Add predict_proba Support to PegasosQSVC and NeuralNetworkClassifier (#871)

OkuyanBoga · FrancescaSchiav · oscar-wallis · web-flow · commit 94ccb0a70ab4 · 2024-12-09T11:21:39.000+02:00
* Adding a predict_proba function to classifiers. (#57) * Update README.md * Predict proba for NNC and PegQSVC * Rewriting predict proba features and docstring It was very inefficient before and didn't have the validation checks needed. The code is now more clear and docstring has been added. * Tweak documentation for NNC and PegasosQSVC, silence lint E1101 on torch connector * Update test with `QNN.predict_proba` * Update test with `PegasosESVC.predict_proba` * Added a release note and solved conflicts with main --------- Co-authored-by: FrancescaSchiav <FrancescaSchiav@users.noreply.github.com> Co-authored-by: oscar-wallis <108736468+oscar-wallis@users.noreply.github.com> Co-authored-by: Edoardo Altamura <38359901+edoaltamura@users.noreply.github.com> Co-authored-by: smens <88490989+smens@users.noreply.github.com> * Reformatted docs * Fix usage of sklearn --------- Co-authored-by: FrancescaSchiav <FrancescaSchiav@users.noreply.github.com> Co-authored-by: oscar-wallis <108736468+oscar-wallis@users.noreply.github.com> Co-authored-by: Edoardo Altamura <38359901+edoaltamura@users.noreply.github.com> Co-authored-by: smens <88490989+smens@users.noreply.github.com>
diff --git a/qiskit_machine_learning/algorithms/classifiers/neural_network_classifier.py b/qiskit_machine_learning/algorithms/classifiers/neural_network_classifier.py
@@ -140,23 +140,76 @@ def _create_objective(self, X: np.ndarray, y: np.ndarray) -> ObjectiveFunction:
         return function
 
     def predict(self, X: np.ndarray) -> np.ndarray:
-        self._check_fitted()
+        """
+        Perform classification on samples in X.
+
+        Args:
+            X (np.ndarray): Input features. For a callable kernel (an instance of
+                :class:`~qiskit_machine_learning.kernels.BaseKernel`), the shape
+                should be ``(m_samples, n_features)``. For a pre-computed kernel, the shape should be
+                ``(m_samples, n_samples)``. Here, ``m_*`` denotes the set to be
+                predicted, and ``n_*`` denotes the size of the training set.
+                In the case of a pre-computed kernel, the kernel values in ``X`` must be calculated
+                with respect to the elements of the set to be predicted and the training set.
+
+        Returns:
+            np.ndarray: An array of shape ``(n_samples,)``, representing the predicted class labels for
+                each sample in ``X``.
 
+        Raises:
+            QiskitMachineLearningError:
+                - If the :meth:`predict` method is called before the model has been fit.
+            ValueError:
+                - If the pre-computed kernel matrix has the wrong shape and/or dimension.
+        """
+        self._check_fitted()
         X, _ = self._validate_input(X)
 
         if self._neural_network.output_shape == (1,):
-            predict = np.sign(self._neural_network.forward(X, self._fit_result.x))
+            # Binary classification
+            raw_output = self._neural_network.forward(X, self._fit_result.x)
+            predict = np.sign(raw_output)
         else:
+            # Multi-class classification
             forward = self._neural_network.forward(X, self._fit_result.x)
             predict_ = np.argmax(forward, axis=1)
+
             if self._one_hot:
+                # Convert class indices to one-hot encoded format
                 predict = np.zeros(forward.shape)
                 for i, v in enumerate(predict_):
                     predict[i, v] = 1
             else:
                 predict = predict_
+
         return self._validate_output(predict)
 
+    def predict_proba(self, X: np.ndarray) -> np.ndarray:
+        """
+        Extracts the predicted probabilities for each class based on the output of a neural
+        network.
+
+        Args:
+            X (np.ndarray): Input features. For a callable kernel (an instance of
+                :class:`~qiskit_machine_learning.kernels.BaseKernel`), the shape
+                should be ``(m_samples, n_features)``. For a pre-computed kernel, the shape should be
+                ``(m_samples, n_samples)``. Here, ``m_*`` denotes the set to be
+                predicted, and ``n_*`` denotes the size of the training set. In the case of a
+                pre-computed kernel, the kernel values in ``X`` must be calculated with respect to
+                the elements of the set to be predicted and the training set.
+
+        Returns:
+            np.ndarray: An array of shape ``(n_samples, n_classes)`` representing the predicted class
+                probabilities (in the range :math:`[0, 1]`) for each sample in ``X``.
+        """
+        self._check_fitted()
+        X, _ = self._validate_input(X)
+
+        # Assumes an activation function is applied within the forward method
+        proba = self._neural_network.forward(X, self._fit_result.x)
+
+        return proba
+
     def score(self, X: np.ndarray, y: np.ndarray, sample_weight: np.ndarray | None = None) -> float:
         return ClassifierMixin.score(self, X, y, sample_weight)
 
