Inzynierka/Lib/site-packages/sklearn/decomposition/tests/test_online_lda.py

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2023-06-02 12:51:02 +02:00
import sys
import numpy as np
from scipy.linalg import block_diag
from scipy.sparse import csr_matrix
from scipy.special import psi
from numpy.testing import assert_array_equal
import pytest
from sklearn.decomposition import LatentDirichletAllocation
from sklearn.decomposition._online_lda_fast import (
_dirichlet_expectation_1d,
_dirichlet_expectation_2d,
)
from sklearn.utils._testing import assert_allclose
from sklearn.utils._testing import assert_array_almost_equal
from sklearn.utils._testing import assert_almost_equal
from sklearn.utils._testing import if_safe_multiprocessing_with_blas
from sklearn.exceptions import NotFittedError
from io import StringIO
def _build_sparse_mtx():
# Create 3 topics and each topic has 3 distinct words.
# (Each word only belongs to a single topic.)
n_components = 3
block = np.full((3, 3), n_components, dtype=int)
blocks = [block] * n_components
X = block_diag(*blocks)
X = csr_matrix(X)
return (n_components, X)
def test_lda_default_prior_params():
# default prior parameter should be `1 / topics`
# and verbose params should not affect result
n_components, X = _build_sparse_mtx()
prior = 1.0 / n_components
lda_1 = LatentDirichletAllocation(
n_components=n_components,
doc_topic_prior=prior,
topic_word_prior=prior,
random_state=0,
)
lda_2 = LatentDirichletAllocation(n_components=n_components, random_state=0)
topic_distr_1 = lda_1.fit_transform(X)
topic_distr_2 = lda_2.fit_transform(X)
assert_almost_equal(topic_distr_1, topic_distr_2)
def test_lda_fit_batch():
# Test LDA batch learning_offset (`fit` method with 'batch' learning)
rng = np.random.RandomState(0)
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components,
evaluate_every=1,
learning_method="batch",
random_state=rng,
)
lda.fit(X)
correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
for component in lda.components_:
# Find top 3 words in each LDA component
top_idx = set(component.argsort()[-3:][::-1])
assert tuple(sorted(top_idx)) in correct_idx_grps
def test_lda_fit_online():
# Test LDA online learning (`fit` method with 'online' learning)
rng = np.random.RandomState(0)
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components,
learning_offset=10.0,
evaluate_every=1,
learning_method="online",
random_state=rng,
)
lda.fit(X)
correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
for component in lda.components_:
# Find top 3 words in each LDA component
top_idx = set(component.argsort()[-3:][::-1])
assert tuple(sorted(top_idx)) in correct_idx_grps
def test_lda_partial_fit():
# Test LDA online learning (`partial_fit` method)
# (same as test_lda_batch)
rng = np.random.RandomState(0)
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components,
learning_offset=10.0,
total_samples=100,
random_state=rng,
)
for i in range(3):
lda.partial_fit(X)
correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
for c in lda.components_:
top_idx = set(c.argsort()[-3:][::-1])
assert tuple(sorted(top_idx)) in correct_idx_grps
def test_lda_dense_input():
# Test LDA with dense input.
rng = np.random.RandomState(0)
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components, learning_method="batch", random_state=rng
)
lda.fit(X.toarray())
correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
for component in lda.components_:
# Find top 3 words in each LDA component
top_idx = set(component.argsort()[-3:][::-1])
assert tuple(sorted(top_idx)) in correct_idx_grps
def test_lda_transform():
# Test LDA transform.
# Transform result cannot be negative and should be normalized
rng = np.random.RandomState(0)
X = rng.randint(5, size=(20, 10))
n_components = 3
lda = LatentDirichletAllocation(n_components=n_components, random_state=rng)
X_trans = lda.fit_transform(X)
assert (X_trans > 0.0).any()
assert_array_almost_equal(np.sum(X_trans, axis=1), np.ones(X_trans.shape[0]))
@pytest.mark.parametrize("method", ("online", "batch"))
def test_lda_fit_transform(method):
# Test LDA fit_transform & transform
# fit_transform and transform result should be the same
rng = np.random.RandomState(0)
X = rng.randint(10, size=(50, 20))
lda = LatentDirichletAllocation(
n_components=5, learning_method=method, random_state=rng
)
X_fit = lda.fit_transform(X)
X_trans = lda.transform(X)
assert_array_almost_equal(X_fit, X_trans, 4)
def test_lda_negative_input():
# test pass dense matrix with sparse negative input.
X = np.full((5, 10), -1.0)
lda = LatentDirichletAllocation()
regex = r"^Negative values in data passed"
with pytest.raises(ValueError, match=regex):
lda.fit(X)
def test_lda_no_component_error():
# test `perplexity` before `fit`
rng = np.random.RandomState(0)
X = rng.randint(4, size=(20, 10))
lda = LatentDirichletAllocation()
regex = (
"This LatentDirichletAllocation instance is not fitted yet. "
"Call 'fit' with appropriate arguments before using this "
"estimator."
