def variables_relevantes_arbol(X, Y, alpha=None):
if len(X) == 0:
logger.info("No se ingreso informacion de variables")
return []
features = list(X.columns)
if alpha == None:
alpha = 1.0 / len(features)
logger.info(
'Se calcula el valor minimo de aceptacion de importancia: {0}'.
format(alpha))
try:
model = ExtraTreeClassifier()
model.fit(X, Y)
importance = model.feature_importances_
relevant_features = []
for i in range(len(features)):
if importance[i] > alpha:
relevant_features.append(features[i])
except Exception as e:
logger.info(
'Error con el metodo de arboles, no se determinaron variables relevantes: {0}'
.format(e))
relevant_features = []
return importance, relevant_features
def dTree(data, labels, test, impurity="gini", mdepth=None):
newData = pd.DataFrame()
newTest = pd.DataFrame()
le = LabelEncoder()
for datum in data:
newData[datum] = le.fit_transform(data[datum])
for testItem in test:
newTest[testItem] = le.fit_transform(test[testItem])
tree1 = DecisionTreeClassifier(criterion=impurity,
max_depth=mdepth,
random_state=42)
tree2 = ExtraTreeClassifier(criterion=impurity,
max_depth=mdepth,
random_state=42)
tree3 = RandomForestClassifier(criterion=impurity,
max_depth=mdepth,
random_state=42)
tree1.fit(newData, labels)
tree2.fit(newData, labels)
tree3.fit(newData, labels)
predict1 = tree1.predict(newTest)
print("tree1", evaluate(predict1, validation_genres))
predict2 = tree2.predict(newTest)
print("tree2", evaluate(predict2, validation_genres))
predict3 = tree3.predict(newTest)
print("tree3", evaluate(predict3, validation_genres))
combined_prediction = voting([predict1, predict2, predict3], [1, 1, 1])
return combined_prediction
def variables_relevantes_arbol(X, Y, alpha=None):
if len(X) == 0:
logger.info("No information was passed")
return []
features = list(X.columns)
if alpha == None:
alpha = 1.0 / len(features)
logger.info(
'Aceptance threshold for variable importance is calculated: {0}'.
format(alpha))
try:
model = ExtraTreeClassifier()
model.fit(X, Y)
importance = model.feature_importances_
relevant_features = []
for i in range(len(features)):
if importance[i] > alpha:
relevant_features.append(features[i])
except Exception as e:
logger.info(
'Error with the tree based model, : There was not relevant variables found{0}'
.format(e))
relevant_features = []
return importance, relevant_features
def apply_extra_trees_classifier(trainData, targetTrain, testData, targetTest):
"""
Applies decision tree algorithm on the dataset, by tuning various parameters
Args:
dataframe: The input trainData, testData and class label on which the decision tree algorithm has to be applied
"""
# fit a CART model to the data
etc = ExtraTreeClassifier(class_weight=None,
criterion='gini',
max_depth=None,
max_features='auto',
max_leaf_nodes=None,
min_samples_leaf=1,
min_samples_split=2,
min_weight_fraction_leaf=0.0,
random_state=None,
splitter='random')
etc.fit(trainData, targetTrain)
print(etc)
# make predictions
expected = targetTest
predicted = etc.predict(testData)
# summarize the fit of the model
print(accuracy_score(expected, predicted))
def extratree(typ, X_train, Y_train, X_test, Y_test, text):
text.delete(1.0, tk.END)
text.insert(
tk.END,
"\n\nIMPORTING ExtraTree" + "\nProcessing this might take a while...",
"bold")
text.update_idletasks()
from sklearn.tree import ExtraTreeClassifier
ETC = ExtraTreeClassifier()
ETC.fit(X_train, Y_train)
Y_pred = ETC.predict(X_test)
text.insert(
tk.END, "\n\nExtra Tree Classifier report \n" +
classification_report(Y_pred, Y_test), "bold")
text.insert(
tk.END,
"*****roc_auc_score: %0.3f*****\n" % roc_auc_score(Y_pred, Y_test),
"bold")
text.insert(
tk.END, "Extra Tree Classifier confusion matrix \n" +
str(confusion_matrix(Y_pred, Y_test)), "bold")
score = accuracy_score(Y_pred, Y_pred)
text.insert(tk.END, "Extra tree score= ", score)
text.update_idletasks()
roc_curve_acc(Y_test, Y_pred, 'ETC')
if typ == "s":
plt.show()
elif typ == "a":
pass
class ExtraTreeClassifierTestCase(SchemaValidationTestCase, unittest.TestCase):
def setUp(self):
super().setUp()
self.model = ExtraTreeClassifier()
iris = load_iris()
X = iris.data.astype(np.float32)
y = iris.target.astype(np.int32)
self.model.fit(X, y)
def tree_select(self):
# 树模型嵌入式特征选取
clf = ExtraTreeClassifier(max_depth=7)
clf.fit(self.X, self.y.ravel())
feature_var = list(clf.feature_importances_)
features = dict(zip(self.feature_names, feature_var))
# print(features)
features = list(dict(sorted(features.items(), key=lambda d: d[1])).keys())[:self.select_feature_num]
return set(features)
def get_feature_relevance_tree(X, y):
vect = DictVectorizer()
X = vect.fit_transform(X)
tree = ExtraTreeClassifier(criterion='entropy')
tree.fit(X, y)
return zip(['general'],
vect.inverse_transform(tree.feature_importances_.reshape(-1,
1)))
def get_decision_tree(X, y, depth=None):
vect = DictVectorizer()
X = vect.fit_transform(X)
tree = ExtraTreeClassifier(max_depth=depth)
tree.fit(X, y)
return export_graphviz(tree,
feature_names=vect.feature_names_,
class_names=tree.classes_,
filled=True)
def trees_models(x_train, y_train):
from sklearn.tree import DecisionTreeClassifier
classifier1 = DecisionTreeClassifier(criterion='entropy', random_state=0)
classifier1.fit(x_train, y_train)
from sklearn.tree import ExtraTreeClassifier
classifier2 = ExtraTreeClassifier()
classifier2.fit(x_train, y_train)
print('DecisionTreeClassifier training accuracy: ',
classifier1.score(x_train, y_train))
print('ExtraTreesClassifier training accuracy: ',
classifier2.score(x_train, y_train))
return classifier1, classifier2
def test_extra_tree_clf():
X, y = load_iris(return_X_y=True)
X_ = X.tolist()
for y_ in [y, (y == 0).astype(int), (y == 2).astype(int)]:
for max_depth in [5, 10, None]:
clf = ExtraTreeClassifier()
clf.fit(X, y_)
clf_ = convert_estimator(clf)
for method in METHODS:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
scores = getattr(clf, method)(X)
scores_ = getattr(clf_, method)(X_)
assert np.allclose(scores.shape, shape(scores_))
assert np.allclose(scores, scores_, equal_nan=True)
def RecommendByET(train_data, train_data_y, test_data, test_data_y, recommendNum=5):
"""多标签分类 """
clf = ExtraTreeClassifier()
clf.fit(train_data, train_data_y)
predictions = clf.predict_proba(test_data)
"""预测结果转化为data array"""
predictions = DataProcessUtils.convertMultilabelProbaToDataArray(predictions)
print(predictions)
recommendList = DataProcessUtils.getListFromProbable(predictions, range(1, train_data_y.shape[1] + 1),
recommendNum)
answerList = test_data_y
print(predictions)
print(test_data_y)
print(recommendList)
print(answerList)
return [recommendList, answerList]
def extra_tree_classifier(self):
self.log.writeToLog('Running Extra Tree Classifier Model...')
