478 lines
16 KiB
Python
478 lines
16 KiB
Python
import sys
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from io import StringIO
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import numpy as np
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import pytest
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from numpy.testing import assert_array_equal
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from scipy.linalg import block_diag
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from scipy.special import psi
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from sklearn.decomposition import LatentDirichletAllocation
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from sklearn.decomposition._online_lda_fast import (
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_dirichlet_expectation_1d,
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_dirichlet_expectation_2d,
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)
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from sklearn.exceptions import NotFittedError
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from sklearn.utils._testing import (
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assert_allclose,
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assert_almost_equal,
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assert_array_almost_equal,
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if_safe_multiprocessing_with_blas,
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)
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from sklearn.utils.fixes import CSR_CONTAINERS
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def _build_sparse_array(csr_container):
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# Create 3 topics and each topic has 3 distinct words.
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# (Each word only belongs to a single topic.)
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n_components = 3
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block = np.full((3, 3), n_components, dtype=int)
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blocks = [block] * n_components
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X = block_diag(*blocks)
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X = csr_container(X)
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return (n_components, X)
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_default_prior_params(csr_container):
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# default prior parameter should be `1 / topics`
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# and verbose params should not affect result
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n_components, X = _build_sparse_array(csr_container)
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prior = 1.0 / n_components
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lda_1 = LatentDirichletAllocation(
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n_components=n_components,
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doc_topic_prior=prior,
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topic_word_prior=prior,
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random_state=0,
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)
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lda_2 = LatentDirichletAllocation(n_components=n_components, random_state=0)
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topic_distr_1 = lda_1.fit_transform(X)
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topic_distr_2 = lda_2.fit_transform(X)
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assert_almost_equal(topic_distr_1, topic_distr_2)
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_fit_batch(csr_container):
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# Test LDA batch learning_offset (`fit` method with 'batch' learning)
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rng = np.random.RandomState(0)
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components,
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evaluate_every=1,
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learning_method="batch",
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random_state=rng,
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)
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lda.fit(X)
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correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
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for component in lda.components_:
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# Find top 3 words in each LDA component
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top_idx = set(component.argsort()[-3:][::-1])
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assert tuple(sorted(top_idx)) in correct_idx_grps
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_fit_online(csr_container):
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# Test LDA online learning (`fit` method with 'online' learning)
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rng = np.random.RandomState(0)
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components,
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learning_offset=10.0,
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evaluate_every=1,
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learning_method="online",
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random_state=rng,
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)
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lda.fit(X)
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correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
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for component in lda.components_:
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# Find top 3 words in each LDA component
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top_idx = set(component.argsort()[-3:][::-1])
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assert tuple(sorted(top_idx)) in correct_idx_grps
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_partial_fit(csr_container):
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# Test LDA online learning (`partial_fit` method)
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# (same as test_lda_batch)
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rng = np.random.RandomState(0)
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components,
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learning_offset=10.0,
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total_samples=100,
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random_state=rng,
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)
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for i in range(3):
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lda.partial_fit(X)
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correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
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for c in lda.components_:
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top_idx = set(c.argsort()[-3:][::-1])
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assert tuple(sorted(top_idx)) in correct_idx_grps
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_dense_input(csr_container):
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# Test LDA with dense input.
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rng = np.random.RandomState(0)
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components, learning_method="batch", random_state=rng
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)
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lda.fit(X.toarray())
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correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
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for component in lda.components_:
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# Find top 3 words in each LDA component
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top_idx = set(component.argsort()[-3:][::-1])
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assert tuple(sorted(top_idx)) in correct_idx_grps
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def test_lda_transform():
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# Test LDA transform.
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# Transform result cannot be negative and should be normalized
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rng = np.random.RandomState(0)
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X = rng.randint(5, size=(20, 10))
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n_components = 3
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lda = LatentDirichletAllocation(n_components=n_components, random_state=rng)
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X_trans = lda.fit_transform(X)
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assert (X_trans > 0.0).any()
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assert_array_almost_equal(np.sum(X_trans, axis=1), np.ones(X_trans.shape[0]))
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@pytest.mark.parametrize("method", ("online", "batch"))
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def test_lda_fit_transform(method):
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# Test LDA fit_transform & transform
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# fit_transform and transform result should be the same
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rng = np.random.RandomState(0)
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X = rng.randint(10, size=(50, 20))
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lda = LatentDirichletAllocation(
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n_components=5, learning_method=method, random_state=rng
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)
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X_fit = lda.fit_transform(X)
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X_trans = lda.transform(X)
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assert_array_almost_equal(X_fit, X_trans, 4)
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def test_lda_negative_input():
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# test pass dense matrix with sparse negative input.
