def test_transformer(self):
X, y = datasets.make_classification(
n_samples=100,
n_features=10,
n_informative=6,
n_redundant=1,
n_classes=2,
n_clusters_per_class=3,
n_repeated=0,
shuffle=False,
random_state=0,
)
df = pd.DataFrame(X, columns=[f"f{i}" for i in range(X.shape[1])])
print(df)
with tempfile.TemporaryDirectory() as tmpdir:
gft = GoldenFeaturesTransformer(tmpdir, "binary_classification")
gft.fit(df, y)
df = gft.transform(df)
print(df)
print(gft.to_json())
gft3 = GoldenFeaturesTransformer(tmpdir, "binary_classification")
gft3.from_json(gft.to_json())
def test_features_count(self):
N_COLS = 10
X, y = datasets.make_classification(
n_samples=100,
n_features=N_COLS,
n_informative=6,
n_redundant=1,
n_classes=2,
n_clusters_per_class=3,
n_repeated=0,
shuffle=False,
random_state=0,
)
df = pd.DataFrame(X, columns=[f"f{i}" for i in range(X.shape[1])])
with tempfile.TemporaryDirectory() as tmpdir:
FEATURES_COUNT = 42
gft = GoldenFeaturesTransformer(
tmpdir, "binary_classification", features_count=FEATURES_COUNT
)
gft.fit(df, y)
self.assertEqual(len(gft._new_features), FEATURES_COUNT)
gft3 = GoldenFeaturesTransformer(tmpdir, "binary_classification")
gft3.from_json(gft.to_json(), tmpdir)
df = gft3.transform(df)
self.assertEqual(df.shape[1], N_COLS + FEATURES_COUNT)
class Preprocessing(object):
def __init__(
self,
preprocessing_params={
"target_preprocessing": [],
"columns_preprocessing": {}
},
model_name=None,
k_fold=None,
repeat=None,
):
self._params = preprocessing_params
if "target_preprocessing" not in preprocessing_params:
self._params["target_preprocessing"] = []
if "columns_preprocessing" not in preprocessing_params:
self._params["columns_preprocessing"] = {}
# preprocssing step attributes
self._categorical_y = None
self._scale_y = None
self._missing_values = []
self._categorical = []
self._scale = []
self._remove_columns = []
self._datetime_transforms = []
self._text_transforms = []
self._golden_features = None
self._kmeans = None
self._add_random_feature = self._params.get("add_random_feature",
False)
self._drop_features = self._params.get("drop_features", [])
self._model_name = model_name
self._k_fold = k_fold
self._repeat = repeat
def _exclude_missing_targets(self, X=None, y=None):
# check if there are missing values in target column
if y is None:
return X, y
y_missing = pd.isnull(y)
if np.sum(np.array(y_missing)) == 0:
return X, y
y = y.drop(y.index[y_missing])
y.index = range(y.shape[0])
if X is not None:
X = X.drop(X.index[y_missing])
X.index = range(X.shape[0])
return X, y
# fit and transform
def fit_and_transform(self, X_train, y_train, sample_weight=None):
logger.debug("Preprocessing.fit_and_transform")
if y_train is not None:
# target preprocessing
# this must be used first, maybe we will drop some rows because of missing target values
target_preprocessing = self._params.get("target_preprocessing")
logger.debug(
"target_preprocessing params: {}".format(target_preprocessing))
X_train, y_train, sample_weight = ExcludeRowsMissingTarget.transform(
X_train, y_train, sample_weight)
if PreprocessingCategorical.CONVERT_INTEGER in target_preprocessing:
logger.debug("Convert target to integer")
self._categorical_y = LabelEncoder(try_to_fit_numeric=True)
self._categorical_y.fit(y_train)
y_train = pd.Series(self._categorical_y.transform(y_train))
if PreprocessingCategorical.CONVERT_ONE_HOT in target_preprocessing:
logger.debug("Convert target to one-hot coding")
self._categorical_y = LabelBinarizer()
self._categorical_y.fit(pd.DataFrame({"target": y_train}),
"target")
y_train = self._categorical_y.transform(
pd.DataFrame({"target": y_train}), "target")
if Scale.SCALE_LOG_AND_NORMAL in target_preprocessing:
logger.debug("Scale log and normal")
self._scale_y = Scale(["target"],
scale_method=Scale.SCALE_LOG_AND_NORMAL)
y_train = pd.DataFrame({"target": y_train})
self._scale_y.fit(y_train)
y_train = self._scale_y.transform(y_train)
y_train = y_train["target"]
if Scale.SCALE_NORMAL in target_preprocessing:
logger.debug("Scale normal")
self._scale_y = Scale(["target"],
scale_method=Scale.SCALE_NORMAL)
y_train = pd.DataFrame({"target": y_train})
self._scale_y.fit(y_train)
y_train = self._scale_y.transform(y_train)
y_train = y_train["target"]
# columns preprocessing
columns_preprocessing = self._params.get("columns_preprocessing")
