def visualize_class_separation(X, labels):
_, (ax1,ax2) = pyplot.subplots(ncols=2)
label_order = np.argsort(labels)
ax1.imshow(pairwise_distances(X[label_order]), interpolation='nearest')
ax2.imshow(pairwise_distances(labels[label_order,None]),
interpolation='nearest')
pyplot.show()
def _hdbscan_generic(X, min_samples=5, alpha=1.0,
metric='minkowski', p=2, leaf_size=None, gen_min_span_tree=False):
if metric == 'minkowski':
if p is None:
raise TypeError('Minkowski metric given but no p value supplied!')
if p < 0:
raise ValueError('Minkowski metric with negative p value is not defined!')
distance_matrix = pairwise_distances(X, metric=metric, p=p)
else:
distance_matrix = pairwise_distances(X, metric=metric)
mutual_reachability_ = mutual_reachability(distance_matrix,
min_samples, alpha)
min_spanning_tree = mst_linkage_core(mutual_reachability_)
if gen_min_span_tree:
result_min_span_tree = min_spanning_tree.copy()
for index, row in enumerate(result_min_span_tree[1:], 1):
candidates = np.where(np.isclose(mutual_reachability_[row[1]], row[2]))[0]
candidates = np.intersect1d(candidates, min_spanning_tree[:index, :2].astype(int))
candidates = candidates[candidates != row[1]]
assert (len(candidates) > 0)
row[0] = candidates[0]
else:
result_min_span_tree = None
min_spanning_tree = min_spanning_tree[np.argsort(min_spanning_tree.T[2]), :]
single_linkage_tree = label(min_spanning_tree)
return single_linkage_tree, result_min_span_tree
def test_silhouette():
# Tests the Silhouette Coefficient.
dataset = datasets.load_iris()
X = dataset.data
y = dataset.target
D = pairwise_distances(X, metric='euclidean')
# Given that the actual labels are used, we can assume that S would be
# positive.
silhouette = silhouette_score(D, y, metric='precomputed')
assert(silhouette > 0)
# Test without calculating D
silhouette_metric = silhouette_score(X, y, metric='euclidean')
assert_almost_equal(silhouette, silhouette_metric)
# Test with sampling
silhouette = silhouette_score(D, y, metric='precomputed',
sample_size=int(X.shape[0] / 2),
random_state=0)
silhouette_metric = silhouette_score(X, y, metric='euclidean',
sample_size=int(X.shape[0] / 2),
random_state=0)
assert(silhouette > 0)
assert(silhouette_metric > 0)
assert_almost_equal(silhouette_metric, silhouette)
# Test with sparse X
X_sparse = csr_matrix(X)
D = pairwise_distances(X_sparse, metric='euclidean')
silhouette = silhouette_score(D, y, metric='precomputed')
assert(silhouette > 0)
def smart_initialize(data, k, seed=None):
"""
Use k-means++ to initialize a good set of centroids
:param data: whole dataset
:param k: number of centroids
:param seed: random seed
:return: initial centroids
"""
if seed is not None: # useful for obtaining consistent results
np.random.seed(seed)
centroids = np.zeros((k, data.shape[1]))
# Randomly choose the first centroid.
# Since we have no prior knowledge, choose uniformly at random
idx = np.random.randint(data.shape[0])
centroids[0] = data[idx, :].toarray()
# Compute distances from the first centroid chosen to all the other data points
distances = pairwise_distances(data, centroids[0:1], metric='euclidean').flatten()
for i in range(1, k):
# Choose the next centroid randomly, so that the probability for each data point to be chosen
# is directly proportional to its squared distance from the nearest centroid.
# Roughly speaking, a new centroid should be as far as from other centroids as possible.
idx = np.random.choice(data.shape[0], 1, p=distances / sum(distances))
centroids[i] = data[idx, :].toarray()
# Now compute distances from the centroids to all data points
distances = np.min(pairwise_distances(data, centroids[0:i + 1], metric='euclidean'), axis=1)
return centroids
def _rsl_small_kdtree(X, cut, k=5, alpha=1.4142135623730951, gamma=5, metric='minkowski', p=2):
if metric == 'minkowski':
if p is None:
raise TypeError('Minkowski metric given but no p value supplied!')
