def test_with_concat_features2(self):
import warnings
warnings.filterwarnings("ignore")
from sklearn.datasets import load_iris
from sklearn.metrics import accuracy_score
from lale.lib.lale import Hyperopt
data = load_iris()
X, y = data.data, data.target
pca = PCA(n_components=3)
nys = Nystroem(n_components=10)
concat = ConcatFeatures()
lr = LogisticRegression(random_state=42, C=0.1)
from lale.operators import make_pipeline
pipeline = make_pipeline(
((((SimpleImputer() | NoOp()) >> pca) & nys) >> concat >> lr)
| KNeighborsClassifier()
)
clf = Hyperopt(estimator=pipeline, max_evals=1, handle_cv_failure=True)
trained = clf.fit(X, y)
predictions = trained.predict(X)
print(accuracy_score(y, predictions))
warnings.resetwarnings()
def _fit_gbt_num(self, X, y):
from lale.lib.lale import Project
from lale.lib.sklearn import SimpleImputer
gbt = auto_gbt(self.prediction_type)
trainable = (Project(columns={'type': 'number'}) >>
SimpleImputer(strategy='mean') >> gbt())
self._try_and_add('gbt_num', trainable, X, y)
def _fit_gbt_num(self, X, y):
from lale.lib.lale import Project
from lale.lib.sklearn import SimpleImputer
gbt = auto_gbt(self.prediction_type)
trainable = (Project(columns={"type": "number"}) >>
SimpleImputer(strategy="mean") >> gbt())
self._try_and_add("gbt_num", trainable, X, y)
def test_pipeline_AWTTR_1(self):
trainable = AutoaiTSPipeline(steps=[(
"AutoaiWindowTransformedTargetRegressor",
AutoaiWindowTransformedTargetRegressor(
regressor=SmallDataWindowTransformer() >> SimpleImputer() >>
RandomForestRegressor()),
)])
self.doTestPipeline(trainable, self.y, self.y, self.y, self.y)
def auto_prep(X):
from lale.lib.lale import ConcatFeatures, Project, categorical
from lale.lib.sklearn import OneHotEncoder, SimpleImputer
n_cols = X.shape[1]
n_cats = len(categorical()(X))
prep_num = SimpleImputer(strategy="mean")
prep_cat = SimpleImputer(strategy="most_frequent") >> OneHotEncoder(
handle_unknown="ignore")
if n_cats == 0:
result = prep_num
elif n_cats == n_cols:
result = prep_cat
else:
result = (
(Project(columns={"type": "number"}, drop_columns=categorical()) >>
prep_num)
& (Project(columns=categorical()) >> prep_cat)) >> ConcatFeatures
return result
def test_nested_pipeline1(self):
from sklearn.datasets import load_iris
from lale.lib.lale import Hyperopt
from sklearn.metrics import accuracy_score
data = load_iris()
X, y = data.data, data.target
#pipeline = KNeighborsClassifier() | (OneHotEncoder(handle_unknown = 'ignore') >> LogisticRegression())
pipeline = KNeighborsClassifier() | (SimpleImputer() >> LogisticRegression())
clf = Hyperopt(estimator=pipeline, max_evals=1)
trained = clf.fit(X, y)
predictions = trained.predict(X)
print(accuracy_score(y, predictions))
def auto_prep(X):
from lale.lib.lale import ConcatFeatures
from lale.lib.lale import Project
from lale.lib.lale import categorical
from lale.lib.sklearn import OneHotEncoder
from lale.lib.sklearn import SimpleImputer
n_cols = X.shape[1]
n_cats = len(categorical()(X))
prep_num = SimpleImputer(strategy='mean')
prep_cat = (SimpleImputer(strategy='most_frequent') >>
OneHotEncoder(handle_unknown='ignore'))
if n_cats == 0:
result = prep_num
elif n_cats == n_cols:
result = prep_cat
else:
result = (
(Project(columns={'type': 'number'}, drop_columns=categorical()) >>
prep_num)
& (Project(columns=categorical()) >> prep_cat)) >> ConcatFeatures
return result
def test_pipeline_AWWR(self):
trainable = AutoaiTSPipeline(steps=[(
"AutoaiWindowTransformedTargetRegressor",
AutoaiWindowedWrappedRegressor(
regressor=SmallDataWindowTransformer() >> SimpleImputer() >>
RandomForestRegressor()),
)])
self.doTestPipeline(trainable,
self.y,
self.y,
self.y,
self.y,
optimization=True)
def test_pipeline_AWTTR_2(self):
trainable = AutoaiTSPipeline(steps=[(
"AutoaiWindowTransformedTargetRegressor",
AutoaiWindowTransformedTargetRegressor(
regressor=SmallDataWindowTransformer() >> SimpleImputer() >>
RandomForestRegressor(),
estimator_prediction_type="rowwise",
),
)])
self.doTestPipeline(trainable,
self.y,
self.y,
self.y,
self.y,
optimization=True)
def fetch(dataset_name, task_type, verbose=False, preprocess=True):
