def _sklearn2weka(self, features, labels=None):
encoder = CategoricalEncoder(encoding='ordinal')
labels_nominal = encoder.fit_transform(np.array(labels).reshape(-1, 1))
if not hasattr(self, 'dict') and labels is not None:
dict = {}
for label, nominal in zip(labels, labels_nominal):
if nominal.item(0) not in dict:
dict[nominal.item(0)] = label
self._dict = dict
labels_column = np.reshape(labels_nominal,[labels_nominal.shape[0], 1])
weka_dataset = ndarray_to_instances(np.ascontiguousarray(features, dtype=np.float_), 'weka_dataset')
weka_dataset.insert_attribute(Attribute.create_nominal('tag', [str(float(i)) for i in range(len(self._dict))]), features.shape[1])
if labels is not None:
for index, inst in enumerate(weka_dataset):
inst.set_value(features.shape[1], labels_column[index])
weka_dataset.set_instance(index,inst)
return weka_dataset
def encode_cat(dat):
cat_encoder = CategoricalEncoder(encoding='onehot-dense')
dat = dat.astype('str')
dat_reshaped = dat.values.reshape(-1, 1)
dat_1hot = cat_encoder.fit_transform(dat_reshaped)
col_names = [
dat.name + '_' + str(x) for x in list(cat_encoder.categories_[0])
]
return pd.DataFrame(dat_1hot, columns=col_names)
def encode_cat(dat):
""" functon to return a labeled data frame with one hot encoding """
cat_encoder = CategoricalEncoder(encoding="onehot-dense")
dat = dat.astype('str')
dat_reshaped = dat.values.reshape(-1, 1)
dat_1hot = cat_encoder.fit_transform(dat_reshaped)
col_names = [
dat.name + "_" + str(x) for x in list(cat_encoder.categories_[0])
]
return pd.DataFrame(dat_1hot, columns=col_names)
def train(self,
d,
report_dir=None,
dropout=0.5,
batch_size=32,
epochs=5,
validation_split=0.,
**params):
d = d.sample(frac=1)
x = d[[c for c in d.columns if c != self.target]]
y = d[[self.target]]
self.preprocessor = dict(
x=StandardScaler(),
y=CategoricalEncoder(encoding='onehot-dense'),
)
x = self.preprocessor['x'].fit_transform(x)
y = self.preprocessor['y'].fit_transform(y)
self.build(dropout=dropout)
self.model.compile(optimizer='adam',
loss='categorical_crossentropy',
metrics=['accuracy'])
callbacks_used = [callbacks.TerminateOnNaN()]
if validation_split:
callbacks_used += [
callbacks.TensorBoard(report_dir,
batch_size=batch_size,
histogram_freq=1,
write_grads=True),
callbacks.ModelCheckpoint(os.path.join(report_dir,
'network.h5'),
verbose=0,
save_best_only=True)
]
report = self.model.fit(x,
y,
batch_size=batch_size,
epochs=epochs,
verbose=0,
callbacks=callbacks_used,
validation_split=validation_split,
validation_data=None,
shuffle=True,
class_weight=None,
sample_weight=None,
initial_epoch=0,
steps_per_epoch=None,
validation_steps=None)
if not validation_split:
models.save_model(self.model, os.path.join(report_dir,
'network.h5'))
return {k: [float(_v) for _v in v] for k, v in report.history.items()}
def create_pipelines(housing_num):
num_attribs = list(housing_num)
cat_attribs = ["ocean_proximity"]
num_pipeline = Pipeline([('selector', DataFrameSelector(num_attribs)),
('imputer', Imputer(strategy="median")),
('attribs_adder', CombinedAttributesAdder()),
('std_caller', StandardScaler())])
cat_pipeline = Pipeline([('selector', DataFrameSelector(cat_attribs)),
('cat_encoder',
CategoricalEncoder(encoding="onehot-dense"))])
return num_pipeline, cat_pipeline
def make_encode_pipeline():
numerical_cols = NUMERICAL_COLS
categorical_cols = CATEGORICAL_COLS + ['AgeBin', 'FamilyBin']
cat_pipe = Pipeline([
('cat_selector', DataFrameSelector(categorical_cols)),
('cat_encoder', CategoricalEncoder('onehot-dense')),
])
final_pipe = FeatureUnion([
('num_selector', DataFrameSelector(numerical_cols)),
('cat_pipe', cat_pipe),
])
return final_pipe
def convert_categorical_features(df):
enc = CategoricalEncoder(encoding='ordinal')
encoded_features = enc.fit_transform(df[[
'dim_is_requested', 'dim_market', 'dim_room_type', 'cancel_policy',
'dim_is_instant_bookable'
]])
encoded_df = pd.DataFrame(encoded_features,
index=df.index,
columns=[
'dim_is_requested', 'dim_market',
'dim_room_type', 'cancel_policy',
'dim_is_instant_bookable'
])
col = df.columns.tolist()
col_non_cat = col[1:3] + col[5:6] + col[7:10] + col[11:]
df_non_cat = df[col_non_cat]
col_cat = encoded_df.columns.tolist()
col_full = col_cat[:] + col_non_cat[:]
stack_full = np.column_stack([encoded_df, df_non_cat])
stack_df = pd.DataFrame(stack_full, index=df.index, columns=col_full)
return stack_df
def make_impute_pipeline():
categorical_cols = CATEGORICAL_COLS
numerical_cols = NUMERICAL_COLS
categorical_pre = Pipeline([
('selector', DataFrameSelector(categorical_cols)),
('impute', CustomImputer(strategy='mode')),
])
categorical_pipeline = Pipeline([
('categorical_pre', categorical_pre),
('encoder', CategoricalEncoder(encoding='onehot-dense')),
])
num_init_quantile_transformer = QuantileTransformer(
output_distribution='normal')
numerical_pipeline = Pipeline([
('selector', DataFrameSelector(numerical_cols)),
('scale', num_init_quantile_transformer),
])
combined_features = FeatureUnion([
('numerical_pipeline', numerical_pipeline),
('cat_ordinal_pipeline', categorical_pipeline),
])
mice_pipeline = Pipeline([
('combined_features', combined_features),
('mice_impute', MICEImputer(verbose=True)),
])
impute_pipeline = Pipeline([
('mice_pipeline', mice_pipeline),
('inverse_qt',
SelectiveAction(
col=list(range(len(numerical_cols))),
action=FunctionTransformer(
inverse_func,
kw_args={'transformer': num_init_quantile_transformer}))),
