def _fit_async(X_path, grp_hash, tmp_folder):
"""
Fits a FB Prophet model for a particular time group
:param X_path: Path to the data used to fit the FB Prophet model
:param grp_hash: Time group identifier
:return: time group identifier and path to the pickled model
"""
np.random.seed(1234)
random.seed(1234)
X = load_obj(X_path)
# Commented for performance, uncomment for debug
# print("prophet - fitting on data of shape: %s for group: %s" % (str(X.shape), grp_hash))
if X.shape[0] < 20:
# print("prophet - small data work-around for group: %s" % grp_hash)
return grp_hash, None
# Import FB Prophet package
mod = importlib.import_module('fbprophet')
Prophet = getattr(mod, "Prophet")
model = Prophet()
with suppress_stdout_stderr():
model.fit(X[['ds', 'y']])
model_path = os.path.join(tmp_folder,
"fbprophet_model" + str(uuid.uuid4()))
save_obj(model, model_path)
remove(X_path) # remove to indicate success
return grp_hash, model_path
def _fit_async(X_path, grp_hash, time_column, tmp_folder):
"""
Fits an ARIMA model for a particular time group
:param X_path: Path to the data used to fit the ARIMA model
:param grp_hash: Time group identifier
:param time_column: Name of the time column in the input data
:return: time group identifier and path to the pickled model
"""
np.random.seed(1234)
random.seed(1234)
X = load_obj(X_path)
pm = importlib.import_module('pmdarima')
with suppress_stdout_stderr():
try:
order = order = np.argsort(X[time_column])
model = pm.auto_arima(X['y'].values[order],
error_action='ignore')
except:
model = None
model_path = os.path.join(tmp_folder,
"autoarima_model" + str(uuid.uuid4()))
save_obj(model, model_path)
remove(X_path) # remove to indicate success
return grp_hash, model_path
def _transform_async(model_path, X_path, nan_value, has_is_train_attr, time_column):
model = load_obj(model_path)
XX_path = os.path.join(temporary_files_path, "autoarima_XXt" + str(uuid.uuid4()))
X = load_obj(X_path)
# Facebook Prophet returns the predictions ordered by time
# So we should keep track of the time order for each group so that
# predictions are ordered the same as the imput frame
# Keep track of the order
order = np.argsort(X[time_column])
if model is not None:
yhat = model.predict_in_sample() \
if has_is_train_attr else model.predict(n_periods=X.shape[0])
yhat = yhat[order]
XX = pd.DataFrame(yhat, columns=['yhat'])
else:
XX = pd.DataFrame(np.full((X.shape[0], 1), nan_value), columns=['yhat']) # invalid model
# Sync index
XX.index = X.index
assert XX.shape[1] == 1
save_obj(XX, XX_path)
remove(model_path) # indicates success, no longer need
remove(X_path) # indicates success, no longer need
return XX_path
def _transform_async(model_path, X_path, nan_value, tmp_folder):
"""
Predicts target for a particular time group
:param model_path: path to the stored model
:param X_path: Path to the data used to fit the FB Prophet model
:param nan_value: Value of target prior, used when no fitted model has been found
:return: self
"""
model = load_obj(model_path)
XX_path = os.path.join(tmp_folder, "fbprophet_XX" + str(uuid.uuid4()))
X = load_obj(X_path)
# Facebook Prophet returns the predictions ordered by time
# So we should keep track of the time order for each group so that
# predictions are ordered the same as the imput frame
# Keep track of the order
order = np.argsort(pd.to_datetime(X["ds"]))
if model is not None:
# Run prophet
yhat = model.predict(X)['yhat'].values
XX = pd.DataFrame(yhat, columns=['yhat'])
else:
XX = pd.DataFrame(np.full((X.shape[0], 1), nan_value), columns=['yhat']) # invalid models
XX.index = X.index[order]
assert XX.shape[1] == 1
save_obj(XX, XX_path)
remove(model_path) # indicates success, no longer need
remove(X_path) # indicates success, no longer need
return XX_path
def _transform_async(model_path, X_path, nan_value, tmp_folder):
"""
Predicts target for a particular time group
:param model_path: path to the stored model
:param X_path: Path to the data used to fit the FB Prophet model
:param nan_value: Value of target prior, used when no fitted model has been found
:return: self
"""
model = load_obj(model_path)
XX_path = os.path.join(tmp_folder, "fbprophet_XX" + str(uuid.uuid4()))
X = load_obj(X_path)
X_time = X[['ds']].groupby('ds').first().reset_index()
with suppress_stdout_stderr():
y_avg = model.predict(X_time)[['ds', 'yhat']]
# Prophet transforms the date column to datetime so we need to transfrom that to merge back
X_time.sort_values('ds', inplace=True)
X_time['yhat'] = y_avg['yhat']
X_time.sort_index(inplace=True)
# Merge back into original frame on 'ds'
# pd.merge wipes the index ... so keep it to provide it again
indices = X.index
X = pd.merge(left=X, right=X_time[['ds', 'yhat']], on='ds', how='left')
X.index = indices
save_obj(X[['yhat']], XX_path)
remove(model_path) # indicates success, no longer need
remove(X_path) # indicates success, no longer need
return XX_path
def _fit_async(X_path, grp_hash, tmp_folder, params):
"""
Fits a FB Prophet model for a particular time group
:param X_path: Path to the data used to fit the FB Prophet model
:param grp_hash: Time group identifier
:return: time group identifier and path to the pickled model
"""
np.random.seed(1234)
random.seed(1234)
X = load_obj(X_path)
# Commented for performance, uncomment for debug
# print("prophet - fitting on data of shape: %s for group: %s" % (str(X.shape), grp_hash))
if X.shape[0] < 20:
# print("prophet - small data work-around for group: %s" % grp_hash)
return grp_hash, None
# Import FB Prophet package
mod = importlib.import_module('fbprophet')
Prophet = getattr(mod, "Prophet")
model = Prophet(yearly_seasonality=True, weekly_seasonality=True, daily_seasonality=True)
if params["country_holidays"] is not None:
model.add_country_holidays(country_name=params["country_holidays"])
if params["monthly_seasonality"]:
model.add_seasonality(name='monthly', period=30.5, fourier_order=5)
with suppress_stdout_stderr():
model.fit(X[['ds', 'y']])
model_path = os.path.join(tmp_folder, "fbprophet_model" + str(uuid.uuid4()))
save_obj(model, model_path)
remove(X_path) # remove to indicate success
return grp_hash, model_path
def fit(self, X: dt.Frame, y: np.array = None):
XX = X[:, self.tgc].to_pandas()
XX = XX.replace([None, np.nan], 0)
XX.rename(columns={self.time_column: "ds"}, inplace=True)
if self.labels is not None:
y = LabelEncoder().fit(self.labels).transform(y)
XX['y'] = np.array(y)
self.nan_value = np.mean(y) # TODO - store mean per group, not just global
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
self.models = {}
num_tasks = len(XX_grp)
def processor(out, res):
out[res[0]] = res[1]
pool_to_use = small_job_pool
pool = pool_to_use(logger=None, processor=processor, num_tasks=num_tasks)
for key, X in XX_grp:
X_path = os.path.join(temporary_files_path, "fbprophet_X" + str(uuid.uuid4()))
X = X.reset_index(drop=True)
save_obj(X, X_path)
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
args = (X_path, grp_hash,)
kwargs = {}
pool.submit_tryget(None, MyParallelProphetTransformer_fit_async, args=args, kwargs=kwargs, out=self.models)
pool.finish()
for k, v in self.models.items():
self.models[k] = load_obj(v) if v is not None else None
remove(v)
return self
def _transform_async(model_path, X_path, nan_value, has_is_train_attr, time_column, tmp_folder):
"""
Predicts target for a particular time group
:param model_path: path to the stored model
:param X_path: Path to the data used to fit the ARIMA model