X_train, X_test, y_train, y_test = self.train_test_split()
et = ExtraTreeClassifier()
trained_model = et.fit(X_train, y_train)
self.save_pickle(trained_model)
y_pred = et.predict(X_test)
self.model_auc_roc(y_test, y_pred, "Extra Tree Classifier Model")
self.model_evaluation(y_test, y_pred, "Extra Tree Classifier Model")
def extra_tree(self):
x_train, x_test, y_train, y_test = self.preprocessing()
extra_tree_model = ExtraTreeClassifier()
y_pred = extra_tree_model.fit(x_train, y_train).predict(x_test)
acc = accuracy_score(y_test, y_pred)
print('Extra Tree Classifier:- ', acc)
conf = confusion_matrix(y_test, y_pred)
f1 = f1_score(y_test, y_pred, average='micro')
print('and its f1 score- ', f1)
print('confusion matrix: \n', conf)
def fit(self, X, y):
"""Build a random decision tree based classifier from the training set (X, y)."""
# Remove protected features
X_protect = np.delete(X, [self.prot_class], axis=1)
num_tr = len(y)
num_prot_1 = sum(X[:, self.prot_class])
num_prot_0 = num_tr - num_prot_1
#X_protect = X
i = 0
fair_trees = []
predictions = []
# Pick up fair trees
while i < self.num_fair_trees:
new_tree = ExtraTreeClassifier(
max_depth=self.max_depth,
min_samples_leaf=self.min_samples_leaf,
max_features=1)
new_tree.fit(X_protect, y)
new_prediction = new_tree.predict(X_protect)
# Calculate the probability we predict someone will dropout between groups (Statistical Parity)
num_pred_1 = len([
e for e in range(0, num_tr)
if new_prediction[e] == 0 and X[e, self.prot_class] == 1
])
num_pred_0 = len([
e for e in range(0, num_tr)
if new_prediction[e] == 0 and X[e, self.prot_class] == 0
])
stat_parity = abs(num_pred_1 / num_prot_1 -
num_pred_0 / num_prot_0)
if stat_parity < self.rho:
i += 1
fair_trees.append(new_tree)
predictions.append(new_prediction)
self.ridge_model.fit(np.transpose(np.asarray(predictions)), y)
self.decision_trees = fair_trees
def read_results(data, model_name):
with open('data.json') as data_json:
data_params = json.load(data_json)
# Prepare data
data_path = os.path.join(DATA_PATH, data_params['data'][data]['file_name'])
print('Read file: {}'.format(data_path))
X, y = load_csv(data_path)
# Apply scaling
scaler = MinMaxScaler().fit(X)
X = scaler.transform(X)
n_test = data_params['data'][data]['n_test']
random_state = RANDOM_STATE
X_train, X_test, y_train, y_test = train_test_split(
X, y, test_size=n_test, random_state=random_state)
model = ExtraTreeClassifier(random_state=RANDOM_STATE)
model.fit(X_train, y_train)
acc_train = model.score(X_train, y_train)
acc_test = model.score(X_test, y_test)
print(('Train Acc: {:.4f}, ' + 'Test Acc: {:.4f}').format(
acc_train, acc_test))
df = pd.DataFrame(columns=COLUMNS)
for attack in ATTACKS_NUM:
for defence in DEFENCES_NUM:
try:
df = get_dataframe_sklearn(df, model, data, model_name, attack,
defence)
except FileNotFoundError as err:
print(err)
continue
# These attacks have no hyperparameter
df.loc[(df['Attack'] == 'boundary') | (df['Attack'] == 'tree'),
'Adv_param'] = np.nan
output_file = os.path.join(
OUTPUT_PATH, '{}_{}_{}.csv'.format(data, model_name, VERSION))
df.to_csv(output_file)
print('Save to:', output_file)
def train_extratree_model():
results_extratree_model = {}
results_extratree_model['acc'] = []
results_extratree_model['p_r_f1_s'] = []
for i in range(30):
train_features, train_labels = get_train_data()
test_features, test_labels = get_test_data()
clf = ExtraTreeClassifier()
clf.fit(train_features, train_labels)
predictions = clf.predict(test_features)
p_r_f1_s = precision_recall_fscore_support(test_labels, predictions)
acc = accuracy_score(test_labels, predictions)
print("ExtraTree Model Classifier : ", acc)
print(
"ExtraTree Model Classifier Precision, Recall, F1-Score, Support: ",
p_r_f1_s)
results_extratree_model['acc'].append(acc)
results_extratree_model['p_r_f1_s'].append(p_r_f1_s)
time.sleep(10)
pickle.dump(results_extratree_model,
open('results_extratree_model.pkl', 'wb'))
class ExtraTreeClassifier(Classifier):
def __init__(self, matrixdatabase):
self._matrix_database = matrixdatabase
self._has_fit = False
self._etc = ETC()
def learn(self, ingredients, cuisine):
return
def classify(self, ingredients):
if not self._has_fit:
matrix, classes = self._matrix_database.make_train_matrix()
self._etc = self._etc.fit(matrix, classes)
print('Fitting complete...')