if p < 0:
raise ValueError('Minkowski metric with negative p value is not defined!')
distance_matrix = pairwise_distances(X, metric=metric, p=p)
else:
distance_matrix = pairwise_distances(X, metric=metric)
mutual_reachability_ = kdtree_mutual_reachability(X,
distance_matrix,
metric,
p=p,
min_points=k,
alpha=alpha)
min_spanning_tree = mst_linkage_core(mutual_reachability_)
min_spanning_tree = min_spanning_tree[np.argsort(min_spanning_tree.T[2]), :]
single_linkage_tree = label(min_spanning_tree)
single_linkage_tree = SingleLinkageTree(single_linkage_tree)
labels = single_linkage_tree.get_clusters(cut, gamma)
return labels, single_linkage_tree
def _hdbscan_small_kdtree(X, min_cluster_size=5, min_samples=None,
metric='minkowski', p=2):
if metric == 'minkowski':
if p is None:
raise TypeError('Minkowski metric given but no p value supplied!')
if p < 0:
raise ValueError('Minkowski metric with negative p value is not defined!')
distance_matrix = pairwise_distances(X, metric=metric, p=p)
else:
distance_matrix = pairwise_distances(X, metric=metric)
mutual_reachability_ = kdtree_mutual_reachability(X,
distance_matrix,
metric,
p=p,
min_points=min_samples)
min_spanning_tree = mst_linkage_core(mutual_reachability_)
min_spanning_tree = min_spanning_tree[np.argsort(min_spanning_tree.T[2]), :]
single_linkage_tree = label(min_spanning_tree)
condensed_tree = condense_tree(single_linkage_tree,
min_cluster_size)
stability_dict = compute_stability(condensed_tree)
cluster_list = get_clusters(condensed_tree, stability_dict)
labels = -1 * np.ones(X.shape[0], dtype=int)
for index, cluster in enumerate(cluster_list):
labels[cluster] = index
return labels, condensed_tree, single_linkage_tree, min_spanning_tree
def class_separation(X, labels):
unique_labels, label_inds = np.unique(labels, return_inverse=True)
ratio = 0
for li in xrange(len(unique_labels)):
Xc = X[label_inds==li]
Xnc = X[label_inds!=li]
ratio += pairwise_distances(Xc).mean() / pairwise_distances(Xc,Xnc).mean()
return ratio / len(unique_labels)
def eval(self, X):
"""Evaluate the kernel density estimation
Parameters
----------
X : array_like
array of points at which to evaluate the KDE. Shape is
(n_points, n_dim), where n_dim matches the dimension of
the training points.
Returns
-------
dens : ndarray
array of shape (n_points,) giving the density at each point.
The density will be normalized for metric='gaussian' or
metric='tophat', and will be unnormalized otherwise.
