def test_n_neighbors():
X = np.arange(12).reshape(4, 3)
y = [1, 1, 2, 2]
lmnn = LargeMarginNearestNeighbor(n_neighbors=2)
assert_warns_message(
UserWarning, '`n_neighbors` (=2) is not less than the number of '
'samples in the smallest non-singleton class (=2). '
'`n_neighbors_` will be set to 1 for estimation.', lmnn.fit, X, y)
def test_neighbors_params():
from scipy.spatial.distance import hamming
params = {'algorithm': 'brute', 'metric': hamming}
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, neighbors_params=params)
lmnn.fit(iris_data, iris_target)
components_hamming = lmnn.components_
lmnn = LargeMarginNearestNeighbor(n_neighbors=3)
lmnn.fit(iris_data, iris_target)
components_euclidean = lmnn.components_
assert (not np.allclose(components_hamming, components_euclidean))
def test_warm_start_validation():
X, y = datasets.make_classification(n_samples=30,
n_features=5,
n_classes=4,
n_redundant=0,
n_informative=5,
random_state=0)
lmnn = LargeMarginNearestNeighbor(warm_start=True, max_iter=5)
lmnn.fit(X, y)
X_less_features, y = \
datasets.make_classification(n_samples=30, n_features=4, n_classes=4,
n_redundant=0, n_informative=4,
random_state=0)
assert_raise_message(
ValueError, 'The new inputs dimensionality ({}) does not '
'match the input dimensionality of the '
'previously learned transformation ({}).'.format(
X_less_features.shape[1], lmnn.components_.shape[1]), lmnn.fit,
X_less_features, y)
def test_pipeline_equivalency():
X = iris_data
y = iris_target
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3)
# Use init='identity' to ensure reproducibility
lmnn_params = dict(n_neighbors=3,
max_iter=10,
init='identity',
random_state=42)
n_neighbors = 3
lmnn = LargeMarginNearestNeighbor(**lmnn_params)
lmnn.fit(X_train, y_train)
lmnn_pipe = make_lmnn_pipeline(**lmnn_params)
lmnn_pipe.fit(X_train, y_train)
pipe_transformation = lmnn_pipe.named_steps.lmnn.components_
assert_array_almost_equal(lmnn.components_, pipe_transformation)
knn = KNeighborsClassifier(n_neighbors=n_neighbors)
knn.fit(lmnn.transform(X_train), y_train)
score = knn.score(lmnn.transform(X_test), y_test)
score_pipe = lmnn_pipe.score(X_test, y_test)
assert (score == score_pipe)
def test_callback():
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, callback='my_cb')
assert_raise_message(ValueError, '`callback` is not callable.', lmnn.fit,
iris_data, iris_target)
max_iter = 10
def my_cb(transformation, n_iter):
rem_iter = max_iter - n_iter
print('{} iterations remaining...'.format(rem_iter))
# assert that my_cb is called
old_stdout = sys.stdout
sys.stdout = StringIO()
lmnn = LargeMarginNearestNeighbor(n_neighbors=3,
callback=my_cb,
max_iter=max_iter,
verbose=1)
try:
lmnn.fit(iris_data, iris_target)
finally:
out = sys.stdout.getvalue()
sys.stdout.close()
sys.stdout = old_stdout
# check output
assert ('{} iterations remaining...'.format(max_iter - 1) in out)
def test_singleton_class():
X = iris_data
y = iris_target
X_tr, X_te, y_tr, y_te = train_test_split(X, y, test_size=0.3, stratify=y)
# one singleton class
singleton_class = 1
ind_singleton, = np.where(y_tr == singleton_class)
y_tr[ind_singleton] = 2
y_tr[ind_singleton[0]] = singleton_class
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, max_iter=30)
lmnn.fit(X_tr, y_tr)
# One non-singleton class
X_tr, X_te, y_tr, y_te = train_test_split(X, y, test_size=0.3, stratify=y)
ind_1, = np.where(y_tr == 1)
ind_2, = np.where(y_tr == 2)
y_tr[ind_1] = 0
y_tr[ind_1[0]] = 1
y_tr[ind_2] = 0
y_tr[ind_2[0]] = 2
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, max_iter=30)
assert_raise_message(
ValueError, 'LargeMarginNearestNeighbor needs at least 2 '
'non-singleton classes, got 1.', lmnn.fit, X_tr, y_tr)
def test_same_lmnn_parallel():
X, y = datasets.make_classification(n_samples=30,
n_features=5,
n_redundant=0,
random_state=0)
X_train, X_test, y_train, y_test = train_test_split(X, y)
lmnn = LargeMarginNearestNeighbor(n_neighbors=3)
lmnn.fit(X_train, y_train)
components = lmnn.components_
lmnn.set_params(n_jobs=3)
lmnn.fit(X_train, y_train)
components_parallel = lmnn.components_
assert_array_almost_equal(components, components_parallel)
def test_neighbors_iris():
