.data)) < 0.2
def ValAccuracyLoss():
imagesVal = os.path.join(path_to_model, "macval.txt")
y_true, \
y_predict, \
y_predict_float, \
runtime_times = ForwardNet(imagesVal,False)
report = classification_report(y_true, y_predict)
print "Val Accuracy = ", accuracy_score(y_true, y_predict)
print "Val Loss = ", zero_one_loss(y_true, y_predict)
print "Val Loss Cross Entropy = ", CrossEntropyLoss(y_true, y_predict_float)
print report