"""
X = np.atleast_2d(X)
if X.ndim != 2:
raise ValueError('X must be two-dimensional')
if X.shape[1] != self.X_.shape[1]:
raise ValueError('dimensions of X do not match training dimension')
if self.metric == 'gaussian':
# wrangle gaussian into scikit-learn's 'rbf' kernel
gamma = 0.5 / self.h / self.h
D = pairwise_kernels(X, self.X_, metric='rbf', gamma=gamma)
D /= np.sqrt(2 * np.pi * self.h ** (2 * X.shape[1]))
dens = D.sum(1)
elif self.metric == 'tophat':
# use Ball Tree to efficiently count neighbors
bt = BallTree(self.X_)
counts = bt.query_radius(X, self.h,
count_only=True)
dens = counts / n_volume(self.h, X.shape[1])
elif self.metric == 'exponential':
D = pairwise_distances(X, self.X_)
dens = np.exp(-abs(D) / self.h)
dens = dens.sum(1)
dens /= n_volume(self.h, X.shape[1]) * special.gamma(X.shape[1])
elif self.metric == 'quadratic':
D = pairwise_distances(X, self.X_)
dens = (1 - (D / self.h) ** 2)
dens[D > self.h] = 0
dens = dens.sum(1)
dens /= 2. * n_volume(self.h, X.shape[1]) / (X.shape[1] + 2)
else:
D = pairwise_kernels(X, self.X_, metric=self.metric, **self.kwargs)
dens = D.sum(1)
return dens
def __call__(self, X_train, X_test, y_train, y_test):
X = np.vstack([X_train, X_test])
y = np.hstack([y_train, y_test])
unique_labels, label_inds = np.unique(y, return_inverse=True)
ratio = 0
for li in range(len(unique_labels)):
Xc = X[label_inds == li]
Xnc = X[label_inds != li]
ratio += pairwise_distances(Xc).mean() \
/ pairwise_distances(Xc, Xnc).mean()
return -ratio / len(unique_labels)
def outlier_clusters_ward(x, y, skill=None, memory=None):
# TODO: incorporate skill
data = np.vstack((x, y)).T
if len(data) == 0:
# uh.
print 'clustering: NO cluster members!'
cluster_centers = np.array([[-1, -1]])
cluster_labels = []
labels = []
n_clusters = 0
dist_within = np.array([])
elif len(data) == 1:
print 'clustering: only 1 data point!'
cluster_centers = data
cluster_labels = [0]
labels = np.array([0])
n_clusters = 1
dist_within = np.array([0])
else:
dist_within = 1000
dist_max = 75
n_clusters = 0
n_clusters_max = 10
clusterer = AgglomerativeClustering(n_clusters=n_clusters,
memory=memory)
# while dist_within > dist_max, keep adding clusters
while (dist_within > dist_max) * (n_clusters < n_clusters_max):
# iterate n_clusters
n_clusters += 1
clusterer.set_params(n_clusters=n_clusters)
# cluster
labels = clusterer.fit_predict(data)
# get cluster_centers
cluster_labels = range(n_clusters)
cluster_centers = np.array([np.mean(data[labels == i], axis=0)
for i in cluster_labels])
# find dist_within: the maximum pairwise distance inside a cluster
dist_within = np.max([np.max(pairwise_distances(
data[labels == i]))
for i in cluster_labels])
dist_within_final = np.array([np.max(pairwise_distances(
data[labels == i])) for i in cluster_labels])
return cluster_centers, cluster_labels, labels, n_clusters, dist_within_final
def test_precomputed(random_state=42):
"""Tests unsupervised NearestNeighbors with a distance matrix."""
# Note: smaller samples may result in spurious test success
rng = np.random.RandomState(random_state)
X = rng.random_sample((10, 4))
Y = rng.random_sample((3, 4))
DXX = metrics.pairwise_distances(X, metric='euclidean')
DYX = metrics.pairwise_distances(Y, X, metric='euclidean')
for method in ['kneighbors']:
# TODO: also test radius_neighbors, but requires different assertion
# As a feature matrix (n_samples by n_features)
nbrs_X = neighbors.NearestNeighbors(n_neighbors=3)
nbrs_X.fit(X)
dist_X, ind_X = getattr(nbrs_X, method)(Y)
# As a dense distance matrix (n_samples by n_samples)
nbrs_D = neighbors.NearestNeighbors(n_neighbors=3, algorithm='brute',
metric='precomputed')
nbrs_D.fit(DXX)
dist_D, ind_D = getattr(nbrs_D, method)(DYX)
assert_array_almost_equal(dist_X, dist_D)
assert_array_almost_equal(ind_X, ind_D)
# Check auto works too
nbrs_D = neighbors.NearestNeighbors(n_neighbors=3, algorithm='auto',
