def f1_average(y_true, y_pred):
"""
returns average of f1 score for both classes.
"""
f1_survived = f1_score(y_true, y_pred, pos_label=1, average="binary")
f1_died = f1_score(y_true, y_pred, pos_label=0, average="binary")
return np.mean([f1_survived, f1_died])
def test_auto_weight():
# Test class weights for imbalanced data
from sklearn.linear_model import LogisticRegression
# We take as dataset the two-dimensional projection of iris so
# that it is not separable and remove half of predictors from
# class 1.
# We add one to the targets as a non-regression test: class_weight="balanced"
# used to work only when the labels where a range [0..K).
from sklearn.utils import compute_class_weight
X, y = iris.data[:, :2], iris.target + 1
unbalanced = np.delete(np.arange(y.size), np.where(y > 2)[0][::2])
classes = np.unique(y[unbalanced])
class_weights = compute_class_weight('balanced', classes, y[unbalanced])
assert_true(np.argmax(class_weights) == 2)
for clf in (svm.SVC(kernel='linear'), svm.LinearSVC(random_state=0),
LogisticRegression()):
# check that score is better when class='balanced' is set.
y_pred = clf.fit(X[unbalanced], y[unbalanced]).predict(X)
clf.set_params(class_weight='balanced')
y_pred_balanced = clf.fit(X[unbalanced], y[unbalanced],).predict(X)
assert_true(metrics.f1_score(y, y_pred, average='weighted')
<= metrics.f1_score(y, y_pred_balanced,
average='weighted'))
def f1(self, X, y):
n_class = len(np.unique(y))
prediction = self.predict(X)
if n_class > 2:
return f1_score(y, prediction, average='weighted')
else:
return f1_score(y, prediction)
def evaluation(y_test=None, y_predict=None, n_classes=None):
"""
Input the predicted results, targets results and
the number of class, return the confusion matrix, F1-score of each class,
accuracy and macro F1-score.
Parameters
----------
y_test : list
The target results
y_predict : list
The predicted results
n_classes : int
The number of classes
Examples
--------
>>> c_mat, f1, acc, f1_macro = tl.utils.evaluation(y_test, y_predict, n_classes)
"""
c_mat = confusion_matrix(y_test, y_predict, labels=[x for x in range(n_classes)])
f1 = f1_score(y_test, y_predict, average=None, labels=[x for x in range(n_classes)])
f1_macro = f1_score(y_test, y_predict, average='macro')
acc = accuracy_score(y_test, y_predict)
tl.logging.info('confusion matrix: \n%s' % c_mat)
tl.logging.info('f1-score : %s' % f1)
tl.logging.info('f1-score(macro) : %f' % f1_macro) # same output with > f1_score(y_true, y_pred, average='macro')
tl.logging.info('accuracy-score : %f' % acc)
return c_mat, f1, acc, f1_macro
def compute_ref(true_tags, out_file, data_type='svm_light'):
tag_map = {'OK': 1, 'BAD': 0, u'OK': 1, u'BAD': 0}
predicted = []
if data_type == 'svm_light':
tag_map_pred = {'+1': 1, '-1': 0}
for line in open(out_file):
label = line[line.find(':')+1:line.find(' ')]
predicted.append(tag_map_pred[label])
elif data_type == 'crfpp' or data_type == 'crf_suite':
for line in open(out_file):
line = line.strip('\n')
if line == '':
continue
tag = line.split('\t')[-1]
if tag == 'OK' or tag == 'BAD':
predicted.append(tag)
predicted = [tag_map[t] for t in predicted]
# if (type(true_tags[0]) is str or type(true_tags[0]) is unicode) and not true_tags[0].isdigit():
true_tags = [tag_map[t] for t in true_tags]
# if type(predicted[0]) is str and not predicted[0].isdigit():
print(true_tags[:10])
print(predicted[:10])
print(f1_score(predicted, true_tags, average=None))
print(f1_score(predicted, true_tags, average='weighted', pos_label=None))
def get_f1_and_classification_report(embeddings_dict, classifier):
xs, ys, y_pred = get_xs_ys_predictions(embeddings_dict, classifier)
class_names = ['verbs', 'nouns', 'adjectives', 'closed class words']
report = classification_report(y_true=ys, y_pred=y_pred, target_names=class_names)
micro_f1 = f1_score(y_true=ys, y_pred=y_pred, average='micro')
macro_f1 = f1_score(y_true=ys, y_pred=y_pred, average='macro')
return micro_f1, macro_f1, report
def evaluation(y_test=None, y_predict=None, n_classes=None):
"""
Input the predicted results, targets results and
the number of class, return the confusion matrix, F1-score of each class,
accuracy and macro F1-score.
Parameters
----------
y_test : numpy.array or list
target results
y_predict : numpy.array or list
predicted results
n_classes : int
number of classes
Examples
--------
>>> c_mat, f1, acc, f1_macro = evaluation(y_test, y_predict, n_classes)
"""
from sklearn.metrics import confusion_matrix, f1_score, accuracy_score
c_mat = confusion_matrix(y_test, y_predict, labels = [x for x in range(n_classes)])
f1 = f1_score(y_test, y_predict, average = None, labels = [x for x in range(n_classes)])
f1_macro = f1_score(y_test, y_predict, average='macro')
acc = accuracy_score(y_test, y_predict)
print('confusion matrix: \n',c_mat)
print('f1-score:',f1)
print('f1-score(macro):',f1_macro) # same output with > f1_score(y_true, y_pred, average='macro')
print('accuracy-score:', acc)
return c_mat, f1, acc, f1_macro
def benchmark(clf, train_X, train_y, test_X, test_y, encoder):
"""
benchmark based on f1 score
"""
t0 = time()
clf.fit(train_X, train_y)
train_time = time() - t0
t0 = time()
pred = clf.predict(test_X)
test_time = time() - t0
score = metrics.f1_score(test_y, pred, average='micro')
scores = metrics.f1_score(test_y, pred, average=None)
counter = Counter(train_y)
counter = [(k, v) for k, v in counter.iteritems()]
counter.sort(key=lambda a: a[1], reverse=True)
if len(counter) > 20:
tops = [v[0] for v in counter[0:20]]
else:
tops = [v[0] for v in counter]
labels = encoder.inverse_transform(tops)
s = [scores[v] for v in tops]
labeled_scores = zip(labels, s)
return clf, score, labeled_scores, train_time, test_time
def on_epoch_end(self, epoch, logs={}):
print logs
corr=0
tot=0
preds = self.model.predict(self.dev_data, verbose=1)
preds_text=[]
for l in preds:
preds_text.append(self.index2label[np.argmax(l)])
print "Micro f-score:", f1_score(self.dev_labels_text,preds_text,average=u"micro")
print "Macro f-score:", f1_score(self.dev_labels_text,preds_text,average=u"macro")
print "Macro recall:", recall_score(self.dev_labels_text,preds_text,average=u"macro")
if self.best_mr < recall_score(self.dev_labels_text,preds_text,average=u"macro"):
self.best_mr = recall_score(self.dev_labels_text,preds_text,average=u"macro")
model.save_weights(self.model_name + '_full_' + str(epoch) + '_MR_' + str(self.best_mr) + '.hdf5')
print 'Saved Weights!'
print classification_report(self.dev_labels_text, preds_text)
for i in xrange(len(self.dev_labels)):
# next_index = sample(preds[i])
next_index = np.argmax(preds[i])
# print preds[i],next_index,index2label[next_index]
l = self.index2label[next_index]
# print "correct:", index2label[np.argmax(dev_labels[i])], "predicted:",l
if self.index2label[np.argmax(self.dev_labels[i])]==l:
corr+=1
tot+=1
print corr,"/",tot
def predict_evaluate_models(fn ,ax=None, sel=["Penalties_Conceeded","Tries_Scored"], goal="Referee", verbosity=0):
class_weight = 'auto'
X, y, names = data_prepare(fn, sel=sel, goal=goal, verbosity=verbosity-1)
if verbosity > 2:
y_shuffled = y.copy()
np.random.shuffle(y_shuffled)
print ("All zeros accuracy:",1.0-np.sum(y)/len(y))
print ("y_shuffled f1_csore:",metrics.f1_score(y, y_shuffled))
n_folds = 10
cv = cross_validation.StratifiedKFold(y, n_folds=n_folds)
#cv = cross_validation.LeaveOneOut(n=len(y))
results = []
for sclf in ('svm','svmp','svmr','lgCV','gnb','rf','knc'):
clf = get_clf(sclf,class_weight=class_weight)
y_pred = cross_validation.cross_val_predict(clf, X, y, cv=cv)
#print "pred:",y_pred
res = [
metrics.accuracy_score(y, y_pred),
metrics.precision_score(y, y_pred),
metrics.recall_score(y, y_pred),
metrics.f1_score(y, y_pred),
]
if verbosity > 0:
print (sclf,res)
results.append( (sclf,res) )
return results
def compare_2_models(model1, model2, X, y, h):
h = min(X.shape[0], h)
hidden_layer = features[np.random.choice(X.shape[0],
h,
replace=False)]
print('training 1st model')
pr = cProfile.Profile()
pr.enable()
model1.fit(X, y, hidden_layer=hidden_layer)
y1 = model1.predict(X)
pr.disable()
ps = pstats.Stats(pr).sort_stats('cumulative')
ps.print_stats()
print('training 2nd model')
pr = cProfile.Profile()
pr.enable()
model2.fit(X, y, hidden_layer=hidden_layer)
y2 = model2.predict(X)
pr.disable()
ps = pstats.Stats(pr).sort_stats('cumulative')
ps.print_stats()
print(f1_score(y, y2))
print(f1_score(y, y1))
return np.allclose(y1, y2)
def baseline_graph_experiment(model, data_fn, data_name, model_name):
print "Running graph experiment (%s)..." % (data_name,)
A, X, Y = data_fn()
A = np.asarray(A)
X = np.asarray(X)
Y = np.asarray(Y)
n_nodes = A.shape[0]
indices = np.arange(n_nodes)
np.random.shuffle(indices)
train_indices = indices[: n_nodes // 3]
valid_indices = indices[n_nodes // 3 : (2 * n_nodes) // 3]
test_indices = indices[(2 * n_nodes) // 3 :]
model.fit_with_validation(A, X, Y, train_indices, valid_indices)
preds = model.predict(A, X, test_indices)
actuals = Y[test_indices, :]