)
with pytest.raises(NotFittedError, match=regex):
lda.perplexity(X)
@if_safe_multiprocessing_with_blas
@pytest.mark.parametrize("method", ("online", "batch"))
def test_lda_multi_jobs(method):
n_components, X = _build_sparse_mtx()
# Test LDA batch training with multi CPU
rng = np.random.RandomState(0)
lda = LatentDirichletAllocation(
n_components=n_components,
n_jobs=2,
learning_method=method,
evaluate_every=1,
random_state=rng,
)
lda.fit(X)
correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
for c in lda.components_:
top_idx = set(c.argsort()[-3:][::-1])
assert tuple(sorted(top_idx)) in correct_idx_grps
@if_safe_multiprocessing_with_blas
def test_lda_partial_fit_multi_jobs():
# Test LDA online training with multi CPU
rng = np.random.RandomState(0)
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components,
n_jobs=2,
learning_offset=5.0,
total_samples=30,
random_state=rng,
)
for i in range(2):
lda.partial_fit(X)
correct_idx_grps = [(0, 1, 2), (3, 4, 5), (6, 7, 8)]
for c in lda.components_:
top_idx = set(c.argsort()[-3:][::-1])
assert tuple(sorted(top_idx)) in correct_idx_grps
def test_lda_preplexity_mismatch():
# test dimension mismatch in `perplexity` method
rng = np.random.RandomState(0)
n_components = rng.randint(3, 6)
n_samples = rng.randint(6, 10)
X = np.random.randint(4, size=(n_samples, 10))
lda = LatentDirichletAllocation(
n_components=n_components,
learning_offset=5.0,
total_samples=20,
random_state=rng,
)
lda.fit(X)
# invalid samples
invalid_n_samples = rng.randint(4, size=(n_samples + 1, n_components))
with pytest.raises(ValueError, match=r"Number of samples"):
lda._perplexity_precomp_distr(X, invalid_n_samples)
# invalid topic number
invalid_n_components = rng.randint(4, size=(n_samples, n_components + 1))
with pytest.raises(ValueError, match=r"Number of topics"):
lda._perplexity_precomp_distr(X, invalid_n_components)
@pytest.mark.parametrize("method", ("online", "batch"))
def test_lda_perplexity(method):
# Test LDA perplexity for batch training
# perplexity should be lower after each iteration
n_components, X = _build_sparse_mtx()
lda_1 = LatentDirichletAllocation(
n_components=n_components,
max_iter=1,
learning_method=method,
total_samples=100,
random_state=0,
)
lda_2 = LatentDirichletAllocation(
n_components=n_components,
max_iter=10,
learning_method=method,
total_samples=100,
random_state=0,
)
lda_1.fit(X)
perp_1 = lda_1.perplexity(X, sub_sampling=False)
lda_2.fit(X)
perp_2 = lda_2.perplexity(X, sub_sampling=False)
assert perp_1 >= perp_2
perp_1_subsampling = lda_1.perplexity(X, sub_sampling=True)
perp_2_subsampling = lda_2.perplexity(X, sub_sampling=True)
assert perp_1_subsampling >= perp_2_subsampling
@pytest.mark.parametrize("method", ("online", "batch"))
def test_lda_score(method):
# Test LDA score for batch training
# score should be higher after each iteration
n_components, X = _build_sparse_mtx()
lda_1 = LatentDirichletAllocation(
n_components=n_components,
max_iter=1,
learning_method=method,
total_samples=100,
random_state=0,
)
lda_2 = LatentDirichletAllocation(
n_components=n_components,
max_iter=10,
learning_method=method,
total_samples=100,
random_state=0,
)
lda_1.fit_transform(X)
score_1 = lda_1.score(X)
lda_2.fit_transform(X)
score_2 = lda_2.score(X)
assert score_2 >= score_1
def test_perplexity_input_format():
# Test LDA perplexity for sparse and dense input
# score should be the same for both dense and sparse input
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components,
max_iter=1,
learning_method="batch",
total_samples=100,
random_state=0,
)
lda.fit(X)
perp_1 = lda.perplexity(X)
perp_2 = lda.perplexity(X.toarray())
assert_almost_equal(perp_1, perp_2)
def test_lda_score_perplexity():
# Test the relationship between LDA score and perplexity
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components, max_iter=10, random_state=0
)
lda.fit(X)
perplexity_1 = lda.perplexity(X, sub_sampling=False)
score = lda.score(X)
perplexity_2 = np.exp(-1.0 * (score / np.sum(X.data)))
assert_almost_equal(perplexity_1, perplexity_2)
def test_lda_fit_perplexity():
# Test that the perplexity computed during fit is consistent with what is
# returned by the perplexity method
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components,
max_iter=1,
learning_method="batch",
random_state=0,
evaluate_every=1,
)
lda.fit(X)
# Perplexity computed at end of fit method
perplexity1 = lda.bound_
# Result of perplexity method on the train set
perplexity2 = lda.perplexity(X)
assert_almost_equal(perplexity1, perplexity2)
def test_lda_empty_docs():
"""Test LDA on empty document (all-zero rows)."""