('numerical_selection', ColumnSelector(range(len(numerical_cols))))
])
final_pipeline = FeatureUnion([('impute_pipeline', impute_pipeline),
('categorical_pre', categorical_pre)])
return final_pipeline
# In[37]: from sklearn.preprocessing import OneHotEncoder encoder = OneHotEncoder() housing_cat_1hot = encoder.fit_transform(housing_cat_encoded.reshape(-1, 1)) housing_cat_1hot # In[38]: housing_cat_1hot.toarray() # In[39]: from sklearn.preprocessing import CategoricalEncoder cat_encoder = CategoricalEncoder() housing_cat_reshaped = housing_cat.values.reshape(-1, 1) housing_cat_1hot = cat_encoder.fit_transform(housing_cat_reshaped) housing_cat_1hot # In[40]: cat_encoder = CategoricalEncoder(encoding="onehot-dense") housing_cat_1hot = cat_encoder.fit_transform(housing_cat_reshaped) housing_cat_1hot # In[41]: cat_encoder.categories_ # In[42]:
X_q = np.array([[
'66', 'retired', 'married', 'primary', 'no', '206', 'no', 'no', 'cellular',
'9', 'feb', '479', '1', '-1', '0', 'unknown'
],
[
'54', 'technician', 'married', 'tertiary', 'no', '876',
'no', 'no', 'cellular', '27', 'oct', '269', '3', '541',
'3', 'success'
]])
# ### Replacing nominal relations
# To use this data we must replace nominal relations. We can encode labels with value between 0 and n_classes-1 or add n_classes dummy values and remove original column. Here we used second option, replaced nominal columns with onehot versions. I used this option because the first one would imply some categories were closer then others, for example encoded value 5 would be "closer" to encoded category 4 than 1. Downside of one-hot option is we will greatly increase number of features, but we can later use PCA to reduce number of features, or just keep the most informative ones.
# In[4]:
enc = CategoricalEncoder(encoding='onehot-dense')
X_2 = np.array(X[:, 0].reshape(-1, 1))
Xq_2 = np.array(X_q[:, 0].reshape(-1, 1))
attributes = [dataset['attributes'][0][0]]
for i, (name, relation) in enumerate(dataset['attributes'][1:-1]):
if relation == 'NUMERIC':
X_2 = np.hstack((X_2, X[:, i + 1].reshape(-1, 1)))
Xq_2 = np.hstack((Xq_2, X_q[:, i + 1].reshape(-1, 1)))
attributes.append(name)
continue
X_2 = np.hstack((X_2, enc.fit_transform(X[:, i + 1].reshape(-1, 1))))
Xq_2 = np.hstack((Xq_2, enc.transform(X_q[:, i + 1].reshape(-1, 1))))
# - age: float.
# - fare: float.
# Categorical Features:
# - embarked: categories encoded as strings {'C', 'S', 'Q'}.
# - sex: categories encoded as strings {'female', 'male'}.
# - pclass: ordinal integers {1, 2, 3}.
numeric_features = ['age', 'fare']
categorical_features = ['embarked', 'sex', 'pclass']
# Provisionally, use pd.fillna() to impute missing values for categorical
# features; SimpleImputer will eventually support strategy="constant".
data[categorical_features] = data[categorical_features].fillna(value='missing')
# We create the preprocessing pipelines for both numeric and categorical data.
numeric_transformer = make_pipeline(SimpleImputer(), StandardScaler())
categorical_transformer = CategoricalEncoder('onehot-dense',
handle_unknown='ignore')
preprocessing_pl = make_column_transformer(
(numeric_features, numeric_transformer),
(categorical_features, categorical_transformer),
remainder='drop'
)
# Append classifier to preprocessing pipeline.
# Now we have a full prediction pipeline.
clf = make_pipeline(preprocessing_pl, LogisticRegression())
X = data.drop('survived', axis=1)
y = data.survived.values
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2,
for t in transition:
transit.append(t)
# feat.append(features)
# transit.append(transition)
print(len(feat), 25)
GloveDimOption = '50' # this could be 50 (171.4 MB), 100 (347.1 MB), 200 (693.4 MB), or 300 (1 GB)
embeddings_index = loadGloveModel('data/glove.6B.' + GloveDimOption + 'd.txt')
# print(embeddings_index['apple'])
# print(embeddings_index['mango'])
embeddings_index[''] = np.zeros(50)
embeddings_index['*root'] = np.ones(50)
enc = CategoricalEncoder(encoding='onehot')
X_pos = [['ADJ'], ['ADP'], ['ADV'], ['AUX'], ['CCONJ'], ['DET'], ['INTJ'],
['NOUN'], ['NUM'], ['PART'], ['PRON'], ['PROPN'], ['PUNCT'],
['SCONJ'], ['SYM'], ['VERB'], ['X']]
enc.fit(X_pos)
for i in X_pos:
embeddings_index[i[0]] = pad_sequences(enc.transform([[i[0]]]).toarray(),
maxlen=50,
padding='post')[0]
#embeddings_index[i[0]] = pad_sequences(enc.transform([[i[0]]]).toarray(), maxlen=18, padding='post')[0]
# print(embeddings_index[i[0]])
# print(embeddings_index['apple'])
feat_vect, transit_vect = [], []
# feat_vect = np.array(())
def kfold_validation(self, k=10):
sem.acquire()
available_ram = psutil.virtual_memory()[1]
available_ram = int(int(available_ram) * .9 * 1e-9)
if available_ram > 5:
jvm.start(max_heap_size='5g')
else:
jvm.start(max_heap_size=str(available_ram)+'g')
###
print('\nCaricando '+self.input_file+' con opts -f'+str(self.features_number)+' -c'+self.classifier_name+'\n')
# load .arff file
dataset = arff.load(open(self.input_file, 'r'))
data = np.array(dataset['data'])
self.features_names = [x[0] for x in dataset['attributes']]
self.attributes_number = data.shape[1]
self.dataset_features_number = self.attributes_number - self.levels_number
# Factorization of Nominal features_index
encoder = CategoricalEncoder(encoding='ordinal')
nominal_features_index = [i for i in range(len(dataset['attributes'][:-self.levels_number])) if dataset['attributes'][i][1] != u'NUMERIC']