accuracy = accuracy_score(actuals, preds)
f1_micro = f1_score(actuals, preds, average="micro")
f1_macro = f1_score(actuals, preds, average="macro")
print "form: name,micro_f,macro_f,accuracy"
print "###RESULTS###: %s,%s,%.8f,%.8f,%.8f" % (data_name, model_name, f1_micro, f1_macro, accuracy)
def getScores(y, yPredTrain, yTest, yPredTest):
scores = dict()
scores['f1Train'] = f1_score(y, yPredTrain)
scores['f1Test'] = f1_score(yTest, yPredTest)
scores['accTrain'] = accuracy_score(y, yPredTrain)
scores['accTest'] = accuracy_score(yTest, yPredTest)
scores['rocTrain'] = roc_auc_score(y, yPredTrain)
scores['rocTest'] = roc_auc_score(yTest, yPredTest)
scores['cMatrixTrain'] = confusion_matrix(y, yPredTrain)
scores['cMatrixTest'] = confusion_matrix(yTest, yPredTest)
proba = float(len(np.where(y==1)[0]))/len(y)
if proba < 0.50:
proba = 1 - proba
scores['random'] = proba
return scores
def main():
f = open("me.stdout", "r").read()
print f
(confusionMatrix, labels, ytrue, ypred, trueCount) = readConfusionMatrix.readText(f)
for row in confusionMatrix:
print row
precisionMicro = np.float(metrics.precision_score(ytrue, ypred, average="micro"))
recallMicro = np.float(metrics.recall_score(ytrue, ypred, average="micro"))
f1Micro = np.float(metrics.f1_score(ytrue, ypred, average="micro"))
f1Macro = np.float(metrics.f1_score(ytrue, ypred, pos_label=1, average="macro"))
precisionMacro = np.float(metrics.precision_score(ytrue, ypred, average="macro"))
recallMacro = np.float(metrics.recall_score(ytrue, ypred, average="macro"))
mConf = metrics.confusion_matrix(ytrue, ypred)
print mConf
print labels
print len(ytrue)
print len(ypred)
print trueCount
print metrics.accuracy_score(ytrue, ypred)
print precisionMicro
print recallMicro
print f1Micro
print f1Macro
print precisionMacro
print recallMacro
def kernel_graph_experiment(model, data_fn, data_name, model_name):
print "Running graph experiment (%s)..." % (data_name,)
A, X, Y = data_fn()
n_nodes = len(A)
indices = np.arange(n_nodes)
np.random.shuffle(indices)
print indices
train_indices = indices[: n_nodes // 3]
valid_indices = indices[n_nodes // 3 : (2 * n_nodes) // 3]
test_indices = indices[(2 * n_nodes) // 3 :]
# train_indices = indices[:int(n_nodes*0.8)]
# valid_indices = indices[int(n_nodes*0.8):int(n_nodes*0.9)]
# test_indices = indices[int(n_nodes*0.9):]
model.fit_with_validation(Y, train_indices, valid_indices, test_indices)
preds = model.predict(Y, np.asarray([]), test_indices)
actuals = Y[test_indices, :]
accuracy = accuracy_score(actuals, preds)
f1_micro = f1_score(actuals, preds, average="micro")
f1_macro = f1_score(actuals, preds, average="macro")
print "form: name,micro_f,macro_f,accuracy"
print "###RESULTS###: %s,%s,%.8f,%.8f,%.8f" % (data_name, model_name, f1_micro, f1_macro, accuracy)
def single_test(feature, attribute):
from sklearn.metrics import f1_score
from sklearn.metrics import recall_score
from sklearn.metrics import accuracy_score
from data_generator import load_vector_from_text
import random
data=merge_different_vectors([feature],attribute)
none_attribute_uids=load_vector_from_text('uids_none_attributes.vector',feature,'list')
none_attribute_uids=filter(lambda x:x in data[0],none_attribute_uids)
alpha=0.2*len(data[0])/len(none_attribute_uids)
train_data=[[],[]]
test_data=[[],[]]
for index,uid in enumerate(data[0]):
if uid in none_attribute_uids and random.random()<alpha:
#if random.random()<0.2:
test_data[0].append(data[1][index])
test_data[1].append(data[2][index])
else:
train_data[0].append(data[1][index])
train_data[1].append(data[2][index])
print len(test_data[1]),sum(test_data[1]),len(train_data[1]),sum(train_data[1])
clf=LogisticRegression()
clf.fit(train_data[0], train_data[1])
predicted_y=clf.predict(test_data[0])
test_accuracy=accuracy_score(test_data[1],predicted_y)
test_recall=recall_score(test_data[1],predicted_y)
test_f1=f1_score(test_data[1],predicted_y)
print 'F1 of test data (%d %d): %0.2f'%(sum(test_data[1]),len(test_data[1])-sum(test_data[1]),test_f1)
print 'Accuracy of test data (%d %d): %0.2f'%(sum(test_data[1]),len(test_data[1])-sum(test_data[1]),test_accuracy)
predicted_y=clf.predict(train_data[0])
train_accuracy=accuracy_score(train_data[1],predicted_y)
train_recall=recall_score(train_data[1],predicted_y)
train_f1=f1_score(train_data[1],predicted_y)
print 'F1 of train data (%d %d): %0.2f'%(sum(train_data[1]),len(train_data[1])-sum(train_data[1]),train_f1)
return [test_accuracy,test_recall,test_f1,train_accuracy,train_recall,train_f1]
def benchmark(clf_current):
print('_' * 80)
print("Test performance for: ")
clf_descr = str(clf_current).split('(')[0]
print(clf_descr)
t0 = time()
classif = OneVsRestClassifier(clf_current)
classif.fit(X_train, Y_train.toarray())
train_time = time() - t0
print("train time: %0.3fs" % train_time)
t0 = time()
if hasattr(clf_current,"decision_function"):
dfmatrix = classif.decision_function(X_test)
score = metrics.f1_score(Y_test.toarray(), df_to_preds(dfmatrix, k = 5))
else:
probsmatrix = classif.predict_proba(X_test)
score = metrics.f1_score(Y_test.toarray(), probs_to_preds(probsmatrix, k = 5))
test_time = time() - t0
print("f1-score: %0.7f" % score)
print("test time: %0.3fs" % test_time)
print('_' * 80)
return clf_descr, score, train_time, test_time
def findBestDistance(self):
print '*** start ****'
d = 0.1
# y_true = []
# y_pred = []
result = {}
for x in range(0,10):
y_true = []
y_pred = []
for dataIndex in range(0, len(self.lstTest)):
dataTest = self.lstTest[dataIndex]
# y_true.append(dataTest[0])
y_true.append(self.scoreConvert(dataTest[0]))
isFilter = self.computeWithNoCorpus(dataTest[1], self.lstTrain, d)
y_pred.append(self.scoreConvert(isFilter))
print y_true
print y_pred
f1 = metrics.f1_score(y_true, y_pred)
f1_mac = f1_score(y_true, y_pred, average='macro')
print 'd : ',d,' f1 : ',f1,' f1 mac : ',f1_mac
result[d] = f1
print classification_report(y_true, y_pred)
# print 'result ', result
d = d+0.1
print result
print '*** end ******'
def ternary_metrics(polarities, lexicon, eval_words, tau_lexicon=None):
if not tau_lexicon == None:
kendall_words = list(set(eval_words).intersection(tau_lexicon))
y_prob, y_true = [], []
polarities = {word:polarities[word] for word in eval_words}
for w in polarities:
y_prob.append(polarities[w])
y_true.append(lexicon[w])
y_prob = np.array(y_prob)
y_true = np.array(y_true)
y_prob = 2*(y_prob - np.min(y_prob)) / (np.max(y_prob) - np.min(y_prob)) - 1
neg_prop = np.sum(np.array(lexicon.values()) == -1) / float(len(lexicon))
pos_prop = np.sum(np.array(lexicon.values()) == 1) / float(len(lexicon))
sorted_probs = sorted(y_prob)
neg_thresh = sorted_probs[int(np.round(neg_prop*len(sorted_probs)))]
pos_thresh = sorted_probs[-int(np.round(pos_prop*len(sorted_probs)))]
cmn_labels = [1 if val >= pos_thresh else -1 if val <= neg_thresh else 0 for val in y_prob]
if not tau_lexicon == None:
tau = kendalltau(*zip(*[(polarities[word], tau_lexicon[word]) for word in kendall_words]))[0]
else:
tau = None
maj_f1 = f1_score(y_true, np.repeat(sp.stats.mode(y_true)[0][0], len(y_true)), average="macro")
cmn_f1 = f1_score(y_true, cmn_labels, average="macro")
label_func = lambda entry : 1 if entry > pos_thresh else -1 if entry < neg_thresh else 0
conf_mat = confusion_matrix(y_true, [label_func(entry) for entry in y_prob])
return tau, cmn_f1, maj_f1, conf_mat
def compareModels(model):
"""
This evaluates the pre-trained model agaisnt
metamind's API on sentences in `data/validation`
Parameters
----------
model: test.MODEL
Namedtuple containing model parameters (dictionary, tfidf
learner and labels)
"""
set_api_key("MohJ53r6kUvoPjHS8tStX1vnfssvN5EDetVcp2uCNISwXus2BS")
with open('data/validation', 'r') as fin:
validations = fin.read()
truth = [model.labels.label2class[i] for i in
['positive']*9 + ['negative']*8]
scores_mm = []
scores_joe = []
for validation in validations.split('\n'):
mmLabel = testMetaMind(validation)[0]['label']
scores_mm.append(model.labels.label2class[mmLabel])
joeLabel = testDeepModel(validation, model)
scores_joe.append(model.labels.label2class[joeLabel])
print 'MetaMind F1 score is %s' % f1_score(truth, scores_mm)
print 'My F1 score is %s' % f1_score(truth, scores_joe)
def test_standard_svm_blobs_2d_class_weight():
# no edges, reduce to crammer-singer svm
X, Y = make_blobs(n_samples=210, centers=3, random_state=1, cluster_std=3,
shuffle=False)
X = np.hstack([X, np.ones((X.shape[0], 1))])
X, Y = X[:170], Y[:170]
X_graphs = [(x[np.newaxis, :], np.empty((0, 2), dtype=np.int)) for x in X]
pbl = GraphCRF(n_features=3, n_states=3, inference_method='unary')
svm = OneSlackSSVM(pbl, check_constraints=False, C=1000)
svm.fit(X_graphs, Y[:, np.newaxis])
weights = 1. / np.bincount(Y)
weights *= len(weights) / np.sum(weights)
pbl_class_weight = GraphCRF(n_features=3, n_states=3, class_weight=weights,
inference_method='unary')
svm_class_weight = OneSlackSSVM(pbl_class_weight, C=10,
check_constraints=False,
break_on_bad=False)
svm_class_weight.fit(X_graphs, Y[:, np.newaxis])