diff --git a/qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py b/qiskit_machine_learning/algorithms/classifiers/pegasos_qsvc.py
@@ -203,7 +203,7 @@ def fit(
 
         self.fit_status_ = PegasosQSVC.FITTED
 
-        logger.debug("fit completed after %s", str(datetime.now() - t_0)[:-7])
+        logger.debug("Fit completed after %s", str(datetime.now() - t_0)[:-7])
 
         return self
 
@@ -213,33 +213,62 @@ def predict(self, X: np.ndarray) -> np.ndarray:
         Perform classification on samples in X.
 
         Args:
-            X: Features. For a callable kernel (an instance of
-               :class:`~qiskit_machine_learning.kernels.BaseKernel`) the shape
-               should be ``(m_samples, n_features)``, for a precomputed kernel the shape should be
-               ``(m_samples, n_samples)``. Where ``m`` denotes the set to be predicted and ``n`` the
-               size of the training set. In that case, the kernel values in X have to be calculated
-               with respect to the elements of the set to be predicted and the training set.
+            X (np.ndarray): Input features. For a callable kernel (an instance of
+                :class:`~qiskit_machine_learning.kernels.BaseKernel`), the shape
+                should be ``(m_samples, n_features)``. For a pre-computed kernel, the shape should be
+                ``(m_samples, n_samples)``. Here, ``m_*`` denotes the set to be
+                predicted, and ``n_*`` denotes the size of the training set. In the case of a
+                pre-computed kernel, the kernel values in ``X`` must be calculated with respect to
+                the elements of the set to be predicted and the training set.
 
         Returns:
-            An array of the shape (n_samples), the predicted class labels for samples in X.
+            np.ndarray: An array of shape ``(n_samples,)``, representing the predicted class labels for
+                each sample in ``X``.
 
         Raises:
             QiskitMachineLearningError:
-                - predict is called before the model has been fit.
+                - If the :meth:`predict` method is called before the model has been fit.
             ValueError:
-                - Pre-computed kernel matrix has the wrong shape and/or dimension.
+                - If the pre-computed kernel matrix has the wrong shape and/or dimension.
         """
 
         t_0 = datetime.now()
         values = self.decision_function(X)
         y = np.array([self._label_pos if val > 0 else self._label_neg for val in values])
-        logger.debug("prediction completed after %s", str(datetime.now() - t_0)[:-7])
+        logger.debug("Prediction completed after %s", str(datetime.now() - t_0)[:-7])
 
         return y
 
+    def predict_proba(self, X: np.ndarray) -> np.ndarray:
+        """
+        Extract class prediction probabilities. The decision function values are
+        not bounded in the range :math:`[0, 1]`. Therefore, these values are
+        converted into probabilities using the sigmoid activation
+        function, which maps the real-valued outputs to the :math:`[0, 1]` range.
+
+        Args:
+            X (np.ndarray): Input features. For a callable kernel (an instance of
+                :class:`~qiskit_machine_learning.kernels.BaseKernel`), the shape
+                should be ``(m_samples, n_features)``. For a pre-computed kernel, the shape should be
+                ``(m_samples, n_samples)``. Here, ``m_*`` denotes the set to be
+                predicted, and ``n_*`` denotes the size of the training set. In the case of a
+                pre-computed kernel, the kernel values in ``X`` must be calculated with respect to
+                the elements of the set to be predicted and the training set.
+
+        Returns:
+            np.ndarray: An array of shape ``(n_samples, 2)``, representing the predicted class
+                probabilities (in the range :math:`[0, 1]`) for each sample in ``X``.
+        """
+        values = self.decision_function(X)
+
+        probabilities = 1 / (1 + np.exp(-values))  # Sigmoid activation function
+        probabilities = np.dstack((1 - probabilities, probabilities))[0]
+
+        return probabilities
+
     def decision_function(self, X: np.ndarray) -> np.ndarray:
         """
-        Evaluate the decision function for the samples in X.
+        Evaluate the decision function for the samples in ``X``.
 