if len(nominal_features_index) > 0:
data[:, nominal_features_index] = encoder.fit_transform(
data[:, nominal_features_index])
# Impute missing value by fitting over training set and transforming both sets
imp = SimpleImputer(missing_values='NaN', strategy='most_frequent')
data[:, :self.dataset_features_number] = imp.fit_transform(data[:, :self.dataset_features_number])
classifiers_per_fold = []
oracles_per_fold = []
predictions_per_fold = []
predictions_per_fold_all = []
print('\n***\nStart testing with '+str(k)+'Fold cross-validation -f'+str(self.features_number)+' -c'+self.classifier_name+'\n***\n')
bar = progressbar.ProgressBar(maxval=k, widgets=[progressbar.Bar(
'=', '[', ']'), ' ', progressbar.Percentage()])
bar.start()
skf = StratifiedKFold(n_splits=k, shuffle=True)
bar_cnt = 0
for train_index, test_index in skf.split(data, data[:,self.attributes_number-1]):
self.classifiers = []
self.training_set = data[train_index, :self.dataset_features_number]
self.testing_set = data[test_index, :self.dataset_features_number]
self.ground_through = data[train_index, self.dataset_features_number:]
self.oracle = data[test_index, self.dataset_features_number:]
self.prediction = np.ndarray(shape=[len(test_index),self.levels_number],dtype='<U24')
self.prediction_all = np.ndarray(shape=[len(test_index),self.levels_number],dtype='<U24')
root = Tree()
root.train_index = [i for i in range(self.training_set.shape[0])]
root.test_index = [i for i in range(self.testing_set.shape[0])]
root.test_index_all = root.test_index
root.children_tags = list(set(self.ground_through[root.train_index, root.level]))
root.children_number = len(root.children_tags)
if self.has_config:
if 'f' in config[root.tag + '_' + str(root.level + 1)]:
root.features_number = config[root.tag + '_' + str(root.level + 1)]['f']
elif 'p' in config[root.tag + '_' + str(root.level + 1)]:
root.packets_number = config[root.tag + '_' + str(root.level + 1)]['p']
root.classifier_name = config[root.tag + '_' + str(root.level + 1)]['c']
print('config','tag',root.tag,'level',root.level,'f',root.features_number,'c',root.classifier_name)
else:
root.features_number = self.features_number
root.packets_number = self.packets_number
root.classifier_name = self.classifier_name
self.classifiers.append(root)
if root.children_number > 1:
classifier_to_call = getattr(self, supported_classifiers[root.classifier_name])
classifier_to_call(node=root)
else:
self.unary_class_results_inferring(root)
# Creating hierarchy recursively
if root.level < self.levels_number-1 and root.children_number > 0:
self.recursive(root)
classifiers_per_fold.append(self.classifiers)
oracles_per_fold.append(self.oracle)
predictions_per_fold.append(self.prediction)
predictions_per_fold_all.append(self.prediction_all)
bar_cnt += 1
bar.update(bar_cnt)
bar.finish()
folder_discriminator = self.classifier_name
if self.has_config:
folder_discriminator = self.config_name
material_folder = './data_'+folder_discriminator+'/material/'
if not os.path.exists('./data_'+folder_discriminator):
os.makedirs('./data_'+folder_discriminator)
os.makedirs(material_folder)
elif not os.path.exists(material_folder):
os.makedirs(material_folder)
type_discr = 'flow'
feat_discr = '_f_' + str(self.features_number)
if not self.has_config and self.packets_number != 0:
type_discr = 'early'
feat_discr = '_p_' + str(self.packets_number)
elif self.has_config:
if 'p' in self.config:
type_discr = 'early'
feat_discr = '_c_' + self.config_name
material_features_folder = './data_'+folder_discriminator+'/material/features/'
if not os.path.exists(material_folder):
os.makedirs(material_folder)
os.makedirs(material_features_folder)
elif not os.path.exists(material_features_folder):
os.makedirs(material_features_folder)
for i in range(self.levels_number):
file = open(material_folder + 'multi_' + type_discr + '_level_' + str(i+1) + feat_discr + '.dat', 'w+')
file.close()
for j in range(k):
file = open(material_folder + 'multi_' + type_discr + '_level_' + str(i+1) + feat_discr + '.dat', 'a')
file.write('@fold\n')
for o, p in zip(oracles_per_fold[j][:,i], predictions_per_fold[j][:,i]):
file.write(str(o)+' '+str(p)+'\n')
file.close()
# Inferring NW metrics per classifier
for classifier in classifiers_per_fold[0]:
file = open(material_folder + 'multi_' + type_discr + '_level_' + str(classifier.level+1) + feat_discr + '_tag_' + str(classifier.tag) + '.dat', 'w+')
file.close()
file = open(material_folder + 'multi_' + type_discr + '_level_' + str(classifier.level+1) + feat_discr + '_tag_' + str(classifier.tag) + '_all.dat', 'w+')
file.close()
file = open(material_features_folder + 'multi_' + type_discr + '_level_' + str(classifier.level+1) + feat_discr + '_tag_' + str(classifier.tag) + '_features.dat', 'w+')
file.close()
for fold_n, classifiers in enumerate(classifiers_per_fold):
for classifier in classifiers:
file = open(material_folder + 'multi_' + type_discr + '_level_' + str(classifier.level+1) + feat_discr + '_tag_' + str(classifier.tag) + '.dat', 'a')
if classifier.level > 0:
index = []
for pred_n, prediction in enumerate(predictions_per_fold[fold_n][classifier.test_index, classifier.level-1]):
if prediction == oracles_per_fold[fold_n][classifier.test_index[pred_n], classifier.level-1]:
index.append(classifier.test_index[pred_n])
prediction_nw = predictions_per_fold[fold_n][index, classifier.level]
oracle_nw = oracles_per_fold[fold_n][index, classifier.level]
