"""Testing for Spectral Biclustering methods""" import numpy as np import pytest from scipy.sparse import csr_matrix, issparse from sklearn.model_selection import ParameterGrid from sklearn.utils._testing import assert_almost_equal from sklearn.utils._testing import assert_array_equal from sklearn.utils._testing import assert_array_almost_equal from sklearn.base import BaseEstimator, BiclusterMixin from sklearn.cluster import SpectralCoclustering from sklearn.cluster import SpectralBiclustering from sklearn.cluster._bicluster import _scale_normalize from sklearn.cluster._bicluster import _bistochastic_normalize from sklearn.cluster._bicluster import _log_normalize from sklearn.metrics import (consensus_score, v_measure_score) from sklearn.datasets import make_biclusters, make_checkerboard class MockBiclustering(BiclusterMixin, BaseEstimator): # Mock object for testing get_submatrix. def __init__(self): pass def get_indices(self, i): # Overridden to reproduce old get_submatrix test. return (np.where([True, True, False, False, True])[0], np.where([False, False, True, True])[0]) def test_get_submatrix(): data = np.arange(20).reshape(5, 4) model = MockBiclustering() for X in (data, csr_matrix(data), data.tolist()): submatrix = model.get_submatrix(0, X) if issparse(submatrix): submatrix = submatrix.toarray() assert_array_equal(submatrix, [[2, 3], [6, 7], [18, 19]]) submatrix[:] = -1 if issparse(X): X = X.toarray() assert np.all(X != -1) def _test_shape_indices(model): # Test get_shape and get_indices on fitted model. for i in range(model.n_clusters): m, n = model.get_shape(i) i_ind, j_ind = model.get_indices(i) assert len(i_ind) == m assert len(j_ind) == n def test_spectral_coclustering(): # Test Dhillon's Spectral CoClustering on a simple problem. param_grid = {'svd_method': ['randomized', 'arpack'], 'n_svd_vecs': [None, 20], 'mini_batch': [False, True], 'init': ['k-means++'], 'n_init': [10]} random_state = 0 S, rows, cols = make_biclusters((30, 30), 3, noise=0.5, random_state=random_state) S -= S.min() # needs to be nonnegative before making it sparse S = np.where(S < 1, 0, S) # threshold some values for mat in (S, csr_matrix(S)): for kwargs in ParameterGrid(param_grid): model = SpectralCoclustering(n_clusters=3, random_state=random_state, **kwargs) model.fit(mat) assert model.rows_.shape == (3, 30) assert_array_equal(model.rows_.sum(axis=0), np.ones(30)) assert_array_equal(model.columns_.sum(axis=0), np.ones(30)) assert consensus_score(model.biclusters_, (rows, cols)) == 1 _test_shape_indices(model) def test_spectral_biclustering(): # Test Kluger methods on a checkerboard dataset. S, rows, cols = make_checkerboard((30, 30), 3, noise=0.5, random_state=0) non_default_params = {'method': ['scale', 'log'], 'svd_method': ['arpack'], 'n_svd_vecs': [20], 'mini_batch': [True]} for mat in (S, csr_matrix(S)): for param_name, param_values in non_default_params.items(): for param_value in param_values: model = SpectralBiclustering( n_clusters=3, n_init=3, init='k-means++', random_state=0, ) model.set_params(**dict([(param_name, param_value)])) if issparse(mat) and model.get_params().get('method') == 'log': # cannot take log of sparse matrix with pytest.raises(ValueError): model.fit(mat) continue else: model.fit(mat) assert model.rows_.shape == (9, 30) assert model.columns_.shape == (9, 30) assert_array_equal(model.rows_.sum(axis=0), np.repeat(3, 30)) assert_array_equal(model.columns_.sum(axis=0), np.repeat(3, 30)) assert consensus_score(model.biclusters_, (rows, cols)) == 1 _test_shape_indices(model) def _do_scale_test(scaled): """Check that rows sum to one constant, and columns to