metric='precomputed')
nbrs_D.fit(DXX)
dist_D, ind_D = getattr(nbrs_D, method)(DYX)
assert_array_almost_equal(dist_X, dist_D)
assert_array_almost_equal(ind_X, ind_D)
# Check X=None in prediction
dist_X, ind_X = getattr(nbrs_X, method)(None)
dist_D, ind_D = getattr(nbrs_D, method)(None)
assert_array_almost_equal(dist_X, dist_D)
assert_array_almost_equal(ind_X, ind_D)
# Must raise a ValueError if the matrix is not of correct shape
assert_raises(ValueError, getattr(nbrs_D, method), X)
target = np.arange(X.shape[0])
for Est in (neighbors.KNeighborsClassifier,
neighbors.RadiusNeighborsClassifier,
neighbors.KNeighborsRegressor,
neighbors.RadiusNeighborsRegressor):
print(Est)
est = Est(metric='euclidean')
est.radius = est.n_neighbors = 1
pred_X = est.fit(X, target).predict(Y)
est.metric = 'precomputed'
pred_D = est.fit(DXX, target).predict(DYX)
assert_array_almost_equal(pred_X, pred_D)
def find_distance_matrix(self, metric='cosine'):
'''
compute distance matrix between topis using cosine or euclidean
distance (default=cosine distance)
'''
if metric == 'cosine':
self.distance_matrix = pairwise_distances(self.topics,
metric='cosine')
# diagonals should be exactly zero, so remove rounding errors
numpy.fill_diagonal(self.distance_matrix, 0)
if metric == 'euclidean':
self.distance_matrix = pairwise_distances(self.topics,
metric='euclidean')
def update_clfs_M(self, clfs, M):
self.clfs = clfs
self.M = M
self.knn_test_dist, self.knn_test = NearestNeighbors(self.k, algorithm='brute', metric='mahalanobis', VI=self.M).fit(self.X_train).kneighbors(self.X_test)
self.preds_train = np.array([e.predict(self.X_train) for e in clfs]).T
self.preds_proba_train = np.array([e.predict_proba(self.X_train) for e in clfs]).swapaxes(0,1)
self.preds_proba_train_smoothed = self.preds_proba_train + 0.01
self.preds_test = np.array([e.predict(self.X_test) for e in clfs]).T
self.preds_proba_test = np.array([e.predict_proba(self.X_test) for e in clfs]).swapaxes(0,1)
self.pp_train = np.array([pt==yt for pt,yt in itertools.izip(self.preds_train, self.y_train)])
self.pp_test = np.array([pt==yt for pt,yt in itertools.izip(self.preds_test, self.y_test)])
self.pd_pp_test = pairwise_distances(self.pp_test, self.pp_train, metric='hamming')
self.pd_preds_test = pairwise_distances(self.preds_test, self.preds_train, metric='hamming')
def update_input(self, clf): preds_train = np.array([e.predict(self.X_train) for e in clf.estimators_]).T self.pp_train = np.array([pt==yt for pt,yt in itertools.izip(preds_train, self.y_train)]) preds_test = np.array([e.predict(self.X_test) for e in clf.estimators_]).T self.pp_test = np.array([pt==yt for pt,yt in itertools.izip(preds_test, self.y_test)]) self.G = np.zeros(self.M.shape) self.active_set = None self.ij = [] self.ijl = [] self.loss = np.inf self.pd_pp = pairwise_distances(self.pp_train, metric='hamming') np.fill_diagonal(self.pd_pp, np.inf) self.pd_pp_test = pairwise_distances(self.pp_test, self.pp_train, metric='hamming') self.step_size = self.alpha self.step_size_break = False
def ds_clustering(clusters,support_vectors, f_values, new_element):
'''
clustering the new element
Efficient Out-of-Sample extension of Dominant set clusters
Massimiliano et. al., NIPS 2004
for all h in S: if sum(a(h,i)*x(h) > f(x) then i is assigned to S)
'''
if clusters ==None or support_vectors==None or new_element == None:
return None
sum_axs = []
for i in np.arange(len(clusters)):
S = clusters[i]
S_old = S.copy()
x = support_vectors[i]
#print 'len S ', len(S), 'len x', len(x)
from sklearn.metrics import euclidean_distances , pairwise_distances
#euclidean_distances(X, Y=None, Y_norm_squared=None, squared=False):
new_arr = [new_element]
dis = pairwise_distances(new_arr,S, metric='sqeuclidean')
sigma2 = np.median(dis)
a_hj = np.exp(-dis / sigma2)
#print dis, a_hj
sum_ax = 0.