self._has_fit = True
output = self._etc.predict(
self._matrix_database.make_row_from_recipe(ingredients))
return output[0]
class ExtraTreeClassifier(Classifier): def __init__(self, matrixdatabase): self._matrix_database = matrixdatabase self._has_fit = False self._etc = ETC() def learn(self, ingredients, cuisine): return def classify(self, ingredients): if not self._has_fit: matrix, classes = self._matrix_database.make_train_matrix() self._etc = self._etc.fit(matrix, classes) print 'Fitting complete...' self._has_fit = True output = self._etc.predict(self._matrix_database.make_row_from_recipe(ingredients)) return output[0]
"去除低方差特征，统计学方法" # np.random.seed(10) # arr = np.random.random((5, 6)) # var = 0.4 # arrnew = VarianceThreshold(0.4 * var * (1 - var)).fit(arr).transform(arr) # print(arr) # print(arrnew) "单变量特征选择，统计学方法" X, y = load_iris(return_X_y=True) print(X.shape, y.shape) "SelectFromModel 只包含两种方法" clf = ExtraTreeClassifier() clf.fit(X, y) print(clf.feature_importances_) model = SelectFromModel(clf, prefit=True) X_new = model.transform(X) print(X_new.shape) # "基于原始数据" # DTC = RandomForestClassifier(n_estimators=20) # DTC.fit(X, y) # score1 = cross_val_score(DTC, X, y, cv=5) # print(np.mean(score1)) # # "单变量特征选择，统计学方法" # Xnew = SelectKBest(chi2, k=2).fit_transform(X, y) # 保留特征的个数
#zero variance removal
#from sklearn.feature_selection import VarianceThreshold
#var=VarianceThreshold()
#
#train_X=var.fit_transform(train_X)
#train_X[train_X._get_numeric_data().columns]=var.fit_transform(train_X._get_numeric_data())
from sklearn.ensemble import RandomForestClassifier
from sklearn.tree import DecisionTreeClassifier
from sklearn.tree import ExtraTreeClassifier
clf=ExtraTreeClassifier(criterion="entropy",random_state=100)
#clf=RandomForestClassifier(n_estimators=100,criterion="entropy",random_state=100)
clf.fit(train_X,train_y)
print(clf.feature_importances_)
for name, importance in zip(train_X.columns, clf.feature_importances_):
print(name, "=", importance)
imp_datafram=pd.DataFrame(list(zip(train_X.columns, clf.feature_importances_)))
#import matplotlib.pyplot as plt
#
#y_pos = np.arange(len(imp_datafram[0]))
#performance = imp_datafram[1]
#
#plt.bar(y_pos, performance, align='center', alpha=0.5)
#plt.xticks(y_pos, imp_datafram[0])
# data = ''
with open(fname) as f:
for s in f:
tmp = map(int, s.split())
labels.append(tmp[-1])
res.append(tmp[:-1])
# data += (str(tmp)[1:-1]).replace(',', '')+'\n'
# with open('out.txt', 'w') as o:
# o.write(str(data)[1:-1])
return res, labels
X, Y = readData('german.data-numeric.txt')
Xt = X[:-200] ; Yt = Y[:-200]
XT = X[-200:] ; YT = Y[-200:]
print len(Xt)
clf = ExtraTreeClassifier(max_depth=None, random_state=0)
clf = clf.fit(Xt, Yt)
#proba = clf.predict_proba(XT)
#print len(proba)
#print proba
err = 0
for i, x in enumerate(XT):
if clf.predict(x) != YT[i]:
prob = clf.predict_proba(x)
# print prob
err += 1
print err
def myclassify(numfiers=5,xtrain=xtrain,ytrain=ytrain,xtest=xtest,ytest=ytest):
count = 0
bagging2 = BaggingClassifier(ETC(),bootstrap=False,bootstrap_features=False)
bagging2.fit(xtrain,ytrain)
#print bagging2.score(xtest,ytest)
count += 1
classifiers = [bagging2.score(xtest,ytest)]
if count < numfiers:
tree2 = ETC()
tree2.fit(xtrain,ytrain)
#print tree2.fit(xtrain,ytrain)
#print tree2.score(xtest,ytest)
count+=1
classifiers = np.append(classifiers,tree2.score(xtest,ytest))
print "1"
print tree2.score(xtest,ytest)
if count < numfiers:
bagging1 = BaggingClassifier(ETC())
bagging1.fit(xtrain,ytrain)
#print bagging1.score(xtest,ytest)
count+=1
classifiers = np.append(classifiers,bagging1.score(xtest,ytest))
print "2"
print bagging1.score(xtest,ytest)
# if count < numfiers:
# # votingClassifiers combine completely different machine learning classifiers and use a majority vote
# clff1 = SVC()
# clff2 = RFC(bootstrap=False)
# clff3 = ETC()
# clff4 = neighbors.KNeighborsClassifier()
# clff5 = quadda()
# print"3"
# eclf = VotingClassifier(estimators = [('svc',clff1),('rfc',clff2),('etc',clff3),('knn',clff4),('qda',clff5)])
# eclf = eclf.fit(xtrain,ytrain)
# #print(eclf.score(xtest,ytest))
# # for claf, label in zip([clff1,clff2,clff3,clff4,clff5,eclf],['SVC','RFC','ETC','KNN','QDA','Ensemble']):
# # cla
# # scores = crossvalidation.cross_val_score(claf,xtrain,ytrain,scoring='accuracy')
# # print ()
# count+=1
# classifiers = np.append(classifiers,eclf.score(xtest,ytest))
# if count < numfiers:
# svc1 = SVC()
# svc1.fit(xtrain,ytrain)
# dec = svc1.score(xtest,ytest)
# count+=1
# classifiers = np.append(classifiers,svc1.score(xtest,ytest))
# print "3"
if count < numfiers:
# Quadradic discriminant analysis - classifier with quadratic decision boundary -
qda = quadda()
qda.fit(xtrain,ytrain)
#print(qda.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,qda.score(xtest,ytest))
print "4"
if count < numfiers:
tree1 = DTC()
tree1.fit(xtrain,ytrain)
#print tree1.fit(xtrain,ytrain)
#print tree1.score(xtest,ytest)
count+=1
classifiers = np.append(classifiers,tree1.score(xtest,ytest))
if count < numfiers:
knn1 = neighbors.KNeighborsClassifier() # this classifies based on the #k nearest neighbors, where k is definted by the user.