:param nan_value: Value of target prior, used when no fitted model has been found
:param has_is_train_attr: indicates if we predict in-sample or out-of-sample
:param time_column: Name of the time column in the input data
:return: self
"""
model = load_obj(model_path)
XX_path = os.path.join(tmp_folder, "autoarima_XXt" + str(uuid.uuid4()))
X = load_obj(X_path)
# Arima returns the predictions ordered by time
# So we should keep track of the time order for each group so that
# predictions are ordered the same as the imput frame
# Keep track of the order
order = np.argsort(X[time_column])
if model is not None:
yhat = model.predict_in_sample() \
if has_is_train_attr else model.predict(n_periods=X.shape[0])
yhat = yhat[order]
XX = pd.DataFrame(yhat, columns=['yhat'])
else:
XX = pd.DataFrame(np.full((X.shape[0], 1), nan_value), columns=['yhat']) # invalid model
# Sync index
XX.index = X.index
assert XX.shape[1] == 1
save_obj(XX, XX_path)
remove(model_path) # indicates success, no longer need
remove(X_path) # indicates success, no longer need
return XX_path
def _transform_async(model_path, X_path, nan_value):
model = load_obj(model_path)
XX_path = os.path.join(temporary_files_path, "fbprophet_XXt" + str(uuid.uuid4()))
X = load_obj(X_path)
if model is not None:
# Facebook Prophet returns the predictions ordered by time
# So we should keep track of the times for each group so that
# predictions are ordered the same as the imput frame
# Make a copy of the input dates
X_ds = X.copy()
X_ds['ds'] = pd.to_datetime(X_ds['ds'])
# Predict with prophet, get the time and prediction and index by time as well
# In the case date repeats inside of a group (this happens at least in acceptance test)
# We groupby date and keep the max (prophet returns the same value for a given date)
# XX will contain the predictions indexed by date
XX = model.predict(X)[['ds', 'yhat']].groupby('ds').max()
# Now put yhat in the right order, simply by maping the dates to the predictions
X_ds['yhat'] = X_ds["ds"].map(XX['yhat'])
# Now set XX back to the predictions and drop the index
XX = X_ds[['yhat']].reset_index(drop=True)
else:
XX = pd.DataFrame(np.full((X.shape[0], 1), nan_value), columns=['yhat']) # invalid models
XX.index = X.index
assert XX.shape[1] == 1
save_obj(XX, XX_path)
remove(model_path) # indicates success, no longer need
remove(X_path) # indicates success, no longer need
return XX_path
def _fit_async(X_path, grp_hash, tmp_folder, params, cap):
"""
Fits a FB Prophet model for a particular time group
:param X_path: Path to the data used to fit the FB Prophet model
:param grp_hash: Time group identifier
:return: time group identifier and path to the pickled model
"""
np.random.seed(1234)
random.seed(1234)
X = load_obj(X_path)
# Commented for performance, uncomment for debug
# print("prophet - fitting on data of shape: %s for group: %s" % (str(X.shape), grp_hash))
if X.shape[0] < 20:
return grp_hash, None
# Import FB Prophet package
mod = importlib.import_module('fbprophet')
Prophet = getattr(mod, "Prophet")
# Fit current model and prior
nrows = X[['ds', 'y']].shape[0]
n_changepoints = max(1, int(nrows * (2 / 3)))
if n_changepoints < 25:
model = Prophet(growth=params["growth"],
n_changepoints=n_changepoints)
else:
model = Prophet(growth=params["growth"])
# Add params
if params["country_holidays"] is not None:
model.add_country_holidays(country_name=params["country_holidays"])
if params["monthly_seasonality"]:
model.add_seasonality(name='monthly',
period=30.5,
fourier_order=params["monthly_seasonality"])
if params["quarterly_seasonality"]:
model.add_seasonality(
name='quarterly',
period=92,
fourier_order=params["quarterly_seasonality"])
with suppress_stdout_stderr():
if params["growth"] == "logistic":
X["cap"] = cap
model.fit(X[['ds', 'y', 'cap']])
else:
model.fit(X[['ds', 'y']])
model_path = os.path.join(tmp_folder,
"fbprophet_model" + str(uuid.uuid4()))
save_obj(model, model_path)
remove(X_path) # remove to indicate success
return grp_hash, model_path
def _fit_async(X_path, grp_hash, time_column):
np.random.seed(1234)
random.seed(1234)
X = load_obj(X_path)
pm = importlib.import_module('pmdarima')
with suppress_stdout_stderr():
try:
order = order = np.argsort(X[time_column])
model = pm.auto_arima(X['y'].values[order], error_action='ignore')
except:
model = None
model_path = os.path.join(temporary_files_path, "autoarima_model" + str(uuid.uuid4()))
save_obj(model, model_path)
remove(X_path) # remove to indicate success
return grp_hash, model_path
def _transform_async(model_path, X_path, nan_value):
model = load_obj(model_path)
XX_path = os.path.join(temporary_files_path,
"fbprophet_XXt" + str(uuid.uuid4()))
X = load_obj(X_path)
if model is not None:
XX = model.predict(X[['ds']])[['yhat']]
else:
XX = pd.DataFrame(np.full((X.shape[0], 1), nan_value),
columns=['yhat']) # invalid models
XX.index = X.index
assert XX.shape[1] == 1
save_obj(XX, XX_path)
remove(model_path) # indicates success, no longer need
remove(X_path) # indicates success, no longer need
return XX_path
def _fit_async(X_path, grp_hash):
np.random.seed(1234)
random.seed(1234)
X = load_obj(X_path)
# Commented for performance, uncomment for debug
# print("prophet - fitting on data of shape: %s for group: %s" % (str(X.shape), grp_hash))
if X.shape[0] < 20:
# print("prophet - small data work-around for group: %s" % grp_hash)
return grp_hash, None
mod = importlib.import_module('fbprophet')
Prophet = getattr(mod, "Prophet")
model = Prophet()
with suppress_stdout_stderr():
model.fit(X[['ds', 'y']])
model_path = os.path.join(temporary_files_path, "fbprophet_model" + str(uuid.uuid4()))
save_obj(model, model_path)
remove(X_path) # remove to indicate success
return grp_hash, model_path
def _fit_async(data_path, grp_hash, tmp_folder, params):
"""
Fits a FB Prophet model for a particular time group
:param data_path: Path to the data used to fit the FB Prophet model
:param grp_hash: Time group identifier
:return: time group identifier and path to the pickled model
"""
np.random.seed(1234)
random.seed(1234)
X = load_obj(data_path)
# if X.shape[0] < 20:
# return grp_hash, None
# Import FB Prophet package
mod = importlib.import_module('fbprophet')
Prophet = getattr(mod, "Prophet")
model = fit_prophet_model(Prophet, X, params)
model_path = os.path.join(tmp_folder, "fbprophet_model" + str(uuid.uuid4()))
save_obj(model, model_path)
remove(data_path) # remove to indicate success
return grp_hash, model_path
def fit(self, X: dt.Frame, y: np.array = None):
pm = importlib.import_module('pmdarima')
self.models = {}
X = X.to_pandas()
XX = X[self.tgc].copy()
XX['y'] = np.array(y)
self.nan_value = np.mean(y)
self.ntrain = X.shape[0]
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
num_tasks = len(XX_grp)
def processor(out, res):
out[res[0]] = res[1]
pool_to_use = small_job_pool
pool = pool_to_use(logger=None, processor=processor, num_tasks=num_tasks)
nb_groups = len(XX_grp)
for _i_g, (key, X) in enumerate(XX_grp):
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
print("Auto ARIMA - ", 100 * (_i_g + 1) // nb_groups, " %% of Groups Fitted")
X_path = os.path.join(temporary_files_path, "autoarima_X" + str(uuid.uuid4()))
X = X.reset_index(drop=True)
save_obj(X, X_path)
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
args = (X_path, grp_hash, self.time_column,)
kwargs = {}
pool.submit_tryget(None, MyParallelAutoArimaTransformer_fit_async, args=args, kwargs=kwargs, out=self.models)
pool.finish()
for k, v in self.models.items():