assert_greater(f1_score(Y, np.hstack(svm_class_weight.predict(X_graphs))),
f1_score(Y, np.hstack(svm.predict(X_graphs))))
def cutoff_f1(clf, X, y):
y_pred = (clf.predict_proba(X)[:,1] > cutoff_value).astype(int)
y_pred2 = clf.predict(X)
s1 = f1_score(y, y_pred)
s2 = f1_score(y, y_pred2)
# print 'f1 = %.4f, %.4f' % (s1, s2)
return s1
def on_epoch_end(self, batch, logs={}):
# losses
self.losses_train.append(self.model.evaluate(X_train, Y_train, batch_size=128,verbose =0))
self.losses_val.append(self.model.evaluate(X_val, Y_val, batch_size=128,verbose = 0))
# Roc train
train_preds = self.model.predict_proba(X_train, verbose=0)
train_preds = train_preds[:, 1]
roc_train = metrics.roc_auc_score(y_train, train_preds)
self.roc_train.append(roc_train)
# Roc val
val_preds = self.model.predict_proba(X_val, verbose=0)
val_preds = val_preds[:, 1]
roc_val = metrics.roc_auc_score(y_val, val_preds)
self.roc_val.append(roc_val)
# Metrics train
y_preds = self.model.predict_classes(X_train,verbose = 0)
self.f1_train.append(metrics.f1_score(y_train,y_preds))
self.recal_train.append(metrics.recall_score(y_train,y_preds))
self.preci_train.append(metrics.precision_score(y_train,y_preds))
# Metrics val
y_preds = self.model.predict_classes(X_val,verbose =0)
self.f1_val.append(metrics.f1_score(y_val,y_preds))
self.recal_val.append(metrics.recall_score(y_val,y_preds))
self.preci_val.append(metrics.precision_score(y_val,y_preds))
def cv_model():
DATA_FILE = './data/train-set-ru-b64-utf-8.txt'
all_data = []
target = []
with open(DATA_FILE) as df:
for i, line in enumerate(df):
print i
line = line.strip()
parts = line.split()
stats_collector = StatsCollector()
#print parts[2]
#print base64.b64decode(parts[3])#.decode('utf-8')
#print parts[2].decode('utf-8'), parts[3].decode('utf-8'), "\n"
stats_collector.collect(int(parts[1]), parts[3], parts[2])
# mark page url
all_data.append(stats_collector.get_features())
target.append(stats_collector.get_target())
#print all_data[-1]
data = np.asarray(all_data, dtype = np.float)
target = np.asarray(target, dtype = np.float)
clf = GradientBoostingClassifier(loss='deviance', learning_rate=0.05, n_estimators=400,\
min_samples_split=30, min_samples_leaf=15, max_depth=5)
kf = KFold(data.shape[0], n_folds = 3, shuffle = True)
for train_index, test_index in kf:
X_train, X_test = data[train_index], data[test_index]
y_train, y_test = target[train_index], target[test_index]
clf.fit(X_train, y_train)
y_pred = clf.predict(X_test)
print f1_score(y_test, y_pred)
def cross_val(data_x, data_y, classifier, kFold, b_cost=1, h_cost=1, w=0.5):
e_h, e_b = 0, 0
y_tests, pred_probas = [], []
for train_index, test_index in kFold:
data_x_, data_y_ = np.array(data_x), np.array(data_y)
X_train, X_test = list(data_x_[train_index]), list(data_x_[test_index])
y_train, y_test = list(data_y_[train_index]), list(data_y_[test_index])
classifier.fit(X_train, y_train)
pred_proba = [r[0] for r in classifier.predict_proba(X_test)]
y_tests += y_test
pred_probas += pred_proba
predictions = [0 if p*b_cost > (1-p)*h_cost else 1 for p in pred_probas]
roc_auc = roc_auc_score(y_tests, pred_probas)
total_acc = accuracy_score(y_tests, predictions)
precision, recall, thresholds = precision_recall_curve(y_tests, pred_probas, pos_label=0)
fpr, tpr, thresholds = roc_curve(y_tests, pred_probas, pos_label=0)
precision_bots = precision_score(y_tests, predictions, pos_label = 0)
precision_humans = precision_score(y_tests, predictions, pos_label = 1)
recall_bots = recall_score(y_tests, predictions, pos_label = 0)
recall_humans = recall_score(y_tests, predictions, pos_label = 1)
f1_bots = f1_score(y_tests, predictions, pos_label = 0)
f1_humans = f1_score(y_tests, predictions, pos_label = 1)
conf_matrix = np.matrix(list(confusion_matrix(y_tests, predictions)))
#plot_curve(fpr, tpr, 'ROC', w)
#plot_curve(recall, precision, 'PR', w)
return [total_acc, precision_bots, precision_humans, recall_bots, recall_humans, f1_bots, f1_humans, roc_auc, conf_matrix]
def logistic_regression_sklearn(self, features, labels):
"""Run a logistic regression, evaluate it, return the LR object
"""
print '\n**** Running logistic regression...'
# Split into train / test segments
features_train, features_test, target_train, target_test = cross_validation.train_test_split(features, labels, test_size=0.20, random_state=0)
lr = LogisticRegression()
lr.fit(features_train, target_train)
# Evaluate the regression
target_predicted = lr.predict(features_test)
accuracy = accuracy_score(target_test, target_predicted)
print 'Logistic regression accuracy score: {0:.0f}%'.format(100 * accuracy)
# coefs = pd.DataFrame(zip(feature_cols, np.transpose(lr.coef_[0])), columns=['Feature', 'Coefficient'])
print 'F1: ',
print f1_score(target_test, target_predicted)
# preds = lr.predict_proba(features_test)[:,1]
# fpr, tpr, _ = roc_curve(target_test, preds)
# print 'AOC: ',
# print '{:.2f}'.format(auc(fpr,tpr))
return lr
def fit_model():
DATA_FILE = './data/train-set-ru-b64-utf-8.txt'
stats_collector = StatsCollector()
i=0
data = []
target = []
with open (DATA_FILE) as df:
for i, line in enumerate(df):
print i
line = line.strip()
parts = line.split()
stats_collector = StatsCollector()
stats_collector.collect(int(parts[1]), parts[3], parts[2])
data.append(stats_collector.get_features())
target.append(stats_collector.get_target())
#print len(data[-1])
data = np.asarray(data, dtype = np.float)
target = np.asarray(target, dtype = np.float)
print data.shape, target.shape
df.close()
clf = GradientBoostingClassifier(loss='deviance', learning_rate=0.07, n_estimators=300, min_samples_split=30,\
min_samples_leaf=15, max_depth=4)
clf.fit(data, target)
y_pred = clf.predict(data)
print f1_score(target, y_pred)
joblib.dump(clf, 'model/model.pkl')
def on_epoch_end(self, epoch, logs={}):
print logs
corr=0
tot=0
preds = self.model.predict(self.dev_data, verbose=1)
preds_text=[]
for l in preds:
preds_text.append(self.index2label[np.argmax(l)])
print "Micro f-score:", f1_score(self.dev_labels_text,preds_text,average=u"micro")
print "Macro f-score:", f1_score(self.dev_labels_text,preds_text,average=u"macro")
print classification_report(self.dev_labels_text, preds_text)
for i in xrange(len(self.dev_labels)):
# next_index = sample(preds[i])
next_index = np.argmax(preds[i])
# print preds[i],next_index,index2label[next_index]
l = self.index2label[next_index]
# print "correct:", index2label[np.argmax(dev_labels[i])], "predicted:",l
if self.index2label[np.argmax(self.dev_labels[i])]==l:
corr+=1
tot+=1
print corr,"/",tot
def evaluate_fold(clf, X_train, y_train, X_test, y_test):
"""
This is the business section
"""
tmp = dict()
tmp['X_train.shape'] = X_train.shape
tmp['X_test.shape'] = X_test.shape
try:
pred_test = clf.predict_proba(X_test)
pred_train = clf.predict_proba(X_train)
tmp['roc'] = roc_info(y_test, pred_test[:,1])
tmp['roc_area'] = roc_auc_score(y_test, pred_test[:,1])
pred_test = clf.predict(X_test)
pred_train = clf.predict(X_train)
tmp['f1_test'] = f1_score(y_test, pred_test, pos_label=1)
tmp['f1_train'] = f1_score(y_train, pred_train, pos_label=1)
except (AttributeError, NotImplementedError):
pred_test = clf.predict(X_test)
pred_train = clf.predict(X_train)
tmp['roc'] = roc_info(y_test, pred_test)
tmp['roc_area'] = roc_auc_score(y_test, pred_test)
tmp['f1_test'] = f1_score(y_test, pred_test, pos_label=1)
tmp['f1_train'] = f1_score(y_train, pred_train, pos_label=1)
return tmp
def scnn_proportion_experiment(data_fn, name, n_hops, prop_valid, prop_test, transform_fn=util.rw_laplacian, transform_name='rwl'):
print 'Running node experiment (%s)...' % (name,)
A, X, Y = data_fn()
n_nodes = A.shape[0]
indices = np.arange(n_nodes)
valid_start = int(n_nodes * (1 - (prop_valid + prop_test)))
test_start = int(n_nodes * (1 - prop_test))
valid_indices = indices[valid_start:test_start]
test_indices = indices[test_start:]
for train_prop in [x / 10.0 for x in range(1, 11)]:
train_end = int(valid_start * train_prop)
train_indices = indices[:train_end]
scnn = SCNN(n_hops=n_hops, transform_fn=transform_fn)
scnn.fit(A, X, Y, train_indices=train_indices, valid_indices=valid_indices)
probs = scnn.predict_proba(X, test_indices)
print probs
preds = scnn.predict(X, test_indices)
actuals = np.argmax(Y[test_indices,:], axis=1)
f1_micro = f1_score(actuals, preds, average='micro')
f1_macro = f1_score(actuals, preds, average='macro')
accuracy = accuracy_score(actuals, preds)
print 'form: name,n_hops,transform_name,micro_f,macro_f,accuracy'
print '###RESULTS###: %s,%d,%.2f,%s,%.8f,%.8f,%.8f' % (name, n_hops, train_prop, transform_name, f1_micro, f1_macro, accuracy)
train, _ = ColumnInfoExtractor(n_files=num_files,
n_rows=num_rows,
train_size=1.,
n_jobs=n_cores,
column_sample=True).transform(
annotations_file=train_file_path,
csv_folder=csv_folder_path)
test, _ = ColumnInfoExtractor(n_files=num_files,
n_rows=num_rows,
train_size=1.,
n_jobs=n_cores,
column_sample=True).transform(
annotations_file=test_file_path,
csv_folder=csv_folder_path)
tqdm.write("Loading data done...")