for column in columns_preprocessing:
transforms = columns_preprocessing[column]
# logger.debug("Preprocess column {} with: {}".format(column, transforms))
# remove empty or constant columns
cols_to_remove = list(
filter(
lambda k: "remove_column" in columns_preprocessing[k],
columns_preprocessing,
))
if X_train is not None:
X_train.drop(cols_to_remove, axis=1, inplace=True)
self._remove_columns = cols_to_remove
numeric_cols = [] # get numeric cols before text transformations
# needed for golden features
if X_train is not None and ("golden_features" in self._params
or "kmeans_features" in self._params):
numeric_cols = X_train.select_dtypes(
include="number").columns.tolist()
# there can be missing values in the text data,
# but we don't want to handle it by fill missing methods
# zeros will be imputed by text_transform method
cols_to_process = list(
filter(
lambda k: "text_transform" in columns_preprocessing[k],
columns_preprocessing,
))
new_text_columns = []
for col in cols_to_process:
t = TextTransformer()
t.fit(X_train, col)
X_train = t.transform(X_train)
self._text_transforms += [t]
new_text_columns += t._new_columns
# end of text transform
for missing_method in [PreprocessingMissingValues.FILL_NA_MEDIAN]:
cols_to_process = list(
filter(
lambda k: missing_method in columns_preprocessing[k],
columns_preprocessing,
))
missing = PreprocessingMissingValues(cols_to_process,
missing_method)
missing.fit(X_train)
X_train = missing.transform(X_train)
self._missing_values += [missing]
# golden features
golden_columns = []
if "golden_features" in self._params:
results_path = self._params["golden_features"]["results_path"]
ml_task = self._params["golden_features"]["ml_task"]
self._golden_features = GoldenFeaturesTransformer(
results_path, ml_task)
self._golden_features.fit(X_train[numeric_cols], y_train)
X_train = self._golden_features.transform(X_train)
golden_columns = self._golden_features._new_columns
kmeans_columns = []
if "kmeans_features" in self._params:
results_path = self._params["kmeans_features"]["results_path"]
self._kmeans = KMeansTransformer(results_path, self._model_name,
self._k_fold)
self._kmeans.fit(X_train[numeric_cols], y_train)
X_train = self._kmeans.transform(X_train)
kmeans_columns = self._kmeans._new_features
for convert_method in [
PreprocessingCategorical.CONVERT_INTEGER,
PreprocessingCategorical.CONVERT_ONE_HOT,
PreprocessingCategorical.CONVERT_LOO,
]:
cols_to_process = list(
filter(
lambda k: convert_method in columns_preprocessing[k],
columns_preprocessing,
))
convert = PreprocessingCategorical(cols_to_process, convert_method)
convert.fit(X_train, y_train)
X_train = convert.transform(X_train)
self._categorical += [convert]
# datetime transform
cols_to_process = list(
filter(
lambda k: "datetime_transform" in columns_preprocessing[k],
columns_preprocessing,
))
new_datetime_columns = []
for col in cols_to_process:
t = DateTimeTransformer()
t.fit(X_train, col)
X_train = t.transform(X_train)
self._datetime_transforms += [t]
new_datetime_columns += t._new_columns
# SCALE
for scale_method in [Scale.SCALE_NORMAL, Scale.SCALE_LOG_AND_NORMAL]:
cols_to_process = list(
filter(
lambda k: scale_method in columns_preprocessing[k],
columns_preprocessing,
))
if (len(cols_to_process) and len(new_datetime_columns)
and scale_method == Scale.SCALE_NORMAL):
cols_to_process += new_datetime_columns
if (len(cols_to_process) and len(new_text_columns)
and scale_method == Scale.SCALE_NORMAL):
cols_to_process += new_text_columns
if (len(cols_to_process) and len(golden_columns)
and scale_method == Scale.SCALE_NORMAL):
cols_to_process += golden_columns
if (len(cols_to_process) and len(kmeans_columns)
and scale_method == Scale.SCALE_NORMAL):
cols_to_process += kmeans_columns
if len(cols_to_process):
scale = Scale(cols_to_process)
scale.fit(X_train)
X_train = scale.transform(X_train)
self._scale += [scale]
if self._add_random_feature:
# -1, 1, with 0 mean
X_train["random_feature"] = np.random.rand(
X_train.shape[0]) * 2.0 - 1.0
if self._drop_features:
available_cols = X_train.columns.tolist()
drop_cols = [c for c in self._drop_features if c in available_cols]
if len(drop_cols) == X_train.shape[1]:
raise AutoMLException(
"All features are droppped! Your data looks like random data."
