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xarray_installed = True + +try: + import shap +except ImportError: + shap_installed = False +else: + shap_installed = True + + +def _check_imports(): + if not shap_installed: + raise ImportError( + "Shap is not installed. Please install it using `pip install shap` first." + ) + elif not xarray_installed: + raise ImportError( + "xarray is not installed. Please install it using `pip install xarray` first." + ) + + +class Explainer: + """Explainer class for returning shap values for each of the three hierarchical classifiers.""" + + def __init__(self, hierarchical_model, data=None, algorithm="auto", mode=""): + """ + Initialize the SHAP explainer for a hierarchical model. + + Parameters + ---------- + hierarchical_model : HierarchicalClassifier + The hierarchical classification model to explain. + data : array-like or None, default=None + The dataset used for creating the SHAP explainer. + algorithm : str, default="auto" + The algorithm to use for SHAP explainer. + mode : str, default="" + The mode of the SHAP explainer. Can be 'tree', 'gradient', 'deep', 'linear', or '' for default SHAP explainer. + """ + self.hierarchical_model = hierarchical_model + self.algorithm = algorithm + self.mode = mode + self.data = data + + _check_imports() + + if mode == "tree": + self.explainer = shap.TreeExplainer + elif mode == "gradient": + self.explainer = shap.GradientExplainer + elif mode == "deep": + self.explainer = shap.DeepExplainer + elif mode == "linear": + self.explainer = shap.LinearExplainer + else: + self.explainer = shap.Explainer + + def explain(self, X): + """ + Generate SHAP values for each node in the hierarchy for the given data. + + Parameters + ---------- + X : array-like + Training data to fit the SHAP explainer. + + Returns + ------- + shap_values_dict : dict + A dictionary of SHAP values for each node. + """ + _check_imports() + if isinstance(self.hierarchical_model, LocalClassifierPerParentNode): + return self._explain_with_xr(X) + elif isinstance(self.hierarchical_model, LocalClassifierPerLevel): + return self._explain_lcpl(X) + elif isinstance(self.hierarchical_model, LocalClassifierPerNode): + return self._explain_lcpn(X) + else: + raise ValueError(f"Invalid model: {self.hierarchical_model}.") + + def _explain_with_dict(self, X): + """ + Generate SHAP values for each node using Local Classifier Per Parent Node (LCPPN) strategy. + + Parameters + ---------- + X : array-like + Sample data for which to generate SHAP values. + + traverse_prediction : True or False + If True, restricts calculation of shap values to only traversed hierarchy as predicted by hiclass model. + + Returns + ------- + shap_values_dict : dict + A dictionary of SHAP values for each node. + """ + shap_values_dict = {} + traversed_nodes = self._get_traversed_nodes(X) + for node in traversed_nodes: + local_classifier = self.hierarchical_model.hierarchy_.nodes[node][ + "classifier" + ] + + # Create explainer with train data + local_explainer = deepcopy(self.explainer)(local_classifier, self.data) + shap_values = np.array(local_explainer.shap_values(X)) + + if len(shap_values.shape) < 3: + shap_values = shap_values.reshape( + 1, shap_values.shape[0], shap_values.shape[1] + ) + + shap_values_dict[node] = shap_values + + for node in self.hierarchical_model.hierarchy_.nodes: + if node not in traversed_nodes: + local_classifier = self.hierarchical_model.hierarchy_.nodes[node] + if len(local_classifier) != 0: + shap_val = np.full( + ( + len(local_classifier["classifier"].classes_), + X.shape[0], + X.shape[1], + ), + np.nan, + ) + shap_values_dict[node] = shap_val + return shap_values_dict + + def _explain_with_xr(self, X): + """ + Generate SHAP values for each node using Local Classifier Per Parent Node (LCPPN) strategy. + + Parameters + ---------- + X : array-like + Sample data for which to generate SHAP values. + + Returns + ------- + shap_values_dict : dict + A dictionary of SHAP values for each node. + """ + explanations = [] + for sample in X: + explanation = self._calculate_shap_values(sample.reshape(1, -1)) + explanations.append(explanation) + return explanations + + def _explain_lcpn(self, X): + shap_values_dict = {} + for node in self.hierarchical_model.hierarchy_.nodes: + if node == self.hierarchical_model.root_: + continue + + if