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X = np.full((5, 10), -1.0)
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lda = LatentDirichletAllocation()
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regex = r"^Negative values in data passed"
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with pytest.raises(ValueError, match=regex):
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lda.fit(X)
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def test_lda_no_component_error():
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# test `perplexity` before `fit`
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rng = np.random.RandomState(0)
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X = rng.randint(4, size=(20, 10))
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lda = LatentDirichletAllocation()
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regex = (
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"This LatentDirichletAllocation instance is not fitted yet. "
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"Call 'fit' with appropriate arguments before using this "
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"estimator."
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)
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with pytest.raises(NotFittedError, match=regex):
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lda.perplexity(X)
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@if_safe_multiprocessing_with_blas
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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@pytest.mark.parametrize("method", ("online", "batch"))
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def test_lda_multi_jobs(method, csr_container):
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n_components, X = _build_sparse_array(csr_container)
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# Test LDA batch training with multi CPU
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rng = np.random.RandomState(0)
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lda = LatentDirichletAllocation(
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n_components=n_components,
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n_jobs=2,
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learning_method=method,
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evaluate_every=1,
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random_state=rng,
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)
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lda.fit(X)
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correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
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for c in lda.components_:
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top_idx = set(c.argsort()[-3:][::-1])
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assert tuple(sorted(top_idx)) in correct_idx_grps
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@if_safe_multiprocessing_with_blas
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_partial_fit_multi_jobs(csr_container):
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# Test LDA online training with multi CPU
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rng = np.random.RandomState(0)
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components,
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n_jobs=2,
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learning_offset=5.0,
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total_samples=30,
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random_state=rng,
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)
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for i in range(2):
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lda.partial_fit(X)
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correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
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for c in lda.components_:
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top_idx = set(c.argsort()[-3:][::-1])
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assert tuple(sorted(top_idx)) in correct_idx_grps
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def test_lda_preplexity_mismatch():
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# test dimension mismatch in `perplexity` method
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rng = np.random.RandomState(0)
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n_components = rng.randint(3, 6)
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n_samples = rng.randint(6, 10)
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X = np.random.randint(4, size=(n_samples, 10))
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lda = LatentDirichletAllocation(
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n_components=n_components,
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learning_offset=5.0,
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total_samples=20,
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random_state=rng,
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)
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lda.fit(X)
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# invalid samples
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invalid_n_samples = rng.randint(4, size=(n_samples + 1, n_components))
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with pytest.raises(ValueError, match=r"Number of samples"):
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lda._perplexity_precomp_distr(X, invalid_n_samples)
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# invalid topic number
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invalid_n_components = rng.randint(4, size=(n_samples, n_components + 1))
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with pytest.raises(ValueError, match=r"Number of topics"):
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lda._perplexity_precomp_distr(X, invalid_n_components)
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@pytest.mark.parametrize("method", ("online", "batch"))
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_perplexity(method, csr_container):
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# Test LDA perplexity for batch training
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# perplexity should be lower after each iteration
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n_components, X = _build_sparse_array(csr_container)
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lda_1 = LatentDirichletAllocation(
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n_components=n_components,
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max_iter=1,
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learning_method=method,
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total_samples=100,
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random_state=0,
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)
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lda_2 = LatentDirichletAllocation(
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n_components=n_components,
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max_iter=10,
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learning_method=method,
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total_samples=100,
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random_state=0,
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)
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lda_1.fit(X)
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perp_1 = lda_1.perplexity(X, sub_sampling=False)
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lda_2.fit(X)
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perp_2 = lda_2.perplexity(X, sub_sampling=False)
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assert perp_1 >= perp_2
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perp_1_subsampling = lda_1.perplexity(X, sub_sampling=True)
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perp_2_subsampling = lda_2.perplexity(X, sub_sampling=True)
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assert perp_1_subsampling >= perp_2_subsampling
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@pytest.mark.parametrize("method", ("online", "batch"))
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_score(method, csr_container):
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# Test LDA score for batch training
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# score should be higher after each iteration
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n_components, X = _build_sparse_array(csr_container)
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lda_1 = LatentDirichletAllocation(
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n_components=n_components,
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max_iter=1,
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learning_method=method,
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total_samples=100,
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random_state=0,
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)
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lda_2 = LatentDirichletAllocation(
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n_components=n_components,
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max_iter=10,
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learning_method=method,
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total_samples=100,
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random_state=0,
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)
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lda_1.fit_transform(X)
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score_1 = lda_1.score(X)
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lda_2.fit_transform(X)
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score_2 = lda_2.score(X)
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assert score_2 >= score_1
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_perplexity_input_format(csr_container):
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# Test LDA perplexity for sparse and dense input
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# score should be the same for both dense and sparse input
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components,
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max_iter=1,
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learning_method="batch",
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total_samples=100,
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random_state=0,
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)
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lda.fit(X)
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perp_1 = lda.perplexity(X)
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perp_2 = lda.perplexity(X.toarray())
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assert_almost_equal(perp_1, perp_2)
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_score_perplexity(csr_container):
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# Test the relationship between LDA score and perplexity
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components, max_iter=10, random_state=0
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)
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lda.fit(X)
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perplexity_1 = lda.perplexity(X, sub_sampling=False)
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score = lda.score(X)
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perplexity_2 = np.exp(-1.0 * (score / np.sum(X.data)))
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assert_almost_equal(perplexity_1, perplexity_2)
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_fit_perplexity(csr_container):
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# Test that the perplexity computed during fit is consistent with what is
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# returned by the perplexity method
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components,
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max_iter=1,
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learning_method="batch",
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random_state=0,
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evaluate_every=1,
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)
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lda.fit(X)
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# Perplexity computed at end of fit method
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perplexity1 = lda.bound_
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# Result of perplexity method on the train set
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perplexity2 = lda.perplexity(X)
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assert_almost_equal(perplexity1, perplexity2)
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_empty_docs(csr_container):
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"""Test LDA on empty document (all-zero rows)."""
