Python sklearn.metrics.pairwise.pairwise_kernels() Examples

def _intertext_score(full_text):
    '''returns tuple of scored sentences
       in order of appearance
       Note: Doing an A/B test to
       compare results, reverting to 
       original algorithm.'''

    sentences = sentence_tokenizer(full_text)
    norm = _normalize(sentences)
    similarity_matrix = pairwise_kernels(norm, metric='cosine')
    scores = _textrank(similarity_matrix)
    scored_sentences = []
    for i, s in enumerate(sentences):
        scored_sentences.append((scores[i],i,s))
    top_scorers = sorted(scored_sentences,
                         key=lambda tup: tup[0], 
                         reverse=True)
    return top_scorers 

def test_pairwise_kernels_callable():
    # Test the pairwise_kernels helper function
    # with a callable function, with given keywords.
    rng = np.random.RandomState(0)
    X = rng.random_sample((5, 4))
    Y = rng.random_sample((2, 4))

    metric = callable_rbf_kernel
    kwds = {'gamma': 0.1}
    K1 = pairwise_kernels(X, Y=Y, metric=metric, **kwds)
    K2 = rbf_kernel(X, Y=Y, **kwds)
    assert_array_almost_equal(K1, K2)

    # callable function, X=Y
    K1 = pairwise_kernels(X, Y=X, metric=metric, **kwds)
    K2 = rbf_kernel(X, Y=X, **kwds)
    assert_array_almost_equal(K1, K2) 

def test_pairwise_similarity_sparse_output(metric, pairwise_func):
    rng = np.random.RandomState(0)
    X = rng.random_sample((5, 4))
    Y = rng.random_sample((3, 4))
    Xcsr = csr_matrix(X)
    Ycsr = csr_matrix(Y)

    # should be sparse
    K1 = pairwise_func(Xcsr, Ycsr, dense_output=False)
    assert issparse(K1)

    # should be dense, and equal to K1
    K2 = pairwise_func(X, Y, dense_output=True)
    assert not issparse(K2)
    assert_array_almost_equal(K1.todense(), K2)

    # show the kernel output equal to the sparse.todense()
    K3 = pairwise_kernels(X, Y=Y, metric=metric)
    assert_array_almost_equal(K1.todense(), K3) 

def test_cosine_similarity():
    # Test the cosine_similarity.

    rng = np.random.RandomState(0)
    X = rng.random_sample((5, 4))
    Y = rng.random_sample((3, 4))
    Xcsr = csr_matrix(X)
    Ycsr = csr_matrix(Y)

    for X_, Y_ in ((X, None), (X, Y),
                   (Xcsr, None), (Xcsr, Ycsr)):
        # Test that the cosine is kernel is equal to a linear kernel when data
        # has been previously normalized by L2-norm.
        K1 = pairwise_kernels(X_, Y=Y_, metric="cosine")
        X_ = normalize(X_)
        if Y_ is not None:
            Y_ = normalize(Y_)
        K2 = pairwise_kernels(X_, Y=Y_, metric="linear")
        assert_array_almost_equal(K1, K2) 

def test_mmk():
    bags = [np.random.normal(size=(np.random.randint(10, 100), 10))
            for _ in range(20)]

    res = MeanMapKernel(gamma=2.38).fit_transform(bags)
    for i in range(20):
        for j in range(20):
            exp = pairwise_kernels(bags[j], bags[i], metric='rbf', gamma=2.38)
            assert_almost_equal(res[i, j], exp.mean(),
                                err_msg="({} to {})".format(i, j))

    res = MeanMapKernel(kernel='linear').fit(bags[:5]).transform(bags[-2:])
    for i in range(5):
        for j in range(18, 20):
            exp = pairwise_kernels(bags[j], bags[i], metric='linear')
            assert_almost_equal(res[j - 18, i], exp.mean(),
                                err_msg="({} to {})".format(i, j))

    # fails on wrong dimension
    assert_raises(
        ValueError,
        lambda:MeanMapKernel().fit(bags).transform([np.random.randn(20, 8)]))


################################################################################ 

def decision_function(self, X):
        """Decision function of the SVM.