isinstance( + self.hierarchical_model.hierarchy_.nodes[node]["classifier"], + ConstantClassifier.ConstantClassifier, + ): + continue + + local_classifier = self.hierarchical_model.hierarchy_.nodes[node][ + "classifier" + ] + + local_explainer = deepcopy(self.explainer)(local_classifier, self.data) + + # Calculate SHAP values for the given sample X + shap_values = np.array(local_explainer.shap_values(X)) + shap_values_dict[node] = shap_values + + return shap_values_dict + + def _explain_lcpl(self, X): + """ + Generate SHAP values for each node using Local Classifier Per Level (LCPL) strategy. + + Parameters + ---------- + X : array-like + Sample data for which to generate SHAP values. + + Returns + ------- + shap_values_dict : dict + A dictionary of SHAP values for each node. + """ + shap_values_dict = {} + start_level = 1 + if len(self.hierarchical_model.local_classifiers_[start_level]) == 1: + start_level = 2 + + for level in range( + start_level, len(self.hierarchical_model.local_classifiers_) + ): + local_classifier = self.hierarchical_model.local_classifiers_[level] + local_explainer = deepcopy(self.explainer)(local_classifier, self.data) + + # Calculate SHAP values for the given sample X + shap_values = np.array(local_explainer.shap_values(X)) + shap_values_dict[level] = shap_values + + return shap_values_dict + + def _get_traversed_nodes(self, samples): + # Helper function to return traversed nodes + if isinstance(self.hierarchical_model, LocalClassifierPerParentNode): + traversals = [] + start_node = self.hierarchical_model.root_ + for x in samples: + current = start_node + traversal_order = [] + while self.hierarchical_model.hierarchy_.neighbors(current): + if ( + "classifier" + not in self.hierarchical_model.hierarchy_.nodes[current] + ): + break # Break if reached leaf node + traversal_order.append(current) + successor = self.hierarchical_model.hierarchy_.nodes[current][ + "classifier" + ].predict(x.reshape(1, -1))[0] + current = successor + traversals.append(traversal_order) + return traversals + elif isinstance(self.hierarchical_model, LocalClassifierPerNode): + pass + elif isinstance(self.hierarchical_model, LocalClassifierPerLevel): + pass + + def _calculate_shap_values(self, X): + if not xarray_installed: + raise ImportError( + "xarray is not installed. Please install it using `pip install xarray` before using " + "this method." + ) + traversed_nodes = self._get_traversed_nodes(X)[0] + datasets = [] + for node in traversed_nodes: + local_classifier = self.hierarchical_model.hierarchy_.nodes[node][ + "classifier" + ] + + # Create a SHAP explainer for the local classifier + local_explainer = deepcopy(self.explainer)(local_classifier, self.data) + + # Calculate SHAP values for the given sample X + shap_values = np.array( + local_explainer.shap_values(X, check_additivity=False) + ) + if len(shap_values.shape) < 3: + shap_values = shap_values.reshape( + 1, shap_values.shape[0], shap_values.shape[1] + ) + + predict_proba = xr.DataArray( + local_classifier.predict_proba(X)[0], + dims=["class"], + coords={ + "class": local_classifier.classes_, + }, + ) + classes = xr.DataArray( + local_classifier.classes_, + dims=["class"], + coords={"class": local_classifier.classes_}, + ) + + shap_val_local = xr.DataArray( + shap_values, + dims=["class", "sample", "feature"], + ) + + local_dataset = xr.Dataset( + { + "node": node.split(self.hierarchical_model.separator_)[-1], + "predicted_class": local_classifier.predict(X), + "predict_proba": predict_proba, + "classes": classes, + "shap_values": shap_val_local, + } + ) + datasets.append(local_dataset) + return datasets diff --git a/hiclass/LocalClassifierPerParentNode.py b/hiclass/LocalClassifierPerParentNode.py index 50a30ca0..e7755a23 100644 --- a/hiclass/LocalClassifierPerParentNode.py +++ b/hiclass/LocalClassifierPerParentNode.py @@ -224,3 +224,44 @@ def _fit_digraph(self, local_mode: bool = False, use_joblib: bool = False): self.logger_.info("Fitting local classifiers") nodes = self._get_parents() self._fit_node_classifier(nodes, local_mode, use_joblib) + + def get_predict_proba(self, X): + """ + Prediction probabilities for each class for the given data. + + Parameters + ---------- + X : {array-like, sparse matrix} of shape (n_samples, n_features) + The input samples. Internally, its dtype will be converted + to ``dtype=np.float32``. If a sparse matrix is provided, it will be + converted into a sparse ``csr_matrix``. + Returns + ------- + prediction_probabilities : dict or list of dicts if X contains multiple samples. + Each dict contains the node as its key and prediction probabilities for + the predicted classes as value. + """ + prediction_probabilities = [] + for sample in X: + predict_proba_dict = {} + y_pred = self.predict(sample.reshape(1, -1)) + traversal_path = str(y_pred[0][0]) + for pred in y_pred[0][1:]: + traversal_path = traversal_path + self.separator_ + pred + + for i in range(self.max_levels_)[:-1]: + node = self.separator_.join( + traversal_path.split(self.separator_)[: i + 1] + ) + + local_classifier = self.hierarchy_.nodes[node]["classifier"] + pred_probabilities = local_classifier.predict_proba( + sample.reshape(1, -1) + ) + predict_proba_dict[node] = pred_probabilities + prediction_probabilities.append(predict_proba_dict) + + if len(prediction_probabilities) == 1: + return prediction_probabilities[0] + + return prediction_probabilities diff --git a/hiclass/__init__.py b/hiclass/__init__.py index 09370436..ec3db00e 100644 --- a/hiclass/__init__.py +++ b/hiclass/__init__.py @@ -1,5 +1,7 @@ """Init module for the library.""" +import os +from ._version import get_versions from .LocalClassifierPerLevel import LocalClassifierPerLevel from .LocalClassifierPerNode import LocalClassifierPerNode from .LocalClassifierPerParentNode import LocalClassifierPerParentNode @@ -7,6 +9,7 @@ from .MultiLabelLocalClassifierPerParentNode import ( MultiLabelLocalClassifierPerParentNode, ) +from .Explainer import Explainer from ._version import get_versions __version__ = get_versions()["version"] @@ -16,6 +19,7 @@ "LocalClassifierPerNode", "LocalClassifierPerParentNode", "LocalClassifierPerLevel", + "Explainer", "MultiLabelLocalClassifierPerNode", "MultiLabelLocalClassifierPerParentNode", ] diff --git a/tests/test_Explainer.py b/tests/test_Explainer.py new file mode 100644 index 00000000..ef1ea0da --- /dev/null +++ b/tests/test_Explainer.py @@ -0,0 +1,153 @@ +import numpy as np +import pytest +from sklearn.ensemble import RandomForestClassifier +from hiclass import ( + LocalClassifierPerParentNode, + LocalClassifierPerNode, + LocalClassifierPerLevel, + Explainer, +) + +try: + import shap +except ImportError: + shap_installed = False +else: + shap_installed = True + +classifiers = [ + LocalClassifierPerLevel, + LocalClassifierPerParentNode, + LocalClassifierPerNode, +] + + +# TODO : Add parametrized tests + + +@pytest.mark.skipif(not shap_installed, reason="shap not installed") +@pytest.fixture +def explainer_data(): + np.random.seed(42) + x_train = np.random.randn(4, 3) + y_train = np.array( + [["a", "b", "d"], ["a", "b", "e"], ["a", "c", "f"], ["a", "c", "g"]] + ) + x_test = np.random.randn(3, 3) + + return x_train, x_test, y_train + + +@pytest.mark.skipif(not shap_installed, reason="shap not installed") +def test_explainer_tree(explainer_data): + rfc = RandomForestClassifier() + lcppn = LocalClassifierPerParentNode( + local_classifier=rfc, replace_classifiers=False + ) + + x_train, x_test, y_train = explainer_data + + lcppn.fit(x_train, y_train) + + explainer = Explainer(lcppn, data=x_train, mode="tree") + shap_dict = explainer.explain(x_test) + assert shap_dict is not None + + # for key, val in shap_dict.items(): + # # Assert on shapes of shap values, must match (target_classes, num_samples, num_features) + # model = lcppn.hierarchy_.nodes[key]["classifier"] + # assert shap_dict[key].shape == ( + # len(model.classes_), + # x_test.shape[0], + # x_test.shape[1], + # ) + + +@pytest.mark.skipif(not shap_installed, reason="shap not installed") +def test_explainer_tree_traversal(explainer_data): + rfc = RandomForestClassifier() + lcppn = LocalClassifierPerParentNode( + local_classifier=rfc, replace_classifiers=False + ) + + x_train, x_test, y_train = explainer_data + + lcppn.fit(x_train, y_train) + + explainer = Explainer(lcppn, data=x_train, mode="tree") + shap_dict = explainer.explain(x_test) + assert shap_dict is not None + # + # for key, val in shap_dict.items(): + # # Assert on shapes of shap values, must match (target_classes, num_samples, num_features) + # model = lcppn.hierarchy_.nodes[key]["classifier"] + # assert shap_dict[key].shape == ( + # len(model.classes_), + # x_test.shape[0], + # x_test.shape[1], + # ) + + +@pytest.fixture +def explainer_data_no_root(): + x_train = np.random.randn(6, 3) + y_train = np.array( + [ + ["a", "b", "c"], + ["x", "y", "z"], + ["a", "b", "c"], + ["x", "y", "z"], + ["a", "b", "c"], + ["x", "y", "z"], + ] + ) + x_test = np.random.randn(1, 3) + return x_train, x_test, y_train + + +@pytest.mark.skipif(not shap_installed, reason="shap not installed") +def test_explainer_tree_no_root(explainer_data_no_root): + rfc = RandomForestClassifier() + lcppn = LocalClassifierPerParentNode( + local_classifier=rfc, replace_classifiers=False + ) + + x_train, x_test, y_train = explainer_data_no_root + + lcppn.fit(x_train, y_train) + + lcppn.predict(x_test) + explainer = Explainer(lcppn, data=x_train, mode="tree") + shap_dict = explainer.explain(x_test) + assert shap_dict is not None + + # for key, val in shap_dict.items(): + # # Assert on shapes of shap values, must match (target_classes, num_samples, num_features) + # model = lcppn.hierarchy_.nodes[key]["classifier"] + # assert shap_dict[key].shape == ( + # len(model.classes_), + # x_test.shape[0], + # x_test.shape[1], + # ) + + +@pytest.mark.skipif(not shap_installed, reason="shap not installed") +@pytest.mark.parametrize("data", ["explainer_data", "explainer_data_no_root"]) +def test_traversal_path(data, request): + x_train, x_test, y_train = request.getfixturevalue(data) + rfc = RandomForestClassifier() + lcppn = LocalClassifierPerParentNode( + local_classifier=rfc, replace_classifiers=False + ) + + lcppn.fit(x_train, y_train) + explainer = Explainer(lcppn, data=x_train, mode="tree") + traversals = explainer._get_traversed_nodes(x_test) + preds = lcppn.predict(x_test) + assert len(preds) == len(traversals) + for i in range(len(x_test)): + for j in range(len(traversals[i])): + if traversals[i][j] == lcppn.root_: + continue + label = traversals[i][j].split("::HiClass::Separator::")[-1] + assert label == preds[i][j - 1] diff --git a/tests/test_LocalClassifierPerLevel.py b/tests/test_LocalClassifierPerLevel.py index 27312f85..144d6d1f 100644 --- a/tests/test_LocalClassifierPerLevel.py +++ b/tests/test_LocalClassifierPerLevel.py @@ -7,9 +7,11 @@ from scipy.sparse import csr_matrix from sklearn.exceptions import NotFittedError from sklearn.linear_model import LogisticRegression +from sklearn.ensemble import RandomForestClassifier from sklearn.utils.estimator_checks import parametrize_with_checks from sklearn.utils.validation import check_is_fitted from hiclass import LocalClassifierPerLevel +from hiclass.Explainer import Explainer @parametrize_with_checks([LocalClassifierPerLevel()]) diff --git a/tests/test_LocalClassifierPerNode.py b/tests/test_LocalClassifierPerNode.py index 670c9823..cd134c10 100644 --- a/tests/test_LocalClassifierPerNode.py +++ b/tests/test_LocalClassifierPerNode.py @@ -7,12 +7,16 @@ from scipy.sparse import csr_matrix from sklearn.exceptions import NotFittedError from sklearn.linear_model import LogisticRegression +from sklearn.ensemble import RandomForestClassifier from sklearn.utils.estimator_checks import parametrize_with_checks from sklearn.utils.validation import check_is_fitted from hiclass import LocalClassifierPerNode + from hiclass.BinaryPolicy import ExclusivePolicy +from hiclass.Explainer import Explainer + @parametrize_with_checks([LocalClassifierPerNode()]) def test_sklearn_compatible_estimator(estimator, check): diff --git a/tests/test_LocalClassifierPerParentNode.py b/tests/test_LocalClassifierPerParentNode.py index 922a03a3..81b38556 100644 --- a/tests/test_LocalClassifierPerParentNode.py +++ b/tests/test_LocalClassifierPerParentNode.py @@ -10,7 +10,7 @@ from sklearn.linear_model import LogisticRegression from sklearn.utils.estimator_checks import parametrize_with_checks from sklearn.utils.validation import check_is_fitted - +from sklearn.ensemble import RandomForestClassifier from hiclass import LocalClassifierPerParentNode @@ -184,3 +184,26 @@ def test_fit_predict(): lcppn.fit(x, y) predictions = lcppn.predict(x) assert_array_equal(y, predictions) + + +def test_predict_proba(): + rfc = RandomForestClassifier() + lcppn = LocalClassifierPerParentNode( + local_classifier=rfc, replace_classifiers=False + ) + + x_train = np.random.randn(4, 3) + y_train = np.array( + [ + ["a", "b", "d", "k"], + ["a", "b", "e", "l"], + ["a", "c", "f", "k"], + ["a", "c", "g", "l"], + ] + ) + x_test = np.random.randn(1, 3) + + lcppn.fit(x_train, y_train) + + pred_proba_dict = lcppn.get_predict_proba(x_test) + assert pred_proba_dict is not None