         Args:
             X: Features. For a callable kernel (an instance of
@@ -259,7 +288,7 @@ def decision_function(self, X: np.ndarray) -> np.ndarray:
                 - Pre-computed kernel matrix has the wrong shape and/or dimension.
         """
         if self.fit_status_ == PegasosQSVC.UNFITTED:
-            raise QiskitMachineLearningError("The PegasosQSVC has to be fit first")
+            raise QiskitMachineLearningError("The PegasosQSVC has to be fit first.")
         if np.ndim(X) != 2:
             raise ValueError("X has to be a 2D array")
         if self._precomputed and self._n_samples != X.shape[1]:
diff --git a/releasenotes/notes/feature-predict-proba-function-for-classifiers-a752c5154a7c988f.yaml b/releasenotes/notes/feature-predict-proba-function-for-classifiers-a752c5154a7c988f.yaml
@@ -0,0 +1,5 @@
+features:
+  - |
+    The :class:`~qiskit_machine_learning.algorithms.PegasosQSVC` and algorithms derived
+    from :class:`~qiskit_machine_learning.algorithms.NeuralNetworkClassifier` module now support `predict_proba` function.
+    This method can be utilized similarly to other `scikit-learn`-based algorithms. 
diff --git a/test/algorithms/classifiers/test_neural_network_classifier.py b/test/algorithms/classifiers/test_neural_network_classifier.py
@@ -160,10 +160,58 @@ def parity(x):
         return qnn, num_inputs, ansatz.num_parameters
 
     def _generate_data(self, num_inputs: int) -> tuple[np.ndarray, np.ndarray]:
-        # construct data
+        """
+        Generates synthetic data consisting of randomly generated features and binary labels.
+        Each label is determined based on the sum of the corresponding feature values. If the sum of
+        the feature values for a sample is less than or equal to 1, the label is 1. Otherwise, the
+        label is 0.
+
+        Args:
+            num_inputs (int): The number of features for each sample.
+
+        Returns:
+            tuple[np.ndarray, np.ndarray]: A tuple containing two numpy arrays:
+                - features: An array of shape ``(6, num_inputs)`` with randomly generated feature values.
+                - labels: An array of shape ``(6,)`` with binary labels for each sample.
+        """
+        # Fixed number of samples for consistency
+        num_samples = 6
+
+        features = algorithm_globals.random.random((num_samples, num_inputs))
+
+        # Assign binary labels based on feature sums
+        labels = (np.sum(features, axis=1) <= 1).astype(float)
+
+        return features, labels
+
+    def _generate_data_multiclass(self, num_inputs: int) -> tuple[np.ndarray, np.ndarray]:
+        """
+        Generates synthetic data consisting of randomly generated features and 3 categorical labels.
+        Each label is determined based on the sum of the corresponding feature values, assigned
+        as follows:
+            - Label 0.0 if the sum of features <= 0.5.
+            - Label 1.0 if 0.5 < sum of features <= 1.0.
+            - Label 2.0 if sum of features > 1.0.
+
+        Args:
+            num_inputs (int): The number of features for each sample.
+
+        Returns:
+            tuple[np.ndarray, np.ndarray]: A tuple containing two numpy arrays:
+                - features: An array of shape ``(6, num_inputs)`` with randomly generated feature values.
+                - labels: An array of shape ``(6,)`` with categorical labels (0, 1, or 2) for each
+                    sample.
+        """
+        # Fixed number of samples for consistency
         num_samples = 6
+
         features = algorithm_globals.random.random((num_samples, num_inputs))
-        labels = 1.0 * (np.sum(features, axis=1) <= 1)
+
+        # Assign categorical labels based on feature sums
+        sums = np.sum(features, axis=1)
+        labels = np.full_like(sums, 2.0)
+        labels[sums <= 0.5] = 0.0
+        labels[(sums > 0.5) & (sums <= 1.0)] = 1.0
 
         return features, labels
 
@@ -247,8 +295,13 @@ def test_classifier_with_sampler_qnn_and_cross_entropy(self, opt):
         (False, "squared_error"),
     )
     def test_categorical_data(self, config):
-        """Test categorical labels using QNN"""
+        """
+        Tests categorical labels using the QNN classifier with categorical labels.
 