        Parameters
        ----------
        X : array-like, shape (n_samples, n_features)
            The input data.

        Returns
        -------
        y : array-like, shape (n_samples,)
            The values of decision function.
        """
        X = check_array(X)
        if self.kernel == "linear":
            return self.intercept_ + np.dot(X, self.coef_)
        else:
            K = pairwise_kernels(X, self.support_vectors_, metric=self.kernel,
                                 **self.kernel_args)
            return (self.intercept_ + np.sum(self.dual_coef_[np.newaxis, :] *
                                             self.y * K, axis=1)) 

def _intertext_score(full_text):
    '''returns tuple of scored sentences
       in order of appearance
       Note: Doing an A/B test to
       compare results, reverting to 
       original algorithm.'''

    sentences = sentence_tokenizer(full_text)
    norm = _normalize(sentences)
    similarity_matrix = pairwise_kernels(norm, metric='cosine')
    scores = _textrank(similarity_matrix)
    scored_sentences = []
    for i, s in enumerate(sentences):
        scored_sentences.append((scores[i],i,s))
    top_scorers = sorted(scored_sentences,
                         key=lambda tup: tup[0], 
                         reverse=True)
    return top_scorers 

def get_pairwise_matrix(self, X, Y=None):
        """Calculates the pairwise similarity of atomic environments with
        scikit-learn, and the pairwise metric configured in the constructor.

        Args:
            X(np.ndarray): Feature vector for the atoms in structure A
            Y(np.ndarray): Feature vector for the atoms in structure B

        Returns:
            np.ndarray: NxM matrix of local similarities between structures A
                and B, with N and M atoms respectively.

        """
        if callable(self.metric):
            params = self.kernel_params or {}
        else:
            params = {"gamma": self.gamma,
                      "degree": self.degree,
                      "coef0": self.coef0}
        return pairwise_kernels(X, Y, metric=self.metric,
                                filter_params=True, **params) 

def _title_similarity_score(full_text, title):
    """Similarity scores for sentences with
       title in descending order"""

    sentences = sentence_tokenizer(full_text)
    norm = _normalize([title]+sentences)
    similarity_matrix = pairwise_kernels(norm, metric='cosine')
    return sorted(zip(
                     similarity_matrix[0,1:],
                     range(len(similarity_matrix)),
                     sentences
                     ),
                 key = lambda tup: tup[0],
                 reverse=True
                 ) 

def test_pairwise_kernels(metric):
    # Test the pairwise_kernels helper function.

    rng = np.random.RandomState(0)
    X = rng.random_sample((5, 4))
    Y = rng.random_sample((2, 4))
    function = PAIRWISE_KERNEL_FUNCTIONS[metric]
    # Test with Y=None
    K1 = pairwise_kernels(X, metric=metric)
    K2 = function(X)
    assert_array_almost_equal(K1, K2)
    # Test with Y=Y
    K1 = pairwise_kernels(X, Y=Y, metric=metric)
    K2 = function(X, Y=Y)
    assert_array_almost_equal(K1, K2)
    # Test with tuples as X and Y
    X_tuples = tuple([tuple([v for v in row]) for row in X])
    Y_tuples = tuple([tuple([v for v in row]) for row in Y])
    K2 = pairwise_kernels(X_tuples, Y_tuples, metric=metric)
    assert_array_almost_equal(K1, K2)