# Sanity checks on the iris dataset
# Puts three points of each label in the plane and performs a
# nearest neighbor query on points near the decision boundary.
lmnn = LargeMarginNearestNeighbor(n_neighbors=1)
lmnn.fit(iris_data, iris_target)
knn = KNeighborsClassifier(n_neighbors=lmnn.n_neighbors_)
LX = lmnn.transform(iris_data)
knn.fit(LX, iris_target)
y_pred = knn.predict(LX)
assert_array_equal(y_pred, iris_target)
lmnn.set_params(n_neighbors=9)
lmnn.fit(iris_data, iris_target)
knn = KNeighborsClassifier(n_neighbors=lmnn.n_neighbors_)
knn.fit(LX, iris_target)
assert (knn.score(LX, iris_target) > 0.95)
def test_impostor_store():
k = 3
lmnn = LargeMarginNearestNeighbor(n_neighbors=k,
init='identity',
impostor_store='list')
lmnn.fit(iris_data, iris_target)
components_list = lmnn.components_
lmnn = LargeMarginNearestNeighbor(n_neighbors=k,
init='identity',
impostor_store='sparse')
lmnn.fit(iris_data, iris_target)
components_sparse = lmnn.components_
assert_array_almost_equal(components_list,
components_sparse,
err_msg='Toggling `impostor_store` results in '
'a different solution.')
def test_neighbors_digits():
# Sanity check on the digits dataset
# the 'brute' algorithm has been observed to fail if the input
# dtype is uint8 due to overflow in distance calculations.
X = digits_data.astype('uint8')
y = digits_target
n_samples, n_features = X.shape
train_test_boundary = int(n_samples * 0.8)
train = np.arange(0, train_test_boundary)
test = np.arange(train_test_boundary, n_samples)
X_train, y_train, X_test, y_test = X[train], y[train], X[test], y[test]
k = 1
lmnn = LargeMarginNearestNeighbor(n_neighbors=k, max_iter=30)
lmnn.fit(X_train, y_train)
knn = KNeighborsClassifier(n_neighbors=k)
knn.fit(lmnn.transform(X_train), y_train)
score_uint8 = knn.score(lmnn.transform(X_test), y_test)
knn.fit(lmnn.transform(X_train.astype(float)), y_train)
score_float = knn.score(lmnn.transform(X_test.astype(float)), y_test)
assert (score_uint8 == score_float)
def test_convergence_warning():
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, max_iter=2, verbose=1)
cls_name = lmnn.__class__.__name__
assert_warns_message(ConvergenceWarning,
'[{}] LMNN did not converge'.format(cls_name),
lmnn.fit, iris_data, iris_target)
def test_random_state():
"""Assert that when having more than max_impostors (forcing sampling),
the same impostors will be sampled given the same random_state and
different impostors will be sampled given a different random_state
leading to a different transformation"""
X = iris_data
y = iris_target
# Use init='identity' to ensure reproducibility
params = {
'n_neighbors': 3,
'max_impostors': 5,
'random_state': 1,
'max_iter': 10,
'init': 'identity'
}
lmnn = LargeMarginNearestNeighbor(**params)
lmnn.fit(X, y)
transformation_1 = lmnn.components_
lmnn = LargeMarginNearestNeighbor(**params)
lmnn.fit(X, y)
transformation_2 = lmnn.components_
# This assertion fails on 32bit systems if init='pca'
assert_allclose(transformation_1, transformation_2)
params['random_state'] = 2
lmnn = LargeMarginNearestNeighbor(**params)
lmnn.fit(X, y)
transformation_3 = lmnn.components_
assert (not np.allclose(transformation_2, transformation_3))
{\displaystyle \min _{\mathbf {M} }\sum _{i,j\in N_{i}}d({\vec {x}}_{i},{\vec {x}}_{j})+\lambda \sum _{i,j,l}\xi _{ijl}}
{\displaystyle \forall _{i,j\in N_{i},l,y_{l}\neq y_{i}}}\forall _{{i,j\in N_{i},l,y_{l}\neq y_{i}}}
{\displaystyle d({\vec {x}}_{i},{\vec {x}}_{j})+1-d({\vec {x}}_{i},{\vec {x}}_{l})\leq \xi _{ijl}}{\displaystyle d({\vec {x}}_{i},{\vec {x}}_{j})+1-d({\vec {x}}_{i},{\vec {x}}_{l})\leq \xi _{ijl}}
{\displaystyle \xi _{ijl}\geq 0}\xi _{{ijl}}\geq 0
{\displaystyle \mathbf {M} \succeq 0}{\mathbf {M}}\succeq 0