)
if drop_cols:
X_train.drop(drop_cols, axis=1, inplace=True)
self._drop_features = drop_cols
if X_train is not None:
# there can be catagorical columns (in CatBoost) which cant be clipped
numeric_cols = X_train.select_dtypes(
include="number").columns.tolist()
X_train[numeric_cols] = X_train[numeric_cols].clip(
lower=np.finfo(np.float32).min + 1000,
upper=np.finfo(np.float32).max - 1000,
)
return X_train, y_train, sample_weight
def transform(self,
X_validation,
y_validation,
sample_weight_validation=None):
logger.debug("Preprocessing.transform")
# doing copy to avoid SettingWithCopyWarning
if X_validation is not None:
X_validation = X_validation.copy(deep=False)
if y_validation is not None:
y_validation = y_validation.copy(deep=False)
# target preprocessing
# this must be used first, maybe we will drop some rows because of missing target values
if y_validation is not None:
target_preprocessing = self._params.get("target_preprocessing")
logger.debug(
"target_preprocessing -> {}".format(target_preprocessing))
(
X_validation,
y_validation,
sample_weight_validation,
) = ExcludeRowsMissingTarget.transform(X_validation, y_validation,
sample_weight_validation)
if PreprocessingCategorical.CONVERT_INTEGER in target_preprocessing:
if y_validation is not None and self._categorical_y is not None:
y_validation = pd.Series(
self._categorical_y.transform(y_validation))
if PreprocessingCategorical.CONVERT_ONE_HOT in target_preprocessing:
if y_validation is not None and self._categorical_y is not None:
y_validation = self._categorical_y.transform(
pd.DataFrame({"target": y_validation}), "target")
if Scale.SCALE_LOG_AND_NORMAL in target_preprocessing:
if self._scale_y is not None and y_validation is not None:
logger.debug("Transform log and normalize")
y_validation = pd.DataFrame({"target": y_validation})
y_validation = self._scale_y.transform(y_validation)
y_validation = y_validation["target"]
if Scale.SCALE_NORMAL in target_preprocessing:
if self._scale_y is not None and y_validation is not None:
logger.debug("Transform normalize")
y_validation = pd.DataFrame({"target": y_validation})
y_validation = self._scale_y.transform(y_validation)
y_validation = y_validation["target"]
# columns preprocessing
if len(self._remove_columns) and X_validation is not None:
cols_to_remove = [
col for col in X_validation.columns
if col in self._remove_columns
]
X_validation.drop(cols_to_remove, axis=1, inplace=True)
# text transform
for tt in self._text_transforms:
if X_validation is not None and tt is not None:
X_validation = tt.transform(X_validation)
for missing in self._missing_values:
if X_validation is not None and missing is not None:
X_validation = missing.transform(X_validation)
# to be sure that all missing are filled
# in case new data there can be gaps!
if (X_validation is not None
and np.sum(np.sum(pd.isnull(X_validation))) > 0
and len(self._params["columns_preprocessing"]) > 0):
