def __tsne_test_helper(self, data, n_com):
tsne_def = TSNE(n_components=n_com, metric="euclidean")
tsne_def = tsne_def(data)
tsne_euc = TSNE(n_components=n_com, metric=Euclidean)
tsne_euc = tsne_euc(data)
tsne_pre = TSNE(n_components=n_com, metric="precomputed")
tsne_pre = tsne_pre(Euclidean(data))
self.assertEqual((data.X.shape[0], n_com), tsne_def.embedding_.shape)
self.assertEqual((data.X.shape[0], n_com), tsne_euc.embedding_.shape)
self.assertEqual((data.X.shape[0], n_com), tsne_pre.embedding_.shape)
def _reduce_dimensions(data, method="MDS", use_cosine=False):
"""
Reduce the dimensionality of the data to 2D.
Parameters
----------
data: Orange.data.Table
The image embeddings (vectors of length 2048).
method: string
The method to use (default MDS).
use_cosine: bool
Precompute cosine distances and pass them to MDS.
Returns
-------
array-like
The data, reduced to 2 dimensions.
"""
if method == "MDS":
if use_cosine:
mds = MDS(n_init=1, dissimilarity="precomputed")
dist_matrix = Cosine(data)
return mds(dist_matrix).embedding_
else:
mds = MDS(n_init=1, init_type="PCA")
return mds(data).embedding_
elif method == "PCA":
pca = PCA(n_components=2)
return pca(data)(data)
elif method == "TSNE":
tsne = TSNE(init="pca")
return tsne(data).embedding_
def test_transform(self):
# Set perplexity to avoid warnings
tsne = TSNE(perplexity=10)
model = tsne(self.iris[::2])
new_embedding = model(self.iris[1::2])
# The new embedding should not contain NaNs
self.assertFalse(np.any(np.isnan(new_embedding.X)))
def compute_tsne(data, perplexity, iter, init):
negative_gradient_method = 'fft' if len(data.X) > 10000 else 'bh'
neighbor_method = 'approx' if len(data.X) > 10000 else 'exact'
tsne = TSNE(
perplexity=perplexity, n_iter=iter, initialization=init, theta=.8,
early_exaggeration_iter=0, negative_gradient_method=negative_gradient_method,
neighbors=neighbor_method, random_state=0
)
return tsne(data)
def test_continue_optimization_inplace(self):
tsne = TSNE(n_iter=100)
model = tsne(self.iris)
new_model = model.optimize(100, inplace=True)
# If we don't do things inplace, then the instances should be the same
self.assertIs(model, new_model)
self.assertIs(model.embedding, new_model.embedding)
self.assertIs(model.embedding_, new_model.embedding_)
# The embeddings in the table should match the embedding object
np.testing.assert_equal(new_model.embedding.X, new_model.embedding_)
def test_fit(self):
n_components = 2
tsne = TSNE(n_components=n_components)
model = tsne(self.iris)
# The embedding should have the correct number of dimensions
self.assertEqual(model.embedding.X.shape, (self.iris.X.shape[0], n_components))
# The embedding should not contain NaNs
self.assertFalse(np.any(np.isnan(model.embedding.X)))
# The embeddings in the table should match the embedding object
np.testing.assert_equal(model.embedding.X, model.embedding_)
def test_continue_optimization(self):
tsne = TSNE(n_iter=100)
model = tsne(self.iris)
new_model = model.optimize(100, inplace=False)
# If we don't do things inplace, then the instances should be different
self.assertIsNot(model, new_model)
self.assertIsNot(model.embedding, new_model.embedding)
self.assertIsNot(model.embedding_, new_model.embedding_)
self.assertFalse(np.allclose(model.embedding.X, new_model.embedding.X),
'Embedding should change after further optimization.')
# The embeddings in the table should match the embedding object
np.testing.assert_equal(new_model.embedding.X, new_model.embedding_)
def test_pickle(self):
for neighbors in ("exact", "approx"):
tsne = TSNE(early_exaggeration_iter=0,
n_iter=10,
perplexity=30,
neighbors=neighbors,
random_state=0)
model = tsne(self.iris[::2])
loaded_model = pickle.loads(pickle.dumps(model))
new_embedding = loaded_model(self.iris[1::2]).X
knn = KNeighborsClassifier(n_neighbors=5)
knn.fit(new_embedding, self.iris[1::2].Y)
predicted = knn.predict(new_embedding)
self.assertTrue(
accuracy_score(predicted, self.iris[1::2].Y) > 0.95,
msg=f"Pickling failed with `neighbors={neighbors}`",
)
def test_fft_correctness(self):
knn = KNeighborsClassifier(n_neighbors=5)
# Set iterations to 0 so we check that the initialization is fairly random
tsne = TSNE(early_exaggeration_iter=0, n_iter=0, perplexity=30,
negative_gradient_method='fft', initialization='random',
random_state=0)
model = tsne(self.iris)
# Evaluate KNN on the random initialization
knn.fit(model.embedding_, self.iris.Y)
predicted = knn.predict(model.embedding_)
self.assertTrue(accuracy_score(predicted, self.iris.Y) < 0.6)
# 100 iterations should be enough for iris
model.optimize(n_iter=100, inplace=True)
# Evaluate KNN on the tSNE embedding
knn.fit(model.embedding_, self.iris.Y)
predicted = knn.predict(model.embedding_)
self.assertTrue(accuracy_score(predicted, self.iris.Y) > 0.95)
def __start(self):
self.pca_preprocessing()
# We call PCA through fastTSNE because it involves scaling. Instead of
# worrying about this ourselves, we'll let the library worry for us.
initialization = TSNE.default_initialization(self.pca_data.X,
n_components=2,
random_state=0)
# Compute perplexity settings for multiscale
n_samples = self.pca_data.X.shape[0]
if self.multiscale:
perplexity = min((n_samples - 1) / 3, 50), min((n_samples - 1) / 3,
500)
else:
perplexity = self.perplexity
# Determine whether to use settings for large data sets
if n_samples > 10_000:
neighbor_method, gradient_method = "approx", "fft"
else:
neighbor_method, gradient_method = "exact", "bh"
# Set number of iterations to 0 - these will be run subsequently
self.projection = TSNE(n_components=2,
perplexity=perplexity,
multiscale=self.multiscale,
early_exaggeration_iter=0,
n_iter=0,
initialization=initialization,
exaggeration=self.exaggeration,
neighbors=neighbor_method,
negative_gradient_method=gradient_method,
random_state=0)(self.pca_data)
self.tsne_runner = TSNERunner(self.projection, step_size=50)
self.tsne_iterator = self.tsne_runner.run_optimization()
self.__set_update_loop(self.tsne_iterator)
self.progressBarInit(processEvents=None)
def test_multiscale(self):
tsne = TSNE(perplexity=(10, 10), multiscale=True)
model = tsne(self.iris[::2])
embedding = model(self.iris[1::2])
self.assertFalse(np.any(np.isnan(embedding.X)))