self.models[k] = load_obj(v) if v is not None else None
remove(v)
return self
def transform(self, X: dt.Frame):
X = X.to_pandas()
X = X.replace([None, np.nan], 0)
XX = X[self.tgc].copy()
XX.rename(columns={self.time_column: "ds"}, inplace=True)
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
assert len(XX_grp) > 0
num_tasks = len(XX_grp)
def processor(out, res):
out.append(res)
pool_to_use = small_job_pool
pool = pool_to_use(logger=None,
processor=processor,
max_workers=self.n_jobs,
num_tasks=num_tasks)
XX_paths = []
model_paths = []
for key, X in XX_grp:
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
X_path = os.path.join(temporary_files_path,
"fbprophet_Xt" + str(uuid.uuid4()))
print("prophet - transforming data of shape: %s for group: %s" %
(str(X.shape), grp_hash))
if grp_hash in self.models:
model = self.models[grp_hash]
model_path = os.path.join(
temporary_files_path,
"fbprophet_modelt" + str(uuid.uuid4()))
save_obj(model, model_path)
save_obj(X, X_path)
model_paths.append(model_path)
args = (model_path, X_path, self.nan_value)
kwargs = {}
pool.submit_tryget(
None,
MyParallelProphetTransformer_transform_async,
args=args,
kwargs=kwargs,
out=XX_paths)
else:
XX = pd.DataFrame(np.full((X.shape[0], 1), self.nan_value),
columns=['yhat']) # unseen groups
save_obj(XX, X_path)
XX_paths.append(X_path)
pool.finish()
XX = pd.concat((load_obj(XX_path) for XX_path in XX_paths),
axis=0).sort_index()
for p in XX_paths + model_paths:
remove(p)
return XX
def _transform_async(model_path, X_path, nan_value):
model = load_obj(model_path)
XX_path = os.path.join(temporary_files_path,
"fbprophet_XXt" + str(uuid.uuid4()))
X = load_obj(X_path)
# Facebook Prophet returns the predictions ordered by time
# So we should keep track of the time order for each group so that
# predictions are ordered the same as the imput frame
# Keep track of the order
order = np.argsort(pd.to_datetime(X["ds"]))
if model is not None:
# Run prophet
yhat = model.predict(X)['yhat'].values
XX = pd.DataFrame(yhat, columns=['yhat'])
else:
XX = pd.DataFrame(np.full((X.shape[0], 1), nan_value),
columns=['yhat']) # invalid models
XX.index = X.index[order]
assert XX.shape[1] == 1
save_obj(XX, XX_path)
remove(model_path) # indicates success, no longer need
remove(X_path) # indicates success, no longer need
return XX_path
def transform(self, X: dt.Frame):
X = X.to_pandas()
XX = X[self.tgc].copy()
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
assert len(XX_grp) > 0
num_tasks = len(XX_grp)
def processor(out, res):
out.append(res)
pool_to_use = small_job_pool
pool = pool_to_use(logger=None, processor=processor, num_tasks=num_tasks)
XX_paths = []
model_paths = []
nb_groups = len(XX_grp)
for _i_g, (key, X) in enumerate(XX_grp):
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
print("Auto ARIMA - ", 100 * (_i_g + 1) // nb_groups, " %% of Groups Transformed")
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
X_path = os.path.join(temporary_files_path, "autoarima_Xt" + str(uuid.uuid4()))
# Commented for performance, uncomment for debug
# print("prophet - transforming data of shape: %s for group: %s" % (str(X.shape), grp_hash))
if grp_hash in self.models:
model = self.models[grp_hash]
model_path = os.path.join(temporary_files_path, "autoarima_modelt" + str(uuid.uuid4()))
save_obj(model, model_path)
save_obj(X, X_path)
model_paths.append(model_path)
args = (model_path, X_path, self.nan_value, hasattr(self, 'is_train'), self.time_column,)
kwargs = {}
pool.submit_tryget(None, MyParallelAutoArimaTransformer_transform_async, args=args, kwargs=kwargs,
out=XX_paths)
else:
# Don't go through pools
XX = pd.DataFrame(np.full((X.shape[0], 1), self.nan_value), columns=['yhat']) # unseen groups
# Sync indices
XX.index = X.index
save_obj(XX, X_path)
XX_paths.append(X_path)
pool.finish()
XX = pd.concat((load_obj(XX_path) for XX_path in XX_paths), axis=0).sort_index()
for p in XX_paths + model_paths:
remove(p)
return XX
def fit(self,
X,
y,
sample_weight=None,
eval_set=None,
sample_weight_eval_set=None,
**kwargs):
# Get TGC and time column
self.tgc = self.params_base.get('tgc', None)
self.time_column = self.params_base.get('time_column', None)
self.nan_value = np.mean(y)
self.cap = np.max(
y
) * 1.5 # TODO Don't like this we should compute a cap from average yearly growth
self.prior = np.mean(y)
if self.time_column is None:
self.time_column = self.tgc[0]
# Get the logger if it exists
logger = None
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir)
loggerinfo(
logger,
"Start Fitting Prophet Model with params : {}".format(self.params))
# Get temporary folders for multi process communication
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
# Convert to pandas
XX = X[:, self.tgc].to_pandas()
XX = XX.replace([None, np.nan], 0)
XX.rename(columns={self.time_column: "ds"}, inplace=True)
# Make target available in the Frame
XX['y'] = np.array(y)
# Set target prior
self.nan_value = np.mean(y)
# Group the input by TGC (Time group column) excluding the time column itself
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
self.models = {}
self.priors = {}
# Prepare for multi processing
num_tasks = len(XX_grp)
def processor(out, res):
out[res[0]] = res[1]
pool_to_use = small_job_pool
loggerdebug(logger,
"Prophet will use {} workers for fitting".format(n_jobs))
pool = pool_to_use(logger=None,
processor=processor,
num_tasks=num_tasks,
max_workers=n_jobs)
# Fit 1 FB Prophet model per time group columns
nb_groups = len(XX_grp)
for _i_g, (key, X) in enumerate(XX_grp):
# Just log where we are in the fitting process
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(
logger, "FB Prophet : %d%% of groups fitted" %
(100 * (_i_g + 1) // nb_groups))
X_path = os.path.join(tmp_folder,
"fbprophet_X" + str(uuid.uuid4()))
X = X.reset_index(drop=True)
save_obj(X, X_path)
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
self.priors[grp_hash] = X['y'].mean()
args = (X_path, grp_hash, tmp_folder, self.params, self.cap)
kwargs = {}
pool.submit_tryget(None,
MyParallelProphetTransformer_fit_async,
args=args,
kwargs=kwargs,
out=self.models)
pool.finish()
for k, v in self.models.items():
self.models[k] = load_obj(v) if v is not None else None
remove(v)
self._clean_tmp_folder(logger, tmp_folder)
return None
def fit(self, X: dt.Frame, y: np.array = None, **kwargs):
"""
Fits ARIMA models (1 per time group) using historical target values contained in y
Model fitting is distributed over a pool of processes and uses file storage to share the data with workers
:param X: Datatable frame containing the features
:param y: numpy array containing the historical values of the target
:return: self
"""
# Get the logger if it exists
logger = None
tmp_folder = str(uuid.uuid4()) + "_arima_folder/"
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir)
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
# Import the ARIMA python module
pm = importlib.import_module('pmdarima')
# Init models
self.models = {}
# Convert to pandas
X = X.to_pandas()
XX = X[self.tgc].copy()
XX['y'] = np.array(y)
self.nan_value = np.mean(y)
self.ntrain = X.shape[0]
# Group the input by TGC (Time group column) excluding the time column itself
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
# Prepare for multi processing
num_tasks = len(XX_grp)
def processor(out, res):
out[res[0]] = res[1]
pool_to_use = small_job_pool
loggerinfo(
logger,
"Arima will use {} workers for parallel processing".format(n_jobs))
pool = pool_to_use(logger=None,
processor=processor,