    # Test with sparse X and Y
    X_sparse = csr_matrix(X)
    Y_sparse = csr_matrix(Y)
    if metric in ["chi2", "additive_chi2"]:
        # these don't support sparse matrices yet
        assert_raises(ValueError, pairwise_kernels,
                      X_sparse, Y=Y_sparse, metric=metric)
        return
    K1 = pairwise_kernels(X_sparse, Y=Y_sparse, metric=metric)
    assert_array_almost_equal(K1, K2) 

def test_pairwise_kernels_filter_param():
    rng = np.random.RandomState(0)
    X = rng.random_sample((5, 4))
    Y = rng.random_sample((2, 4))
    K = rbf_kernel(X, Y, gamma=0.1)
    params = {"gamma": 0.1, "blabla": ":)"}
    K2 = pairwise_kernels(X, Y, metric="rbf", filter_params=True, **params)
    assert_array_almost_equal(K, K2)

    assert_raises(TypeError, pairwise_kernels, X, Y, "rbf", **params) 

def _get_kernel(self, X, Y=None):
        kernel_params = self._get_kernel_params()
        if self.kernel == "gak":
            return cdist_gak(X, Y, n_jobs=self.n_jobs, verbose=self.verbose,
                             **kernel_params)
        else:
            X_sklearn = to_sklearn_dataset(X)
            if Y is not None:
                Y_sklearn = to_sklearn_dataset(Y)
            else:
                Y_sklearn = Y
            return pairwise_kernels(X_sklearn, Y_sklearn, metric=self.kernel,
                                    n_jobs=self.n_jobs, **kernel_params) 

def transform(self, X):
        '''
        Compute kernels from X to :attr:`features_`.

        Parameters
        ----------
        X : list of arrays or :class:`skl_groups.features.Features`
            The bags to compute "from". Must have same dimension as
            :attr:`features_`.

        Returns
        -------
        K : array of shape ``[len(X), len(features_)]``
            The kernel evaluations from X to :attr:`features_`.
        '''

        X = as_features(X, stack=True, bare=True)
        Y = self.features_

        if X.dim != Y.dim:
            raise ValueError("MMK transform got dimension {} but had {} at fit"
                             .format(X.dim, Y.dim))

        pointwise = pairwise_kernels(X.stacked_features, Y.stacked_features,
                                     metric=self.kernel,
                                     filter_params=True,
                                     **self._get_kernel_params())

        # TODO: is there a way to do this without a Python loop?
        K = np.empty((len(X), len(Y)))
        for i in range(len(X)):
            for j in range(len(Y)):
                K[i, j] = pointwise[X._boundaries[i]:X._boundaries[i+1],
                                    Y._boundaries[j]:Y._boundaries[j+1]].mean()

        return K 

def _get_kernel(self, X, Y=None):
        if callable(self.kernel_):
            params = self.kernel_params_ or {}
        else:
            params = {'gamma': self.gamma_,
                      'degree': self.degree_,
                      'coef0': self.coef0_}

        return pairwise_kernels(X, Y, metric=self.kernel_, filter_params=True, **params) 

def _title_similarity_score(full_text, title):
    """Similarity scores for sentences with
       title in descending order"""

    sentences = sentence_tokenizer(full_text)
    norm = _normalize([title]+sentences)
    similarity_matrix = pairwise_kernels(norm, metric='cosine')
    return sorted(zip(
                     similarity_matrix[0,1:],
                     range(len(similarity_matrix)),
                     sentences
                     ),
                 key = lambda tup: tup[0],
                 reverse=True
                 ) 

def test_pairwise_precomputed():
    for func in [pairwise_distances, pairwise_kernels]:
        # Test correct shape
        assert_raises_regexp(ValueError, '.* shape .*',
                             func, np.zeros((5, 3)), metric='precomputed')
        # with two args
        assert_raises_regexp(ValueError, '.* shape .*',
                             func, np.zeros((5, 3)), np.zeros((4, 4)),
                             metric='precomputed')
        # even if shape[1] agrees (although thus second arg is spurious)
        assert_raises_regexp(ValueError, '.* shape .*',
                             func, np.zeros((5, 3)), np.zeros((4, 3)),
                             metric='precomputed')

        # Test not copied (if appropriate dtype)
        S = np.zeros((5, 5))
        S2 = func(S, metric="precomputed")
        assert_true(S is S2)
        # with two args
        S = np.zeros((5, 3))
        S2 = func(S, np.zeros((3, 3)), metric="precomputed")
        assert_true(S is S2)