for h in np.arange(len(S_old)):
sum_ax = sum_ax + a_hj[0][h]*x[h]
#print 'i =',i,' sum_ax', sum_ax, 'f_values ', f_values[i]
sum_axs.append(sum_ax)
#print np.argmax(sum_axs), ' ', np.max(sum_axs)
if np.max(sum_axs) >= 0.5*f_values[np.argmax(sum_axs)]:
return np.argmax(sum_axs)
return None
def display_single_tf_idf_cluster(cluster, df_map):
'''map_index_to_word: SFrame specifying the mapping betweeen words and column indices'''
wiki_subset = cluster['dataframe']
tf_idf_subset = cluster['matrix']
centroid = cluster['centroid']
# Print top 5 words with largest TF-IDF weights in the cluster
idx = centroid.argsort()[::-1]
for i in range(5):
print('{0:s}:{1:.3f}'.format(df_map[df_map['idx'] == idx[i]]['word'].values[0], centroid[idx[i]]))
print('')
# Compute distances from the centroid to all data points in the cluster.
distances = pairwise_distances(tf_idf_subset, [centroid], metric='euclidean').flatten()
# compute nearest neighbors of the centroid within the cluster.
nearest_neighbors = distances.argsort()
# For 8 nearest neighbors, print the title as well as first 180 characters of text.
# Wrap the text at 80-character mark.
for i in range(8):
text = ' '.join(wiki_subset.iloc[nearest_neighbors[i]]['text'].split(None, 25)[0:25])
print('* {0:50s} {1:.5f}\n {2:s}\n {3:s}'.format(wiki_subset.iloc[nearest_neighbors[i]]['name'],
distances[nearest_neighbors[i]], text[:90], text[90:180] if len(text) > 90 else ''))
print(text)
print()
def test_l1_precomputed(self):
dist = pairwise_distances(self.pts, metric='l1')
k_range = range(1, 5)
incr_gen = incremental_neighbor_graph(dist, precomputed=True, k=k_range)
for k, G in zip_longest(k_range, incr_gen):
expected = ngraph(dist, precomputed=True, k=k)
assert_array_almost_equal(G.matrix(dense=True), expected)
def test_spectral_amg_mode():
# Test the amg mode of SpectralClustering
centers = np.array([
[0., 0., 0.],
[10., 10., 10.],
[20., 20., 20.],
])
X, true_labels = make_blobs(n_samples=100, centers=centers,
cluster_std=1., random_state=42)
D = pairwise_distances(X) # Distance matrix
S = np.max(D) - D # Similarity matrix
S = sparse.coo_matrix(S)
try:
from pyamg import smoothed_aggregation_solver
amg_loaded = True
except ImportError:
amg_loaded = False
if amg_loaded:
labels = spectral_clustering(S, n_clusters=len(centers),
random_state=0, mode="amg")