# there is something missing, fill it
# we should notice user about it!
# warnings should go to the separate file ...
# warnings.warn(
# "There are columns {} with missing values which didnt have missing values in train dataset.".format(
# list(
# X_validation.columns[np.where(np.sum(pd.isnull(X_validation)))]
# )
# )
# )
missing = PreprocessingMissingValues(
X_validation.columns,
PreprocessingMissingValues.FILL_NA_MEDIAN)
missing.fit(X_validation)
X_validation = missing.transform(X_validation)
# golden features
if self._golden_features is not None:
X_validation = self._golden_features.transform(X_validation)
if self._kmeans is not None:
X_validation = self._kmeans.transform(X_validation)
for convert in self._categorical:
if X_validation is not None and convert is not None:
X_validation = convert.transform(X_validation)
for dtt in self._datetime_transforms:
if X_validation is not None and dtt is not None:
X_validation = dtt.transform(X_validation)
for scale in self._scale:
if X_validation is not None and scale is not None:
X_validation = scale.transform(X_validation)
if self._add_random_feature:
# -1, 1, with 0 mean
X_validation["random_feature"] = (
np.random.rand(X_validation.shape[0]) * 2.0 - 1.0)
if self._drop_features and X_validation is not None:
X_validation.drop(self._drop_features, axis=1, inplace=True)
if X_validation is not None:
# there can be catagorical columns (in CatBoost) which cant be clipped
numeric_cols = X_validation.select_dtypes(
include="number").columns.tolist()
X_validation[numeric_cols] = X_validation[numeric_cols].clip(
lower=np.finfo(np.float32).min + 1000,
upper=np.finfo(np.float32).max - 1000,
)
return X_validation, y_validation, sample_weight_validation
def inverse_scale_target(self, y):
if self._scale_y is not None:
y = pd.DataFrame({"target": y})
y = self._scale_y.inverse_transform(y)
y = y["target"]
return y
def inverse_categorical_target(self, y):
if self._categorical_y is not None:
y = self._categorical_y.inverse_transform(
pd.DataFrame({"target": np.array(y)}))
y = y.astype(str)
return y
def get_target_class_names(self):
pos_label, neg_label = "1", "0"
if self._categorical_y is not None:
if self._params["ml_task"] == BINARY_CLASSIFICATION:
# binary classification
for label, value in self._categorical_y.to_json().items():
if value == 1:
pos_label = label
else:
neg_label = label
return [neg_label, pos_label]
else:
# multiclass classification
# logger.debug(self._categorical_y.to_json())
if "unique_values" not in self._categorical_y.to_json():
labels = dict(
(v, k)
for k, v in self._categorical_y.to_json().items())
else:
labels = {
i: v
for i, v in enumerate(self._categorical_y.to_json()
["unique_values"])
}
return list(labels.values())
else: # self._categorical_y is None
if "ml_task" in self._params:
if self._params["ml_task"] == BINARY_CLASSIFICATION:
return ["0", "1"]
return []
def prepare_target_labels(self, y):
pos_label, neg_label = "1", "0"
if self._categorical_y is not None:
if len(y.shape) == 1:
# binary classification
for label, value in self._categorical_y.to_json().items():
if value == 1:
pos_label = label
else:
neg_label = label
# threshold is applied in AutoML class
return pd.DataFrame({
"prediction_{}".format(neg_label): 1 - y,
"prediction_{}".format(pos_label): y,
})
else:
# multiclass classification
if "unique_values" not in self._categorical_y.to_json():
labels = dict(
(v, k)
for k, v in self._categorical_y.to_json().items())
else:
labels = {
i: v
for i, v in enumerate(self._categorical_y.to_json()
["unique_values"])
}
d = {}
cols = []
for i in range(y.shape[1]):
d["prediction_{}".format(labels[i])] = y[:, i]
cols += ["prediction_{}".format(labels[i])]
df = pd.DataFrame(d)
df["label"] = np.argmax(np.array(df[cols]), axis=1)
df["label"] = df["label"].map(labels)
return df
else: # self._categorical_y is None
if "ml_task" in self._params:
if self._params["ml_task"] == BINARY_CLASSIFICATION:
return pd.DataFrame({
"prediction_0": 1 - y,