ablation_results = defaultdict(dict)
for pp_name, pp in tqdm(all_pipelines.items()):
tqdm.write(f"Fitting pipeline {pp_name}")
pp.fit(train, train["y"])
y_test = test["y"]
y_pred = pp.predict(test)
f_score = f1_score(y_true=y_test, y_pred=y_pred, average='macro')
ablation_results[pp_name]["f_score"] = f_score
ablation_results[pp_name]["confusion_matrix"] = confusion_matrix(
y_true=y_test, y_pred=y_pred).tolist()
ablation_results["tags"] = list(np.unique(test["y"]))
json.dump(ablation_results, open("./data/ablation_results.json", "w"))
from sklearn.metrics import f1_score y_true = [0, 0, 0, 0, 0, 1, 1, 1, 1, 1] y_pred = [0, 1, 1, 1, 1, 0, 0, 0, 1, 1] print(f1_score(y_true, y_pred)) # 0.3636363636363636
def train1():
with open(opt.pickle_train_path, 'rb') as inp:
word2id = pickle.load(inp)
id2word = pickle.load(inp)
tag2id = pickle.load(inp)
id2tag = pickle.load(inp)
x_train = pickle.load(inp)
y_train = pickle.load(inp)
x_valid = pickle.load(inp)
y_valid = pickle.load(inp)
print("train len:", len(x_train))
print("valid len", len(x_valid))
# print("test len", len(x_test))
train_dataset = NERDataset(x_train,y_train)
valid_dataset = NERDataset(x_valid, y_valid)
# valid_dataset = NERDataset(x_valid, y_valid)
# test_dataset = NERDataset(x_test, y_test)
train_dataloader = DataLoader(train_dataset, batch_size=opt.batch_size, shuffle=True, num_workers=opt.num_workers)
valid_dataloader = DataLoader(valid_dataset, batch_size=opt.batch_size, shuffle=True, num_workers=opt.num_workers)
# test_dataloader = DataLoader(test_dataset, batch_size=opt.batch_size, shuffle=True, num_workers=opt.num_workers)
# x = train_dataset[0]
# print(x)
# for index, batch in enumerate(train_dataloader):
# print(index)
# print(batch)
models = {'NERLSTM': NERLSTM,
'NERLSTM_CRF': NERLSTM_CRF}
all_vec = load_vec(opt.load_vec_path)
# device = torch.device('cuda')
# model = models[opt.model](opt.embedding_dim, opt.hidden_dim, opt.dropout, word2id, tag2id).cuda()
model = models[opt.model](opt.word_dim, opt.embedding_dim, opt.hidden_dim, opt.filter_size, opt.cnn_out_dim,
opt.dropout, word2id, tag2id, all_vec).cuda()
criterion = nn.CrossEntropyLoss(ignore_index=0)
optimizer = optim.Adam(model.parameters(), lr=opt.lr, weight_decay=opt.weight_decay)
if opt.model == 'NERLSTM':
for epoch in range(opt.max_epoch):
model.train()
for index, batch in enumerate(train_dataloader):
optimizer.zero_grad()
X = batch['x'].cuda()
y = batch['y'].cuda()
y = y.view(-1, 1)
y = y.squeeze(-1)
pred = model(X)
pred = pred.view(-1, pred.size(-1))
loss = criterion(pred, y)
loss.backward()
optimizer.step()
if index % 200 == 0:
print('epoch:%04d,------------loss:%f' % (epoch, loss.item()))
aver_loss = 0
preds, labels = [], []
for index, batch in enumerate(valid_dataloader):
model.eval()
val_x, val_y = batch['x'].cuda(), batch['y'].cuda()
predict = model(val_x)
predict = torch.argmax(predict, dim=-1)
if index % 500 == 0:
print([id2word[i.item()] for i in val_x[0].cpu() if i.item() > 0])
length = [id2tag[i.item()] for i in val_y[0].cpu() if i.item() > 0]
print(length)
print([id2tag[i.item()] for i in predict[0][:len(length)].cpu() if i.item() > 0])
# 统计非0的，也就是真实标签的长度
leng = []
for i in val_y.cpu():
tmp = []
for j in i:
if j.item() > 0:
tmp.append(j.item())
leng.append(tmp)
# 提取真实长度的预测标签
for index, i in enumerate(predict.tolist()):
preds.extend(i[:len(leng[index])])
# 提取真实长度的真实标签
for index, i in enumerate(val_y.tolist()):
labels.extend(i[:len(leng[index])])
precision = precision_score(labels, preds, average='macro')
recall = recall_score(labels, preds, average='macro')
f1 = f1_score(labels, preds, average='macro')
report = classification_report(labels, preds)
print(report)
elif opt.model == 'NERLSTM_CRF':
best_score = 0.0
for epoch in range(opt.max_epoch):
model.train()
for index, batch in enumerate(train_dataloader):
optimizer.zero_grad()
X = batch['x'].cuda()
y = batch['y'].cuda()
# CRF
loss = model.log_likelihood(X, y)
loss.backward()
# CRF
torch.nn.utils.clip_grad_norm_(parameters=model.parameters(), max_norm=10)
optimizer.step()
if index % 200 == 0:
print('best_score:%f' % (best_score))
print('epoch:%02d,idnex%4d------------loss:%f' % (epoch, index, loss.item()))
aver_loss = 0
preds, labels = [], []
for index, batch in enumerate(valid_dataloader):
model.eval()
val_x, val_y = batch['x'].cuda(), batch['y'].cuda()
predict = model(val_x)
# CRF
loss = model.log_likelihood(val_x, val_y)
aver_loss += loss.item()
# 统计非0的，也就是真实标签的长度
leng = []
for i in val_y.cpu():
tmp = []
for j in i:
if j.item() > 0:
tmp.append(j.item())
leng.append(tmp)
for index, i in enumerate(predict):
preds += i[:len(leng[index])]
for index, i in enumerate(val_y.tolist()):
labels += i[:len(leng[index])]
aver_loss /= (len(valid_dataloader) * 64)
precision = precision_score(labels, preds, average='macro')
recall = recall_score(labels, preds, average='macro')
f1 = f1_score(labels, preds, average='macro')
# report = classification_report(labels, preds)
# print(report)
print('p', precision)
print('r', recall)
print('f1', f1)
if f1 > best_score:
best_score = f1
path_name = './model/model' + str(epoch) + '----' + str(f1) + '.pkl'
torch.save(model, path_name)
print('model has been saved')
def test1(model_path,output_file,output_file1):
def list2tags(l_list):
r = []
for l in l_list:
r.append(id2tag[l])
return r
with open(opt.pickle_train_path, 'rb') as inp:
word2id = pickle.load(inp)
id2word = pickle.load(inp)
tag2id = pickle.load(inp)
id2tag = pickle.load(inp)
x_train = pickle.load(inp)
y_train = pickle.load(inp)
x_test = pickle.load(inp)
y_test = pickle.load(inp)
print("valid len", len(x_test))
test_dataset = NERDataset(x_test, y_test)
test_dataloader = DataLoader(test_dataset, batch_size=opt.batch_size, shuffle=False, num_workers=opt.num_workers)
model = torch.load(model_path)
model.eval()
aver_loss = 0
preds, labels = [], []
for index, batch in enumerate(test_dataloader):
model.eval()
val_x, val_y = batch['x'].cuda(), batch['y'].cuda()
predict = model(val_x)
# CRF
loss = model.log_likelihood(val_x, val_y)
aver_loss += loss.item()
# 统计非0的，也就是真实标签的长度
leng = []
for i in val_y.cpu():
tmp = []
for j in i:
if j.item() > 0:
tmp.append(j.item())
leng.append(tmp)
for index, i in enumerate(predict):
preds += i[:len(leng[index])]
for index, i in enumerate(val_y.tolist()):
labels += i[:len(leng[index])]
print('prediction\n' + str(len(list2tags(preds))) + '\n', list2tags(preds))
print('labels\n'+ str(len(list2tags(labels))) + '\n', list2tags(labels))
aver_loss /= (len(test_dataloader) * 64)
# precision = precision_score(labels, preds, average='macro')
# recall = recall_score(labels, preds, average='macro')
# f1 = f1_score(labels, preds, average='macro')
precision = precision_score(labels, preds, average='macro')
recall = recall_score(labels, preds, average='macro')
f1 = f1_score(labels, preds, average='macro')
# report = classification_report(labels, preds)
# print(report)
print('p',precision)
print('r',recall)
print('f1',f1)
p, r, f = get_f1score(list2tags(preds), list2tags(labels))
print('p', p)
print('r', r)
print('f1', f)
skf = StratifiedKFold(n_splits=5)
confusion_matrices = []
accuracies = []
precisions = []
recalls = []
f1s = []
for train, test in skf.split(X, Y):
xtrain, xtest = X[train], X[test]
ytrain, ytest = Y[train], Y[test]
clf.fit(xtrain, ytrain)
ypredict = clf.predict(xtest)
confusion_matrices.append(confusion_matrix(ytest, ypredict))
accuracies.append(accuracy_score(ytest, ypredict))
precisions.append(precision_score(ytest, ypredict))
recalls.append(recall_score(ytest, ypredict))
f1s.append(f1_score(ytest, ypredict))
print '5-fold cross-validation'
print 'sum of confusion matrices'
print sum(confusion_matrices)
print 'average accuracy'
print np.mean(accuracies)
print 'average precision'
print np.mean(precisions)
print 'average recall'
print np.mean(recalls)
print 'average f1'
print np.mean(f1s)
# train a classifier on the full training set
final_classifier = naive_bayes.BernoulliNB()
def get_metrics(path):
precision = []
recall = []
fscore = []
roc_auc = []
results = []
valid_dataset = 67
test_scores = np.load(path)
threshold = 0
for i in range(67):
values = np.load("data/A1X_" + str(i + 1) + ".npy")
labels = np.load("data/A1Y_" + str(i + 1) + ".npy")
test_portion = 0.2
test_n = int(len(labels) * test_portion)
train_values, test_values = values[:-test_n], values[-test_n:]
train_labels, test_labels = labels[:-test_n], labels[-test_n:]
test_score = test_scores[i]
threshold = np.sum(test_score) / test_score.shape[0]
test_correct = np.zeros(len(test_score))
for j in range(len(test_labels) - window_size + 1):
for k in range(window_size):
if (test_labels[j + k] == 1):
test_correct[j] = 1
break