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Z = np.zeros((5, 4))
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for X in [Z, csr_container(Z)]:
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lda = LatentDirichletAllocation(max_iter=750).fit(X)
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assert_almost_equal(
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lda.components_.sum(axis=0), np.ones(lda.components_.shape[1])
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)
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def test_dirichlet_expectation():
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"""Test Cython version of Dirichlet expectation calculation."""
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x = np.logspace(-100, 10, 10000)
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expectation = np.empty_like(x)
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_dirichlet_expectation_1d(x, 0, expectation)
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assert_allclose(expectation, np.exp(psi(x) - psi(np.sum(x))), atol=1e-19)
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x = x.reshape(100, 100)
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assert_allclose(
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_dirichlet_expectation_2d(x),
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psi(x) - psi(np.sum(x, axis=1)[:, np.newaxis]),
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rtol=1e-11,
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atol=3e-9,
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)
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def check_verbosity(
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verbose, evaluate_every, expected_lines, expected_perplexities, csr_container
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):
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(
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n_components=n_components,
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max_iter=3,
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learning_method="batch",
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verbose=verbose,
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evaluate_every=evaluate_every,
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random_state=0,
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)
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out = StringIO()
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old_out, sys.stdout = sys.stdout, out
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try:
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lda.fit(X)
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finally:
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sys.stdout = old_out
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n_lines = out.getvalue().count("\n")
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n_perplexity = out.getvalue().count("perplexity")
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assert expected_lines == n_lines
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assert expected_perplexities == n_perplexity
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@pytest.mark.parametrize(
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"verbose,evaluate_every,expected_lines,expected_perplexities",
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[
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(False, 1, 0, 0),
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(False, 0, 0, 0),
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(True, 0, 3, 0),
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(True, 1, 3, 3),
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(True, 2, 3, 1),
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],
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)
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_verbosity(
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verbose, evaluate_every, expected_lines, expected_perplexities, csr_container
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):
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check_verbosity(
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verbose, evaluate_every, expected_lines, expected_perplexities, csr_container
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)
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@pytest.mark.parametrize("csr_container", CSR_CONTAINERS)
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def test_lda_feature_names_out(csr_container):
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"""Check feature names out for LatentDirichletAllocation."""
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n_components, X = _build_sparse_array(csr_container)
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lda = LatentDirichletAllocation(n_components=n_components).fit(X)
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names = lda.get_feature_names_out()
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assert_array_equal(
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[f"latentdirichletallocation{i}" for i in range(n_components)], names
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)
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@pytest.mark.parametrize("learning_method", ("batch", "online"))
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def test_lda_dtype_match(learning_method, global_dtype):
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"""Check data type preservation of fitted attributes."""
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rng = np.random.RandomState(0)
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X = rng.uniform(size=(20, 10)).astype(global_dtype, copy=False)
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lda = LatentDirichletAllocation(
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n_components=5, random_state=0, learning_method=learning_method
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)
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lda.fit(X)
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assert lda.components_.dtype == global_dtype
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assert lda.exp_dirichlet_component_.dtype == global_dtype
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@pytest.mark.parametrize("learning_method", ("batch", "online"))
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def test_lda_numerical_consistency(learning_method, global_random_seed):
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"""Check numerical consistency between np.float32 and np.float64."""
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rng = np.random.RandomState(global_random_seed)
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X64 = rng.uniform(size=(20, 10))
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X32 = X64.astype(np.float32)
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lda_64 = LatentDirichletAllocation(
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n_components=5, random_state=global_random_seed, learning_method=learning_method
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).fit(X64)
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lda_32 = LatentDirichletAllocation(
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n_components=5, random_state=global_random_seed, learning_method=learning_method
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).fit(X32)
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assert_allclose(lda_32.components_, lda_64.components_)
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assert_allclose(lda_32.transform(X32), lda_64.transform(X64))
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