def test_experiment(self):
output_filename_header = FileLoader.create_output_file()
time.sleep(1)
loaded_algorithm_combinations = FileLoader.read_csv_file("../Datasets/test.csv")
file_path = "../Datasets/HIV_37_Samples/MergedDataset.csv"
loaded_data = FileLoader.load_file(file_path)
# feature_eliminator = SelectKBest(f_regression,k=k_value)
print (loaded_algorithm_combinations[0])
output_filename = FileLoader.create_output_file()
for i in range(0, 80):
normalizer = self.getnormalizer(loaded_algorithm_combinations[i][0])
feature_eliminator = self.getfeature_eliminator(loaded_algorithm_combinations[i][1])
the_model = self.get_model(loaded_algorithm_combinations[i][2])
print "taking ", type(normalizer).__name__, "and feature selector ", type(
feature_eliminator
).__name__, "model", type(the_model).__name__
FileLoader.write_model_in_file(
output_filename_header,
type(normalizer).__name__,
type(feature_eliminator).__name__,
type(the_model).__name__,
"",
"",
"",
"",
"",
)
the_data_manager = DataManager(feature_eliminator, normalizer=normalizer)
the_data_manager.set_data(loaded_data)
the_data_manager.split_data(test_split=0.15, train_split=0.70)
exp = Experiment(the_data_manager, the_model)
exp.run_experiment()
# arr_selected = feature_eliminator.get_support(indices=True)
# if(exp.get_r2(SplitTypes.Train) > 0 and exp.get_r2(SplitTypes.Valid) > 0 and exp.get_r2(SplitTypes.Test) > 0):
FileLoader.write_model_in_file(
output_filename,
type(normalizer).__name__,
type(feature_eliminator).__name__,
type(the_model).__name__,
"",
exp.fitness_matrix[0],
exp.get_r2(SplitTypes.Train),
exp.get_r2(SplitTypes.Valid),
exp.get_r2(SplitTypes.Test),
)
def test_experiment_not_transformed_test(self):
file_path = "../Datasets/HIV_37_Samples/MergedDataset.csv"
loaded_data = FileLoader.load_file(file_path)
data_manager = DataManager()
data_manager.set_data(loaded_data)
data_manager.split_data(test_split=0.19, train_split=0.62)
learning_model = FakePredictionModel()
exp = Experiment(data_manager, learning_model)
exp.run_experiment()
self.assertEquals(0, exp.get_r2(SplitTypes.Test))
def test_experiment_svm_svr_37dataset_r2_train(self):
file_path = "../Datasets/HIV_37_Samples/MergedDataset.csv"
loaded_data = FileLoader.load_file(file_path)
the_data_manager = DataManager()
the_data_manager.set_data(loaded_data)
the_data_manager.split_data(test_split=0.19, train_split=0.62)
the_model = svm.SVR()
exp = Experiment(the_data_manager, the_model)
exp.run_experiment()
r2_train = exp.get_r2(SplitTypes.Train)
expected_svm_r2_value = 0.93994377385638073
self.assertEqual(r2_train, expected_svm_r2_value)
def test_experiment_all_zeros_r2_1(self):
the_data_manager = DataManager()
array_all_zeroes = np.zeros((37, 397))
the_data_manager.set_data(array_all_zeroes)
the_data_manager.split_data(test_split=0.19, train_split=0.62)
the_model = svm.SVR()
exp = Experiment(the_data_manager, the_model)
exp.run_experiment()
r2_train = exp.get_r2(SplitTypes.Train)
expected = 1.0
self.assertEqual(r2_train, expected)
def test_experiment_svr_37dataset_r2_test(self):
file_path = "../Datasets/HIV_37_Samples/MergedDataset.csv"
loaded_data = FileLoader.load_file(file_path)
the_data_manager = DataManager()
the_data_manager.set_data(loaded_data)
the_data_manager.split_data(test_split=0.19, train_split=0.62)
the_model = svm.SVR()
exp = Experiment(the_data_manager, the_model)
exp.run_experiment()
r2_test = exp.get_r2(SplitTypes.Test)
expected_svm_r2_value = -0.33005242525900247
self.assertEqual(r2_test, expected_svm_r2_value)
type(the_model).__name__,
)
file_path = "../Datasets/HIV_37_Samples/MergedDataset.csv"
loaded_data = FileLoader.load_file(file_path)
# feature_eliminator = SelectKBest(f_regression,k=k_value)
the_data_manager = DataManager(feature_eliminator, normalizer=normalizer)
the_data_manager.set_data(loaded_data)
the_data_manager.split_data(test_split=0.15, train_split=0.70)
exp = Experiment(the_data_manager, the_model)
exp.run_experiment()
arr_selected = feature_eliminator.get_support(indices=True)
if (
exp.get_r2(SplitTypes.Train) > 0
and exp.get_r2(SplitTypes.Valid) > 0
and exp.get_r2(SplitTypes.Test) > 0
):
print(
feature_eliminator.get_support(indices=True),
type(normalizer).__name__,
type(feature_eliminator).__name__,
type(the_model).__name__,
"Fitness",
exp.fitness_matrix[0],
"Train",
exp.get_r2(SplitTypes.Train),
"Valid",
exp.get_r2(SplitTypes.Valid),
"Test",