# We don't care too much that it's good, just that it *worked*.
# There does have to be some lower limit on the performance though.
assert_greater(np.mean(labels == true_labels), .3)
else:
assert_raises(ValueError, spectral_embedding, S,
n_components=len(centers), random_state=0, mode="amg")
def visualize_document_clusters(wiki, tf_idf, centroids, cluster_assignment, k,
map_index_to_word, display_content=True):
'''wiki: original dataframe
tf_idf: data matrix, sparse matrix format
map_index_to_word: SFrame specifying the mapping betweeen words and column indices
display_content: if True, display 8 nearest neighbors of each centroid'''
print('==========================================================')
# Visualize each cluster c
for c in xrange(k):
# Cluster heading
print('Cluster {0:d} '.format(c)),
# Print top 5 words with largest TF-IDF weights in the cluster
idx = centroids[c].argsort()[::-1]
for i in xrange(5): # Print each word along with the TF-IDF weight
print('{0:s}:{1:.3f}'.format(map_index_to_word['category'][idx[i]], centroids[c,idx[i]])),
print('')
if display_content:
# Compute distances from the centroid to all data points in the cluster,
# and compute nearest neighbors of the centroids within the cluster.
distances = pairwise_distances(tf_idf, [centroids[c]], metric='euclidean').flatten()
distances[cluster_assignment!=c] = float('inf') # remove non-members from consideration
nearest_neighbors = distances.argsort()
# For 8 nearest neighbors, print the title as well as first 180 characters of text.
# Wrap the text at 80-character mark.
for i in xrange(8):
text = ' '.join(wiki[nearest_neighbors[i]]['text'].split(None, 25)[0:25])
print('\n* {0:50s} {1:.5f}\n {2:s}\n {3:s}'.format(wiki[nearest_neighbors[i]]['name'],
distances[nearest_neighbors[i]], text[:90], text[90:180] if len(text) > 90 else ''))
print('==========================================================')
def precompute_gaussian_kernels(XX, YY, verbose=False):
"""For each unit, precompute Gaussian kernel between the trials of
the two samples XX and YY. Estimate each sigma2 parameter as median
distance between the trials of each sample.
"""
if verbose: print("Pre-computing the kernel matrix for each unit.")
n_units = XX.shape[1] # or YY.shape[1]
Ks = [] # here we store all the kernel matrices
sigma2s = np.zeros(n_units) # here we store all the sigma2s, one per unit
m = XX.shape[0]
n = YY.shape[0]
for i in range(n_units):
if verbose: print("Unit %s" % i),
X = XX[:,i,:].copy()
Y = YY[:,i,:].copy()
if verbose: print("Computing Gaussian kernel."),
dm = pairwise_distances(np.vstack([X, Y]), metric='sqeuclidean')
# Heuristic: sigma2 is the median value among all pairwise
# distances between X and Y. Note: should we use just
# dm[:m,m:] or all dm?
sigma2 = np.median(dm[:m,m:])**2
sigma2s[i] = sigma2
if verbose: print("sigma2 = %s" % sigma2)
K = np.exp(-dm / sigma2)
Ks.append(K)
return Ks, sigma2s
def assign_clusters(data, centroids):
# Compute distances between each data point and the set of centroids:
distances_from_centroids = pairwise_distances(data, centroids, metric='euclidean')
# Compute cluster assignments for each data point:
cluster_assignment = np.apply_along_axis(np.argmin, axis = 1, arr = distances_from_centroids)
return cluster_assignment
def sim_calc(self):
nt = self.corpora[0]
self.scores = {}
for corp in self.corpora:
i_nt = []
i_c2 = []
rows = self.ekk_rows[corp[0]]
for i, word in enumerate(self.ekk_rows['NT']):
if word in rows:
i_nt.append(i)
i_c2.append(self.ekk_rows[corp[0]].index(word))
d_c2 = np.memmap(
'{0}{1}/{4}/{2}/{5}_{2}_lems=False_{4}_min_occ={3}_{6}no_stops=False_NORMED.dat'.format(
self.base, corp[0], corp[1], corp[2], self.english, self.prefix, self.svd),
dtype='float32', shape=(len(rows), len(rows)))[i_c2]
d_c2 = d_c2[:, i_c2]
d_nt = np.memmap(
'{0}{1}/{4}/{2}/{5}_{2}_lems=False_{4}_min_occ={3}_{6}no_stops=False_NORMED.dat'.format(
self.base, nt[0], nt[1], nt[2], self.english, self.prefix,
self.svd), dtype='float32',
shape=(len(self.ekk_rows['NT']), len(self.ekk_rows['NT'])))[
i_nt]
d_nt = d_nt[:, i_nt]
self.scores['{0}_{1}'.format('NT', corp[0])] = np.average(np.diag(
1 - pairwise_distances(d_nt, d_c2, metric='cosine',
n_jobs=12)))
def logpdf_diagonal_gaussian(x, mean, cov):
"""
Compute log-pdf of a multivariate Gaussian distribution with diagonal covariance at a given point x.