if verbose:
print('Loading dataset:', dataset_name)
#Check that the dataset name exists in experiments_dict
try:
dataset_name_found = experiments_dict[dataset_name]
if experiments_dict[dataset_name]['task_type'] != task_type.lower():
raise ValueError("The task type {} does not match with the given datasets task type {}"\
.format(task_type, experiments_dict[dataset_name]['task_type']))
except KeyError:
raise KeyError("Dataset name {} not found in the supported datasets".format(dataset_name))
data_file_name = os.path.join(download_data_dir, dataset_name+".arff")
if verbose:
print(data_file_name)
if not os.path.exists(data_file_name):
#TODO: Download the data
if not os.path.exists(download_data_dir):
os.makedirs(download_data_dir)
if verbose:
print('created directory {}'.format(download_data_dir))
urllib.request.urlretrieve(experiments_dict[dataset_name]['download_arff_url'], data_file_name)
assert os.path.exists(data_file_name)
with open(data_file_name) as f:
dataDictionary = arff.load(f)
f.close()
from lale.datasets.data_schemas import liac_arff_to_schema
schema_orig = liac_arff_to_schema(dataDictionary)
target_col = experiments_dict[dataset_name]['target']
if preprocess:
arffData = pd.DataFrame(dataDictionary['data'])
#arffData = arffData.fillna(0)
attributes = dataDictionary['attributes']
if verbose:
print(attributes)
categorical_cols = []
numeric_cols = []
X_columns = []
for i, item in enumerate(attributes):
if item[0].lower() == target_col:
target_indx = i
#remove it from attributes so that the next loop indices are adjusted accordingly.
del attributes[i]
y = arffData.iloc[:,target_indx]
arffData = arffData.drop(i, axis = 1)
for i, item in enumerate(attributes):
X_columns.append(i)
if (((isinstance(item[1], str) and item[1].lower() not in numeric_data_types_list) \
or isinstance(item[1], list)) and (item[0].lower() != 'class')):
categorical_cols.append(i)
elif (isinstance(item[1], str) and item[1].lower() in numeric_data_types_list) and (item[0].lower() != 'class'):
numeric_cols.append(i)
if verbose:
print(f'categorical columns: {categorical_cols}')
print(f'numeric columns: {numeric_cols}')
X = arffData.iloc[:,X_columns]
#Check whether there is any error
num_classes_from_last_row = len(list(set(y)))
if verbose:
print('num_classes_from_last_row', num_classes_from_last_row)
transformers1 = [
( 'imputer_str',
SimpleImputer(missing_values=None, strategy='most_frequent'),
categorical_cols),
( 'imputer_num',
SimpleImputer(strategy='mean'), numeric_cols)]
txm1 = ColumnTransformer(transformers1, sparse_threshold=0.0)
transformers2 = [
( 'ohe', OneHotEncoder(sparse=False),
list(range(len(categorical_cols)))),
( 'no_op', 'passthrough',
list(range(len(categorical_cols),
len(categorical_cols) + len(numeric_cols))))]
txm2 = ColumnTransformer(transformers2, sparse_threshold=0.0)
if verbose:
print("Shape of X before preprocessing", X.shape)
from lale.operators import make_pipeline
preprocessing = make_pipeline(txm1, txm2)
X = preprocessing.fit(X).transform(X)
if verbose:
print("Shape of X after preprocessing", X.shape)
else:
col_names = [attr[0] for attr in dataDictionary['attributes']]
df_all = pd.DataFrame(dataDictionary['data'], columns=col_names)
y = df_all[target_col]
y = y.squeeze()
cols_X = [col for col in col_names if col != target_col]
X = df_all[cols_X]
labelencoder = LabelEncoder()
y = labelencoder.fit_transform(y)
X_train, X_test, y_train, y_test = \
train_test_split(X, y, test_size = 0.33, random_state = 0)
if verbose:
print(f'training set shapes: X {X_train.shape}, y {y_train.shape}')
print(f'test set shapes: X {X_test.shape}, y {y_test.shape}')
X_train, X_test, y_train, y_test = add_schemas( \
schema_orig, target_col, X_train, X_test, y_train, y_test)
return (X_train, y_train), (X_test, y_test)
def test_simple_imputer(self):
from lale.lib.sklearn import SimpleImputer
reg = SimpleImputer(strategy='mean', fill_value=10)
reg.fit(self.X_train, self.y_train)
def test_simple_imputer(self):
reg = SimpleImputer(strategy="mean", fill_value=10)
reg.fit(self.X_train, self.y_train)