knn1.fit(xtrain,ytrain)
#print(knn1.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,knn1.score(xtest,ytest))
if count < numfiers:
# linear discriminant analysis - classifier with linear decision boundary -
lda = linda()
lda.fit(xtrain,ytrain)
#print(lda.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,lda.score(xtest,ytest))
if count < numfiers:
tree3 = RFC()
tree3.fit(xtrain,ytrain)
#print tree3.score(xtest,ytest)
count+=1
classifiers = np.append(classifiers,tree3.score(xtest,ytest))
if count < numfiers:
bagging3 = BaggingClassifier(RFC(),bootstrap=False,bootstrap_features=False)
bagging3.fit(xtrain,ytrain)
#print bagging3.score(xtest,ytest)
count+=1
classifiers = np.append(classifiers,bagging3.score(xtest,ytest))
if count < numfiers:
bagging4 = BaggingClassifier(SVC(),bootstrap=False,bootstrap_features=False)
bagging4.fit(xtrain,ytrain)
#print bagging4.score(xtest,ytest)
count+=1
classifiers = np.append(classifiers,bagging4.score(xtest,ytest))
if count < numfiers:
tree4 = RFC(bootstrap=False)
tree4.fit(xtrain,ytrain)
#print tree4.score(xtest,ytest)
count+=1
classifiers = np.append(classifiers,tree4.score(xtest,ytest))
if count < numfiers:
tree6 = GBC()
tree6.fit(xtrain,ytrain)
#print(tree6.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,tree6.score(xtest,ytest))
if count < numfiers:
knn2 = neighbors.KNeighborsClassifier(n_neighbors = 10)
knn2.fit(xtrain,ytrain)
#print(knn2.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,knn2.score(xtest,ytest))
if count < numfiers:
knn3 = neighbors.KNeighborsClassifier(n_neighbors = 3)
knn3.fit(xtrain,ytrain)
#print(knn3.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,knn3.score(xtest,ytest))
if count < numfiers:
knn4 = neighbors.KNeighborsClassifier(algorithm = 'ball_tree')
knn4.fit(xtrain,ytrain)
#print(knn4.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,knn4.score(xtest,ytest))
if count < numfiers:
knn5 = neighbors.KNeighborsClassifier(algorithm = 'kd_tree')
knn5.fit(xtrain,ytrain)
#print(knn5.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,knn5.score(xtest,ytest))
if count < numfiers:
ncc1 = NearestCentroid()
ncc1.fit(xtrain,ytrain)
#print (ncc1.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,ncc1.score(xtest,ytest))
if count < numfiers:
# Nearest shrunken Centroid
for shrinkage in [None,0.05,0.1,0.2,0.3,0.4,0.5]:
ncc2 = NearestCentroid(shrink_threshold = shrinkage)
ncc2.fit(xtrain,ytrain)
#print(ncc2.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,ncc2.score(xtest,ytest))
if count < numfiers:
tree5 = ABC()
tree5.fit(xtrain,ytrain)
#print(tree5.score(xtest,ytest))
count+=1
classifiers = np.append(classifiers,tree5.score(xtest,ytest))
classifierlabel = ["BaggingETC (with bootstraps set to false)","ETC","BaggingETC","Voting Classifier","svm","QDA","DTC","KNN (default)","LDA","RFC",
"BaggingRFC (with bootstraps set to false)","BaggingSVC (with bootstraps set to false)","RFC (bootstrap false)","GBC",
"knn (n_neighbors = 10)","knn (n_neighbors = 3)","knn (ball tree algorithm)","knn (kd_tree algorithm)",
"Nearest Centroid","Shrunken Centroid?","ABC"]
classifierlabel = classifierlabel[:len(classifiers)]
#print len(classifiers)
#print classifiers
for i in range(len(classifiers)):
print ("{} classifier has percent correct {}".format(classifierlabel[i],classifiers[i]))
print("Test set Accuracy: ", metrics.accuracy_score(y_test, yhat))
# In[ ]:
DTree = DecisionTreeClassifier(max_depth=3)
DTree.fit(x_train, y_train)
yhat = DTree.predict(x_test)
print("DecisionTreeClassifier")
print("Train set Accuracy: ",
metrics.accuracy_score(y_train, DTree.predict(x_train)))
print("Test set Accuracy: ", metrics.accuracy_score(y_test, yhat))
# In[ ]:
ETree = ExtraTreeClassifier(max_depth=3)
ETree.fit(x_train, y_train)
yhat = ETree.predict(x_test)
print("ExtraTreeClassifier")
print("Train set Accuracy: ",
metrics.accuracy_score(y_train, ETree.predict(x_train)))
print("Test set Accuracy: ", metrics.accuracy_score(y_test, yhat))
# In[ ]:
Ada = AdaBoostClassifier()
Ada.fit(x_train, y_train)
yhat = Ada.predict(x_test)
print("AdaBoostClassifier")
print("Train set Accuracy: ",
metrics.accuracy_score(y_train, Ada.predict(x_train)))
print("Test set Accuracy: ", metrics.accuracy_score(y_test, yhat))
def main():
# filepath: sentence data file path
# vecfile: word vector file path pre-generated from other
# vectype: compression methods. Average, avg+tf-idf one line, agg+tf-idf whole data
# vec_path: vector file save path
filepath = '/home/junlinux/Desktop/CSCI544_Last/hw7/data/stem_testdata' # 'data/data_test'
vecfile = '/home/junlinux/Desktop/CSCI544_Last/hw7/data/glove.6B/glove.6B.50d.txt'
vec_files = [
'/home/junlinux/Desktop/CSCI544_Last/hw7/data/glove.6B/glove.6B.50d.txt',
'/home/junlinux/Desktop/CSCI544_Last/hw7/data/glove.6B/glove.6B.100d.txt',
'/home/junlinux/Desktop/CSCI544_Last/hw7/data/glove.6B/glove.6B.200d.txt',
'/home/junlinux/Desktop/CSCI544_Last/hw7/data/glove.6B/glove.6B.300d.txt',
'/home/junlinux/Desktop/CSCI544_Last/hw7/data/glove.6B/glove.42B.300d.txt',
'/home/junlinux/Desktop/CSCI544_Last/hw7/data/glove.6B/glove.840B.300d.txt'
]
# don't know why yet, relative file path having permission deny
# so we're using absolute path for now
vec_path = '/home/junlinux/Desktop/CSCI544_Last/hw7/data/word_vector/'
# Here, we can choose type of vectorization
# there are 6 word vector file downloaded from glove
"""
vectype = 1
for v in vec_files:
start_time = time.time()
name = v.split('/')[-1][:-4] + '_vec'
print(name, 'vectorization in process')
word_vec_gen(filepath, v, vectype, vec_path+name)
print("--- %s seconds ---" % (time.time() - start_time))
vectype = 2
for v in vec_files:
start_time = time.time()
name = v.split('/')[-1][:-4] + '_vec_OnelineTF'
print(name, 'vectorization in process')
word_vec_gen(filepath, v, vectype, vec_path + name)
print("--- %s seconds ---" % (time.time() - start_time))
vectype = 3
for v in vec_files:
start_time = time.time()
name = v.split('/')[-1][:-4] + '_vec_WholeDataTF'
print(name, 'vectorization in process')
word_vec_gen(filepath, v, vectype, vec_path + name)
print("--- %s seconds ---" % (time.time() - start_time))
"""