num_tasks=num_tasks,
max_workers=n_jobs)
# Build 1 ARIMA model per time group columns
nb_groups = len(XX_grp)
for _i_g, (key, X) in enumerate(XX_grp):
# Just say where we are in the fitting process
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(
logger, "Auto ARIMA : %d%% of groups fitted" %
(100 * (_i_g + 1) // nb_groups))
X_path = os.path.join(tmp_folder,
"autoarima_X" + str(uuid.uuid4()))
X = X.reset_index(drop=True)
save_obj(X, X_path)
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
args = (X_path, grp_hash, self.time_column, tmp_folder)
kwargs = {}
pool.submit_tryget(None,
MyParallelAutoArimaTransformer_fit_async,
args=args,
kwargs=kwargs,
out=self.models)
pool.finish()
for k, v in self.models.items():
self.models[k] = load_obj(v) if v is not None else None
remove(v)
self._clean_tmp_folder(logger, tmp_folder)
return self
def transform(self, X: dt.Frame, **kwargs):
"""
Uses fitted models (1 per time group) to predict the target
If self.is_train exists, it means we are doing in-sample predictions
if it does not then we Arima is used to predict the future
:param X: Datatable Frame containing the features
:return: ARIMA predictions
"""
# Get the logger if it exists
logger = None
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir)
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
X = X.to_pandas()
XX = X[self.tgc].copy()
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
assert len(XX_grp) > 0
num_tasks = len(XX_grp)
def processor(out, res):
out.append(res)
pool_to_use = small_job_pool
loggerinfo(logger,
"Arima will use {} workers for transform".format(n_jobs))
pool = pool_to_use(logger=None,
processor=processor,
num_tasks=num_tasks,
max_workers=n_jobs)
XX_paths = []
model_paths = []
nb_groups = len(XX_grp)
for _i_g, (key, X) in enumerate(XX_grp):
# Just print where we are in the process of fitting models
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(
logger, "Auto ARIMA : %d%% of groups transformed" %
(100 * (_i_g + 1) // nb_groups))
# Create time group key to store and retrieve fitted models
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
# Create file path to store data and pass it to the fitting pool
X_path = os.path.join(tmp_folder,
"autoarima_Xt" + str(uuid.uuid4()))
# Commented for performance, uncomment for debug
# print("ARIMA - transforming data of shape: %s for group: %s" % (str(X.shape), grp_hash))
if grp_hash in self.models:
model = self.models[grp_hash]
model_path = os.path.join(
tmp_folder, "autoarima_modelt" + str(uuid.uuid4()))
save_obj(model, model_path)
save_obj(X, X_path)
model_paths.append(model_path)
args = (model_path, X_path, self.nan_value,
hasattr(self, 'is_train'), self.time_column,
self.pred_gap, tmp_folder)
kwargs = {}
pool.submit_tryget(
None,
MyParallelAutoArimaTransformer_transform_async,
args=args,
kwargs=kwargs,
out=XX_paths)
else:
# Don't go through pools
XX = pd.DataFrame(np.full((X.shape[0], 1), self.nan_value),
columns=['yhat']) # unseen groups
# Sync indices
XX.index = X.index
save_obj(XX, X_path)
XX_paths.append(X_path)
pool.finish()
XX = pd.concat((load_obj(XX_path) for XX_path in XX_paths),
axis=0).sort_index()
for p in XX_paths + model_paths:
remove(p)
self._clean_tmp_folder(logger, tmp_folder)
return XX
def fit(self,
X,
y,
sample_weight=None,
eval_set=None,
sample_weight_eval_set=None,
**kwargs):
logger = None
if self._make_logger:
# Example use of logger, with required import of:
# from h2oaicore.systemutils import make_experiment_logger, loggerinfo
# Can use loggerwarning, loggererror, etc. for different levels
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir)
if self._show_logger_test:
loggerinfo(logger, "TestLOGGER: Fit CatBoost")
if self._show_task_test:
# Example task sync operations
if hasattr(self, 'testcount'):
self.test_count += 1
else:
self.test_count = 0
# The below generates a message in the GUI notifications panel
if self.test_count == 0 and self.context and self.context.experiment_id:
warning = "TestWarning: First CatBoost fit for this model instance"
loggerwarning(logger, warning)
task = kwargs.get('task')
if task:
task.sync(key=self.context.experiment_id,
progress=dict(type='warning', data=warning))
task.flush()
# The below generates a message in the GUI top-middle panel above the progress wheel
if self.test_count == 0 and self.context and self.context.experiment_id:
message = "Tuning CatBoost"
loggerinfo(logger, message)
task = kwargs.get('task')
if task:
task.sync(key=self.context.experiment_id,
progress=dict(type='update', message=message))
task.flush()
from catboost import CatBoostClassifier, CatBoostRegressor, EFstrType
# label encode target and setup type of problem
lb = LabelEncoder()
if self.num_classes >= 2:
lb.fit(self.labels)
y = lb.transform(y)
if eval_set is not None:
valid_X = eval_set[0][0]
valid_y = eval_set[0][1]
valid_y = lb.transform(valid_y)
eval_set = [(valid_X, valid_y)]
self.params.update({'objective': 'Logloss'})
if self.num_classes > 2:
self.params.update({'objective': 'MultiClass'})
if isinstance(X, dt.Frame):
orig_cols = list(X.names)
numeric_cols = list(X[:, [bool, int, float]].names)
else:
orig_cols = list(X.columns)
numeric_cols = list(X.select_dtypes([np.number]).columns)
# unlike lightgbm that needs label encoded categoricals, catboots can take raw strings etc.
self.params['cat_features'] = [
i for i, x in enumerate(orig_cols)
if 'CatOrig:' in x or 'Cat:' in x or x not in numeric_cols
]
if not self.get_uses_gpus(self.params):
# monotonicity constraints not available for GPU for catboost
# get names of columns in same order
X_names = list(dt.Frame(X).names)
X_numeric = self.get_X_ordered_numerics(X)
X_numeric_names = list(X_numeric.names)
_, _, constraints, self.set_monotone_constraints(X=X_numeric, y=y)
# if non-numerics, then fix those to have 0 constraint
self.params['monotone_constraints'] = [0] * len(X_names)
colnumi = 0
for coli in X_names:
if X_names[coli] in X_numeric_names:
self.params['monotone_constraints'][coli] = constraints[
colnumi]
colnumi += 1
if isinstance(X, dt.Frame) and len(self.params['cat_features']) == 0:
# dt -> catboost internally using buffer leaks, so convert here
# assume predict is after pipeline collection or in subprocess so needs no protection
X = X.to_numpy(
) # don't assign back to X so don't damage during predict
X = np.ascontiguousarray(X,
dtype=np.float32 if config.data_precision
== "float32" else np.float64)
if eval_set is not None:
valid_X = eval_set[0][0].to_numpy(
) # don't assign back to X so don't damage during predict
valid_X = np.ascontiguousarray(
valid_X,
dtype=np.float32
if config.data_precision == "float32" else np.float64)
valid_y = eval_set[0][1]
eval_set = [(valid_X, valid_y)]
if eval_set is not None:
valid_X_shape = eval_set[0][0].shape
else:
valid_X_shape = None
X, eval_set = self.process_cats(X, eval_set, orig_cols)
# modify self.params_base['gpu_id'] based upon actually-available GPU based upon training and valid shapes
self.acquire_gpus_function(train_shape=X.shape,
valid_shape=valid_X_shape)
params = copy.deepcopy(
self.params
) # keep separate, since then can be pulled form lightgbm params
params = self.transcribe_params(params=params, **kwargs)
if logger is not None:
loggerdata(
logger,
"CatBoost parameters: params_base : %s params: %s catboost_params: %s"
% (str(self.params_base), str(self.params), str(params)))
if self.num_classes == 1:
self.model = CatBoostRegressor(**params)
else:
self.model = CatBoostClassifier(**params)