# This is used for "threshold" detector (Detector 1 in report)
predictions = (test_score < threshold).astype(np.int32)
# Use the anomalous_num if taking advanced detection method (Detector 2 in report)
#anomalous_num = np.where(test_correct==1)[0].shape[0]
#predictions = np.zeros_like(test_correct)
#predictions_idx = heapq.nsmallest(anomalous_num, range(len(test_score)), test_score.take)
#predictions[predictions_idx] = 1
precision.append(
precision_score(test_correct, predictions, average="binary"))
recall.append(recall_score(test_correct, predictions,
average="binary"))
fscore.append(f1_score(test_correct, predictions, average="binary"))
if (np.sum(test_correct == 1) == 0
or np.sum(test_correct == 1) == test_correct.shape[0]):
roc_auc.append(0)
valid_dataset -= 1
else:
roc_auc.append(roc_auc_score(test_correct, test_score))
# This part is for augmenting the dataset with infrequent normal sampels
"""
train_score = np.load("scores_on_trained_S.npy")
train_correct = np.zeros(len(train_score[i]))
for j in range(len(train_labels)-window_size+1):
for k in range(window_size):
if (train_labels[j+k] == 1):
train_correct[j] = 1
break
a_n = np.where(train_correct==1)[0].shape[0]
pred = np.zeros_like(train_correct)
pred_idx = heapq.nsmallest(a_n, range(len(train_score[i])), train_score[i].take)
pred[pred_idx] = 1
augment_data(train_correct, train_values[:-119], pred, 50, "aug_data/A1X_"+str(i+1)+".npy", "aug_data/A1Y_"+str(i+1)+".npy")
"""
precision = np.array(precision)
recall = np.array(recall)
fscore = np.array(fscore)
roc_auc = np.array(roc_auc)
#np.save("precision.npy", precision)
#np.save("recall.npy", recall)
#np.save("fscore.npy", fscore)
#np.save("roc_auc.npy", roc_auc)
print("Precision:", float(np.sum(precision)) / valid_dataset)
print("Recall:", float(np.sum(recall)) / valid_dataset)
print("Fscore:", float(np.sum(fscore)) / valid_dataset)
print("AUC_Score:", float(np.sum(roc_auc)) / valid_dataset)
models_report = pd.DataFrame(columns=[
'Model', 'Precision_score', 'Recall_score', 'F1_score', 'Accuracy'
])
for clf, clf_name in zip(clfs.values(), clfs.keys()):
clf.fit(X_train_up, y_train_up)
y_pred = clf.predict(X_test_up)
y_score = clf.score(X_test_up, y_test_up)
#print('Calculating {}'.format(clf_name))
t = pd.Series({
'Model': clf_name,
'Precision_score': metrics.precision_score(y_test_up, y_pred),
'Recall_score': metrics.recall_score(y_test_up, y_pred),
'F1_score': metrics.f1_score(y_test_up, y_pred),
'Accuracy': metrics.accuracy_score(y_test_up, y_pred)
})
models_report = models_report.append(t, ignore_index=True)
models_report
from sklearn.ensemble import RandomForestClassifier
classifier = RandomForestClassifier(n_estimators=300,
n_jobs=1,
random_state=0,
bootstrap=False)
classifier.fit(X_train_up, y_train_up)
y_pred = classifier.predict(X_test_up)
auc_scores = []
for train_index, test_index in kf.split(idx_train):
X_train_fold, X_test_fold = X_train[train_index], X_train[test_index]
y_train_fold, y_test_fold = y_train[train_index], y_train[test_index]
elm.fit(X_train_fold,y_train_fold)
y_pred = elm.predict_proba(X_test_fold)[:, 1]
yhat_classes = y_pred.copy()
yhat_classes[yhat_classes>=threshold] = np.float64(1)
yhat_classes[yhat_classes<threshold] = np.float64(0)
accuracy = accuracy_score(y_test_fold, yhat_classes)
loss = log_loss(y_test_fold, yhat_classes)
f1 = f1_score(y_test_fold, yhat_classes)
precision = precision_score(y_test_fold, yhat_classes)
recall = recall_score(y_test_fold, yhat_classes)
auc_score = roc_auc_score(y_test_fold, y_pred)
accuracies.append(accuracy)
losses.append(loss)
f1s.append(f1)
precisions.append(precision)
recalls.append(recall)
auc_scores.append(auc_score)
end = time.time()
print('Accuracy: %f' % np.array(accuracies).mean())
print('Precision: %f' % np.array(precisions).mean())
print('Recall: %f' % np.array(recalls).mean())
def CNN_model(X_training,
X_test,
y_training,
y_test,
n_epochs=100,
batch_size=256,
model_name='model',
history_file='model_accuracies.csv',
conf_matrix=False,
accuracy_report=False):
while os.path.isfile(model_name + ".h5"):
model_name = model_name + str(1)
csv_logger = CSVLogger('model_training.log')
plot_losses = my_callbacks.PlotLosses()
metrics = my_callbacks.Metrics()
f1_accuracy = my_callbacks.F1Metric()
earlystop = EarlyStopping(monitor='val_acc', patience=10, mode='auto')
adam = Adam(lr=0.00001,
beta_1=0.9,
beta_2=0.999,
epsilon=None,
decay=0.0,
amsgrad=False)
model = Sequential()
model.add(
Conv1D(32,
9,
input_shape=(X_training.shape[1], 1),
kernel_initializer=he_normal(seed=12),
activation='relu',
W_regularizer=l1_l2(0.01)))
model.add(BatchNormalization())
model.add(MaxPooling1D(1))
model.add(
Conv1D(32,
3,
activation='relu',
W_regularizer=l1_l2(0.01),
padding='same'))
model.add(MaxPooling1D(3, padding='same'))
model.add(BatchNormalization())
model.add(
Conv1D(9,
3,
activation='relu',
W_regularizer=l1_l2(0.01),
padding='same'))
model.add(MaxPooling1D(3, padding='same'))
model.add(BatchNormalization())
model.add(
Conv1D(9,
3,
activation='relu',
W_regularizer=l1_l2(0.01),
padding='same'))
model.add(MaxPooling1D(3, padding='same'))
model.add(BatchNormalization())
model.add(Flatten())
model.add(Dense(512, activation='relu'))
model.add(Dropout(0.2))
model.add(Dense(256, activation='relu'))
model.add(BatchNormalization())
model.add(Dropout(0.2))
model.add(Dense(17, activation='softmax', input_shape=(1, )))
model.compile(optimizer=adam,
loss='sparse_categorical_crossentropy',
metrics=['accuracy'])
print('starts fitting model ...')
start = time.time()
model.fit(X_training,
y_training,
batch_size=batch_size,
epochs=n_epochs,
validation_data=(X_test, y_test),
callbacks=[metrics, csv_logger])
end = time.time()
delta = end - start
print('fitting time: ', delta)
print('starts predicting model ...')
start_prediction = time.time()
model.predict(X_test)
end_prediction = time.time()
delta_prediction = end_prediction - start_prediction
print('prediction time: ', delta_prediction)
y_pred = model.predict_classes(X_test)
model.save_weights(model_name + ".h5")
print('weights saved to disk')
model_json = model.to_json()
with open(model_name + '.json', 'w') as json_file:
json_file.write(model_json)
print('model saved to disk')
with open(history_file, 'a', newline='') as history:
writer = csv.writer(history, delimiter=';')
writer.writerow([
model_name,
accuracy_score(y_test, y_pred),
cohen_kappa_score(y_test, y_pred),
f1_score(y_test, y_pred, average='weighted'), delta,
delta_prediction
])
if conf_matrix:
cm_filename = model_name + '_cm.csv'
cm = pd.DataFrame(confusion_matrix(y_test, y_pred))
cm.to_csv(cm_filename)
if accuracy_report:
raport_filename = model_name + '_report.csv'
report = classification_report(y_test, y_pred)
with open(raport_filename, 'w') as acc_report:
acc_report.write(report)
return y_pred
'KNeighborsClassifier'
], [pe_v, nb_v, dt_v, rf_v, lr_v, kn_v]):
print(x)
error = (Y_test != y).sum()
p[0].append(error)
print("Errors : %d" % error)
acc = accuracy_score(y, Y_test) * 100
p[1].append(acc)
print("Accuracy : %.2f%%" % acc)
ps = precision_score(y, Y_test) * 100
p[2].append(ps)
print("Precision : %.2f%%" % ps)
rs = recall_score(y, Y_test) * 100
p[3].append(rs)
print("Recall : %.2f%%" % rs)
f1 = f1_score(y, Y_test) * 100
p[4].append(f1)
print("F1 Score : %.2f%% \n" % f1)
print("\n")
print("WITHOUT PCA")
# Perceptron Model
pe = Perceptron(n_iter=10, eta0=10, n_jobs=-1)
pe.fit(X_train_sd, Y_train)
# Naive Bayes Classification
nb = GaussianNB()
nb.fit(X_train, Y_train)
# Decision Tree Classifier
def main():
# Could/should refactor this whole thing
args = parseCmdLine()
myModule = sklearnHelperLib.importPyFile(args.pipelineDefs)
pipelines = myModule.pipelines
if type(pipelines) != type([]):
pipelines = [ pipelines ]
if args.vote: nPipelinesAndVotes = len(pipelines)+1 # include votes
else: nPipelinesAndVotes = len(pipelines)
# totals across all the split tries for each pipeline + voted predictions
# for computing averages
pipelineTotals = [ {'fscores':0,
'precisions': 0,
'f1': 0,
'recalls': 0, } for i in range(nPipelinesAndVotes) ]
# formats for output lines, Pipeline line, votes line, avg line
pf="Pipeline %d: F1: %5.3f F%d: %5.3f Precision: %4.2f Recall: %4.2f"
vf="Votes... %d: F1: %5.3f F%d: %5.3f Precision: %4.2f Recall: %4.2f"
af="Average. %d: F1: %5.3f F%d: %5.3f Precision: %4.2f Recall: %4.2f"
dataSet = load_files( args.trainingData )
labelIndex = dataSet['target_names'].index(args.label)
for sp in range(args.numSplits):
docs_train, docs_test, y_train, y_test = \
train_test_split( dataSet.data, dataSet.target,
test_size=args.testSize, random_state=None)
predictions = [] # predictions[i]= predictions for ith Pipeline
# on this split (for voting)
print "Sample Split %d" % sp