        # Test always returns float dtype
        S = func(np.array([[1]], dtype='int'), metric='precomputed')
        assert_equal('f', S.dtype.kind)

        # Test converts list to array-like
        S = func([[1.]], metric='precomputed')
        assert_true(isinstance(S, np.ndarray)) 

def test_pairwise_parallel():
    wminkowski_kwds = {'w': np.arange(1, 5).astype('double'), 'p': 1}
    metrics = [(pairwise_distances, 'euclidean', {}),
               (pairwise_distances, wminkowski, wminkowski_kwds),
               (pairwise_distances, 'wminkowski', wminkowski_kwds),
               (pairwise_kernels, 'polynomial', {'degree': 1}),
               (pairwise_kernels, callable_rbf_kernel, {'gamma': .1}),
               ]
    for func, metric, kwds in metrics:
        yield check_pairwise_parallel, func, metric, kwds 

def test_pairwise_kernels_filter_param():
    rng = np.random.RandomState(0)
    X = rng.random_sample((5, 4))
    Y = rng.random_sample((2, 4))
    K = rbf_kernel(X, Y, gamma=0.1)
    params = {"gamma": 0.1, "blabla": ":)"}
    K2 = pairwise_kernels(X, Y, metric="rbf", filter_params=True, **params)
    assert_array_almost_equal(K, K2)

    assert_raises(TypeError, pairwise_kernels, X, Y, "rbf", **params) 

def test_cosine_similarity_sparse_output():
    # Test if cosine_similarity correctly produces sparse output.

    rng = np.random.RandomState(0)
    X = rng.random_sample((5, 4))
    Y = rng.random_sample((3, 4))
    Xcsr = csr_matrix(X)
    Ycsr = csr_matrix(Y)

    K1 = cosine_similarity(Xcsr, Ycsr, dense_output=False)
    assert_true(issparse(K1))

    K2 = pairwise_kernels(Xcsr, Y=Ycsr, metric="cosine")
    assert_array_almost_equal(K1.todense(), K2) 

def test_kernel_ridge_precomputed():
    for kernel in ["linear", "rbf", "poly", "cosine"]:
        K = pairwise_kernels(X, X, metric=kernel)
        pred = KernelRidge(kernel=kernel).fit(X, y).predict(X)
        pred2 = KernelRidge(kernel="precomputed").fit(K, y).predict(K)
        assert_array_almost_equal(pred, pred2) 

def test(self, dataset: BaseADDataset, device: str = 'cpu', n_jobs_dataloader: int = 0):
        """Tests the SSAD model on the test data."""
        logger = logging.getLogger()

        _, test_loader = dataset.loaders(batch_size=128, num_workers=n_jobs_dataloader)

        # Get data from loader
        idx_label_score = []
        X = ()
        idxs = []
        labels = []
        for data in test_loader:
            inputs, label_batch, _, idx = data
            inputs, label_batch, idx = inputs.to(device), label_batch.to(device), idx.to(device)
            if self.hybrid:
                inputs = self.ae_net.encoder(inputs)  # in hybrid approach, take code representation of AE as features
            X_batch = inputs.view(inputs.size(0), -1)  # X_batch.shape = (batch_size, n_channels * height * width)
            X += (X_batch.cpu().data.numpy(),)
            idxs += idx.cpu().data.numpy().astype(np.int64).tolist()
            labels += label_batch.cpu().data.numpy().astype(np.int64).tolist()
        X = np.concatenate(X)

        # Testing
        logger.info('Starting testing...')
        start_time = time.time()

        # Build kernel
        kernel = pairwise_kernels(X, self.X_svs, metric=self.kernel, gamma=self.gamma)

        scores = (-1.0) * self.model.apply(kernel)

        self.results['test_time'] = time.time() - start_time
        scores = scores.flatten()
        self.rho = -self.model.threshold

        # Save triples of (idx, label, score) in a list
        idx_label_score += list(zip(idxs, labels, scores.tolist()))
        self.results['test_scores'] = idx_label_score

