def save_model(self, model, sub_dir='model', name='model', seed=None):
model_dir = self._get_dir(sub_dir)
create_path(model_dir, merge=True)
model_file = os.path.join(model_dir,
'{}.pkl'.format(name) if seed is None
else '{}_{}.pkl'.format(name, seed))
joblib.dump(model, model_file)
def save_predictions_as_pickle(self, predictions, sub_dir='prediction',
name='prediction', seed=None):
output_dir = self._get_prediction_output_dir(sub_dir)
create_path(output_dir, merge=True)
predict_file = os.path.join(output_dir,
'{}.pickle'.format(name) if seed is None
else '{}_{}.pickle'.format(name, seed))
pickle.dump(predictions.astype(np.float32), predict_file)
def save_json(self, data, sub_dir='json', name='json_file', seed=None):
json_dir = self._get_dir(sub_dir)
create_path(json_dir, merge=True)
json_file = os.path.join(json_dir,
'{}.json'.format(name) if seed is None
else '{}_{}.json'.format(name, seed))
with open(json_file, 'w') as wf:
json.dump(data, wf)
def save_predictions_as_npy(self, predictions, sub_dir='prediction',
name='prediction', seed=None):
output_dir = self._get_prediction_output_dir(sub_dir)
create_path(output_dir, merge=True)
predict_file = os.path.join(output_dir,
'{}.npy'.format(name) if seed is None
else '{}_{}.npy'.format(name, seed))
np.save(predict_file, predictions)
def save_featurizer_as_dataframe(self, output_df, name='featurizer',
save_type='pickle.gz'):
featurizer_dir = self._get_featurizer_output_dir()
create_path(featurizer_dir, merge=True)
featurizer_file = os.path.join(
featurizer_dir, '{}.{}'.format(name, save_type))
if save_type == 'csv':
output_df.to_csv(featurizer_file)
elif save_type.startswith('pickle'):
output_df.to_pickle(featurizer_file)
def save_predictions_as_txt(self, predictions, sub_dir='prediction',
name='prediction', seed=None):
output_dir = self._get_prediction_output_dir(sub_dir)
create_path(output_dir, merge=True)
predict_file = os.path.join(output_dir,
'{}.txt'.format(name) if seed is None
else '{}_{}.txt'.format(name, seed))
with open(predict_file, 'w') as wf:
wf.write("\n".join(list(map(str, predictions))))
def save_predictions_as_dataframe(self, predictions, subdir='prediction',
name='prediction', seed=None):
predict_dir = self._get_prediction_output_dir(subdir)
create_path(predict_dir, merge=True)
predict_file = os.path.join(predict_dir,
'{}.csv'.format(name) if seed is None
else '{}_{}.csv'.format(name, seed))
predict_df = pd.DataFrame(predictions,
columns=['target', 'predict']
if isinstance(predictions[0], np.ndarray)
else ['predict'])
predict_df.to_csv(predict_file)
def _prepare_paths(self, output_path=None, auto_rename=False):
timestamp = time.time()
pid = os.getpid()
if output_path == 'tmp' or output_path == 'default':
output_path = \
'/tmp/amlearn/task_%d/output_%d' % (pid, int(timestamp))
self.output_path_ = output_path
if output_path is not None:
if auto_rename and os.path.exists(self.output_path_):
self.output_path_ = auto_rename_file(self.output_path_)
create_path(self.output_path_,
overwrite=self.overwrite_path, merge=self.merge_path)
self.output_path_created_ = True
def _fit_cv(self,
X,
y,
random_state=None,
scoring=None,
cv_num=1,
cv_params=None,
val_size=0.3,
save_model=False,
save_score=True,
save_prediction=False,
prediction_types='dataframe',
save_feature_importances=True,
save_train_val_idx=False,
**fit_params):
# If user's cv_params contains 'cv_num' parameter, use the max value
# between function parameter 'cv_num' and cv_params's 'cv_num'.
if not self.imblearn:
self.backend.logger.info('Start Cross Validation.')