for i, pl in enumerate(pipelines): # for each Pipeline
pl.fit(docs_train, y_train)
y_pred = pl.predict(docs_test)
predictions.append(y_pred)
precision, recall, fscore, support = \
precision_recall_fscore_support( \
y_test, y_pred, args.beta,
pos_label=labelIndex,
average='binary')
f1 = f1_score(y_test, y_pred, pos_label=labelIndex,
average='binary')
pipelineTotals[i]['fscores'] += fscore
pipelineTotals[i]['f1'] += f1
pipelineTotals[i]['precisions'] += precision
pipelineTotals[i]['recalls'] += recall
l = pf % (i, f1, args.beta, fscore, precision, recall)
print l
if args.vote:
vote_pred = y_vote( predictions )
precision, recall, fscore, support = \
precision_recall_fscore_support( \
y_test, vote_pred, args.beta,
pos_label=labelIndex,
average='binary')
f1 = f1_score(y_test, vote_pred, pos_label=labelIndex,
average='binary')
i = len(pipelines)
pipelineTotals[i]['fscores'] += fscore
pipelineTotals[i]['f1'] += f1
pipelineTotals[i]['precisions'] += precision
pipelineTotals[i]['recalls'] += recall
l = vf % (i , f1, args.beta, fscore, precision, recall)
print l
# averages across all the Splits
print
for i in range(nPipelinesAndVotes):
avgFscore = pipelineTotals[i]['fscores'] / args.numSplits
avgF1 = pipelineTotals[i]['f1'] / args.numSplits
avgPrecision = pipelineTotals[i]['precisions'] / args.numSplits
avgRecall = pipelineTotals[i]['recalls'] / args.numSplits
l = af % (i, avgF1, args.beta, avgFscore, avgPrecision, avgRecall)
print l
# pipeline info
print "\nTraining data: %s" % args.trainingData
print time.strftime("%Y/%m/%d-%H-%M-%S")
for i,p in enumerate(pipelines):
print "\nPipeline %d -------------" % i
for s in p.steps:
print s
model_xgb = XGBClassifier(scale_pos_weight=3,
learning_rate=0.2,
n_estimators=200,
min_child_weight=20,
max_depth=3,
base_score=0.5,
gamma=0,
n_jobs=4)
# eval = [(X_test, y_test)]
# model_xgb.fit(X_train, y_train, eval_set=eval, eval_metric='auc', early_stopping_rounds=20, verbose=True)
model_xgb.fit(X, Y)
y_pred = model_xgb.predict(X_test)
p = precision_score(y_test, y_pred, average='binary')
r = recall_score(y_test, y_pred, average='binary')
f1score = f1_score(y_test, y_pred, average='binary')
print(p)
print(r)
print(f1score)
plot_importance(model_xgb, importance_type='gain')
pyplot.rcParams["font.sans-serif"] = ["Microsoft YaHei"]
pyplot.rcParams['axes.unicode_minus'] = False
pyplot.show()
# y_real_pred = model_xgb.predict(X_real_test)
# y_real_pred = grid_search.predict(X_real_test)
# y_real_id = pd.read_csv('data\df_id_test.csv', index_col=0, names=["个人编码", "result"])
# temp = pd.DataFrame({"result": y_real_pred}, index=X_real_test.index)
# print(temp["result"].sum())
# y_real_id["result"] = temp["result"]
for i in range(0, np.shape(features)[0], predict_batch):
predictions[i:i+predict_batch] = clf.predict(features[
i:i+predict_batch])
predictions_prob = np.zeros((np.shape(features)[0],len(np.unique(label))))
for i in range(0, np.shape(features)[0], predict_batch):
predictions_prob[i:i+predict_batch] = clf.predict_proba(features[
i:i+predict_batch])
np.save('predictions.npy',predictions)
np.save('predictions_prob.npy',predictions_prob)
predictions=predictions.astype(np.uint8)
print("predictions",predictions.shape,np.unique(predictions),predictions.dtype)
print("label_test",label.shape,np.unique(label),label.dtype)
predictions=predictions.astype(np.uint8)
metrics={}
metrics['f1_score']=f1_score(label,predictions,average=None)
metrics['f1_score_weighted']=f1_score(label,predictions,average='weighted')
metrics['overall_acc']=accuracy_score(label,predictions)
confusion_matrix_=confusion_matrix(label,predictions)
metrics['per_class_acc']=(confusion_matrix_.astype('float') / confusion_matrix_.sum(axis=1)[:, np.newaxis]).diagonal()
metrics['average_acc']=np.average(metrics['per_class_acc'][~np.isnan(metrics['per_class_acc'])])
print(metrics)
print(confusion_matrix_)
# A prediction is made on the test dataset based on the model fitted on train set
y_pred = clf.predict(x_test)
# Various performance metrics were found and reported for each k
print "k =", k
"""
Report all performance metrics and append values to their respective arrays
"""
accuracies.append(accuracy_score(y_test, y_pred))
print 'Accuracy:', accuracy_score(y_test, y_pred)
precisions.append(precision_score(y_test, y_pred))
print 'Precision:', precision_score(y_test, y_pred)
recalls.append(recall_score(y_test, y_pred))
print 'Recall:', recall_score(y_test, y_pred)
fscores.append(f1_score(y_test, y_pred))
print 'F1-Score:', f1_score(y_test, y_pred)
# Find best fit k based on their accuracies
best_k_index = np.argmax(accuracies)
"""
Display performance metrics for best fit k value
"""
print "Best fit k =", best_k_index + 3
print 'Best fit Accuracy:', accuracies[best_k_index]
print 'Best fit Precision:', precisions[best_k_index]
print 'Best fit Recall:', recalls[best_k_index]
print 'Best fit F1-Score:', fscores[best_k_index]
def gini_samples_f1(truth, predictions):
return f1_score(truth, predictions.argmax(axis=1), average='samples')
def train(self, data_dir):
'''
Trains a single layer model on the data contained in the specified
directory. Labels found in the directory are augmented with an
unknown label.
Args:
data_dir: Directory containing the training data
'''
print("Reading data")
# First read the data directory for the features and labels
X_all, y_all, new_labels = read_data(
data_dir,
duration=self.duration,
labels=self.labels
)
self.labels = new_labels
print("Making data splits")
# Split the data into training, validation, and testing sets
X_train, X_test, y_train, y_test = train_test_split(
X_all,
y_all,
test_size=0.2,
random_state=0
)
print("Normalizing features")
# Mean normalize the features, saving the means and variances
self.means = X_train.mean(axis=0)
self.stds = X_train.std(axis=0)
# Set the zero standard deviations to 1
zero_stds = self.stds <= 1
self.stds[zero_stds] = 1
# Apply the mean normalization transformation to the training dataj
X_normed = X_train - np.expand_dims(self.means, 0)
X_normed /= np.expand_dims(self.stds, 0)
print("Doing feature selection")
# Select the relevant features from the training set
self.feature_list = select_features(X_normed, y_train)
print(self.feature_list)
# If hidden size wasn't specified, default to the mean of the number
# of features and the size of the label space
if self.hidden_size is None:
self.hidden_size = int(1/2*(
len(self.labels) + \
len(self.feature_list)
)
)
# Augment the data with randomly permuted samples
X_aug, y_aug = self._augment_data(X_normed, y_train)
# Fit the one layer model to the augmented training data
X_input = X_aug[:, self.feature_list]
self.model = MLPClassifier(
(self.hidden_size),
alpha=0.1,
activation='relu',
max_iter=1000
)
self.model.fit(X_input, y_aug)
# Evaulate the model on the augmented test data
X_test_input = X_test - np.expand_dims(self.means, 0)
X_test_input /= np.expand_dims(self.stds, 0)
X_test_aug, y_test_aug = self._augment_data(X_test_input, y_test)
predictions = self.model.predict(X_test_aug[:, self.feature_list])
print("F1 score:",
f1_score(y_test_aug, predictions, average='weighted'))
def gini_weighted_f1(truth, predictions):
return f1_score(truth, predictions.argmax(axis=1), average='weighted')
def score(self, X, y, print_report=False):
predictions = self.predict(X)
if print_report:
print(confusion_matrix(y, predictions))
print(classification_report(y, predictions, digits=3))
return f1_score(y, predictions, average="macro")
string_files = string_files[int(len(string_files) *
args['split']):]
struct_files = struct_files[int(len(struct_files) *
args['split']):]
dynamc_files = dynamc_files[int(len(dynamc_files) *
args['split']):]
print('---------- ENSEMBLE MODEL ----------')
res = ensemble(
string_files, struct_files, dynamc_files,
string_model.predict(map(itemgetter(1), string_files)),
structure_model.predict(map(itemgetter(1), struct_files)),
dynamic_model.predict(map(itemgetter(1), dynamc_files)))
# Write the sklearn step here please on x=res[1] and y=res[2]
print("accuracy:\t\t\t", metrics.accuracy_score(res[1], res[2]))
print("f1 score (micro):\t\t",
metrics.f1_score(res[1], res[2], average='micro'))
print("precision score (micro):\t",
metrics.precision_score(res[1], res[2], average='micro'))
print("recall score (micro):\t\t",
metrics.recall_score(res[1], res[2], average='micro'))
print("f1 score (macro):\t\t",
metrics.f1_score(res[1], res[2], average='macro'))
print("precision score (macro):\t",
metrics.precision_score(res[1], res[2], average='macro'))
print("recall score (macro):\t\t",
metrics.recall_score(res[1], res[2], average='macro'))
elif mode == 'validate':
if args['choose']:
print(
'The parameter "choose" is unavailable for this operation.'
