def test_forward_selection(self, mocker, max_predictors: int):
# create list of elements [var1_enc, var2_c, ..., var10_enc]
predictors_list = [f"var{i+1}_enc" for i in range(10)]
# extract sublist [var1_enc, var5_enc, var9_enc]:
forced_predictors = predictors_list[::4]
# remove these from predictors list to have clean version
predictors = [
pred for pred in predictors_list if pred not in forced_predictors
]
ordered_output_list = forced_predictors + predictors
def mock_find_next_best_model(self, train_data, target_column_name,
candidate_predictors,
current_predictors):
return mock_model(current_predictors + candidate_predictors[0:1])
mocker.patch(("cobra.model_building.ForwardFeatureSelection."
"_find_next_best_model"), mock_find_next_best_model)
fw_selection = ForwardFeatureSelection(max_predictors=max_predictors)
fitted_models = (fw_selection._forward_selection(
pd.DataFrame(), "target", predictors, forced_predictors))
actual = [sorted(model.predictors) for model in fitted_models]
expected = [
sorted(ordered_output_list[:i + 1])
for i in range(min(max_predictors, len(predictors_list)))
]
assert actual == expected
def test_fit(self, mocker, max_predictors: int, expectation):
# create list of elements [var1_enc, var2_c, ..., var10_enc]
predictors_list = [f"var{i+1}_enc" for i in range(10)]
# extract sublist [var1_enc, var5_enc, var9_enc]:
forced_predictors_list = predictors_list[::4]
ordered_output_list = (forced_predictors_list + [
pred
for pred in predictors_list if pred not in forced_predictors_list
])
fw_selection = ForwardFeatureSelection(max_predictors=max_predictors)
def mock_train_model(self, train_data, target_column_name, predictors):
return mock_model(predictors)
def mock_forward_selection(self, train_data, target_column_name,
predictors, forced_predictors):
n_models = min(max_predictors,
len(predictors) + len(forced_predictors))
return [
mock_model(ordered_output_list[:i + 1])
for i in range(n_models)
]
(mocker.patch(
"cobra.model_building.ForwardFeatureSelection._train_model",
mock_train_model))
mocker.patch(("cobra.model_building.ForwardFeatureSelection"
"._forward_selection"), mock_forward_selection)
with expectation:
fw_selection.fit(pd.DataFrame(),
"target",
predictors=predictors_list,
forced_predictors=forced_predictors_list,
excluded_predictors=[])
# for each fitted model, check number of predictors
actual = [
model.predictors for model in fw_selection._fitted_models
]
expected = [
ordered_output_list[:i + 1]
for i in range(min(max_predictors, len(predictors_list)))
]
if max_predictors == len(forced_predictors_list):
expected = [forced_predictors_list]
assert actual == expected
def test_compute_model_performances(self, mocker, model_type):
data = mock_data(add_split_col=True, model_type=model_type)
fw_selection = ForwardFeatureSelection(model_type=model_type)
fw_selection._fitted_models = [
mock_model_num_pred(1, model_type=model_type),
mock_model_num_pred(2, model_type=model_type),
mock_model_num_pred(3, model_type=model_type)
]
def mock_evaluate(self, X, y, split, metric): # on AUC scale, but gives the same for RMSE as it is a mock
if split == "train":
return 0.612
else:
return 0.609
if model_type == "classification":
patch_fct = "cobra.model_building.forward_selection.LogisticRegressionModel.evaluate"
elif model_type == "regression":
patch_fct = "cobra.model_building.forward_selection.LinearRegressionModel.evaluate"
mocker.patch(patch_fct, mock_evaluate)
actual = (fw_selection
.compute_model_performances(data, "target",
splits=["train", "selection"],
metric=None))
expected = pd.DataFrame([
{"predictors": ["var1_enc"],
"last_added_predictor": "var1_enc",
"train_performance": 0.612, "selection_performance": 0.609,
"model_type": model_type},
{"predictors": ["var1_enc", "var2_enc"],
"last_added_predictor": "var2_enc",
"train_performance": 0.612, "selection_performance": 0.609,
"model_type": model_type},
{"predictors": ["var1_enc", "var2_enc", "var3_enc"],
"last_added_predictor": "var3_enc",
"train_performance": 0.612, "selection_performance": 0.609,
"model_type": model_type}
])
pd.testing.assert_frame_equal(actual, expected)
def test_compute_model_performances(self, mocker):
data = mock_data(add_split_col=True)
fw_selection = ForwardFeatureSelection()
fw_selection._fitted_models = [
mock_model_num_pred(1),
mock_model_num_pred(2),
mock_model_num_pred(3)
]
def mock_evaluate(self, X, y, split):
if split == "train":
return 0.612
else:
return 0.609
(mocker.patch(("cobra.model_building.forward_selection"
".MLModel.evaluate"), mock_evaluate))
actual = (fw_selection.compute_model_performances(
data, "target", splits=["train", "selection"]))
expected = pd.DataFrame([{
"predictors": ["var1_enc"],
"last_added_predictor": "var1_enc",
"train_performance": 0.612,
"selection_performance": 0.609
}, {
"predictors": ["var1_enc", "var2_enc"],
"last_added_predictor": "var2_enc",
"train_performance": 0.612,
"selection_performance": 0.609
}, {
"predictors": ["var1_enc", "var2_enc", "var3_enc"],
"last_added_predictor":
"var3_enc",
"train_performance":
0.612,
"selection_performance":
0.609
}])
pd.testing.assert_frame_equal(actual, expected)
def test_ffs_train_data_assertions(self, model_type):
fw_selection = ForwardFeatureSelection(model_type=model_type)
with pytest.raises(AssertionError): # no split column
fw_selection.fit(pd.DataFrame(), "target", predictors=[""])
df = mock_data(add_split_col=True, model_type=model_type)
with pytest.raises(AssertionError): # not at least train & selection sets
fw_selection.fit(df[df["split"] == "train"], "target", predictors=[""])
def test_get_model_from_step(self):
forward_selection = ForwardFeatureSelection()
with pytest.raises(ValueError):
forward_selection.get_model_from_step(2)