# from here, will earase.
filepath = '/home/junlinux/Desktop/CSCI544_Last/hw7/data/data_test' # 'data/stem_testdata'
#filepath = '/home/junlinux/Desktop/CSCI544_Last/hw7/data/hyp1-hyp2-ref'
vectype = 1
start_time = time.time()
name = vecfile.split('/')[-1][:-4] + '_vec_diffOrder'
#print(name, 'vectorization in process')
#word_vec_gen(filepath, vecfile, vectype, vec_path + name)
#print("--- %s seconds ---" % (time.time() - start_time))
filepath = '/home/junlinux/Desktop/CSCI544_Last/hw7/data/data_test' # 'data/stem_testdata'
vectype = 2
start_time = time.time()
name = vecfile.split('/')[-1][:-4] + '_vec_OnelineTF'
#print(name, 'vectorization in process')
#word_vec_gen(filepath, vecfile, vectype, vec_path + name)
#print("--- %s seconds ---" % (time.time() - start_time))
filepath = '/home/junlinux/Desktop/CSCI544_Last/hw7/data/data_test' # 'data/stem_testdata'
vectype = 3
start_time = time.time()
name = vecfile.split('/')[-1][:-4] + '_vec_WholeDataTF'
#print(name, 'vectorization in process')
#word_vec_gen(filepath, vecfile, vectype, vec_path + name)
#print("--- %s seconds ---" % (time.time() - start_time))
vec_path = 'data/word_vector/glove.6B.50d_vec_diffOrder'
wvec = load_wordvec(vec_path)
target_path = 'data/dev.answers'
answer = load_target(target_path)
from sklearn.model_selection import train_test_split
from sklearn.naive_bayes import BernoulliNB
from sklearn.tree import DecisionTreeClassifier
from sklearn.tree import ExtraTreeClassifier
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.neural_network import MLPClassifier
from sklearn.neighbors import KNeighborsClassifier
from sklearn.linear_model import LogisticRegression
from sklearn.svm import NuSVC
from sklearn.multiclass import OneVsOneClassifier
from sklearn.multiclass import OneVsRestClassifier
from sklearn.svm import LinearSVC
clf1 = KNeighborsClassifier()
clf2 = DecisionTreeClassifier()
clf3 = ExtraTreeClassifier()
clf4 = MLPClassifier()
clf5nu = NuSVC()
clf6lin = LinearSVC()
# 'sag', 'saga' and 'lbfgs' ’
print("Training Starts")
X_train, X_test, y_train, y_test = train_test_split(wvec,
answer,
test_size=0.10,
random_state=42)
#clf1.fit(X_train, y_train)
clf1.fit(X_train, y_train)
print('KNeighborsClassifier score 50d', clf1.score(X_test, y_test))
clf2.fit(X_train, y_train)
print('DecisionTreeClassifier score 50d', clf2.score(X_test, y_test))
clf3.fit(X_train, y_train)
print('ExtraTreeClassifier score 50d', clf3.score(X_test, y_test))
clf4.fit(X_train, y_train)
print('MLPClassifier score 50d', clf4.score(X_test, y_test))
clf1 = OneVsRestClassifier(KNeighborsClassifier())
clf2 = OneVsRestClassifier(DecisionTreeClassifier())
clf3 = OneVsRestClassifier(ExtraTreeClassifier())
clf4 = OneVsRestClassifier(MLPClassifier())
clf5 = OneVsOneClassifier(NuSVC())
clf6 = OneVsRestClassifier(LinearSVC())
from sklearn.linear_model import SGDClassifier
from sklearn.linear_model import Perceptron
from sklearn.linear_model import PassiveAggressiveClassifier
clf7 = OneVsRestClassifier(SGDClassifier())
clf8 = OneVsRestClassifier(Perceptron())
clf9 = OneVsRestClassifier(PassiveAggressiveClassifier())
print('One vs Rest methods case::')
print('KNeighborsClassifier score 50d',
clf1.fit(X_train, y_train).score(X_test, y_test))
print('DecisionTreeClassifier score 50d',
clf2.fit(X_train, y_train).score(X_test, y_test))
print('ExtraTreeClassifier score 50d',
clf3.fit(X_train, y_train).score(X_test, y_test))
print('MLPClassifier score 50d',
clf4.fit(X_train, y_train).score(X_test, y_test))
print('SGDClassifier score 50d',
clf7.fit(X_train, y_train).score(X_test, y_test))
print('Perceptron score 50d',
clf8.fit(X_train, y_train).score(X_test, y_test))
print('PassiveAggressiveClassifier score 50d',
clf9.fit(X_train, y_train).score(X_test, y_test))
print('NuSVC score 50d', clf5.fit(X_train, y_train).score(X_test, y_test))
print('LinearSVC score 50d',
clf6.fit(X_train, y_train).score(X_test, y_test))
clf5nu.fit(X_train, y_train)
print('NuSVC score 50d', clf5nu.score(X_test, y_test))
clf6lin.fit(X_train, y_train)
print('LinearSVC score 50d', clf6lin.score(X_test, y_test))
from sklearn.datasets import make_friedman1
from sklearn.feature_selection import RFECV
from sklearn.neighbors import KNeighborsClassifier
estimator = DecisionTreeClassifier()
test_set = df.iloc[train_data_len:, :]
#print(train_set.head(5))
train_x = train_set.iloc[:, 0:6]
train_y = train_set.iloc[:, 6:]
#print(type(train_y))
#train_y.reshape(len(train_y), )
#print(train_y.head(5))
test_x = test_set.iloc[:, 0:6]
test_y = test_set.iloc[:, 6:]
#test_y.reshape(len(test_y), )
#print(train_x.head(5))
#print(train_y.head(5))
from sklearn.tree import ExtraTreeClassifier
classifier = ExtraTreeClassifier(random_state=0,
criterion="entropy",
splitter="best")
classifier.fit(train_x, train_y.values.ravel())
info = classifier.score(test_x, test_y.values.ravel())
print(info)
#model = Sequential()
f1_score(y_test, smote_pred) recall_score(y_test, smote_pred) ################################################################### ########################## Feature Selection ###################### ################################################################### #Feature Selection using Tree Classifier a = r2.iloc[:,0:19] #independent columns b = r2.iloc[:,-1] #target column model = ExtraTreeClassifier() model.fit(a,b) print(model.feature_importances_) #use inbuilt class feature_importances of tree based classifiers #plot graph of feature importances for better visualization feat_importances = pd.Series(model.feature_importances_, index=a.columns) feat_importances.nlargest(19).plot(kind='barh') ############################################################### ####################### Cross Validation ###################### ############################################################### colnames = list(r2.columns) predictors = colnames[:19]
def myclassify_AudPow(numfiers,xtrain_1,xtrain_2,ytrain_1,ytrain_2,xtest):
# remove NaN, Inf, and -Inf values from the xtest feature matrix
xtest = xtest[~np.isnan(xtest).any(axis=1),:]
xtest = xtest[~np.isinf(xtest).any(axis=1),:]
xtrain = np.append(xtrain_1,xtrain_2,0)
ytrain = np.append(ytrain_1,ytrain_2)
ytrain = np.ravel(ytrain)
xtrunclength = sio.loadmat('../Files/xtrunclength.mat')
xtrunclength = xtrunclength['xtrunclength'][0]
#if xtest is NxM matrix, returns Nxnumifiers matrix where each column corresponds to a classifiers prediction vector
count = 0
# print numfiers
predictionMat = np.empty((xtest.shape[0],numfiers))
predictionStringMat = []
finalPredMat = []
bagging2 = BaggingClassifier(ETC(),bootstrap=False,bootstrap_features=False)
bagging2.fit(xtrain,ytrain)
#print bagging2.score(xtest,ytest)
ytest = bagging2.predict(xtest)
predictionMat[:,count] = ytest
count += 1
if count < numfiers:
tree2 = ETC()
tree2.fit(xtrain,ytrain)
ytest = tree2.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
bagging1 = BaggingClassifier(ETC())
bagging1.fit(xtrain,ytrain)
#print bagging1.score(xtest,ytest)
ytest = bagging1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
# votingClassifiers combine completely different machine learning classifiers and use a majority vote
clff1 = SVC()
clff2 = RFC(bootstrap=False)
clff3 = ETC()
clff4 = neighbors.KNeighborsClassifier()
clff5 = quadda()
eclf = VotingClassifier(estimators = [('svc',clff1),('rfc',clff2),('etc',clff3),('knn',clff4),('qda',clff5)])
eclf = eclf.fit(xtrain,ytrain)
#print(eclf.score(xtest,ytest))
# for claf, label in zip([clff1,clff2,clff3,clff4,clff5,eclf],['SVC','RFC','ETC','KNN','QDA','Ensemble']):
# cla
# scores = crossvalidation.cross_val_score(claf,xtrain,ytrain,scoring='accuracy')
# print ()
ytest = eclf.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
svc1 = SVC()
svc1.fit(xtrain,ytrain)
ytest = svc1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
# Quadradic discriminant analysis - classifier with quadratic decision boundary -
qda = quadda()
qda.fit(xtrain,ytrain)
#print(qda.score(xtest,ytest))
ytest = qda.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree1 = DTC()
tree1.fit(xtrain,ytrain)
ytest = tree1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn1 = neighbors.KNeighborsClassifier() # this classifies based on the #k nearest neighbors, where k is definted by the user.