def gini_micro_f1(truth, predictions):
return f1_score(truth, predictions.argmax(axis=1), average='micro')
params,
n_jobs=1,
cv=5,
return_train_score=True,
scoring={'f1_score': make_scorer(f1_score, average='macro'),
'accuracy': 'accuracy'},
refit='f1_score',
verbose=10,
error_score='raise')
best = search.fit(X[:, :, :], Y[:])
print(best.__dict__)
print("BEST PARAMS: ", best.best_params_)
model_dir = 'models'
if not os.path.exists(model_dir):
os.makedirs(model_dir)
best_estimator = best.best_estimator_
best_estimator.fit(X, Y)
predicted_y = best_estimator.predict(X_test)
print("TEST EVALUATION")
print("F1-SCORE: ", f1_score(Y_test, predicted_y, average='macro'))
print("ACCURACY: ", accuracy_score(Y_test, predicted_y))
auc_roc = roc_auc_score(Y_test, predicted_y)
print("AUROC score : %s "% acc)
precision, recall, _ = precision_recall_curve(Y_test, predicted_y)
auc_prc = auc(recall, precision)
print("AUPRC score : %s "% auc_prc)
print(confusion_matrix(Y_test, predicted_y))
best_estimator.model.save(os.path.join(model_dir, str(datetime.now().strftime("%Y%m%d-%H%M%S"))))
def gini_f1(truth, predictions, pos_label=1):
return f1_score(truth, predictions, average=None)[pos_label]
Xtrain, Xtest, Ytrain, Ytest = train_test_split(X,
label,
test_size=.3,
random_state=1984)
print("len(X) = %d" % (len(X)))
print("len(Xtrain) = %d" % (len(Xtrain)))
print("len(Xtest) = %d" % (len(Xtest)))
model = BernoulliNB()
model.fit(Xtrain, Ytrain)
prediction = model.predict(Xtest)
accuracy = (Ytest == prediction).mean()
precision_score = precision_score(Ytest, prediction, average="macro")
recall_score = recall_score(Ytest, prediction, average="macro")
f1_score = f1_score(Ytest, prediction, average="macro")
print("accuracy %.3f" % accuracy)
print("precision_score %.3f" % precision_score)
print("recall_score %.3f" % recall_score)
print("f1_score %.3f" % f1_score)
confusion_matrix = confusion_matrix(Ytest, prediction, labels=[0, 1, 2, 3])
print(confusion_matrix)
print("VOIR LE RESULTAT DANS FICHIER NBLibrary.xlsx")
############ Ecrire resultat sur un fichier Excel ###############
export("NBLibrary.xlsx", confusion_matrix, len(X), len(Xtrain), len(Xtest),
accuracy, precision_score, recall_score, f1_score)
'''
import os
#print(classifier_Y.shape[0])
k_means_classifier = KNeighborsClassifier(n_neighbors=10)
k_means_classifier.fit(c_x_train, c_y_train)
svm_classifier = SVC(kernel='linear')
svm_classifier.fit(c_x_train, c_y_train)
k_means_guesses = k_means_classifier.predict(c_x_test)
svm_guesses = svm_classifier.predict(c_x_test)
print("K-Means Accuracy, Recall, Precision, and F1 score are as follows:")
print(accuracy_score(c_y_test, k_means_guesses))
print(recall_score(c_y_test, k_means_guesses, average='macro'))
print(precision_score(c_y_test, k_means_guesses, average='macro'))
print(f1_score(c_y_test, k_means_guesses, average='macro'))
print(
"Support Vector Machine Accuracy, Recall, Precision, and F1 score are as follows:"
)
print(accuracy_score(c_y_test, svm_guesses))
print(recall_score(c_y_test, svm_guesses, average='macro'))
print(precision_score(c_y_test, svm_guesses, average='macro'))
print(f1_score(c_y_test, svm_guesses, average='macro'))
#print(guesses)
### ----- Normalization of Regression Data
# ----------------------------------------------------------------------------------
feature_data1 = df[['sex_code', 'education_code']]
X = pd.read_csv('D:/SKRIPSI/percobaan/1332data9klas/tfidf1332.csv')
# In[2]:
kf = KFold(len(X), n_folds=10, shuffle=True, random_state=9999)
model_train_index = []
model_test_index = []
model = 0
for k, (index_train, index_test) in enumerate(kf):
X_train, X_test, y_train, y_test = X.ix[index_train,:], X.ix[index_test,:],y[index_train], y[index_test]
clf = MultinomialNB(alpha=0.1, fit_prior=True, class_prior=None).fit(X_train, y_train)
score = clf.score(X_test, y_test)
f1score = f1_score(y_test, clf.predict(X_test))
precision = precision_score(y_test, clf.predict(X_test))
recall = recall_score(y_test, clf.predict(X_test))
print('Model %d has accuracy %f with | f1score: %f | precision: %f | recall : %f'%(k,score, f1score, precision, recall))
model_train_index.append(index_train)
model_test_index.append(index_test)
model+=1
# In[5]:
temp = df.klasifikasi
# In[ ]:
def main(_):
# word_id_mapping_o, w2v_o = load_w2v(FLAGS.embedding_file, FLAGS.embedding_dim, True)
word_id_mapping_o, w2v_o = load_word_embedding(FLAGS.word_id_file, FLAGS.embedding_file, FLAGS.embedding_dim, True)
word_embedding_o = tf.constant(w2v_o, dtype=tf.float32)
# word_id_mapping_r, w2v_r = load_w2v(FLAGS.embedding_file_r, FLAGS.embedding_dim, True)
# word_id_mapping_r, w2v_r = load_word_embedding(FLAGS.word_id_file, FLAGS.embedding_file_r, FLAGS.embedding_dim, True)
word_id_mapping_r = word_id_mapping_o
word_embedding_r = tf.constant(w2v_o, dtype=tf.float32)
with tf.name_scope('inputs'):
keep_prob1 = tf.placeholder(tf.float32)
keep_prob2 = tf.placeholder(tf.float32)
x_o = tf.placeholder(tf.int32, [None, FLAGS.max_doc_len, FLAGS.max_sentence_len])
x_r = tf.placeholder(tf.int32, [None, FLAGS.max_doc_len, FLAGS.max_sentence_len])
sen_len_o = tf.placeholder(tf.int32, [None, FLAGS.max_doc_len])
sen_len_r = tf.placeholder(tf.int32, [None, FLAGS.max_doc_len])
doc_len_o = tf.placeholder(tf.int32, None)
doc_len_r = tf.placeholder(tf.int32, None)
y = tf.placeholder(tf.float32, [None, FLAGS.n_class])
inputs_o = tf.nn.embedding_lookup(word_embedding_o, x_o)
inputs_o = tf.reshape(inputs_o, [-1, FLAGS.max_sentence_len, FLAGS.embedding_dim])
inputs_r = tf.nn.embedding_lookup(word_embedding_r, x_r)
inputs_r = tf.reshape(inputs_r, [-1, FLAGS.max_sentence_len, FLAGS.embedding_dim])
prob = hn_inter_att(inputs_o, sen_len_o, doc_len_o, inputs_r, sen_len_r, doc_len_r, keep_prob1, keep_prob2)
with tf.name_scope('loss'):
reg_loss = tf.get_collection(tf.GraphKeys.REGULARIZATION_LOSSES)
loss = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(logits=prob, labels=y)) + tf.add_n(reg_loss)
all_vars = [var for var in tf.global_variables()]
with tf.name_scope('train'):
global_step = tf.Variable(0, name='global_step', trainable=False)
optimizer = tf.train.AdamOptimizer(learning_rate=FLAGS.learning_rate)
grads, global_norm = tf.clip_by_global_norm(tf.gradients(loss, all_vars), 5.0)
train_op = optimizer.apply_gradients(zip(grads, all_vars), name='train_op', global_step=global_step)
with tf.name_scope('predict'):
cor_pred = tf.equal(tf.argmax(prob, 1), tf.argmax(y, 1))
accuracy = tf.reduce_mean(tf.cast(cor_pred, tf.float32))
accuracy_num = tf.reduce_sum(tf.cast(cor_pred, tf.int32))
true_y = tf.argmax(y, 1)
pred_y = tf.argmax(prob, 1)
title = '-d1-{}d2-{}b-{}r-{}l2-{}sen-{}dim-{}h-{}c-{}'.format(
FLAGS.keep_prob1,
FLAGS.keep_prob2,
FLAGS.batch_size,
FLAGS.learning_rate,
FLAGS.l2_reg,
FLAGS.max_sentence_len,
FLAGS.embedding_dim,
FLAGS.n_hidden,
FLAGS.n_class
)
def get_batch_data(xo, slo, dlo, xr, slr, dlr, yy, batch_size, kp1, kp2, is_shuffle=True):
for index in batch_index(len(yy), batch_size, 1, is_shuffle):
feed_dict = {
x_o: xo[index],
x_r: xr[index],
y: yy[index],
sen_len_o: slo[index],
sen_len_r: slr[index],
doc_len_o: dlo[index],
doc_len_r: dlr[index],
keep_prob1: kp1,
keep_prob2: kp2,
}
yield feed_dict, len(index)
conf = tf.ConfigProto(allow_soft_placement=True)
conf.gpu_options.allow_growth = True
with tf.Session(config=conf) as sess:
import time
timestamp = str(int(time.time()))
_dir = 'summary/' + str(timestamp) + '_' + title
test_loss = tf.placeholder(tf.float32)
test_acc = tf.placeholder(tf.float32)
train_summary_op, test_summary_op, validate_summary_op, train_summary_writer, test_summary_writer, \
validate_summary_writer = summary_func(loss, accuracy, test_loss, test_acc, _dir, title, sess)
save_dir = 'temp_model/' + str(timestamp) + '_' + title + '/'
saver = saver_func(save_dir)
init = tf.global_variables_initializer()
sess.run(init)
# saver.restore(sess, '/-')
tr_x, tr_y, tr_sen_len, tr_doc_len = load_inputs_document(
FLAGS.train_file,
word_id_mapping_o,
FLAGS.max_sentence_len,
FLAGS.max_doc_len
)
te_x, te_y, te_sen_len, te_doc_len = load_inputs_document(
FLAGS.test_file,
word_id_mapping_o,
FLAGS.max_sentence_len,
FLAGS.max_doc_len
)
tr_x_r, tr_y_r, tr_sen_len_r, tr_doc_len_r = load_inputs_document(
FLAGS.train_file_r,
word_id_mapping_r,
FLAGS.max_sentence_len,
FLAGS.max_doc_len
)
te_x_r, te_y_r, te_sen_len_r, te_doc_len_r = load_inputs_document(
FLAGS.test_file_r,
word_id_mapping_r,
FLAGS.max_sentence_len,
FLAGS.max_doc_len
)
# v_x, v_y, v_sen_len, v_doc_len = load_inputs_document(
# FLAGS.validate_file_path,
# word_id_mapping,
# FLAGS.max_sentence_len,
# FLAGS.max_doc_len
# )
# v_x, v_y, v_sen_len, v_doc_len = load_inputs_document(
# FLAGS.validate_file_path,
# word_id_mapping,
# FLAGS.max_sentence_len,
# FLAGS.max_doc_len
# )
max_acc, max_prob, step = 0., None, None
max_ty, max_py = None, None
for i in xrange(FLAGS.n_iter):
for train, _ in get_batch_data(tr_x, tr_sen_len, tr_doc_len, tr_x_r, tr_sen_len_r, tr_doc_len_r, tr_y,
FLAGS.batch_size, FLAGS.keep_prob1, FLAGS.keep_prob2):
_, step, summary = sess.run([train_op, global_step, train_summary_op], feed_dict=train)
train_summary_writer.add_summary(summary, step)
# embed_update = tf.assign(word_embedding, tf.concat([tf.zeros([1, FLAGS.embedding_dim]), word_embedding[1:]]), 0)
# sess.run(embed_update)
acc, cost, cnt = 0., 0., 0
p, ty, py = [], [], []
for test, num in get_batch_data(te_x, te_sen_len, te_doc_len, te_x_r, te_sen_len_r, te_doc_len_r, te_y, FLAGS.batch_size, 1.0, 1.0, False):
_loss, _acc, _p, _ty, _py = sess.run([loss, accuracy_num, prob, true_y, pred_y], feed_dict=test)
p += list(_p)
ty += list(_ty)
py += list(_py)
acc += _acc
cost += _loss * num
cnt += num
print 'all samples={}, correct prediction={}'.format(cnt, acc)
acc = acc / cnt
cost = cost / cnt
print 'Iter {}: mini-batch loss={:.6f}, test acc={:.6f}'.format(i, cost, acc)
summary = sess.run(test_summary_op, feed_dict={test_loss: cost, test_acc: acc})
test_summary_writer.add_summary(summary, step)
if acc > max_acc:
max_acc = acc
max_prob = p
max_ty = ty
max_py = py
# saver.save(sess, save_dir, global_step=step)
print 'P:', precision_score(max_ty, max_py, average=None)
print 'R:', recall_score(max_ty, max_py, average=None)
print 'F:', f1_score(max_ty, max_py, average=None)
fp = open(FLAGS.prob_file, 'w')
for item in max_prob:
fp.write(' '.join([str(it) for it in item]) + '\n')
print 'Optimization Finished! Max acc={}'.format(max_acc)
print 'Learning_rate={}, iter_num={}, batch_size={}, hidden_num={}, l2={}'.format(
FLAGS.learning_rate,
FLAGS.n_iter,
FLAGS.batch_size,
FLAGS.n_hidden,
FLAGS.l2_reg
)
for i in features: ## run for every feature
my_list.append(i)
X = df.loc[:, my_list].values # data
## cross-validation
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.20,
random_state=0)
#machine learning algorithm is applied in this section
clf = ml_list[j] #
clf.fit(X_train, y_train)
predict = clf.predict(X_test)
f1 = clf.score(X_test, y_test)
result = f1_score(y_test, predict, average='macro')
accuracy = round(clf.score(X_test, y_test), 2)
temp = "["
for ii in my_list:
temp += str(
my_list.index(ii) + 1
) + ", " #translate property list to sequence number for less space
if result >= least: # If the F-criterion is equal to or greater than the highest value previously accessed, keep the new feature.