else:
prediction_nw = predictions_per_fold[fold_n][classifier.test_index, classifier.level]
oracle_nw = oracles_per_fold[fold_n][classifier.test_index, classifier.level]
file.write('@fold\n')
for o, p in zip(oracle_nw, prediction_nw):
file.write(str(o)+' '+str(p)+'\n')
file.close()
file = open(material_folder + 'multi_' + type_discr + '_level_' + str(classifier.level+1) + feat_discr + '_tag_' + str(classifier.tag) + '_all.dat', 'a')
if classifier.level > 0:
index = []
for pred_n, prediction in enumerate(predictions_per_fold_all[fold_n][classifier.test_index, classifier.level-1]):
if prediction == oracles_per_fold[fold_n][classifier.test_index[pred_n], classifier.level-1]:
index.append(classifier.test_index[pred_n])
prediction_all = predictions_per_fold_all[fold_n][index, classifier.level]
oracle_all = oracles_per_fold[fold_n][index, classifier.level]
else:
prediction_all = predictions_per_fold_all[fold_n][classifier.test_index_all, classifier.level]
oracle_all = oracles_per_fold_all[fold_n][classifier.test_index_all, classifier.level]
file.write('@fold\n')
for o, p in zip(oracle_all, prediction_all):
file.write(str(o)+' '+str(p)+'\n')
file.close()
file = open(material_features_folder + 'multi_' + type_discr + '_level_' + str(classifier.level+1) + feat_discr + '_tag_' + str(classifier.tag) + '_features.dat', 'a')
file.write('@fold\n')
file.write(self.features_names[classifier.features_index[0]])
for feature_index in classifier.features_index[1:]:
file.write(','+self.features_names[feature_index])
file.write('\n')
file.close()
graph_folder = './data_'+folder_discriminator+'/graph/'
if not os.path.exists('./data_'+folder_discriminator):
os.makedirs('./data_'+folder_discriminator)
os.makedirs(graph_folder)
elif not os.path.exists(graph_folder):
os.makedirs(graph_folder)
# Graph plot
G = nx.DiGraph()
for info in classifiers_per_fold[0]:
G.add_node(str(info.level)+' '+info.tag, level=info.level,
tag=info.tag, children_tags=info.children_tags)
for node_parent, data_parent in G.nodes.items():
for node_child, data_child in G.nodes.items():
if data_child['level']-data_parent['level'] == 1 and any(data_child['tag'] in s for s in data_parent['children_tags']):
G.add_edge(node_parent, node_child)
nx.write_gpickle(G, graph_folder+'multi_' + type_discr + feat_discr +'_graph.gml')
###
jvm.stop()
sem.release()
from sklearn.tree import DecisionTreeClassifier
from sklearn.tree import export_graphviz
from sklearn.ensemble import RandomForestClassifier
from sklearn.preprocessing import Imputer
from sklearn.metrics import f1_score
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import OneHotEncoder
from sklearn.preprocessing import LabelBinarizer
from sklearn.preprocessing import CategoricalEncoder
train = pd.read_csv('train.csv')
# Cabin allocations https://www.encyclopedia-titanica.org/cabins.html
# label = LabelBinarizer()
# hot = OneHotEncoder(handle_unknown = 'ignore', n_values=['male', 'female'])
categorical = CategoricalEncoder()
pipe = Pipeline([('Categorical Encoder', categorical)])
# pipe = Pipeline([('Label Binarizer', label)])
# train['Sex'] = train['Sex'].replace({'male': 0, 'female': 1})
# train.head()
# train.describe()
train = train[['Pclass', 'Sex', 'SibSp', 'Parch', 'Fare', 'Age', 'Survived']]
pipe.fit(train)
imputer = Imputer()
train.describe()
encoding_methods = ['one-hot', 'target', 'similarity']
dirty_column = 'Employee Position Title'
#########################################################################
#########################################################################
# Creating a learning pipeline
# ----------------------------
# The encoders for both clean and dirty data are first imported:
from sklearn.preprocessing import FunctionTransformer
from sklearn.preprocessing import CategoricalEncoder
from dirty_cat import SimilarityEncoder, TargetEncoder
encoders_dict = {
'one-hot': CategoricalEncoder(handle_unknown='ignore',
encoding='onehot-dense'),
'similarity': SimilarityEncoder(similarity='ngram',
handle_unknown='ignore'),
'target': TargetEncoder(handle_unknown='ignore'),
'numerical': FunctionTransformer(None)}
# We then create a function that takes one key of our ``encoders_dict``,
# returns a pipeline object with the associated encoder,
# as well as a Scaler and a RidgeCV regressor:
from sklearn.compose import ColumnTransformer
from sklearn.pipeline import Pipeline
def make_pipeline(encoding_method):
# static transformers from the other columns
y_train,
test_size=0.5)
# Unsupervised transformation based on totally random trees
rt = RandomTreesEmbedding(max_depth=3, n_estimators=n_estimator,
random_state=0)
rt_lm = LogisticRegression()
pipeline = make_pipeline(rt, rt_lm)
pipeline.fit(X_train, y_train)
y_pred_rt = pipeline.predict_proba(X_test)[:, 1]
fpr_rt_lm, tpr_rt_lm, _ = roc_curve(y_test, y_pred_rt)
# Supervised transformation based on random forests
rf = RandomForestClassifier(max_depth=3, n_estimators=n_estimator)
rf_enc = CategoricalEncoder()
rf_lm = LogisticRegression()
rf.fit(X_train, y_train)
rf_enc.fit(rf.apply(X_train))
rf_lm.fit(rf_enc.transform(rf.apply(X_train_lr)), y_train_lr)
y_pred_rf_lm = rf_lm.predict_proba(rf_enc.transform(rf.apply(X_test)))[:, 1]
fpr_rf_lm, tpr_rf_lm, _ = roc_curve(y_test, y_pred_rf_lm)
grd = GradientBoostingClassifier(n_estimators=n_estimator)
grd_enc = CategoricalEncoder()
grd_lm = LogisticRegression()
grd.fit(X_train, y_train)