another.""" row_sum = scaled.sum(axis=1) col_sum = scaled.sum(axis=0) if issparse(scaled): row_sum = np.asarray(row_sum).squeeze() col_sum = np.asarray(col_sum).squeeze() assert_array_almost_equal(row_sum, np.tile(row_sum.mean(), 100), decimal=1) assert_array_almost_equal(col_sum, np.tile(col_sum.mean(), 100), decimal=1) def _do_bistochastic_test(scaled): """Check that rows and columns sum to the same constant.""" _do_scale_test(scaled) assert_almost_equal(scaled.sum(axis=0).mean(), scaled.sum(axis=1).mean(), decimal=1) def test_scale_normalize(): generator = np.random.RandomState(0) X = generator.rand(100, 100) for mat in (X, csr_matrix(X)): scaled, _, _ = _scale_normalize(mat) _do_scale_test(scaled) if issparse(mat): assert issparse(scaled) def test_bistochastic_normalize(): generator = np.random.RandomState(0) X = generator.rand(100, 100) for mat in (X, csr_matrix(X)): scaled = _bistochastic_normalize(mat) _do_bistochastic_test(scaled) if issparse(mat): assert issparse(scaled) def test_log_normalize(): # adding any constant to a log-scaled matrix should make it # bistochastic generator = np.random.RandomState(0) mat = generator.rand(100, 100) scaled = _log_normalize(mat) + 1 _do_bistochastic_test(scaled) def test_fit_best_piecewise(): model = SpectralBiclustering(random_state=0) vectors = np.array([[0, 0, 0, 1, 1, 1], [2, 2, 2, 3, 3, 3], [0, 1, 2, 3, 4, 5]]) best = model._fit_best_piecewise(vectors, n_best=2, n_clusters=2) assert_array_equal(best, vectors[:2]) def test_project_and_cluster(): model = SpectralBiclustering(random_state=0) data = np.array([[1, 1, 1], [1, 1, 1], [3, 6, 3], [3, 6, 3]]) vectors = np.array([[1, 0], [0, 1], [0, 0]]) for mat in (data, csr_matrix(data)): labels = model._project_and_cluster(mat, vectors, n_clusters=2) assert_almost_equal(v_measure_score(labels, [0, 0, 1, 1]), 1.0) def test_perfect_checkerboard(): # XXX Previously failed on build bot (not reproducible) model = SpectralBiclustering(3, svd_method="arpack", random_state=0) S, rows, cols = make_checkerboard((30, 30), 3, noise=0, random_state=0) model.fit(S) assert consensus_score(model.biclusters_, (rows, cols)) == 1 S, rows, cols = make_checkerboard((40, 30), 3, noise=0, random_state=0) model.fit(S) assert consensus_score(model.biclusters_, (rows, cols)) == 1 S, rows, cols = make_checkerboard((30, 40), 3, noise=0, random_state=0) model.fit(S) assert consensus_score(model.biclusters_, (rows, cols)) == 1 @pytest.mark.parametrize( "args", [{'n_clusters': (3, 3, 3)}, {'n_clusters': 'abc'}, {'n_clusters': (3, 'abc')}, {'method': 'unknown'}, {'n_components': 0}, {'n_best': 0}, {'svd_method': 'unknown'}, {'n_components': 3, 'n_best': 4}] ) def test_errors(args): data = np.arange(25).reshape((5, 5)) model = SpectralBiclustering(**args) with pytest.raises(ValueError): model.fit(data) def test_wrong_shape(): model = SpectralBiclustering() data = np.arange(27).reshape((3, 3, 3)) with pytest.raises(ValueError): model.fit(data) @pytest.mark.parametrize('est', (SpectralBiclustering(), SpectralCoclustering())) def test_n_features_in_(est): X, _, _ = make_biclusters((3, 3), 3, random_state=0) assert not hasattr(est, 'n_features_in_') est.fit(X) assert est.n_features_in_ == 3 @pytest.mark.parametrize("klass", [SpectralBiclustering, SpectralCoclustering]) @pytest.mark.parametrize("n_jobs", [None, 1]) def test_n_jobs_deprecated(klass, n_jobs): # FIXME: remove in 1.0 depr_msg = ("'n_jobs' was deprecated in version 0.23 and will be removed " "in 1.0") S, _, _ = make_biclusters((30, 30), 3, noise=0.5, random_state=0) est = klass(random_state=0, n_jobs=n_jobs) with pytest.warns(FutureWarning, match=depr_msg): est.fit(S)