For this coursework, PyLMNN package is used to compute LMNN for metric learning:https://pypi.org/project/PyLMNN/
"""
# need pip install pylmnn
from pylmnn import LargeMarginNearestNeighbor as LMNN
# Set up the hyperparameters
k_train, n_components, max_iter = 5, 25, 1000
# Instantiate the metric learner
lmnn = LMNN(n_neighbors=k_train, max_iter=max_iter, n_components= n_components)
# Train the metric learner
lmnn_original = lmnn.fit(original_train_list, Y_train)
lmnn_test = lmnn_original.transform(original_test_list)
lmnn_test= lmnn_test.T
print(lmnn_test.shape)
rank_k = []
for i in range(1,lmnn_test.shape[1]):
rank_k.append(i)
#initialise maP and accuracy scores
avg_prec = 0
rank1_prec = []
def test_warm_start_effectiveness():
# A 1-iteration second fit on same data should give almost same result
# with warm starting, and quite different result without warm starting.
X, y = datasets.make_classification(n_samples=30,
n_features=5,
n_redundant=0,
random_state=0)
X_train, X_test, y_train, y_test = train_test_split(X, y)
n_iter = 10
lmnn_warm = LargeMarginNearestNeighbor(n_neighbors=3,
warm_start=True,
max_iter=n_iter,
random_state=0)
lmnn_warm.fit(X_train, y_train)
transformation_warm = lmnn_warm.components_
lmnn_warm.max_iter = 1
lmnn_warm.fit(X_train, y_train)
transformation_warm_plus_one = lmnn_warm.components_
lmnn_cold = LargeMarginNearestNeighbor(n_neighbors=3,
warm_start=False,
max_iter=n_iter,
random_state=0)
lmnn_cold.fit(X_train, y_train)
transformation_cold = lmnn_cold.components_
lmnn_cold.max_iter = 1
lmnn_cold.fit(X_train, y_train)
transformation_cold_plus_one = lmnn_cold.components_
diff_warm = np.sum(
np.abs(transformation_warm_plus_one - transformation_warm))
diff_cold = np.sum(
np.abs(transformation_cold_plus_one - transformation_cold))
assert (diff_warm < 2.0,
"Transformer changed significantly after one iteration even "
"though it was warm-started.")
assert (diff_cold > diff_warm,
"Cold-started transformer changed less significantly than "
"warm-started transformer after one iteration.")
# embedding
loreal_data = np.load('/export/home//loreal_135_classification/em_training.npz')
X_train, y_train = loreal_data['X'], loreal_data['y']
loreal_data = np.load('/export/home//loreal_135_classification/em_test.npz')
X_test, y_test = loreal_data['X'], loreal_data['y']
'''
knn = KNeighborsClassifier(n_neighbors=10)
# Train with no transformation (euclidean metric)
knn.fit(X_train, y_train)
# Test with euclidean metric
acc = knn.score(X_test, y_test)
print('KNN accuracy on test set: {}'.format(acc))
# LMNN is no longer a classifier but a transformer
lmnn = LargeMarginNearestNeighbor(n_neighbors=10, verbose=1, max_iter=300)
lmnn.fit(X_train, y_train)
# Train with transformation learned by LMNN
knn.fit(lmnn.transform(X_train), y_train)
# Test with transformation learned by LMNN
acc = knn.score(lmnn.transform(X_test), y_test)
print('LMNN accuracy on test set: {}'.format(acc))
def test_init_transformation():
X, y = datasets.make_classification(n_samples=30,
n_features=5,
n_redundant=0,
random_state=0)
X_train, X_test, y_train, y_test = train_test_split(X, y)
# Initialize with identity
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, init='identity')
lmnn.fit(X_train, y_train)
# Initialize with PCA
lmnn_pca = LargeMarginNearestNeighbor(n_neighbors=3, init='pca')
lmnn_pca.fit(X_train, y_train)
# Initialize with a transformation given by the user
init = np.random.rand(X.shape[1], X.shape[1])
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, init=init)
lmnn.fit(X_train, y_train)
# init.shape[1] must match X.shape[1]
init = np.random.rand(X.shape[1], X.shape[1] + 1)