grd_enc.fit(grd.apply(X_train)[:, :, 0])
grd_lm.fit(grd_enc.transform(grd.apply(X_train_lr)[:, :, 0]), y_train_lr)
def kfold_validation(self, k=10):
sem.acquire()
available_ram = psutil.virtual_memory()[1]
available_ram = int(int(available_ram) * .9 * 1e-9)
if available_ram > 5:
jvm.start(max_heap_size='5g')
else:
jvm.start(max_heap_size=str(available_ram)+'g')
###
print('\nCaricando '+self.input_file+' con opts -f'+str(self.features_number)+' -c'+self.classifier_name+'\n')
# load .arff file
dataset = arff.load(open(input_file, 'r'))
data = np.array(dataset['data'])
self.features_names = [x[0] for x in dataset['attributes']]
self.attributes_number = data.shape[1]
self.dataset_features_number = self.attributes_number - self.levels_number
# Factorization of Nominal features_index
encoder = CategoricalEncoder(encoding='ordinal')
nominal_features_index = [i for i in range(len(dataset['attributes'][:-self.levels_number])) if dataset['attributes'][i][1] != u'NUMERIC']
if len(nominal_features_index) > 0:
data[:, nominal_features_index] = encoder.fit_transform(
data[:, nominal_features_index])
# Impute missing value by fitting over training set and transforming both sets
imp = SimpleImputer(missing_values='NaN', strategy='most_frequent')
data[:, :self.dataset_features_number] = imp.fit_transform(
data[:, :self.dataset_features_number])
prediction = []
probability = []
oracle = []
print('\n***\nStart testing with ' + str(k)+'Fold cross-validation -f'+str(self.features_number)+' -c'+self.classifier_name+'\n***\n')
bar = progressbar.ProgressBar(maxval=k, widgets=[progressbar.Bar(
'=', '[', ']'), ' ', progressbar.Percentage()])
bar.start()
temp_metrics = []
skf = StratifiedKFold(n_splits=k, shuffle=True)
bar_cnt = 0
for train_index, test_index in skf.split(data, data[:, self.dataset_features_number + self.tag_under_test]):
self.training_set = data[train_index, :self.dataset_features_number]
self.testing_set = data[test_index, :self.dataset_features_number]
self.ground_through = data[train_index,
self.dataset_features_number + self.tag_under_test]
self.oracle = data[test_index,
self.dataset_features_number + self.tag_under_test]
self.prediction = np.ndarray(
shape=[len(test_index), 1], dtype='<U24')
self.probability = np.ndarray(
shape=[len(test_index), len(set(self.ground_through))], dtype='<U24')
classifier_to_call = getattr(self, supported_classifiers[self.classifier_name])
classifier_to_call()
prediction.append(self.prediction)
probability.append(self.probability)
oracle.append(self.oracle)
# print(type(prediction[bar_cnt]))
# print(type(probability[bar_cnt]))
bar_cnt += 1
bar.update(bar_cnt)
bar.finish()
relations = []
relations = []
relations.append({ # Lv2:Lv1
u'Tor': u'Tor',
u'TorPT': u'Tor',
u'TorApp': u'Tor',
u'I2PApp80BW': u'I2P',
u'I2PApp0BW': u'I2P',
u'I2PApp': u'I2P',
u'JonDonym': u'JonDonym'
})
relations.append({ # Lv3:Lv2
u'JonDonym': u'JonDonym',
u'I2PSNARK_App80BW': u'I2PApp80BW',
u'IRC_App80BW': u'I2PApp80BW',
u'Eepsites_App80BW': u'I2PApp80BW',
u'I2PSNARK_App0BW': u'I2PApp0BW',
u'IRC_App0BW': u'I2PApp0BW',
u'Eepsites_App0BW': u'I2PApp0BW',
u'I2PSNARK_App': u'I2PApp',
u'IRC_App': u'I2PApp',
u'Eepsites_App': u'I2PApp',
u'ExploratoryTunnels_App': u'I2PApp',
u'ParticipatingTunnels_App': u'I2PApp',
u'Tor': u'Tor',
u'Streaming': u'TorApp',
u'Torrent': u'TorApp',
u'Browsing': u'TorApp',
u'Flashproxy': u'TorPT',
u'FTE': u'TorPT',
u'Meek': u'TorPT',
u'Obfs3': u'TorPT',
u'scramblesuit': u'TorPT'
})
oracle_inferred = []
prediction_inferred = []
for i in range(self.tag_under_test):
oracle_inferred.append(list())
prediction_inferred.append(list())
# Infering superior levels
for i in range(k):
# Assign of prediction to a dummy to use this one in consecutive label swaps
inferred_prediction = prediction[i].copy()
inferred_oracle = oracle[i].copy()
for j in reversed(range(self.tag_under_test)):
inferred_oracle = np.vectorize(
relations[j].get)(list(inferred_oracle))
inferred_prediction = np.vectorize(
relations[j].get)(list(inferred_prediction))
oracle_inferred[j].append(inferred_oracle)
prediction_inferred[j].append(inferred_prediction)
print('\n***\nStart testing with incremental gamma threshold\n***\n')
bar = progressbar.ProgressBar(maxval=9, widgets=[progressbar.Bar(
'=', '[', ']'), ' ', progressbar.Percentage()])
bar.start()
oracle_gamma = []
prediction_gamma = []
classified_ratio = []
for i in range(9):
gamma = float(i+1)/10.0
oracle_gamma.append(list())
prediction_gamma.append(list())
classified_ratio.append(list())
for j in range(k):
indexes = []
p_cnt = 0
for p in probability[j]:
if max(p) < gamma:
indexes.append(p_cnt)
p_cnt += 1
gamma_oracle = np.delete(oracle[j], [indexes])
gamma_prediction = np.delete(prediction[j], [indexes])
oracle_gamma[i].append(gamma_oracle)
prediction_gamma[i].append(gamma_prediction)
classified_ratio[i].append(
float(len(gamma_prediction))/float(len(prediction[j])))
bar.update(i)
bar.finish()
data_folder = './data_'+self.classifier_name+'/material/'
if not os.path.exists('./data_'+self.classifier_name):
os.makedirs('./data_'+self.classifier_name)
os.makedirs(data_folder)
elif not os.path.exists(data_folder):
os.makedirs(data_folder)
if self.packets_number != 0:
file = open(data_folder+'flat_early_level_'+str(self.level_target) +
'_p_'+str(self.packets_number)+'.dat', 'w+')
else:
file = open(data_folder+'flat_flow_level_'+str(self.level_target) +
'_f_'+str(self.features_number)+'.dat', 'w+')