least = result
print(
'%-17s %-30s %-10s %-10s %-15s %-15s ' %
(j, i, result, accuracy, temp, "------> New feature found!!!"))
else: #If not, remove it from the list
def test(patch_shape, extraction_step):
with tf.Graph().as_default():
test_patches = tf.placeholder(tf.float32, [
F.batch_size, patch_shape[0], patch_shape[1], patch_shape[2],
F.num_mod
],
name='real_patches')
phase = tf.placeholder(tf.bool)
# Define the network
# For using actual 3-D U-Net change ***trained_network*** function both in training and testing
#output_soft = trained_network(test_patches, phase, patch_shape, reuse=None)
output_soft = trained_network_dis(test_patches, reuse=None)
# To convert from one hat form
output = tf.argmax(output_soft, axis=-1)
print("Output Patch Shape:", output.get_shape())
# To load the saved checkpoint
saver = tf.train.Saver()
with tf.Session() as sess:
try:
load_model(F.best_checkpoint_dir, sess, saver)
print(" Checkpoint loaded succesfully!....\n")
except:
print(" [!] Checkpoint loading failed!....\n")
return
# Get patches from test images
patches_test, labels_test = preprocess_dynamic_lab(
F.data_directory,
F.num_classes,
extraction_step,
patch_shape,
F.number_train_images,
validating=F.training,
testing=F.testing,
num_images_testing=F.number_test_images)
total_batches = int(patches_test.shape[0] / F.batch_size)
# Array to store the prediction results
predictions_test = np.zeros((patches_test.shape[0], patch_shape[0],
patch_shape[1], patch_shape[2]))
print("max and min of patches_test:", np.min(patches_test),
np.max(patches_test))
# Batch wise prediction
print("Total number of Batches: ", total_batches)
for batch in range(total_batches):
patches_feed = patches_test[batch * F.batch_size:(batch + 1) *
F.batch_size, :, :, :, :]
preds = sess.run(output,
feed_dict={
test_patches: patches_feed,
phase: False
})
predictions_test[batch * F.batch_size:(batch + 1) *
F.batch_size, :, :, :] = preds
print(("Processed_batch:[%8d/%8d]") % (batch, total_batches))
print("All patches Predicted")
print("Shape of predictions_test, min and max:",
predictions_test.shape, np.min(predictions_test),
np.max(predictions_test))
#To stitch the image back
images_pred = recompose3D_overlap(predictions_test, 144, 192, 256,
extraction_step[0],
extraction_step[1],
extraction_step[2])
print("Shape of Predicted Output Groundtruth Images:",
images_pred.shape, np.min(images_pred), np.max(images_pred),
np.mean(images_pred), np.mean(labels_test))
# To save the images
for i in range(F.number_test_images):
pred2d = np.reshape(images_pred[i], (144 * 192 * 256))
lab2d = np.reshape(labels_test[i], (144 * 192 * 256))
save_image(F.results_dir, images_pred[i],
F.number_train_images + i + 2)
F1_score = f1_score(lab2d, pred2d, [0, 1, 2, 3], average=None)
# Evaluation
pred2d = np.reshape(images_pred,
(images_pred.shape[0] * 144 * 192 * 256))
lab2d = np.reshape(labels_test,
(labels_test.shape[0] * 144 * 192 * 256))
F1_score = f1_score(lab2d, pred2d, [0, 1, 2, 3], average=None)
print("Testing Dice Coefficient.... ")
print("Background:", F1_score[0])
print("CSF:", F1_score[1])
print("GM:", F1_score[2])
print("WM:", F1_score[3])
return
def evaluate(self,dev,avg_best,BLEU=False):
logging.info("STARTING EVALUATION")
acc_avg = 0.0
wer_avg = 0.0
acc_G = 0.0
acc_P = 0.0
acc_V = 0.0
microF1_PRED,microF1_PRED_cal,microF1_PRED_nav,microF1_PRED_wet = [],[],[],[]
microF1_TRUE,microF1_TRUE_cal,microF1_TRUE_nav,microF1_TRUE_wet = [],[],[],[]
ref = []
hyp = []
ref_s = ""
hyp_s = ""
pbar = tqdm(enumerate(dev),total=len(dev))
for j, data_dev in pbar:
# (T,B) a list of list
words = self.evaluate_batch(len(data_dev[1]),data_dev[0],data_dev[1],data_dev[2],data_dev[3],data_dev[4],data_dev[5],data_dev[6])
acc=0
w = 0
temp_gen = []
for i, row in enumerate(np.transpose(words)): # (B,T)
st = ''
for e in row:
if e== '<EOS>':
break
else:
st+= e + ' '
temp_gen.append(st)
correct = data_dev[7][i]
### compute F1 SCORE
if(len(data_dev)>10):
f1_true,f1_pred = computeF1(data_dev[8][i],st.lstrip().rstrip(),correct.lstrip().rstrip())
microF1_TRUE += f1_true
microF1_PRED += f1_pred
f1_true,f1_pred = computeF1(data_dev[9][i],st.lstrip().rstrip(),correct.lstrip().rstrip())
microF1_TRUE_cal += f1_true
microF1_PRED_cal += f1_pred
f1_true,f1_pred = computeF1(data_dev[10][i],st.lstrip().rstrip(),correct.lstrip().rstrip())
microF1_TRUE_nav += f1_true
microF1_PRED_nav += f1_pred
f1_true,f1_pred = computeF1(data_dev[11][i],st.lstrip().rstrip(),correct.lstrip().rstrip())
microF1_TRUE_wet += f1_true
microF1_PRED_wet += f1_pred
if (correct.lstrip().rstrip() == st.lstrip().rstrip()):
acc+=1
w += wer(correct.lstrip().rstrip(),st.lstrip().rstrip())
ref.append(str(correct.lstrip().rstrip()))
hyp.append(str(st.lstrip().rstrip()))
ref_s+=str(correct.lstrip().rstrip())+ "\n"
hyp_s+=str(st.lstrip().rstrip()) + "\n"
acc_avg += acc/float(len(data_dev[1]))
wer_avg += w/float(len(data_dev[1]))
pbar.set_description("R:{:.4f},W:{:.4f}".format(acc_avg/float(len(dev)),wer_avg/float(len(dev))))
if(len(data_dev)>10):
logging.info("F1 SCORE:\t"+str(f1_score(microF1_TRUE, microF1_PRED, average='micro')))
logging.info("F1 CAL:\t"+str(f1_score(microF1_TRUE_cal, microF1_PRED_cal, average='micro')))
logging.info("F1 WET:\t"+str(f1_score(microF1_TRUE_wet, microF1_PRED_wet, average='micro')))
logging.info("F1 NAV:\t"+str(f1_score(microF1_TRUE_nav, microF1_PRED_nav, average='micro')))
if (BLEU):
bleu_score = moses_multi_bleu(np.array(hyp), np.array(ref), lowercase=True)
logging.info("BLEU SCORE:"+str(bleu_score))
if (bleu_score >= avg_best):
self.save_model(str(self.name)+str(bleu_score))
logging.info("MODEL SAVED")
return bleu_score
else:
acc_avg = acc_avg/float(len(dev))
if (acc_avg >= avg_best):
self.save_model(str(self.name)+str(acc_avg))
logging.info("MODEL SAVED")
return acc_avg
def train_or_eval_model(model,
loss_function,
dataloader,
epoch,
optimizer=None,
train=False):
losses = []
preds = []
labels = []
masks = []
alphas, alphas_f, alphas_b, vids = [], [], [], []
assert not train or optimizer != None
if train:
model.train()
else:
model.eval()
for data in dataloader:
if train:
optimizer.zero_grad()
# import ipdb;ipdb.set_trace()
acouf, qmask, umask, label =\
[d.cuda() for d in data[:-1]] if cuda else data[:-1]
#log_prob = model(torch.cat((textf,acouf,visuf),dim=-1), qmask,umask) # seq_len, batch, n_classes
log_prob, alpha, alpha_f, alpha_b = model(
acouf, qmask, umask) # seq_len, batch, n_classes
lp_ = log_prob.transpose(0, 1).contiguous().view(
-1,
log_prob.size()[2]) # batch*seq_len, n_classes
labels_ = label.view(-1) # batch*seq_len
loss = loss_function(lp_, labels_, umask)
pred_ = torch.argmax(lp_, 1) # batch*seq_len
preds.append(pred_.data.cpu().numpy())
labels.append(labels_.data.cpu().numpy())
masks.append(umask.view(-1).cpu().numpy())
losses.append(loss.item() * masks[-1].sum())
if train:
loss.backward()
optimizer.step()
else:
alphas += alpha
alphas_f += alpha_f
alphas_b += alpha_b
vids += data[-1]
if preds != []:
preds = np.concatenate(preds)
labels = np.concatenate(labels)
masks = np.concatenate(masks)
else:
return float('nan'), float('nan'), [], [], [], float('nan'), []
avg_loss = round(np.sum(losses) / np.sum(masks), 4)
avg_accuracy = round(
accuracy_score(labels, preds, sample_weight=masks) * 100, 2)
avg_fscore = round(
f1_score(labels, preds, sample_weight=masks, average='weighted') * 100,
2)
return avg_loss, avg_accuracy, labels, preds, masks, avg_fscore, [
alphas, alphas_f, alphas_b, vids
]