def recursive_feature_elimination(config_learning, config_data, number_features):
output = open(os.path.expanduser(config_data.get("Learner", "models")) + "/" + "feature_ranks.txt", "w")
feature_names = FeatureExtractor.get_combinations_from_config_file_unsorted(config_data)
x_train = read_features_file(config_learning.get('x_train'), '\t')
y_train = read_reference_file(config_learning.get('y_train'), '\t')
x_test = read_features_file(config_learning.get('x_test'), '\t')
estimator, scorers = learn_model.set_learning_method(config_learning, x_train, y_train)
scale = config_learning.get("scale", True)
if scale:
x_train, x_test = scale_datasets(x_train, x_test)
rfe = RFE(estimator, number_features, step=1)
rfe.fit(x_train, y_train)
for i, name in enumerate(feature_names):
output.write(name + "\t" + str(rfe.ranking_[i]) + "\n")
print(name + "\t" + str(rfe.ranking_[i]))
predictions = rfe.predict(x_test)
output.close()
return predictions
def train_model(cfg, model_path):
x_train = read_features_file(cfg.get('x_train'), '\t')
y_train = read_reference_file(cfg.get('y_train'), '\t')
x_test = read_features_file(cfg.get('x_test'), '\t')
scale = cfg.get("scale", True)
if scale:
x_train, x_test = scale_datasets(x_train, x_test)
estimator, scorers = learn_model.set_learning_method(cfg, x_train, y_train)
estimator.fit(x_train, y_train)
joblib.dump(estimator, model_path)
def train_save(config_learning, config_data):
learning_config = config_learning.get("learning", None)
method_name = learning_config.get("method", None)
x_train = read_features_file(config_learning.get('x_train'), '\t')
y_train = read_reference_file(config_learning.get('y_train'), '\t')
x_test = read_features_file(config_learning.get('x_test'), '\t')
scale = config_learning.get("scale", True)
if scale:
x_train, x_test = scale_datasets(x_train, x_test)
estimator, scorers = learn_model.set_learning_method(config_learning, x_train, y_train)
estimator.fit(x_train, y_train)
joblib.dump(estimator, os.path.expanduser(config_data.get('Learner', 'models')) + '/' + method_name + '.pkl')
def recursive_feature_elimination_cv(config_learning, config_data):
output = open(os.path.expanduser(config_data.get("Learner", "models")) + "/" + "feature_ranks.txt", "w")
feature_names = FeatureExtractor.get_features_from_config_file_unsorted(config_data)
combination_methods = FeatureExtractor.get_combinations_from_config_file_unsorted(config_data)
x_train = read_features_file(config_learning.get('x_train'), '\t')
y_train = read_reference_file(config_learning.get('y_train'), '\t')
x_test = read_features_file(config_learning.get('x_test'), '\t')
estimator, scorers = learn_model.set_learning_method(config_learning, x_train, y_train)
scale = config_learning.get("scale", True)
if scale:
x_train, x_test = scale_datasets(x_train, x_test)
rfecv = RFECV(estimator=estimator, step=1, cv=StratifiedKFold(y_train, 2), scoring='accuracy')
rfecv.fit(x_train, y_train)
feature_list = []
for i, feature_name in enumerate(feature_names):
if combination_methods[i] == 'both':
feature_list.append(feature_name)
feature_list.append(feature_name)
else:
feature_list.append(feature_name)
for i, name in enumerate(feature_list):
output.write(name + "\t" + str(rfecv.ranking_[i]) + "\n")
output.close()
predictions = rfecv.predict(x_test)
return predictions