# Hit sometimes: Exception: catboost/libs/data_new/quantization.cpp:779: All features are either constant or ignored.
if self.num_classes == 1:
# assume not mae, which would use median
# baseline = [np.mean(y)] * len(y)
baseline = None
else:
baseline = None
kwargs_fit = dict(baseline=baseline, eval_set=eval_set)
pickle_path = None
if config.debug_daimodel_level >= 2:
self.uuid = str(uuid.uuid4())[:6]
pickle_path = os.path.join(exp_dir(),
"catboost%s.tmp.pickle" % self.uuid)
save_obj((self.model, X, y, sample_weight, kwargs_fit),
pickle_path)
# FIT (with migration safety before hyperopt/Optuna function added)
try:
if hasattr(self, 'dask_or_hyper_or_normal_fit'):
self.dask_or_hyper_or_normal_fit(X,
y,
sample_weight=sample_weight,
kwargs=kwargs,
**kwargs_fit)
else:
self.model.fit(X, y, sample_weight=sample_weight, **kwargs_fit)
except Exception as e:
if "All features are either constant or ignored" in str(e):
raise IgnoreEntirelyError(str(e))
raise
if config.debug_daimodel_level <= 2:
remove(pickle_path)
# https://catboost.ai/docs/concepts/python-reference_catboostclassifier.html
# need to move to wrapper
if self.model.get_best_iteration() is not None:
iterations = self.model.get_best_iteration() + 1
else:
iterations = self.params['n_estimators']
# must always set best_iterations
self.model_path = None
importances = copy.deepcopy(self.model.feature_importances_)
if not self._save_by_pickle:
self.uuid = str(uuid.uuid4())[:6]
model_file = "catboost_%s.bin" % str(self.uuid)
self.model_path = os.path.join(self.context.experiment_tmp_dir,
model_file)
self.model.save_model(self.model_path)
with open(self.model_path, mode='rb') as f:
model = f.read()
else:
model = self.model
self.set_model_properties(
model=
model, # overwrites self.model object with bytes if not using pickle
features=orig_cols,
importances=importances,
iterations=iterations)
def transform(self, X: dt.Frame, **kwargs):
"""
Uses fitted models (1 per time group) to predict the target
:param X: Datatable Frame containing the features
:return: FB Prophet predictions
"""
# Get the logger if it exists
logger = None
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir
)
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
# Reduce X to TGC
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
X = X[:, self.tgc].to_pandas()
# Fill NaNs or None
X = X.replace([None, np.nan], 0)
# Change date feature name to match Prophet requirements
X.rename(columns={self.time_column: "ds"}, inplace=True)
# Predict y using unique dates
X_time = X[['ds']].groupby('ds').first().reset_index()
with suppress_stdout_stderr():
y_avg = self.model.predict(X_time)[['ds', 'yhat']]
# Prophet transforms the date column to datetime so we need to transfrom that to merge back
X_time.sort_values('ds', inplace=True)
X_time['yhat'] = y_avg['yhat']
X_time.sort_index(inplace=True)
# Merge back into original frame on 'ds'
# pd.merge wipes the index ... so keep it to provide it again
indices = X.index
X = pd.merge(
left=X,
right=X_time[['ds', 'yhat']],
on='ds',
how='left'
)
X.index = indices
# Go through groups and recover the scaled target for knowed groups
if len(tgc_wo_time) > 0:
X_groups = X.groupby(tgc_wo_time)
else:
X_groups = [([None], X)]
inverted_ys = []
for key, X_grp in X_groups:
grp_hash = self.get_hash(key)
# Scale target for current group
if grp_hash in self.scalers.keys():
inverted_y = self.scalers[grp_hash].inverse_transform(X_grp[['yhat']])
else:
inverted_y = self.general_scaler.inverse_transform(X_grp[['yhat']])
# Put back in a DataFrame to keep track of original index
inverted_df = pd.DataFrame(inverted_y, columns=['yhat'])
inverted_df.index = X_grp.index
inverted_ys.append(inverted_df)
XX_general = pd.concat(tuple(inverted_ys), axis=0).sort_index()
if self.top_groups:
# Go though the groups and predict only top
XX_paths = []
model_paths = []
def processor(out, res):
out.append(res)
num_tasks = len(self.top_groups)
pool_to_use = small_job_pool
pool = pool_to_use(logger=None, processor=processor, num_tasks=num_tasks, max_workers=n_jobs)
nb_groups = len(X_groups)
for _i_g, (key, X_grp) in enumerate(X_groups):
# Just log where we are in the fitting process
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(logger, "FB Prophet : %d%% of groups predicted" % (100 * (_i_g + 1) // nb_groups))
# Create dict key to store the min max scaler
grp_hash = self.get_hash(key)
X_path = os.path.join(tmp_folder, "fbprophet_Xt" + str(uuid.uuid4()))
if grp_hash not in self.top_groups:
XX = pd.DataFrame(np.full((X_grp.shape[0], 1), np.nan), columns=['yhat']) # unseen groups
XX.index = X_grp.index
save_obj(XX, X_path)
XX_paths.append(X_path)
continue
if self.grp_models[grp_hash] is None:
XX = pd.DataFrame(np.full((X_grp.shape[0], 1), np.nan), columns=['yhat']) # unseen groups
XX.index = X_grp.index
save_obj(XX, X_path)
XX_paths.append(X_path)
continue
model = self.grp_models[grp_hash]
model_path = os.path.join(tmp_folder, "fbprophet_modelt" + str(uuid.uuid4()))
save_obj(model, model_path)
save_obj(X_grp, X_path)
model_paths.append(model_path)
args = (model_path, X_path, self.priors[grp_hash], tmp_folder)
kwargs = {}
pool.submit_tryget(None, MyParallelProphetTransformer_transform_async, args=args, kwargs=kwargs,
out=XX_paths)
pool.finish()
XX_top_groups = pd.concat((load_obj(XX_path) for XX_path in XX_paths), axis=0).sort_index()
for p in XX_paths + model_paths:
remove(p)
self._clean_tmp_folder(logger, tmp_folder)
features_df = pd.DataFrame()
features_df[self.display_name + '_GrpAvg'] = XX_general['yhat']
if self.top_groups:
features_df[self.display_name + f'_Top{self.top_n}Grp'] = XX_top_groups['yhat']
self._output_feature_names = list(features_df.columns)
self._feature_desc = list(features_df.columns)
return features_df
def predict(self, X, y=None, **kwargs):
model, features, importances, iterations = self.get_model_properties()
if not self._save_by_pickle:
from catboost import CatBoostClassifier, CatBoostRegressor, EFstrType
if self.num_classes >= 2:
from_file = CatBoostClassifier()
else:
from_file = CatBoostRegressor()
with open(self.model_path, mode='wb') as f:
f.write(model)
model = from_file.load_model(self.model_path)
# FIXME: Do equivalent throttling of predict size like def _predict_internal(self, X, **kwargs), wrap-up.
if isinstance(X, dt.Frame) and len(self.params['cat_features']) == 0:
# dt -> lightgbm internally using buffer leaks, so convert here
# assume predict is after pipeline collection or in subprocess so needs no protection
X = X.to_numpy(
) # don't assign back to X so don't damage during predict
X = np.ascontiguousarray(X,
dtype=np.float32 if config.data_precision
== "float32" else np.float64)
X, eval_set = self.process_cats(X, None, self.feature_names_fitted)
pred_contribs = kwargs.get('pred_contribs', False)
output_margin = kwargs.get('output_margin', False)
fast_approx = kwargs.pop('fast_approx', False)
if fast_approx:
iterations = min(config.fast_approx_num_trees, iterations)
# implicit import
from catboost import CatBoostClassifier, CatBoostRegressor, EFstrType, Pool
n_jobs = max(1, physical_cores_count)
if not pred_contribs and not output_margin:
if self.num_classes >= 2:
preds = model.predict_proba(
X,
ntree_start=0,
ntree_end=iterations, # index of first tree *not* to be used
thread_count=self.params_base.get(
'n_jobs', n_jobs), # -1 is not supported
)
if preds.shape[1] == 2:
return preds[:, 1]
else:
return preds
else:
return model.predict(
X,
ntree_start=0,
ntree_end=iterations, # index of first tree *not* to be used
thread_count=self.params_base.get(
'n_jobs', n_jobs), # -1 is not supported
)
elif output_margin:
# uses "predict" for raw for any class
preds = model.predict(
X,
prediction_type="RawFormulaVal",
ntree_start=0,
ntree_end=iterations, # index of first tree *not* to be used
thread_count=self.params_base.get(
'n_jobs', n_jobs), # -1 is not supported
)
if len(preds.shape
) > 1 and preds.shape[1] == 2 and self.num_classes == 2:
return preds[:, 1]
else:
return preds
elif pred_contribs:
# For Shapley, doesn't come from predict
# For regression/binary, shap is shape of (rows, features + bias)
# for multiclass, shap is shape of (rows, classes, features + bias)
data = Pool(X, label=y, cat_features=self.params['cat_features'])
if fast_approx:
# https://github.com/catboost/catboost/issues/1146
# https://github.com/catboost/catboost/issues/1535
# can't specify trees, but they have approx version
# Regular, Exact, or Approximate
shap_calc_type = "Approximate"
else:
shap_calc_type = "Regular"
# See also shap_mode
# help(CatBoostClassifier.get_feature_importance)
print_debug("shap_calc_type: %s" % shap_calc_type)
pickle_path = None
if config.debug_daimodel_level >= 2:
self.uuid = str(uuid.uuid4())[:6]
pickle_path = os.path.join(
exp_dir(), "catboost_shappredict%s.tmp.pickle" % self.uuid)
model.save_model(
os.path.join(exp_dir(), "catshapproblem%s.catboost.model" %
self.uuid))
# save_obj((self, self.model, model, X, y, kwargs, shap_calc_type, self.params['cat_features']), pickle_path)
save_obj((model, X, y, kwargs, shap_calc_type,
self.params['cat_features']), pickle_path)
preds_shap = model.get_feature_importance(
data=data,
thread_count=self.params_base.get(
'n_jobs', n_jobs), # -1 is not supported,
type=EFstrType.ShapValues,
shap_calc_type=shap_calc_type,
)
# repair broken shap sum: https://github.com/catboost/catboost/issues/1125
print_debug("shap_fix")
preds_raw = model.predict(
X,
prediction_type="RawFormulaVal",
ntree_start=0,
ntree_end=iterations, # index of first tree *not* to be used
thread_count=self.params_base.get(
'n_jobs', n_jobs), # -1 is not supported
)
if self.num_classes <= 2:
axis = 1
else:
axis = 2
orig_sum = np.sum(preds_shap, axis=axis)
print_debug("shap_fix2")
# avoid division by 0, need different trick, e.g. change baseline, to fix that case
if axis == 1:
orig_sum[orig_sum[:] == 0.0] = 1.0
preds_shap = preds_shap * preds_raw[:, None] / orig_sum[:,
None]
else:
# each feature and each class must sum up
orig_sum[orig_sum[:, :] == 0.0] = 1.0
preds_shap = preds_shap * preds_raw[:, :,
None] / orig_sum[:, :,
None]
if config.hard_asserts and config.debug_daimodel_level >= 2:
print_debug("shap_check")
model.save_model(os.path.join(exp_dir(), "catshapproblem"))
pickle.dump((X, y, self.params['cat_features']),
open(os.path.join(exp_dir(), "catshapproblem.pkl"),
"wb"))
preds_raw = model.predict(
X,
prediction_type="RawFormulaVal",
ntree_start=0,
ntree_end=iterations, # index of first tree *not* to be used
thread_count=self.params_base.get(
'n_jobs', n_jobs), # -1 is not supported
)
assert np.isclose(preds_raw, np.sum(
preds_shap, axis=axis)).all(
), "catboost shapley does not sum up correctly"
if config.debug_daimodel_level <= 2:
remove(pickle_path)
if axis == 1:
return preds_shap
else:
# DAI expects (shape rows) * (classes x (features + 1)) with "columns" as blocks of
# feature_0_class_0 feature_0_class_0 ... feature_0_class_1 feature_1_class_1 ...
return preds_shap.reshape(
preds_shap.shape[0],
preds_shap.shape[1] * preds_shap.shape[2])
else:
raise RuntimeError("No such case")
def fit(self, X: dt.Frame, y: np.array = None, **kwargs):
"""
Fits FB Prophet models (1 per time group) using historical target values contained in y
Model fitting is distributed over a pool of processes and uses file storage to share the data with workers
:param X: Datatable frame containing the features
:param y: numpy array containing the historical values of the target
:return: self
"""
# Get the logger if it exists
logger = None
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir
)
try:
# Add value of prophet_top_n in recipe_dict variable inside of config.toml file
# eg1: recipe_dict="{'prophet_top_n': 200}"
# eg2: recipe_dict="{'prophet_top_n':10}"
self.top_n = config.recipe_dict['prophet_top_n']
except KeyError:
self.top_n = 50
loggerinfo(logger, f"Prophet will use {self.top_n} groups as well as average target data.")
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
# Reduce X to TGC
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
X = X[:, self.tgc].to_pandas()
# Fill NaNs or None
X = X.replace([None, np.nan], 0)
# Add target, Label encoder is only used for Classif. which we don't support...
if self.labels is not None:
y = LabelEncoder().fit(self.labels).transform(y)
X['y'] = np.array(y)
self.nan_value = X['y'].mean()
# Change date feature name to match Prophet requirements
X.rename(columns={self.time_column: "ds"}, inplace=True)
# Create a general scale now that will be used for unknown groups at prediction time
# Can we do smarter than that ?
self.general_scaler = MinMaxScaler().fit(X[['y', 'ds']].groupby('ds').median().values)
# Go through groups and standard scale them
if len(tgc_wo_time) > 0:
X_groups = X.groupby(tgc_wo_time)
else:
X_groups = [([None], X)]
self.scalers = {}
scaled_ys = []
print(f'{datetime.now()} Start of group scaling')
for key, X_grp in X_groups:
# Create dict key to store the min max scaler
grp_hash = self.get_hash(key)
# Scale target for current group
self.scalers[grp_hash] = MinMaxScaler()
y_skl = self.scalers[grp_hash].fit_transform(X_grp[['y']].values)
# Put back in a DataFrame to keep track of original index
y_skl_df = pd.DataFrame(y_skl, columns=['y'])
# (0, 'A') (1, 4) (100, 1) (100, 1)
# print(grp_hash, X_grp.shape, y_skl.shape, y_skl_df.shape)
y_skl_df.index = X_grp.index
scaled_ys.append(y_skl_df)
print(f'{datetime.now()} End of group scaling')
# Set target back in original frame but keep original
X['y_orig'] = X['y']
X['y'] = pd.concat(tuple(scaled_ys), axis=0)
# Now Average groups
X_avg = X[['ds', 'y']].groupby('ds').mean().reset_index()
# Send that to Prophet
params = {
"country_holidays": self.country_holidays,
"monthly_seasonality": self.monthly_seasonality
}
mod = importlib.import_module('fbprophet')
Prophet = getattr(mod, "Prophet")
self.model = Prophet(yearly_seasonality=True, weekly_seasonality=True, daily_seasonality=True)
if params["country_holidays"] is not None:
self.model.add_country_holidays(country_name=params["country_holidays"])
if params["monthly_seasonality"]:
self.model.add_seasonality(name='monthly', period=30.5, fourier_order=5)
with suppress_stdout_stderr():
self.model.fit(X[['ds', 'y']])
print(f'{datetime.now()} General Model Fitted')
self.top_groups = None
if len(tgc_wo_time) > 0:
if self.top_n > 0:
top_n_grp = X.groupby(tgc_wo_time).size().sort_values().reset_index()[tgc_wo_time].iloc[-self.top_n:].values
self.top_groups = [
'_'.join(map(str, key))
for key in top_n_grp
]
if self.top_groups:
self.grp_models = {}
self.priors = {}
# Prepare for multi processing
num_tasks = len(self.top_groups)
def processor(out, res):
out[res[0]] = res[1]
pool_to_use = small_job_pool
loggerinfo(logger, f"Prophet will use {n_jobs} workers for fitting.")
loggerinfo(logger, "Prophet parameters holidays {} / monthly {}".format(self.country_holidays, self.monthly_seasonality))
pool = pool_to_use(
logger=None, processor=processor,
num_tasks=num_tasks, max_workers=n_jobs
)
#
# Fit 1 FB Prophet model per time group columns
nb_groups = len(X_groups)
# Put y back to its unscaled value for top groups
X['y'] = X['y_orig']
for _i_g, (key, X) in enumerate(X_groups):
# Just log where we are in the fitting process
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(logger, "FB Prophet : %d%% of groups fitted" % (100 * (_i_g + 1) // nb_groups))
X_path = os.path.join(tmp_folder, "fbprophet_X" + str(uuid.uuid4()))
X = X.reset_index(drop=True)
save_obj(X, X_path)
grp_hash = self.get_hash(key)
if grp_hash not in self.top_groups:
continue
self.priors[grp_hash] = X['y'].mean()
params = {
"country_holidays": self.country_holidays,
"monthly_seasonality": self.monthly_seasonality
}
args = (X_path, grp_hash, tmp_folder, params)
kwargs = {}
pool.submit_tryget(None, MyParallelProphetTransformer_fit_async,
args=args, kwargs=kwargs, out=self.grp_models)
pool.finish()
for k, v in self.grp_models.items():
self.grp_models[k] = load_obj(v) if v is not None else None
remove(v)
self._clean_tmp_folder(logger, tmp_folder)
return self
def transform(self, X: dt.Frame, **kwargs):
"""
Uses fitted models (1 per time group) to predict the target
:param X: Datatable Frame containing the features
:return: FB Prophet predictions
"""
# Get the logger if it exists
logger = self.get_experiment_logger()
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
# Reduce X to TGC
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
# Change date feature name to match Prophet requirements
X = self.convert_to_prophet(X)
y_predictions = self.predict_with_average_model(X, tgc_wo_time)
y_predictions.columns = ['average_pred']
# Go through groups
for grp_col in tgc_wo_time:
# Get the unique dates to be predicted
X_groups = X[['ds', grp_col]].groupby(grp_col)
# Go though the groups and predict only top
XX_paths = []
model_paths = []
def processor(out, res):
out.append(res)
num_tasks = len(X_groups)
pool_to_use = small_job_pool
pool = pool_to_use(logger=None,
processor=processor,
num_tasks=num_tasks,
max_workers=n_jobs)
for _i_g, (key, X_grp) in enumerate(X_groups):
# Just log where we are in the fitting process
if (_i_g + 1) % max(1, num_tasks // 20) == 0:
loggerinfo(
logger, "FB Prophet : %d%% of groups predicted" %
(100 * (_i_g + 1) // num_tasks))
# Create dict key to store the min max scaler
grp_hash = self.get_hash(key)
X_path = os.path.join(tmp_folder,
"fbprophet_Xt" + str(uuid.uuid4()))
if grp_hash not in self.grp_models[grp_col]:
# unseen groups
XX = pd.DataFrame(np.full((X_grp.shape[0], 1), np.nan),
columns=['yhat'])
XX.index = X_grp.index
save_obj(XX, X_path)
XX_paths.append(X_path)
continue
if self.grp_models[grp_col][grp_hash] is None:
# known groups but not enough train data
XX = pd.DataFrame(np.full((X_grp.shape[0], 1), np.nan),
columns=['yhat'])
XX.index = X_grp.index
save_obj(XX, X_path)
XX_paths.append(X_path)
continue
model = self.grp_models[grp_col][grp_hash]
model_path = os.path.join(
tmp_folder, "fbprophet_modelt" + str(uuid.uuid4()))
save_obj(model, model_path)
save_obj(X_grp, X_path)
model_paths.append(model_path)
args = (model_path, X_path, self.priors[grp_col][grp_hash],
tmp_folder)
kwargs = {}
pool.submit_tryget(
None,
MyProphetOnSingleGroupsTransformer_transform_async,
args=args,
kwargs=kwargs,