for i in range(k):
file.write('@fold\n')
for o, p in zip(oracle[i], prediction[i]):
file.write(str(o)+' '+str(p)+'\n')
file.close()
for i in range(self.tag_under_test):
if self.packets_number != 0:
file = open(data_folder+'flat_early_level_'+str(self.level_target) +
'_p_'+str(self.packets_number)+'_inferred_'+str(i+1)+'.dat', 'w+')
else:
file = open(data_folder+'flat_flow_level_'+str(self.level_target) +
'_f_'+str(self.features_number)+'_inferred_'+str(i+1)+'.dat', 'w+')
for j in range(k):
file.write('@fold\n')
for o, p in zip(oracle_inferred[i][j], prediction_inferred[i][j]):
file.write(str(o)+' '+str(p)+'\n')
file.close()
for i in range(9):
if self.packets_number != 0:
file = open(data_folder+'flat_early_level_'+str(self.level_target)+'_p_' +
str(self.packets_number)+'_gamma_'+str(float(i+1)/10.0)+'.dat', 'w+')
else:
file = open(data_folder+'flat_flow_level_'+str(self.level_target)+'_f_' +
str(self.features_number)+'_gamma_'+str(float(i+1)/10.0)+'.dat', 'w+')
for j in range(k):
file.write('@fold_cr\n')
file.write(str(classified_ratio[i][j])+'\n')
for o, p in zip(oracle_gamma[i][j], prediction_gamma[i][j]):
file.write(str(o)+' '+str(p)+'\n')
file.close()
###
jvm.stop()
sem.release()
import pandas as pd
from sklearn.naive_bayes import GaussianNB
from sklearn import datasets
import numpy as np
from sklearn.preprocessing import CategoricalEncoder
#Read the data and remove labels
mushroom_data = pd.read_csv("../data/agaricus-lepiota.data", header = None)
print(mushroom_data.keys())
target = mushroom_data[[19]]
mushroom_data = mushroom_data.drop([19],axis = 1) # axis 1 for dropping columns
fixed_mushrooms = CategoricalEncoder(mushroom_data)
print(type(x))
#Make Naive Bayes Classifier
nb = GaussianNB()
#y_pred = nb.fit(mushroom_data.as_matrix(),target.as_matrix()).predict(mushroom_data)
# "communication" part (not initially present in the category as a unique word)
# as well as the technician part of this category.
#########################################################################
# Encoding categorical data using SimilarityEncoder
# -------------------------------------------------
#
# A typical data-science workflow uses one-hot encoding to represent
# categories.
from sklearn.preprocessing import CategoricalEncoder
# encoding simply a subset of the observations
n_obs = 20
employee_position_titles = values['Employee Position Title'].head(
n_obs).to_frame()
categorical_encoder = CategoricalEncoder(encoding='onehot-dense')
one_hot_encoded = categorical_encoder.fit_transform(employee_position_titles)
f3, ax3 = plt.subplots(figsize=(6, 6))
ax3.matshow(one_hot_encoded)
ax3.set_title('Employee Position Title values, one-hot encoded')
ax3.axis('off')
f3.tight_layout()
#########################################################################
# The corresponding is very sparse
#
# SimilarityEncoder can be used to replace one-hot encoding capturing the
# similarities:
f4, ax4 = plt.subplots(figsize=(6, 6))
similarity_encoded = similarity_encoder.fit_transform(employee_position_titles)
X_categorical = X[:, :idx_end_categorical + 1]
# Select only the numerical columns of X (including ft_embedding if present)
X_numerical = X[:, idx_end_categorical + 1:]
return X_categorical, X_numerical
else:
return np.zeros((X.shape[0], 0)), X
if __name__ == "__main__":
df_train = load_and_preprocess('TrainingSet(3).csv', nrows=10000)
# print(df_train.combined_str)
# X = pd.concat([df_train[colnames_categ], df_inference[colnames_categ]])
X = df_train[colnames_categ]
X = X.apply(preprocess_categ_series)
enc = CategoricalEncoder(handle_unknown='ignore')
enc.fit(X)
len_onehot = enc.transform(
df_train[colnames_categ].iloc[:1]).toarray().shape[1]
print(len_onehot)
# train_X_onehot = enc.transform(df_train[colnames_categ]).toarray()
# # inference_X_onehot = enc.transform(df_train[colnames_categ]).toarray()
# print(train_X_onehot.shape)
# print(train_X_onehot[0])
# pprint(enc.categories_)
from sklearn.decomposition import PCA
from sklearn.ensemble import RandomForestClassifier
train = titanic_src.utils.read_csv('data/interim/added_features_train.csv',
index_col=0)
y = train['Survived'].as_matrix()
cat_nominal_cols = ['Title', 'IsAlone', 'Sex', 'Embarked', 'HighestDeck']
cat_ordinal_cols = ['Pclass']
numerical_cols = ['Age', 'SibSp', 'Fare', 'FamilySize', 'NumOfCabins']
cat_nominal_pipeline = Pipeline([
('selector', tf.DataFrameSelector(cat_nominal_cols)),
('impute', tf.CustomImputer(strategy='mode')),
('encoder', CategoricalEncoder(encoding='onehot-dense')),
])
cat_ordinal_pipeline = Pipeline([
('selector', tf.DataFrameSelector(cat_ordinal_cols)),
('impute', tf.CustomImputer(strategy='mode')),
('encode_scale', QuantileTransformer(output_distribution='normal'))
])
num_init_quantile_transformer = QuantileTransformer(
output_distribution='normal')
def inverse_func(X):
return num_init_quantile_transformer.inverse_transform(X)
# ---Pipelines with DataFrameSelector
num_attribs = list(housing_num)
cat_attribs = ["ocean_proximity"]
new_df = housing[cat_attribs]
#print(new_df)
# num_pipeline = Pipeline([
# ('selector', DataFrameSelector(num_attribs)),
# ('imputer', Imputer(strategy="median")),
# ('attribs_adder', CombinedAttributesAdder()),
# ('std_scaler', StandardScaler())
# ])
cat_pipeline = Pipeline([
('selector', DataFrameSelector(cat_attribs)),
('cat_encoder', CategoricalEncoder(encoding="onehot-dense"))])