cv_start_time = time.time()
if cv_params is None:
cv_params = {}
if 'cv_num' in cv_params.keys():
cv_num = max(cv_num, cv_params['cv_num'])
cv_params.pop('cv_num')
if 'scoring' in cv_params.keys():
cv_params.pop('scoring')
return_train_score = cv_params.get('return_train_score', True)
if cv_num > 1:
np.random.seed(random_state)
classifier_params = \
appropriate_kwargs(fit_params, self.classifier.fit)
results, scorers = \
cross_validate(estimator=self.classifier, scoring=scoring,
fit_params=classifier_params, X=X, y=y,
cv=cv_num, **cv_params)
else:
results, scorers = self._fit(X,
y,
self.classifier,
val_size=val_size,
return_train_score=return_train_score,
random_state=random_state,
scoring=scoring,
**fit_params)
cv_num = 1
# TODO: now if scoring is more than one, score_name only can be the first of them.
self.score_name = self.score_name if hasattr(self, 'score_name') \
else list(scorers.keys())[0]
self.best_score_, (self.best_model_, self.best_model_tag_)= \
max(zip(results['test_{}'.format(self.score_name)],
zip(results['estimators'],
[''] if cv_num == 1 else
["cv_{}".format(i) for i in range(cv_num)])),
key=lambda x: x[0])
if not self.imblearn:
self.backend.logger.info(
"\tCV classification finish in {:.4f} seconds.".format(
time.time() - cv_start_time))
if save_model or save_score or save_train_val_idx or save_prediction \
or save_feature_importances:
imblearn_output_path = \
os.path.join(self.backend.output_path, self.imblearn_tag)
create_path(imblearn_output_path)
if save_score:
write_file(
os.path.join(imblearn_output_path, 'mean_scores.txt'),
'{}\n{}\n{}'.format(
','.join(['dataset'] + list(scorers.keys())),
','.join(['test'] + [
str(np.mean(results['test_{}'.format(score_name)]))
for score_name in scorers.keys()
]), ','.join(['train'] + [
str(np.mean(results['train_{}'.format(
score_name)]))
for score_name in scorers.keys()
]) if return_train_score else -1))
check_path_while_saving(self.backend.output_path)
for cv_idx in range(cv_num):
sub_path = os.path.join(self.imblearn_tag,
"cv_{}".format(cv_idx))
cv_output_path = \
os.path.join(self.backend.output_path, sub_path)
create_path(cv_output_path)
if save_score:
write_file(
os.path.join(cv_output_path, 'scores.txt'),
'{}\n{}\n{}'.format(
','.join(['dataset'] + list(scorers.keys())),
','.join(['test'] + [
str(results['test_{}'.format(score_name)]
[cv_idx]) for score_name in scorers.keys()
]), ','.join(['train'] + [
str(results['train_{}'.format(score_name)]
[cv_idx]) for score_name in scorers.keys()
]) if return_train_score else -1))
score_model = results['estimators'][cv_idx]
if save_model:
self.backend.save_model(score_model, sub_path)
if save_feature_importances:
self.backend.save_json(
self.feature_importances_dict(score_model),
sub_path,
name='feature_importances')
if save_train_val_idx:
train_idx = results['indices'][cv_idx][0]
val_idx = results['indices'][cv_idx][1]
write_file(os.path.join(cv_output_path, 'train_idx.txt'),
"\n".join(list(map(str, train_idx))))
write_file(os.path.join(cv_output_path, 'val_idx.txt'),
"\n".join(list(map(str, val_idx))))
if save_prediction:
if 'X_val' in fit_params.keys(
) and 'y_val' in fit_params.keys():
test_X = fit_params['X_val']
test_y = fit_params['y_val']
else:
test_X = X[results['indices'][cv_idx][1]] \
if isinstance(X, np.ndarray) \
else X.iloc[results['indices'][cv_idx][1]]
test_y = y[results['indices'][cv_idx][1]] \
if isinstance(y, np.ndarray) \
else y.iloc[results['indices'][cv_idx][1]]
if hasattr(score_model, 'predict_proba'):
predictions = score_model.predict_proba(test_X)
elif hasattr(score_model, 'decision_function'):
predictions = score_model.decision_function(test_X)
else:
predictions = score_model.predict(test_X)
targets_and_predictions = \
np.array(list(zip(test_y, predictions[:, 1])))
if not isinstance(prediction_types, list_like()):
prediction_types = [prediction_types]
for predict_type in prediction_types:
if predict_type in self.backend.valid_predictions_type:
getattr(
self.backend,
'save_predictions_as_{}'.format(predict_type))(
targets_and_predictions, sub_path)
else:
raise ValueError(
'predict_type {} is unknown, '
'Possible values are {}'.format(
predict_type,
self.backend.valid_predictions_type))
return results, scorers
def _fit_cv(self, X, y, val_size=0.3, random_state=None, scoring=None,
cv_num=1, cv_params=None, save_train_val_idx=True,
save_model=True, save_score=True, save_prediction=True,
prediction_types='dataframe', save_feature_importances=True,
**fit_params):
# If user's cv_params contains 'cv_num' parameter, use the max value
# between function parameter 'cv_num' and cv_params's 'cv_num'.
self.backend.logger.info('Start Cross Validation.')