out=XX_paths)
pool.finish()
y_predictions[f'{grp_col}_pred'] = pd.concat(
(load_obj(XX_path) for XX_path in XX_paths),
axis=0).sort_index()
for p in XX_paths + model_paths:
remove(p)
# Now we can invert scale
# But first get rid of NaNs
for grp_col in tgc_wo_time:
# Add time group to the predictions, will be used to invert scaling
y_predictions[grp_col] = X[grp_col]
# Fill NaN
y_predictions[f'{grp_col}_pred'] = y_predictions[
f'{grp_col}_pred'].fillna(y_predictions['average_pred'])
# Go through groups and recover the scaled target for knowed groups
if len(tgc_wo_time) > 0:
X_groups = y_predictions.groupby(tgc_wo_time)
else:
X_groups = [([None], y_predictions)]
for _f in [f'{grp_col}_pred'
for grp_col in tgc_wo_time] + ['average_pred']:
inverted_ys = []
for key, X_grp in X_groups:
grp_hash = self.get_hash(key)
# Scale target for current group
if grp_hash in self.scalers.keys():
inverted_y = self.scalers[grp_hash].inverse_transform(
X_grp[[_f]])
else:
inverted_y = self.general_scaler.inverse_transform(
X_grp[[_f]])
# Put back in a DataFrame to keep track of original index
inverted_df = pd.DataFrame(inverted_y, columns=[_f])
inverted_df.index = X_grp.index
inverted_ys.append(inverted_df)
y_predictions[_f] = pd.concat(tuple(inverted_ys),
axis=0).sort_index()[_f]
self._clean_tmp_folder(logger, tmp_folder)
y_predictions.drop(tgc_wo_time, axis=1, inplace=True)
self._output_feature_names = [
f'{self.display_name}_{_f}' for _f in y_predictions
]
self._feature_desc = [
f'{self.display_name}_{_f}' for _f in y_predictions
]
return y_predictions
def fit(self,
X,
y,
sample_weight=None,
eval_set=None,
sample_weight_eval_set=None,
**kwargs):
# Get TGC and time column
self.tgc = self.params_base.get('tgc', None)
self.time_column = self.params_base.get('time_column', None)
self.nan_value = np.mean(y)
self.cap = np.max(
y
) * 1.5 # TODO Don't like this we should compute a cap from average yearly growth
self.prior = np.mean(y)
if self.time_column is None:
self.time_column = self.tgc[0]
# Get the logger if it exists
logger = None
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir)
loggerinfo(
logger,
"Start Fitting Prophet Model with params : {}".format(self.params))
try:
# Add value of prophet_top_n in recipe_dict variable inside of config.toml file
# eg1: recipe_dict="{'prophet_top_n': 200}"
# eg2: recipe_dict="{'prophet_top_n':10}"
self.top_n = config.recipe_dict['prophet_top_n']
except KeyError:
self.top_n = 50
loggerinfo(
logger,
f"Prophet will use {self.top_n} groups as well as average target data."
)
# Get temporary folders for multi process communication
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
# Reduce X to TGC
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
X = X[:, self.tgc].to_pandas()
# Fill NaNs or None
X = X.replace([None, np.nan], 0)
# Add target, Label encoder is only used for Classif. which we don't support...
if self.labels is not None:
y = LabelEncoder().fit(self.labels).transform(y)
X['y'] = np.array(y)
self.nan_value = X['y'].mean()
# Change date feature name to match Prophet requirements
X.rename(columns={self.time_column: "ds"}, inplace=True)
# Create a general scale now that will be used for unknown groups at prediction time
# Can we do smarter than that ?
general_scaler = MinMaxScaler().fit(
X[['y', 'ds']].groupby('ds').median().values)
# Go through groups and standard scale them
if len(tgc_wo_time) > 0:
X_groups = X.groupby(tgc_wo_time)
else:
X_groups = [([None], X)]
scalers = {}
scaled_ys = []
print('Number of groups : ', len(X_groups))
for g in tgc_wo_time:
print(f'Number of groups in {g} groups : {X[g].unique().shape}')
for key, X_grp in X_groups:
# Create dict key to store the min max scaler
grp_hash = self.get_hash(key)
# Scale target for current group
scalers[grp_hash] = MinMaxScaler()
y_skl = scalers[grp_hash].fit_transform(X_grp[['y']].values)
# Put back in a DataFrame to keep track of original index
y_skl_df = pd.DataFrame(y_skl, columns=['y'])
y_skl_df.index = X_grp.index
scaled_ys.append(y_skl_df)
# Set target back in original frame but keep original
X['y_orig'] = X['y']
X['y'] = pd.concat(tuple(scaled_ys), axis=0)
# Now Average groups
X_avg = X[['ds', 'y']].groupby('ds').mean().reset_index()
# Send that to Prophet
mod = importlib.import_module('fbprophet')
Prophet = getattr(mod, "Prophet")
nrows = X[['ds', 'y']].shape[0]
n_changepoints = max(1, int(nrows * (2 / 3)))
if n_changepoints < 25:
model = Prophet(yearly_seasonality=True,
weekly_seasonality=True,
daily_seasonality=True,
n_changepoints=n_changepoints)
else:
model = Prophet(yearly_seasonality=True,
weekly_seasonality=True,
daily_seasonality=True)
if self.params["country_holidays"] is not None:
model.add_country_holidays(
country_name=self.params["country_holidays"])
if self.params["monthly_seasonality"]:
model.add_seasonality(
name='monthly',
period=30.5,
fourier_order=self.params["monthly_seasonality"])
if self.params["quarterly_seasonality"]:
model.add_seasonality(
name='quarterly',
period=92,
fourier_order=self.params["quarterly_seasonality"])
with suppress_stdout_stderr():
model.fit(X[['ds', 'y']])
top_groups = None
if len(tgc_wo_time) > 0:
if self.top_n > 0:
top_n_grp = X.groupby(tgc_wo_time).size().sort_values(
).reset_index()[tgc_wo_time].iloc[-self.top_n:].values
top_groups = ['_'.join(map(str, key)) for key in top_n_grp]
grp_models = {}
priors = {}
if top_groups:
# Prepare for multi processing
num_tasks = len(top_groups)
def processor(out, res):
out[res[0]] = res[1]
pool_to_use = small_job_pool
loggerinfo(logger,
f"Prophet will use {n_jobs} workers for fitting.")
pool = pool_to_use(logger=None,
processor=processor,
num_tasks=num_tasks,
max_workers=n_jobs)
#
# Fit 1 FB Prophet model per time group columns
nb_groups = len(X_groups)
# Put y back to its unscaled value for top groups
X['y'] = X['y_orig']
for _i_g, (key, X) in enumerate(X_groups):
# Just log where we are in the fitting process
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(
logger, "FB Prophet : %d%% of groups fitted" %
(100 * (_i_g + 1) // nb_groups))
X_path = os.path.join(tmp_folder,
"fbprophet_X" + str(uuid.uuid4()))
X = X.reset_index(drop=True)
save_obj(X, X_path)
grp_hash = self.get_hash(key)
if grp_hash not in top_groups:
continue
priors[grp_hash] = X['y'].mean()
args = (X_path, grp_hash, tmp_folder, self.params, self.cap)
kwargs = {}
pool.submit_tryget(None,
MyParallelProphetTransformer_fit_async,
args=args,
kwargs=kwargs,
out=grp_models)
pool.finish()
for k, v in grp_models.items():
grp_models[k] = load_obj(v) if v is not None else None
remove(v)
self._clean_tmp_folder(logger, tmp_folder)
self.set_model_properties(
model={
'avg': model,
'group': grp_models,
'priors': priors,
'topgroups': top_groups,
'skl': scalers,
'gen_scaler': general_scaler
},
features=self.tgc, # Prophet uses time and timegroups
importances=np.ones(len(self.tgc)),
iterations=-1 # Does not have iterations
)
return None
def fit(self, X: dt.Frame, y: np.array = None, **kwargs):
"""
Fits FB Prophet models (1 per time group) using historical target values contained in y
Model fitting is distributed over a pool of processes and uses file storage to share the data with workers
:param X: Datatable frame containing the features
:param y: numpy array containing the historical values of the target
:return: self
"""
# Get the logger if it exists
logger = self.get_experiment_logger()
loggerinfo(
logger,
f"Prophet will use individual groups as well as average target data."