knn1.fit(xtrain,ytrain)
ytest = knn1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
# linear discriminant analysis - classifier with linear decision boundary -
lda = linda()
lda.fit(xtrain,ytrain)
ytest = lda.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree3 = RFC()
tree3.fit(xtrain,ytrain)
ytest = tree3.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
bagging3 = BaggingClassifier(RFC(),bootstrap=False,bootstrap_features=False)
bagging3.fit(xtrain,ytrain)
ytest = bagging3.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
bagging4 = BaggingClassifier(SVC(),bootstrap=False,bootstrap_features=False)
bagging4.fit(xtrain,ytrain)
ytest = bagging4.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree4 = RFC(bootstrap=False)
tree4.fit(xtrain,ytrain)
ytest = tree4.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree6 = GBC()
tree6.fit(xtrain,ytrain)
ytest = tree6.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn2 = neighbors.KNeighborsClassifier(n_neighbors = 10)
knn2.fit(xtrain,ytrain)
ytest = knn2.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn3 = neighbors.KNeighborsClassifier(n_neighbors = 3)
knn3.fit(xtrain,ytrain)
ytest = knn3.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn4 = neighbors.KNeighborsClassifier(algorithm = 'ball_tree')
knn4.fit(xtrain,ytrain)
ytest = knn4.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn5 = neighbors.KNeighborsClassifier(algorithm = 'kd_tree')
knn5.fit(xtrain,ytrain)
ytest = knn5.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
ncc1 = NearestCentroid()
ncc1.fit(xtrain,ytrain)
ytest = ncc1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree5 = ABC()
tree5.fit(xtrain,ytrain)
ytest = tree5.predict(xtest)
predictionMat[:,count] = ytest
count+=1
for colCount in range(predictionMat.shape[1]):
tempCol = predictionMat[:,colCount]
modeCol = predWindowVecModeFinder(tempCol,xtrunclength)
modeStr = predVec2Str(modeCol)
predictionStringMat.append(modeStr)
finalPredMat += map(int,modeCol)
return predictionStringMat,finalPredMat
filled = True, rounded = True,
special_characters = True)
print(check_output('dot -Tpdf cart.dot -o cart.pdf', shell = True))
print("Accuracy = %s"%accuracy_score(rnd_test_y, clf_cart.predict(rnd_test_X)))
print("Precision = %s"%precision_score(rnd_test_y, clf_cart.predict(rnd_test_X)))
print("Recall = %s"%recall_score(rnd_test_y, clf_cart.predict(rnd_test_X)))
print("F = %s"%fbeta_score(rnd_test_y, clf_cart.predict(rnd_test_X), beta=1))
print("Confusion matrix = %s"%confusion_matrix(rnd_test_y, clf_cart.predict(rnd_test_X)))
roc_auc_scorer = get_scorer("roc_auc")
print("ROC AUC = %s"%roc_auc_scorer(clf_cart, rnd_test_X, rnd_test_y))
fpr, tpr, thresholds = roc_curve(rnd_test_y, clf_cart.predict_proba(rnd_test_X)[:, 1])
axes_roc.plot(fpr, tpr, label = 'CART-2')
## randomized tree with default setting
clf_rnd_tree = ExtraTreeClassifier()
clf_rnd_tree.fit(rnd_training_X, rnd_training_y)
export_graphviz(clf_rnd_tree, out_file = 'default_rnd_tree.dot',
feature_names = attribute_names,
class_names = bi_class_target_attrs,
filled = True, rounded = True,
special_characters = True)
print(check_output('dot -Tpdf default_rnd_tree.dot -o default_rnd_tree.pdf', shell = True))
print("Accuracy = %s"%accuracy_score(rnd_test_y, clf_rnd_tree.predict(rnd_test_X)))
print("Precision = %s"%precision_score(rnd_test_y, clf_rnd_tree.predict(rnd_test_X)))
print("Recall = %s"%recall_score(rnd_test_y, clf_rnd_tree.predict(rnd_test_X)))
print("F = %s"%fbeta_score(rnd_test_y, clf_rnd_tree.predict(rnd_test_X), beta=1))
print("Confusion matrix = %s"%confusion_matrix(rnd_test_y, clf_rnd_tree.predict(rnd_test_X)))
fpr, tpr, thresholds = roc_curve(rnd_test_y, clf_rnd_tree.predict_proba(rnd_test_X)[:, 1])
axes_roc.plot(fpr, tpr, label = "Randomized tree-1")
axes_roc.set_title("ROC of CART and a randomized tree")
axes_roc.set_xlabel("FPR")
# separate the data from the target attributes
test_data = dataset2.drop('change_id', axis=1)
test_data = test_data.drop('411_commit_time', axis=1)
test_data = test_data.drop('412_full_path', axis=1)
# remove unnecessary features
#test_data = test_data.drop('File', axis=1)
# the lables of test data
test_target = dataset2.Buggy
#print(test_target)
from imblearn.over_sampling import RandomOverSampler
ros = RandomOverSampler(random_state=0)
X_resampled, y_resampled = ros.fit_resample(train_data, train_target)
test_data_resampled, test_target_resampled = ros.fit_resample(
test_data, test_target)
clf = ExtraTreeClassifier(splitter='best')
test_pred = clf.fit(X_resampled,
y_resampled).predict(test_data_resampled)
file.write(
classification_report(test_target_resampled,
test_pred,
labels=[0, 1]))
file.write("\n")
file.close()
def build_separate_tree(X,y,max_features,max_depth,min_samples_split): clf = ExtraTreeClassifier(max_features=max_features,max_depth=max_depth,min_samples_split=min_samples_split) clf = clf.fit(X,y) return clf
mix_estimators = [
('le', LogisticRegression(solver='lbfgs', max_iter=1000, multi_class='multinomial')),
('te', rn.choice(tree_estimators)[1]), *rn.sample(boost_estimators, 4), *rn.sample(nb_estimators, 2)]
voting_classifier_mix = VotingClassifier(estimators=mix_estimators)
all_estimators = [('lgr', LogisticRegression(solver='lbfgs', max_iter=1000, multi_class='multinomial')),
*tree_estimators, *boost_estimators, *nb_estimators]
voting_classifier_all = VotingClassifier(estimators=all_estimators)
# Train all models, (it will take some time)
logistic_regression.fit(x_train, y_train)
tree_classifier.fit(x_train, y_train)