cv_start_time = time.time()
if cv_params is None:
cv_params = {}
if 'cv_num' in cv_params.keys():
cv_num = max(cv_num, cv_params['cv_num'])
cv_params.pop('cv_num')
if 'scoring' in cv_params.keys():
cv_params.pop('scoring')
return_train_score = cv_params.get('return_train_score', True)
if cv_num > 1:
if random_state is False:
pass
else:
np.random.seed(random_state)
results, scorers = \
cross_validate(estimator=self.regressor, scoring=scoring,
fit_params=fit_params, X=X, y=y, cv=cv_num,
**cv_params)
else:
results, scorers = self._fit(
X, y, self.regressor, val_size=val_size,
return_train_score=return_train_score,
random_state=random_state, scoring=scoring, **fit_params)
cv_num = 1
# TODO: now if scorers list length is more than 1, score_name only can
# be the first of them.
self.score_name = self.score_name if hasattr(self, 'score_name') \
else list(scorers.keys())[0]
self.best_score_, (self.best_model_, self.best_model_tag_)= \
max(zip(results['test_{}'.format(self.score_name)],
zip(results['estimators'],
[''] if cv_num == 1 else
["cv_{}".format(i) for i in range(cv_num)])),
key=lambda x: x[0])
self.backend.logger.info(
"\tCV regression finish in {:.4f} seconds.".format(
time.time() - cv_start_time))
if save_score:
write_file(
os.path.join(self.backend.output_path, 'mean_scores.txt'),
'{}\n{}\n{}'.format(
','.join(['dataset'] + list(scorers.keys())),
','.join(['test'] +
[str(np.mean(results['test_{}'.format(
score_name)]))
for score_name in scorers.keys()]),
','.join(['train'] +
[str(np.mean(results['train_{}'.format(
score_name)]))
for score_name in scorers.keys()])
if return_train_score else -1))
for cv_idx in range(cv_num):
cv_tag = "cv_{}".format(cv_idx)
cv_output_path = os.path.join(self.backend.output_path, cv_tag)
create_path(cv_output_path, merge=True)
if save_score:
write_file(os.path.join(cv_output_path, 'scores.txt'),
'{}\n{}\n{}'.format(
','.join(['dataset'] + list(scorers.keys())),
','.join(['test'] +
[str(results['test_{}'.format(
score_name)][cv_idx])
for score_name in scorers.keys()]),
','.join(['train'] +
[str(results['train_{}'.format(
score_name)][cv_idx])
for score_name in scorers.keys()])
if return_train_score else -1))
score_model = results['estimators'][cv_idx]
if save_model:
self.backend.save_model(score_model, cv_tag)
if save_feature_importances:
self.backend.save_json(
self.feature_importances_dict(score_model), cv_tag,
name='feature_importances')
if save_train_val_idx:
train_idx = results['indices'][cv_idx][0]
val_idx = results['indices'][cv_idx][1]
write_file(os.path.join(cv_output_path, 'train_idx.txt'),
"\n".join(list(map(str, train_idx))))
write_file(os.path.join(cv_output_path, 'val_idx.txt'),
"\n".join(list(map(str, val_idx))))
if save_prediction:
predictions = \
score_model.predict(X.iloc[results['indices'][cv_idx][1]])
targets_and_predictions = \
np.array(list(zip(y.iloc[results['indices'][cv_idx][1]],
predictions)))
if not isinstance(prediction_types, list_like()):
prediction_types = [prediction_types]
for predict_type in prediction_types:
if predict_type in self.backend.valid_predictions_type:
instance = getattr(self.backend,
'save_predictions_as_{}'.format(
predict_type))
instance(targets_and_predictions, cv_tag)
else:
raise ValueError(
'predict_type {} is unknown, '
'Possible values are {}'.format(
predict_type,
self.backend.valid_predictions_type))
return self