)
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
# Reduce X to TGC
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
X = self.convert_to_prophet(X)
# Add target, Label encoder is only used for Classif. which we don't support...
if self.labels is not None:
y = LabelEncoder().fit(self.labels).transform(y)
X['y'] = np.array(y)
self.prior_value = X['y'].mean()
self.general_scaler = self.fit_scaler_to_median_target(X)
X = self.scale_target_for_each_time_group(X, tgc_wo_time)
self.avg_model = self.fit_prophet_model_on_average_target(X)
# Go through individual time group columns and create avg models
self.grp_models = {}
self.priors = {}
for grp_col in tgc_wo_time:
self.grp_models[grp_col] = {}
self.priors[grp_col] = {}
X_groups = X[['ds', 'y', grp_col]].groupby(grp_col)
nb_groups = len(X_groups)
def processor(out, res):
out[res[0]] = res[1]
pool_to_use = small_job_pool
loggerinfo(logger,
f"Prophet will use {n_jobs} workers for fitting.")
loggerinfo(
logger, "Prophet parameters holidays {} / monthly {}".format(
self.country_holidays, self.monthly_seasonality))
pool = pool_to_use(logger=None,
processor=processor,
num_tasks=nb_groups,
max_workers=n_jobs)
for _i_g, (key, X_grp) in enumerate(X_groups):
# Just log where we are in the fitting process
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(
logger, "FB Prophet : %d%% of groups fitted" %
(100 * (_i_g + 1) // nb_groups))
X_path = os.path.join(tmp_folder,
"fbprophet_X" + str(uuid.uuid4()))
# Save target average for current group
grp_hash = self.get_hash(key)
self.priors[grp_col][grp_hash] = X_grp['y'].mean()
# Average by date
X_grp_avg = X_grp.groupby('ds')['y'].mean().reset_index()
save_obj(X_grp_avg, X_path)
params = {
"country_holidays": self.country_holidays,
"monthly_seasonality": self.monthly_seasonality
}
args = (X_path, grp_hash, tmp_folder, params)
kwargs = {}
pool.submit_tryget(
None,
MyProphetOnSingleGroupsTransformer_fit_async,
args=args,
kwargs=kwargs,
out=self.grp_models[grp_col])
pool.finish()
for k, v in self.grp_models[grp_col].items():
self.grp_models[grp_col][k] = load_obj(
v) if v is not None else None
remove(v)
self._clean_tmp_folder(logger, tmp_folder)
return self
def transform(self, X: dt.Frame, **kwargs):
"""
Uses fitted models (1 per time group) to predict the target
:param X: Datatable Frame containing the features
:return: FB Prophet predictions
"""
# Get the logger if it exists
logger = None
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir)
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
XX = X[:, self.tgc].to_pandas()
XX = XX.replace([None, np.nan], 0)
XX.rename(columns={self.time_column: "ds"}, inplace=True)
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
assert len(XX_grp) > 0
num_tasks = len(XX_grp)
def processor(out, res):
out.append(res)
pool_to_use = small_job_pool
loggerinfo(logger,
"Prophet will use {} workers for transform".format(n_jobs))
pool = pool_to_use(logger=None,
processor=processor,
num_tasks=num_tasks,
max_workers=n_jobs)
XX_paths = []
model_paths = []
nb_groups = len(XX_grp)
print("Nb Groups = ", nb_groups)
for _i_g, (key, X) in enumerate(XX_grp):
# Log where we are in the transformation of the dataset
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(
logger, "FB Prophet : %d%% of groups transformed" %
(100 * (_i_g + 1) // nb_groups))
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
X_path = os.path.join(tmp_folder,
"fbprophet_Xt" + str(uuid.uuid4()))
# Commented for performance, uncomment for debug
# print("prophet - transforming data of shape: %s for group: %s" % (str(X.shape), grp_hash))
if grp_hash in self.models:
model = self.models[grp_hash]
model_path = os.path.join(
tmp_folder, "fbprophet_modelt" + str(uuid.uuid4()))
save_obj(model, model_path)
save_obj(X, X_path)
model_paths.append(model_path)
args = (model_path, X_path, self.priors[grp_hash], tmp_folder)
kwargs = {}
pool.submit_tryget(
None,
MyParallelProphetTransformer_transform_async,
args=args,
kwargs=kwargs,
out=XX_paths)
else:
XX = pd.DataFrame(np.full((X.shape[0], 1), self.nan_value),
columns=['yhat']) # unseen groups
XX.index = X.index
save_obj(XX, X_path)
XX_paths.append(X_path)
pool.finish()
XX = pd.concat((load_obj(XX_path) for XX_path in XX_paths),
axis=0).sort_index()
for p in XX_paths + model_paths:
remove(p)
self._clean_tmp_folder(logger, tmp_folder)
return XX
def fit(self, X: dt.Frame, y: np.array = None, **kwargs):
"""
Fits FB Prophet models (1 per time group) using historical target values contained in y
Model fitting is distributed over a pool of processes and uses file storage to share the data with workers
:param X: Datatable frame containing the features
:param y: numpy array containing the historical values of the target
:return: self
"""
# Get the logger if it exists
logger = None
if self.context and self.context.experiment_id:
logger = make_experiment_logger(
experiment_id=self.context.experiment_id,
tmp_dir=self.context.tmp_dir,
experiment_tmp_dir=self.context.experiment_tmp_dir)
tmp_folder = self._create_tmp_folder(logger)
n_jobs = self._get_n_jobs(logger, **kwargs)
# Convert to pandas
XX = X[:, self.tgc].to_pandas()
XX = XX.replace([None, np.nan], 0)
XX.rename(columns={self.time_column: "ds"}, inplace=True)
# Make sure labales are numeric
if self.labels is not None:
y = LabelEncoder().fit(self.labels).transform(y)
XX['y'] = np.array(y)
# Set target prior
self.nan_value = np.mean(y)
# Group the input by TGC (Time group column) excluding the time column itself
tgc_wo_time = list(np.setdiff1d(self.tgc, self.time_column))
if len(tgc_wo_time) > 0:
XX_grp = XX.groupby(tgc_wo_time)
else:
XX_grp = [([None], XX)]
self.models = {}
self.priors = {}
# Prepare for multi processing
num_tasks = len(XX_grp)
def processor(out, res):
out[res[0]] = res[1]
pool_to_use = small_job_pool
loggerinfo(logger,
"Prophet will use {} workers for fitting".format(n_jobs))
loggerinfo(
logger, "Prophet parameters holidays {} / monthly {}".format(
self.country_holidays, self.monthly_seasonality))
pool = pool_to_use(logger=None,
processor=processor,
num_tasks=num_tasks,
max_workers=n_jobs)
# Fit 1 FB Prophet model per time group columns
nb_groups = len(XX_grp)
for _i_g, (key, X) in enumerate(XX_grp):
# Just log where we are in the fitting process
if (_i_g + 1) % max(1, nb_groups // 20) == 0:
loggerinfo(
logger, "FB Prophet : %d%% of groups fitted" %
(100 * (_i_g + 1) // nb_groups))
X_path = os.path.join(tmp_folder,
"fbprophet_X" + str(uuid.uuid4()))
X = X.reset_index(drop=True)
save_obj(X, X_path)
key = key if isinstance(key, list) else [key]
grp_hash = '_'.join(map(str, key))
self.priors[grp_hash] = X['y'].mean()
params = {
"country_holidays": self.country_holidays,
"monthly_seasonality": self.monthly_seasonality
}
args = (X_path, grp_hash, tmp_folder, params)
kwargs = {}
pool.submit_tryget(None,
MyParallelProphetTransformer_fit_async,
args=args,
kwargs=kwargs,
out=self.models)
pool.finish()
for k, v in self.models.items():
self.models[k] = load_obj(v) if v is not None else None
remove(v)
self._clean_tmp_folder(logger, tmp_folder)
return self