        # Compute AUC
        _, labels, scores = zip(*idx_label_score)
        labels = np.array(labels)
        scores = np.array(scores)
        self.results['test_auc'] = roc_auc_score(labels, scores)

        # If hybrid, also test model with linear kernel
        if self.hybrid:
            start_time = time.time()
            linear_kernel = pairwise_kernels(X, self.linear_X_svs, metric='linear')
            scores_linear = (-1.0) * self.linear_model.apply(linear_kernel)
            self.results['test_time_linear'] = time.time() - start_time
            scores_linear = scores_linear.flatten()
            self.results['test_auc_linear'] = roc_auc_score(labels, scores_linear)
            logger.info('Test AUC linear model: {:.2f}%'.format(100. * self.results['test_auc_linear']))
            logger.info('Test Time linear model: {:.3f}s'.format(self.results['test_time_linear']))

        # Log results
        logger.info('Test AUC: {:.2f}%'.format(100. * self.results['test_auc']))
        logger.info('Test Time: {:.3f}s'.format(self.results['test_time']))
        logger.info('Finished testing.') 

def _kernel(self, X, Y):
        """Calculate the kernel matrix

        Parameters
        ---------
        X : {float, array}, shape = [n_samples, n_features]
            Input data.

        Y : {float, array}, shape = [n_centers, n_targets]
            Kernel centers.

        Returns
        -------
        K : {float, array}, shape = [n_samples, n_centers]
            Kernel matrix.
        """
        if (
            self.kernel != "rbf"
            and self.kernel != "laplace"
            and self.kernel != "cauchy"
        ):
            if callable(self.kernel):
                params = self.kernel_params or {}
            else:
                params = {
                    "gamma": self.gamma_,
                    "degree": self.degree,
                    "coef0": self.coef0,
                }
            return pairwise_kernels(
                X, Y, metric=self.kernel, filter_params=True, **params
            )
        distance = euclidean_distances(X, Y, squared=True)
        bandwidth = np.float32(1.0 / np.sqrt(2.0 * self.gamma_))
        if self.kernel == "rbf":
            distance = -self.gamma_ * distance
            K = np.exp(distance)
        elif self.kernel == "laplace":
            d = np.maximum(distance, 0)
            K = np.exp(-np.sqrt(d) / bandwidth)
        else:  # self.kernel == "cauchy":
            K = 1 / (1 + 2.0 * self.gamma_ * distance)
        return K 

def fit(self, X, y):
        """Fit the model to data matrix X and target y.

        Parameters
        ----------
        X : array-like, shape (n_samples, n_features)
            The input data.

        y : array-like, shape (n_samples,)
            The class labels.

        Returns
        -------
        self : returns a trained SVM
        """
        self.support_vectors_ = check_array(X)
        self.y = check_array(y, ensure_2d=False)

        random_state = check_random_state(self.random_state)

        self.kernel_args = {}
        if self.kernel == "rbf" and self.gamma is not None:
            self.kernel_args["gamma"] = self.gamma
        elif self.kernel == "poly":
            self.kernel_args["degree"] = self.degree
            self.kernel_args["coef0"] = self.coef0
        elif self.kernel == "sigmoid":
            self.kernel_args["coef0"] = self.coef0

        K = pairwise_kernels(X, metric=self.kernel, **self.kernel_args)
        self.dual_coef_ = np.zeros(X.shape[0])
        self.intercept_ = _svm.smo(
            K, y, self.dual_coef_, self.C, random_state, self.tol,
            self.numpasses, self.maxiter, self.verbose)

        # If the user was using a linear kernel, lets also compute and store
        # the weights. This will speed up evaluations during testing time.
        if self.kernel == "linear":
            self.coef_ = np.dot(self.dual_coef_ * self.y, self.support_vectors_)

        # only samples with nonzero coefficients are relevant for predictions
        support_vectors = np.nonzero(self.dual_coef_)
        self.dual_coef_ = self.dual_coef_[support_vectors]
        self.support_vectors_ = X[support_vectors]
        self.y = y[support_vectors]

        return self 

def fit(self, X, y=None):
        """Creates an affinity matrix for X using the selected affinity,
        then applies spectral clustering to this affinity matrix.