extra_tree_classifier.fit(x_train, y_train)
adaboost_classifier.fit(x_train, y_train)
extra_trees_classifier.fit(x_train, y_train)
bagging_classifier.fit(x_train, y_train)
gradient_boost_classifier.fit(x_train, y_train)
mlp_classifier.fit(x_train, y_train)
gaussian_nb.fit(x_train, y_train)
voting_classifier_tree.fit(x_train, y_train)
voting_classifier_boost.fit(x_train, y_train)
voting_classifier_nb.fit(x_train, y_train)
voting_classifier_mix.fit(x_train, y_train)
voting_classifier_all.fit(x_train, y_train)
#data = np.array(data)
print('Finish Label Encode')
clf = ExtraTreeClassifier(random_state=103, splitter='random', max_features=9)
##Get dataset
X = np.array(traindata.iloc[:, :10])
y = np.array(traindata.iloc[:, 10])
##build decision tree
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.1,
random_state=11)
clf.fit(X_train, y_train)
print('Finish Extra tree training')
predicttest = clf.predict(X_test)
##count click (0 or 1)
countClick = [0, 0]
for i in predicttest:
if i == 0:
countClick[0] += 1
else:
countClick[1] += 1
print(countClick)
##get accuracy, precision, recall, f_measure
dfscore.plot(kind='barh') # Label Encoding from sklearn.preprocessing import LabelEncoder le=LabelEncoder() y.iloc[:]=le.fit_transform(y.iloc[:]) # Feature Scaling from sklearn.preprocessing import StandardScaler sc=StandardScaler() x.iloc[:,:]=sc.fit_transform(x.iloc[:,:]) # Feature Importance from sklearn.tree import ExtraTreeClassifier classifier=ExtraTreeClassifier() classifier.fit(x,y) importance=pd.Series(classifier.feature_importances_,index=x.columns) importance.plot(kind='barh') # Segregating training & testing data from sklearn.model_selection import train_test_split x_train,x_test,y_train,y_test=train_test_split(x,y,test_size=0.2,random_state=0) # Modelling # Extreme Gradient Boosting: from sklearn.ensemble import BaggingClassifier from sklearn.tree import DecisionTreeClassifier gb=BaggingClassifier(DecisionTreeClassifier(),n_estimators=20,max_samples=0.5,max_features=1) gb.fit(x_train,y_train) gb.score(x_train,y_train) gb.score(x_test,y_test)
print("Feature ranking:")
for f in range(X.shape[1]):
print("%d. feature %d (%f)" % (f + 1, indices[f], importances[indices[f]]))
# Plotting featre importance
plt.figure(figsize=(10,5))
plt.title("Feature importances")
plt.bar(range(X.shape[1]), importances[indices],
color="g", yerr=std[indices], align="center")
plt.xticks(range(X.shape[1]), features,rotation=90)
plt.xlim([-1, X.shape[1]])
plt.show()
# Importing,intitiating and fitting Extra trees classifier
from sklearn.tree import ExtraTreeClassifier
extree = ExtraTreeClassifier(max_features=11,min_samples_split=21,
random_state=101,max_depth =28)
extree.fit(X_train_sm1,y_train_sm1)
extree_predict=extree.predict(X_test)
#checking performacne of the extra trees classifier
print(confusion_matrix(y_test,extree_predict))
print(classification_report(y_test,extree_predict))
#Importing test data
test=pd.read_csv('FIA_predictions.csv')
# getting columns same as training data
test=test.iloc[:,0:33]
#converting data type for categorical variables
test['NAICS2']=test['NAICS2'].astype('category')
test['NAICS4']=test['NAICS4'].astype('category')
test['NAICS_CD']=test['NAICS_CD'].astype('category')
test['Restricted_Vertical']=test['Restricted_Vertical'].astype('category')
test['LCTN_TYP_VAL']=test['LCTN_TYP_VAL'].astype('category')
test['srvc_five_dgt_zip']=test['srvc_five_dgt_zip'].astype('category')
def extra_tree(self):
x_train, x_test, y_train, y_test = self.preprocessing()
extra_tree_model = ExtraTreeClassifier()
y_pred = extra_tree_model.fit(x_train, y_train).predict(x_test)
self.printing(y_test, y_pred, 'Extra Tree')
### TREESSSSS from sklearn import tree from sklearn.tree import DecisionTreeClassifier as DTC tree1 = DTC() print tree1 tree1.fit(xtrain,ytrain1) print tree1.fit(xtrain,ytrain1) print tree1.score(xtest,ytest1) # In[22]: from sklearn.tree import ExtraTreeClassifier as ETC tree2 = ETC() print tree2 tree2.fit(xtrain,ytrain1) print tree2.fit(xtrain,ytrain1) print tree2.score(xtest,ytest1) # In[23]: from sklearn.ensemble import BaggingClassifier bagging1 = BaggingClassifier(ETC()) bagging1.fit(xtrain,ytrain1) print bagging1.score(xtest,ytest1) # In[24]: from sklearn.ensemble import BaggingClassifier
def myclassify_practice_set(numfiers,xtrain,ytrain,xtltrain,xtltest,xtest,ytarget=None,testing=False,grids='ABCDEFGHI'):
#NOTE we might not need xtltrain
# xtrain and ytrain are your training set. xtltrain is the indices of corresponding recordings in xtrain and ytrain. these will always be present
#xtest is your testing set. xtltest is the corresponding indices of the recording. for the practice set xtltest = xtrunclength
# ytest is optional and depends on if you are using a testing set or the practice set
# remove NaN, Inf, and -Inf values from the xtest feature matrix
xtest,xtltest,ytarget = removeNanAndInf(xtest,xtltest,ytarget)
# print 'finished removal of Nans'
ytrain = np.ravel(ytrain)
ytarget = np.ravel(ytarget)
#if xtest is NxM matrix, returns Nxnumifiers matrix where each column corresponds to a classifiers prediction vector
count = 0
# print numfiers
predictionMat = np.empty((xtest.shape[0],numfiers))
predictionStringMat = []
finalPredMat = []
targetStringMat = []
targets1 = []
predictions1 = []
# svc1 = SVC()
# svc1.fit(xtrain,ytrain)
# ytest = svc1.predict(xtest)
# predictionMat[:,count] = ytest
# count+=1
if count < numfiers:
# votingClassifiers combine completely different machine learning classifiers and use a majority vote
clff1 = SVC()
clff2 = RFC(bootstrap=False)