"prediction_1": y
})
elif self._params["ml_task"] == MULTICLASS_CLASSIFICATION:
return pd.DataFrame(
data=y,
columns=[
"prediction_{}".format(i)
for i in range(y.shape[1])
],
)
return pd.DataFrame({"prediction": y})
def to_json(self):
preprocessing_params = {}
if self._remove_columns:
preprocessing_params["remove_columns"] = self._remove_columns
if self._missing_values is not None and len(self._missing_values):
mvs = [] # refactor
for mv in self._missing_values:
if mv.to_json():
mvs += [mv.to_json()]
if mvs:
preprocessing_params["missing_values"] = mvs
if self._categorical is not None and len(self._categorical):
cats = [] # refactor
for cat in self._categorical:
if cat.to_json():
cats += [cat.to_json()]
if cats:
preprocessing_params["categorical"] = cats
if self._datetime_transforms is not None and len(
self._datetime_transforms):
dtts = []
for dtt in self._datetime_transforms:
dtts += [dtt.to_json()]
if dtts:
preprocessing_params["datetime_transforms"] = dtts
if self._text_transforms is not None and len(self._text_transforms):
tts = []
for tt in self._text_transforms:
tts += [tt.to_json()]
if tts:
preprocessing_params["text_transforms"] = tts
if self._golden_features is not None:
preprocessing_params[
"golden_features"] = self._golden_features.to_json()
if self._kmeans is not None:
preprocessing_params["kmeans"] = self._kmeans.to_json()
if self._scale is not None and len(self._scale):
scs = [sc.to_json() for sc in self._scale if sc.to_json()]
if scs:
preprocessing_params["scale"] = scs
if self._categorical_y is not None:
cat_y = self._categorical_y.to_json()
if cat_y:
preprocessing_params["categorical_y"] = cat_y
if self._scale_y is not None:
preprocessing_params["scale_y"] = self._scale_y.to_json()
if "ml_task" in self._params:
preprocessing_params["ml_task"] = self._params["ml_task"]
if self._add_random_feature:
preprocessing_params["add_random_feature"] = True
if self._drop_features:
preprocessing_params["drop_features"] = self._drop_features
preprocessing_params["params"] = self._params
return preprocessing_params
def from_json(self, data_json, results_path):
self._params = data_json.get("params", self._params)
if "remove_columns" in data_json:
self._remove_columns = data_json.get("remove_columns", [])
if "missing_values" in data_json:
self._missing_values = []
for mv_data in data_json["missing_values"]:
mv = PreprocessingMissingValues()
mv.from_json(mv_data)
self._missing_values += [mv]
if "categorical" in data_json:
self._categorical = []
for cat_data in data_json["categorical"]:
cat = PreprocessingCategorical()
cat.from_json(cat_data)
self._categorical += [cat]
if "datetime_transforms" in data_json:
self._datetime_transforms = []
for dtt_params in data_json["datetime_transforms"]:
dtt = DateTimeTransformer()
dtt.from_json(dtt_params)
self._datetime_transforms += [dtt]
if "text_transforms" in data_json:
self._text_transforms = []
for tt_params in data_json["text_transforms"]:
tt = TextTransformer()
tt.from_json(tt_params)
self._text_transforms += [tt]
if "golden_features" in data_json:
self._golden_features = GoldenFeaturesTransformer()
self._golden_features.from_json(data_json["golden_features"],
results_path)
if "kmeans" in data_json:
self._kmeans = KMeansTransformer()
self._kmeans.from_json(data_json["kmeans"], results_path)
if "scale" in data_json:
self._scale = []
for scale_data in data_json["scale"]:
sc = Scale()
sc.from_json(scale_data)
self._scale += [sc]
if "categorical_y" in data_json:
if "new_columns" in data_json["categorical_y"]:
self._categorical_y = LabelBinarizer()
else:
self._categorical_y = LabelEncoder()
self._categorical_y.from_json(data_json["categorical_y"])
if "scale_y" in data_json:
self._scale_y = Scale()
self._scale_y.from_json(data_json["scale_y"])
if "ml_task" in data_json:
self._params["ml_task"] = data_json["ml_task"]
self._add_random_feature = data_json.get("add_random_feature", False)
self._drop_features = data_json.get("drop_features", [])