Z = np.zeros((5, 4))
for X in [Z, csr_matrix(Z)]:
lda = LatentDirichletAllocation(max_iter=750).fit(X)
assert_almost_equal(
lda.components_.sum(axis=0), np.ones(lda.components_.shape[1])
)
def test_dirichlet_expectation():
"""Test Cython version of Dirichlet expectation calculation."""
x = np.logspace(-100, 10, 10000)
expectation = np.empty_like(x)
_dirichlet_expectation_1d(x, 0, expectation)
assert_allclose(expectation, np.exp(psi(x) - psi(np.sum(x))), atol=1e-19)
x = x.reshape(100, 100)
assert_allclose(
_dirichlet_expectation_2d(x),
psi(x) - psi(np.sum(x, axis=1)[:, np.newaxis]),
rtol=1e-11,
atol=3e-9,
)
def check_verbosity(verbose, evaluate_every, expected_lines, expected_perplexities):
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(
n_components=n_components,
max_iter=3,
learning_method="batch",
verbose=verbose,
evaluate_every=evaluate_every,
random_state=0,
)
out = StringIO()
old_out, sys.stdout = sys.stdout, out
try:
lda.fit(X)
finally:
sys.stdout = old_out
n_lines = out.getvalue().count("\n")
n_perplexity = out.getvalue().count("perplexity")
assert expected_lines == n_lines
assert expected_perplexities == n_perplexity
@pytest.mark.parametrize(
"verbose,evaluate_every,expected_lines,expected_perplexities",
[
(False, 1, 0, 0),
(False, 0, 0, 0),
(True, 0, 3, 0),
(True, 1, 3, 3),
(True, 2, 3, 1),
],
)
def test_verbosity(verbose, evaluate_every, expected_lines, expected_perplexities):
check_verbosity(verbose, evaluate_every, expected_lines, expected_perplexities)
def test_lda_feature_names_out():
"""Check feature names out for LatentDirichletAllocation."""
n_components, X = _build_sparse_mtx()
lda = LatentDirichletAllocation(n_components=n_components).fit(X)
names = lda.get_feature_names_out()
assert_array_equal(
[f"latentdirichletallocation{i}" for i in range(n_components)], names
)
@pytest.mark.parametrize("learning_method", ("batch", "online"))
def test_lda_dtype_match(learning_method, global_dtype):
"""Check data type preservation of fitted attributes."""
rng = np.random.RandomState(0)
X = rng.uniform(size=(20, 10)).astype(global_dtype, copy=False)
lda = LatentDirichletAllocation(
n_components=5, random_state=0, learning_method=learning_method
)
lda.fit(X)
assert lda.components_.dtype == global_dtype
assert lda.exp_dirichlet_component_.dtype == global_dtype
@pytest.mark.parametrize("learning_method", ("batch", "online"))
def test_lda_numerical_consistency(learning_method, global_random_seed):
"""Check numerical consistency between np.float32 and np.float64."""
rng = np.random.RandomState(global_random_seed)
X64 = rng.uniform(size=(20, 10))
X32 = X64.astype(np.float32)
lda_64 = LatentDirichletAllocation(
n_components=5, random_state=global_random_seed, learning_method=learning_method
).fit(X64)
lda_32 = LatentDirichletAllocation(
n_components=5, random_state=global_random_seed, learning_method=learning_method
).fit(X32)
assert_allclose(lda_32.components_, lda_64.components_)
assert_allclose(lda_32.transform(X32), lda_64.transform(X64))