# # ---Combining Pipelines with sklearn class FeatureUnion
# # Give a list of transformers or pipelines.
from sklearn.pipeline import FeatureUnion
#
# full_pipeline = FeatureUnion(transformer_list=[
# ("num_pipeline", num_pipeline),
# ("cat_pipeline", cat_pipeline)
# ])
# # Run entire pipeline:
# housing_prepared = full_pipeline.fit_transform(housing)
# from sklearn.linear_model import LinearRegression
#
# lin_reg = LinearRegression()
# lin_reg.fit(housing_prepared, housing_labels)
#
#data.subset(500, 50, 50)
#Step 9: Specify the features to use, this part is merely for sklearn.
features = ClassifierFeatures()
#features.add('headline', TfidfVectorizer(tokenizer=TextTokenizer.tokenizeText, lowercase=False, analyzer='word', ngram_range=(1,1), min_df=1), 'headline'),#, max_features=100000)),
# features.add('headline_words', TfidfVectorizer(tokenizer=TextTokenizer.tokenizeText, lowercase=False, analyzer='word', ngram_range=(1,1), min_df=1), 'headline'),#, max_features=100000)),
# features.add('headline1_words', TfidfVectorizer(tokenizer=TextTokenizer.tokenizeText, lowercase=False, analyzer='word', ngram_range=(1,1), min_df=1), 'headline1'),#, max_features=100000)),
# features.add('headline2_words', TfidfVectorizer(tokenizer=TextTokenizer.tokenizeText, lowercase=False, analyzer='word', ngram_range=(1,1), min_df=1), 'headline2'),#, max_features=100000)),
# features.add('keyword_words', TfidfVectorizer(tokenizer=TextTokenizer.tokenizeText, lowercase=False, analyzer='word', ngram_range=(1, 1), min_df=1), 'keyword'),#, max_features=100000)),
# #features.add('term_words', TfidfVectorizer(tokenizer=TextTokenizer.tokenizeText, lowercase=False, analyzer='word', ngram_range=(1, 2), min_df=1), 'term'),#, max_features=100000)),
#features.add('display_url', TfidfVectorizer(tokenizer=TextTokenizer.tokenizeText, lowercase=False, analyzer='word', ngram_range=(1, 1), min_df=1), 'display_url'),#, max_features=100000)),
# features.add('quality_score', StandardScaler(), 'quality_score'),
features.add('avg_position', StandardScaler(), 'avg_position'),
features.add('avg_cost', StandardScaler(), 'avg_cost'),
features.add('device', CategoricalEncoder(), 'device'),
features.add('ad_placement', CategoricalEncoder(), 'ad_placement'),
features.add('ad_type', CategoricalEncoder(), 'ad_type'),
features.add('match_type', CategoricalEncoder(), 'match_type'),
#Step 10: Specify the classifier you want to use (additionaly!)
new_classifier = LogisticRegression()
#new_classifier = SVR(kernel='linear')
#new_classifier = LinearRegression(fit_intercept=True, normalize=True)
#new_classifier = Ridge(alpha=.5)
if options.args.print_details >= 2:
printer.labelDistribution(data.Y_train, 'Training Set')
#Step 11: Run our system.
if len(data.labels) > 1: #otherwise, there is nothing to train
# - embarked: categories encoded as strings {'C', 'S', 'Q'}.
# - sex: categories encoded as strings {'female', 'male'}.
# - pclass: ordinal integers {1, 2, 3}.
# We create the preprocessing pipelines for both numeric and categorical data.
numeric_features = ['age', 'fare']
numeric_transformer = Pipeline(
steps=[('imputer',
SimpleImputer(strategy='median')), ('scaler', StandardScaler())])
categorical_features = ['embarked', 'sex', 'pclass']
categorical_transformer = Pipeline(
steps=[('imputer',
SimpleImputer(strategy='constant', fill_value='missing')),
('onehot',
CategoricalEncoder('onehot-dense', handle_unknown='ignore'))])
preprocessor = ColumnTransformer(transformers=[
('num', numeric_transformer, numeric_features),
('cat', categorical_transformer, categorical_features)
],
remainder='drop')