+        Args:
+            config (tuple): Configuration tuple containing whether to use one-hot
+                encoding and the loss function.
+        """
         one_hot, loss = config
 
         optimizer = L_BFGS_B(maxiter=5)
@@ -259,20 +312,29 @@ def test_categorical_data(self, config):
 
         features, labels = self._generate_data(num_inputs)
         labels = labels.astype(str)
-        # convert to categorical
+
+        # Convert to categorical labels
         labels[labels == "0.0"] = "A"
         labels[labels == "1.0"] = "B"
 
-        # fit to data
+        # Fit classifier to the data
         classifier.fit(features, labels)
 
-        # score
+        # Evaluate the classifier
         score = classifier.score(features, labels)
         self.assertGreater(score, 0.5)
 
+        # Predict a single sample
         predict = classifier.predict(features[0, :])
         self.assertIn(predict, ["A", "B"])
 
+        # Test predict_proba method
+        probas = classifier.predict_proba(features)
+        self.assertEqual(probas.shape, (6, 2))
+
+        for proba in probas:
+            self.assertAlmostEqual(np.sum(proba), 1.0, places=5)
+
     @idata(L1L2_ERRORS + ["cross_entropy"])
     def test_sparse_arrays(self, loss):
         """Tests classifier with sparse arrays as features and labels."""
@@ -375,7 +437,7 @@ def test_binary_classification_with_multiclass_data(self):
         """Test that trying to train a binary classifier with multiclass data raises an error."""
 
         optimizer = L_BFGS_B(maxiter=5)
-        qnn, num_inputs, num_parameters = self._create_sampler_qnn(output_shape=1)
+        qnn, _, num_parameters = self._create_sampler_qnn(output_shape=1)
         classifier = self._create_classifier(
             qnn,
             num_parameters,
@@ -385,11 +447,10 @@ def test_binary_classification_with_multiclass_data(self):
 
         # construct data
         num_samples = 3
-        x = algorithm_globals.random.random((num_samples, num_inputs))
-        y = np.asarray([0, 1, 2])
+        features, labels = self._generate_data_multiclass(num_samples)
 
         with self.assertRaises(QiskitMachineLearningError):
-            classifier.fit(x, y)
+            classifier.fit(features, labels)
 
     def test_bad_binary_shape(self):
         """Test that trying to train a binary classifier with misshaped data raises an error."""
@@ -435,6 +496,9 @@ def test_untrained(self):
         with self.assertRaises(QiskitMachineLearningError, msg="classifier.predict()"):
             classifier.predict(np.asarray([]))
 
+        with self.assertRaises(QiskitMachineLearningError, msg="classifier.predict_proba()"):
+            classifier.predict_proba(np.asarray([]))
+
         with self.assertRaises(QiskitMachineLearningError, msg="classifier.fit_result"):
             _ = classifier.fit_result
 
diff --git a/test/algorithms/classifiers/test_pegasos_qsvc.py b/test/algorithms/classifiers/test_pegasos_qsvc.py
@@ -70,15 +70,34 @@ def setUp(self):
         self.label_test_4d = label_4d[15:]
 
     def test_qsvc(self):
-        """Test PegasosQSVC"""
-        qkernel = FidelityQuantumKernel(feature_map=self.feature_map)
-
-        pegasos_qsvc = PegasosQSVC(quantum_kernel=qkernel, C=1000, num_steps=self.tau)
-
-        pegasos_qsvc.fit(self.sample_train, self.label_train)
-        score = pegasos_qsvc.score(self.sample_test, self.label_test)
-
-        self.assertEqual(score, 1.0)
+        """
+        Test the Pegasos QSVC algorithm.
+        """
+        quantum_kernel = FidelityQuantumKernel(feature_map=self.feature_map)
+        classifier = PegasosQSVC(quantum_kernel=quantum_kernel, C=1000, num_steps=self.tau)
+        classifier.fit(self.sample_train, self.label_train)
+
+        # Evaluate the model on the test data
+        test_score = classifier.score(self.sample_test, self.label_test)
+        self.assertEqual(test_score, 1.0)
+
+        # Expected predictions for the given test data
+        predicted_labels = classifier.predict(self.sample_test)
+        self.assertTrue(np.array_equal(predicted_labels, self.label_test))
+
+        # Test predict_proba method (normalization is imposed by definition)
+        probas = classifier.predict_proba(self.sample_test)
+        expected_probas = np.array(
+            [
+                [0.67722117, 0.32277883],
+                [0.35775209, 0.64224791],
+                [0.36540916, 0.63459084],
+                [0.64419096, 0.35580904],
+                [0.35864466, 0.64135534],
+            ]
+        )
+        self.assertEqual(probas.shape, (self.label_test.shape[0], 2))
+        np.testing.assert_array_almost_equal(probas, expected_probas, decimal=5)
 
     def test_decision_function(self):
         """Test PegasosQSVC."""