        Parameters
        ----------
        X : array-like or sparse matrix, shape (n_samples, n_features)
            OR, if affinity==`precomputed`, a precomputed affinity
            matrix of shape (n_samples, n_samples)
        """
        X = check_array(X, accept_sparse=['csr', 'csc', 'coo'],
                        dtype=np.float64)
        if X.shape[0] == X.shape[1] and self.affinity != "precomputed":
            warnings.warn("The spectral clustering API has changed. ``fit``"
                          "now constructs an affinity matrix from data. To use"
                          " a custom affinity matrix, "
                          "set ``affinity=precomputed``.")

        if self.affinity == 'nearest_neighbors':
            connectivity = kneighbors_graph(X, n_neighbors=self.n_neighbors, include_self=True,
                                            n_jobs=self.n_jobs)
            self.affinity_matrix_ = 0.5 * (connectivity + connectivity.T)
        elif self.affinity == 'precomputed':
            self.affinity_matrix_ = X
        else:
            params = self.kernel_params
            if params is None:
                params = {}
            if not callable(self.affinity):
                params['gamma'] = self.gamma
                params['degree'] = self.degree
                params['coef0'] = self.coef0
            self.affinity_matrix_ = pairwise_kernels(X, metric=self.affinity,
                                                     filter_params=True,
                                                     **params)

        random_state = check_random_state(self.random_state)
        self.labels_ = spectral_clustering(self.affinity_matrix_,
                                           n_clusters=self.n_clusters,
                                           eigen_solver=self.eigen_solver,
                                           random_state=random_state,
                                           n_init=self.n_init,
                                           eigen_tol=self.eigen_tol,
                                           assign_labels=self.assign_labels)
        return self 

def test_pairwise_kernels():    # Test the pairwise_kernels helper function.

    rng = np.random.RandomState(0)
    X = rng.random_sample((5, 4))
    Y = rng.random_sample((2, 4))
    # Test with all metrics that should be in PAIRWISE_KERNEL_FUNCTIONS.
    test_metrics = ["rbf", "laplacian", "sigmoid", "polynomial", "linear",
                    "chi2", "additive_chi2"]
    for metric in test_metrics:
        function = PAIRWISE_KERNEL_FUNCTIONS[metric]
        # Test with Y=None
        K1 = pairwise_kernels(X, metric=metric)
        K2 = function(X)
        assert_array_almost_equal(K1, K2)
        # Test with Y=Y
        K1 = pairwise_kernels(X, Y=Y, metric=metric)
        K2 = function(X, Y=Y)
        assert_array_almost_equal(K1, K2)
        # Test with tuples as X and Y
        X_tuples = tuple([tuple([v for v in row]) for row in X])
        Y_tuples = tuple([tuple([v for v in row]) for row in Y])
        K2 = pairwise_kernels(X_tuples, Y_tuples, metric=metric)
        assert_array_almost_equal(K1, K2)

        # Test with sparse X and Y
        X_sparse = csr_matrix(X)
        Y_sparse = csr_matrix(Y)
        if metric in ["chi2", "additive_chi2"]:
            # these don't support sparse matrices yet
            assert_raises(ValueError, pairwise_kernels,
                          X_sparse, Y=Y_sparse, metric=metric)
            continue
        K1 = pairwise_kernels(X_sparse, Y=Y_sparse, metric=metric)
        assert_array_almost_equal(K1, K2)
    # Test with a callable function, with given keywords.
    metric = callable_rbf_kernel
    kwds = {'gamma': 0.1}
    K1 = pairwise_kernels(X, Y=Y, metric=metric, **kwds)
    K2 = rbf_kernel(X, Y=Y, **kwds)
    assert_array_almost_equal(K1, K2)

    # callable function, X=Y
    K1 = pairwise_kernels(X, Y=X, metric=metric, **kwds)
    K2 = rbf_kernel(X, Y=X, **kwds)
    assert_array_almost_equal(K1, K2)