# Append classifier to preprocessing pipeline.
# Now we have a full prediction pipeline.
clf = Pipeline(steps=[('preprocessor',
preprocessor), ('classifier', LogisticRegression())])
X = data.drop('survived', axis=1)
y = data['survived']
test_size=0.5)
# Unsupervised transformation based on totally random trees
rt = RandomTreesEmbedding(max_depth=3,
n_estimators=n_estimator,
random_state=0)
rt_lm = LogisticRegression()
pipeline = make_pipeline(rt, rt_lm)
pipeline.fit(X_train, y_train)
y_pred_rt = pipeline.predict_proba(X_test)[:, 1]
fpr_rt_lm, tpr_rt_lm, _ = roc_curve(y_test, y_pred_rt)
# Supervised transformation based on random forests
rf = RandomForestClassifier(max_depth=3, n_estimators=n_estimator)
rf_enc = CategoricalEncoder()
rf_lm = LogisticRegression()
rf.fit(X_train, y_train)
rf_enc.fit(rf.apply(X_train))
rf_lm.fit(rf_enc.transform(rf.apply(X_train_lr)), y_train_lr)
y_pred_rf_lm = rf_lm.predict_proba(rf_enc.transform(rf.apply(X_test)))[:, 1]
fpr_rf_lm, tpr_rf_lm, _ = roc_curve(y_test, y_pred_rf_lm)
grd = GradientBoostingClassifier(n_estimators=n_estimator)
grd_enc = CategoricalEncoder()
grd_lm = LogisticRegression()
grd.fit(X_train, y_train)
grd_enc.fit(grd.apply(X_train)[:, :, 0])
grd_lm.fit(grd_enc.transform(grd.apply(X_train_lr)[:, :, 0]), y_train_lr)
def extract_features(df_train,
df_inference,
selected_feature_names_categ,
selected_feature_names_interval,
shuffle=True,
fuzzy_matching=True,
use_onehot=True,
use_sentence_vec=False):
features_to_use = []
variable_types = []
if not (use_onehot):
for feature in selected_feature_names_categ:
features_to_use.append(feature + '_encoded')
variable_types.append('categorical_nominal')
# Append interval AFTER categorical!!
for feature in selected_feature_names_interval:
features_to_use.append(feature + '_normed')
variable_types.append('numerical')
# Check to ensure all cols exist (avoid keyerrors)
for df in [df_train, df_inference]:
df[selected_feature_names_categ + selected_feature_names_interval]
print(df['combined_str'])
# for feature in selected_feature_names_categ:
# le = preprocessing.LabelEncoder()
# print(print_attr_overview(df[feature], True, topn=10))
# df[feature + '_encoded'] = le.fit_transform(df[feature])
# features_to_use.append(feature + '_encoded')
if use_onehot:
# Each Feature has its own vocab...
vocabs = defaultdict(list)
X = pd.concat([df_train[colnames_categ], df_inference[colnames_categ]])
X = df_train[colnames_categ]
X = X.apply(preprocess_categ_series)
enc = CategoricalEncoder(handle_unknown='ignore')
enc.fit_transform(X)
# pprint(enc.categories_)
else:
le = preprocessing.LabelEncoder()
all_unique = []
# FIT LABEL_ENCODER (combine vocabs for train and inference)
for df in [df_train, df_inference]:
for feature in selected_feature_names_categ:
# print(print_attr_overview(df[feature]))
s = df[feature]
# Remove categorical entries with less than 10 occurances
a = s.value_counts()
s[s.isin(a.index[a < 12])] = np.nan
s[s.isnull()] = "EMPTY_PLACEHOLDER"
s = s.map(lambda x: x.lower() if type(x) == str else x)
# print(np.unique(df[feature]))
all_unique.extend(np.unique(s))
le.fit(all_unique)
# TRANSFORM LABEL_ENCODER
for df in [df_train, df_inference]:
for feature in selected_feature_names_categ:
print(feature)
# print(df[feature])
s = df[feature]
s = s.map(lambda x: x.lower() if type(x) == str else x)
df[feature + '_encoded'] = le.transform(s)
print(feature, len(np.unique(s)))
for df in [df_train, df_inference]:
for feature in selected_feature_names_interval:
s = df[feature]
s = s.map(lambda x: x.replace(',', '') if type(x) == str else x)
# print(s)
s = pd.to_numeric(s, errors='coerce')
# Set null values to zero
# TODO: try set nan to the mean instead of zero
# TODO: try different types of normalisation
s[np.logical_not(s.notnull())] = 0.0
df[feature + '_normed'] = norm_zscore(s)
# features_to_use.append('sentence_vec')
# variable_types.append('embedding')
if use_sentence_vec:
from ft_embedding import get_sentence_vec
print('Computing sentence vectors for dataset')
train_embedding_mat = np.asarray(
[get_sentence_vec(x) for x in df_train['combined_str']])
inference_embedding_mat = np.asarray(
[get_sentence_vec(x) for x in df_inference['combined_str']])
variable_types.append('ft_embedding')
if use_onehot:
print(features_to_use)
# One-Hot Categorical Encoding
train_X_onehot = enc.transform(df_train[colnames_categ]).toarray()
train_X_interval = df_train[features_to_use].as_matrix()
print(train_X_onehot.shape)
print(train_X_interval.shape)
train_X = np.hstack([train_X_onehot, train_X_interval])
inference_X_onehot = enc.transform(
df_inference[colnames_categ]).toarray()
inference_X_interval = df_inference[features_to_use].as_matrix()
print(inference_X_onehot.shape)
print(inference_X_interval.shape)
inference_X = np.hstack([inference_X_onehot, inference_X_interval])
# Add (one-hot encoded) numerical features to variable_types
len_onehot = train_X_onehot.shape[1]
print(len_onehot)
features_to_use = ['numerical'
for i in range(len_onehot)] + features_to_use
else:
# Index Categorical Encoding (integer)
train_X = df_train[features_to_use].as_matrix()
inference_X = df_inference[features_to_use].as_matrix()
train_y = df_train['case_status'].as_matrix()
if use_sentence_vec:
# Stack with sentence embedding
train_X = np.hstack([train_X.copy(), train_embedding_mat])
inference_X = np.hstack([inference_X.copy(), inference_embedding_mat])
print(train_embedding_mat.shape)
print(inference_embedding_mat.shape)
print(train_X.shape)
print(inference_X.shape)
# exit()
inference_row_id = df_inference['row ID']
if shuffle:
train_X, train_y = skl_shuffle(train_X, train_y)
# print(X.shape)
# print(y.shape)
if use_onehot:
vocab_size = 0
else:
vocab_size = len(list(le.classes_))
return train_X, train_y, inference_row_id, inference_X, vocab_size, variable_types, features_to_use