clff3 = ETC()
clff4 = neighbors.KNeighborsClassifier()
clff5 = quadda()
eclf = VotingClassifier(estimators = [('svc',clff1),('rfc',clff2),('etc',clff3),('knn',clff4),('qda',clff5)])
eclf = eclf.fit(xtrain,ytrain)
#print(eclf.score(xtest,ytest))
# for claf, label in zip([clff1,clff2,clff3,clff4,clff5,eclf],['SVC','RFC','ETC','KNN','QDA','Ensemble']):
# cla
# scores = crossvalidation.cross_val_score(claf,xtrain,ytrain,scoring='accuracy')
# print ()
ytest = eclf.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
bagging2 = BaggingClassifier(ETC(),bootstrap=False,bootstrap_features=False)
bagging2.fit(xtrain,ytrain)
#print bagging2.score(xtest,ytest)
ytest = bagging2.predict(xtest)
predictionMat[:,count] = ytest
count += 1
if count < numfiers:
tree2 = ETC()
tree2.fit(xtrain,ytrain)
ytest = tree2.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
bagging1 = BaggingClassifier(ETC())
bagging1.fit(xtrain,ytrain)
#print bagging1.score(xtest,ytest)
ytest = bagging1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
svc1 = SVC()
svc1.fit(xtrain,ytrain)
ytest = svc1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
# Quadradic discriminant analysis - classifier with quadratic decision boundary -
qda = quadda()
qda.fit(xtrain,ytrain)
#print(qda.score(xtest,ytest))
ytest = qda.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree1 = DTC()
tree1.fit(xtrain,ytrain)
ytest = tree1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn1 = neighbors.KNeighborsClassifier() # this classifies based on the #k nearest neighbors, where k is definted by the user.
knn1.fit(xtrain,ytrain)
ytest = knn1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
# linear discriminant analysis - classifier with linear decision boundary -
lda = linda()
lda.fit(xtrain,ytrain)
ytest = lda.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree3 = RFC()
tree3.fit(xtrain,ytrain)
ytest = tree3.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
bagging3 = BaggingClassifier(RFC(),bootstrap=False,bootstrap_features=False)
bagging3.fit(xtrain,ytrain)
ytest = bagging3.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
bagging4 = BaggingClassifier(SVC(),bootstrap=False,bootstrap_features=False)
bagging4.fit(xtrain,ytrain)
ytest = bagging4.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree4 = RFC(bootstrap=False)
tree4.fit(xtrain,ytrain)
ytest = tree4.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree6 = GBC()
tree6.fit(xtrain,ytrain)
ytest = tree6.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn2 = neighbors.KNeighborsClassifier(n_neighbors = 10)
knn2.fit(xtrain,ytrain)
ytest = knn2.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn3 = neighbors.KNeighborsClassifier(n_neighbors = 3)
knn3.fit(xtrain,ytrain)
ytest = knn3.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn4 = neighbors.KNeighborsClassifier(algorithm = 'ball_tree')
knn4.fit(xtrain,ytrain)
ytest = knn4.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
knn5 = neighbors.KNeighborsClassifier(algorithm = 'kd_tree')
knn5.fit(xtrain,ytrain)
ytest = knn5.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
ncc1 = NearestCentroid()
ncc1.fit(xtrain,ytrain)
ytest = ncc1.predict(xtest)
predictionMat[:,count] = ytest
count+=1
if count < numfiers:
tree5 = ABC()
tree5.fit(xtrain,ytrain)
ytest = tree5.predict(xtest)
predictionMat[:,count] = ytest
count+=1
# print xtltest
# print len(ytest)
for colCount in range(predictionMat.shape[1]):
tempCol = predictionMat[:,colCount]
if testing:
modeCol = temppredWindowVecModeFinder(tempCol,xtltest,4,grids,isPrint=0)
else:
modeCol = predWindowVecModeFinder(tempCol,xtltest,4,isPrint=0)
ytarg = predWindowVecModeFinder(ytarget,xtltest,1,isPrint=0)
if testing:
modeStr = temppredVec2Str(modeCol,grids)
else:
modeStr = predVec2Str(modeCol)
modeStrans = predVec2Str(ytarg)
predictionStringMat.append(modeStr)
predictions1.append(modeCol)
finalPredMat += map(int,modeCol)
targetStringMat.append(modeStrans)
targets1.append(ytarg)
if testing == False:
if ytarget != None:
#print targets1
#print ""
#print predictions1
confusionme = confusion_matrix(targets1[0],predictions1[0])
#print "Confusion Matrix is: "
#print confusionme
return predictionStringMat, targetStringMat, finalPredMat
print("CV error = %f +-%f" % (np.mean(scores), np.std(scores)))
#
print "Cross validation"
scores = cross_val_score(RandomForestClassifier(), training, classes,
cv=KFold(n=len(training), n_folds=5, random_state=42),
scoring="accuracy")
print("CV error = %f +-%f" % (1. - np.mean(scores), np.std(scores)))
print("Accuracy =", accuracy_score(y_test, tlf.predict(X_test)))
print("Precision =", precision_score(y_test, tlf.predict(X_test)))
print("Recall =", recall_score(y_test, tlf.predict(X_test)))
print("F =", fbeta_score(y_test, tlf.predict(X_test), beta=1))
print "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
print "Extra Tree classifier"
rlf = ExtraTreeClassifier()
rlf.fit(training, classes)
print("Training error =", zero_one_loss(classes, rlf.predict(training)))
X_train, X_test, y_train, y_test = train_test_split(training, classes)
rlf = ExtraTreeClassifier()
rlf.fit(X_train, y_train)
print("Training error =", zero_one_loss(y_train, rlf.predict(X_train)))
print("Test error =", zero_one_loss(y_test, rlf.predict(X_test)))
scores = []
print "K-fold cross validation"
for train, test in KFold(n=len(training), n_folds=5, random_state=42):
X_train, y_train = training[train], classes[train]
X_test, y_test = training[test], classes[test]
rlf = ExtraTreeClassifier().fit(X_train, y_train)