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, init=init)
assert_raise_message(
ValueError, 'The input dimensionality ({}) of the given '
'linear transformation `init` must match the '
'dimensionality of the given inputs `X` ({}).'.format(
init.shape[1], X.shape[1]), lmnn.fit, X_train, y_train)
# init.shape[0] must be <= init.shape[1]
init = np.random.rand(X.shape[1] + 1, X.shape[1])
lmnn = LargeMarginNearestNeighbor(n_neighbors=3, init=init)
assert_raise_message(
ValueError, 'The output dimensionality ({}) of the given '
'linear transformation `init` cannot be '
'greater than its input dimensionality ({}).'.format(
init.shape[0], init.shape[1]), lmnn.fit, X_train, y_train)
# init.shape[0] must match n_components
init = np.random.rand(X.shape[1], X.shape[1])
n_components = X.shape[1] - 2
lmnn = LargeMarginNearestNeighbor(n_neighbors=3,
init=init,
n_components=n_components)
assert_raise_message(
ValueError, 'The preferred embedding dimensionality '
'`n_components` ({}) does not match '
'the output dimensionality of the given '
'linear transformation `init` ({})!'.format(n_components,
init.shape[0]), lmnn.fit,
X_train, y_train)
from sklearn.neighbors import KNeighborsClassifier
from sklearn.model_selection import train_test_split
from sklearn.datasets import load_iris
from pylmnn import LargeMarginNearestNeighbor as LMNN
# Load a data set
X, y = load_iris(return_X_y=True)
# Split in training and testing set
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.7, stratify=y, random_state=42)
# Set up the hyperparameters
k_train, k_test, n_components, max_iter = 3, 3, X.shape[1], 180
# Instantiate the metric learner
lmnn = LMNN(n_neighbors=k_train, max_iter=max_iter, n_components=n_components)
# Train the metric learner
lmnn.fit(X_train, y_train)
# Fit the nearest neighbors classifier
knn = KNeighborsClassifier(n_neighbors=k_test)
knn.fit(lmnn.transform(X_train), y_train)
# Compute the k-nearest neighbor test accuracy after applying the learned transformation
lmnn_acc = knn.score(lmnn.transform(X_test), y_test)
print('LMNN accuracy on test set of {} points: {:.4f}'.format(X_test.shape[0], lmnn_acc))
import numpy as np
from pylmnn import LargeMarginNearestNeighbor as LMNN
csv = np.genfromtxt("data/numerical_train.csv", delimiter=',')
csv_test = np.genfromtxt("data/numerical_test.csv", delimiter=',')
n, d = csv.shape
X_train = csv[:, :d - 1]
y_train = csv[:, -1]
X_test = csv_test[:, :d - 1]
y_test = csv_test[:, -1]
k_train, n_components, max_iter = 7, d - 1, 180
lmnn = LMNN(n_neighbors=k_train, max_iter=max_iter, n_components=n_components)
print('learning the metric...')
# Train the metric learner
lmnn.fit(X_train, y_train)
X_train_transformed = lmnn.transform(X_train)
X_test_transformed = lmnn.transform(X_test)
pickle.dump(X_train_transformed,
open("data/numerical_train_transformed.pkl", 'wb'))
pickle.dump(y_train, open("data/numerical_train_labels.pkl", 'wb'))
pickle.dump(X_test_transformed,
open("data/numerical_test_transformed.pkl", 'wb'))
pickle.dump(y_test, open("data/numerical_test_labels.pkl", 'wb'))
acc1 = []
acc2 = []
acc3 = []
acc4 = []
T = []
T1 = []
T2 = []
T3 = []
T4 = []
for k in [9, 11, 12, 13, 14, 16, 17, 18, 19, 21, 22, 23, 24, 26, 27, 28, 29]:
print('Running K={} ... ... '.format(k))
t0 = time.time()
lmnn = LMNN(n_neighbors=k, max_iter=200, n_components=x.shape[1])
lmnn.fit(x_train, y_train)
x_train_ = lmnn.transform(x_train)
x_test_ = lmnn.transform(x_test)
t1 = time.time()
T.append(t1 - t0)
print('LMNN Cost:', t1 - t0)
knn = KNeighborsClassifier(n_neighbors=k,
weights='distance',
metric='cosine',
algorithm='brute')
knn.fit(x_train_, y_train)
lmnn_acc = knn.score(x_test_, y_test)
acc1.append(lmnn_acc)
t2 = time.time()