A multivariate Gaussian distribution with a diagonal covariance is equivalent
to a collection of independent Gaussian random variables.
The log-pdf will be computed for each row of x.
mean and cov should be given as 1D numpy arrays.
:param x: a sparse matrix
:param mean: means of variables
:param cov: covariances of variables
:return: log-pdf of a multivariate Gaussian distribution
"""
n = x.shape[0]
dim = x.shape[1]
assert(dim == len(mean) and dim == len(cov))
# multiply each i-th column of x by (1/(2*sigma_i)), where sigma_i is sqrt of variance of i-th variable.
scaled_x = x.dot(diag(1. / (2 * np.sqrt(cov))))
# multiply each i-th entry of mean by (1/(2*sigma_i))
scaled_mean = mean / (2 * np.sqrt(cov))
# sum of pairwise squared Eulidean distances gives SUM[(x_i - mean_i)^2/(2*sigma_i^2)]
dist_sqr = pairwise_distances(scaled_x, [scaled_mean], 'euclidean').flatten() ** 2
return -np.sum(np.log(np.sqrt(2 * np.pi * cov))) - dist_sqr
def main():
X, theta = swiss_roll(8, 500, return_theta=True)
D = pairwise_distances(X)
graph_info = [
_c('5-NN', neighbor_graph, D, k=6, precomputed=True),
_c('b-matching', b_matching, D, 6),
_c('gabriel', gabriel_graph, X),
_c('rel. neighborhood', relative_neighborhood_graph,D,metric='precomputed'),
_c('manifold spanning', manifold_spanning_graph, X, 2),
_c('L1', sparse_regularized_graph, X, kmax=10, sparsity_param=0.0005),
_c('SMCE', _smce_symm_dist, X, kmax=25, sparsity_param=5),
_c('SAFFRON', saffron, X, q=15, k=5, tangent_dim=2),
_c('MST', mst, D, metric='precomputed'),
_c('dMST', disjoint_mst, D, metric='precomputed'),
]
print('Plotting graphs & embeddings')
fig1, axes1 = plt.subplots(nrows=3, ncols=3, subplot_kw=dict(projection='3d'))
fig2, axes2 = plt.subplots(nrows=3, ncols=3)
fig1.suptitle('Original Coordinates')
fig2.suptitle('Isomap Embeddings')
for ax1, ax2, info in zip(axes1.flat, axes2.flat, graph_info):
label, G, gg, emb, mask = info
G.plot(X, ax=ax1, title=label, vertex_style=dict(c=theta))
gg.plot(emb, ax=ax2, title=label, vertex_style=dict(c=theta[mask]))
ax1.view_init(elev=5, azim=70)
ax1.set_axis_off()
ax2.set_axis_off()
plt.show()
def discriminate_activation_distance(self):
testset = A([ self.get_input_item(t) for t in
self.data.discrimination_stimuli ])
f = self.data.nT
activation = np.array([np.linalg.norm(self.map[:,:,f:] - t[f:],
ord = 2, axis = 2).reshape(1,-1)[0]
for t in testset])
distances = pairwise_distances(activation, metric = 'euclidean')
dn, tn = self.data.dirname, self.data.discrimination_data
tz = self.predict_terms(self.data.discrimination_stimuli).argmax(1)
terms = self.data.terms[tz]
d_fn = '%s/AD_discrimination_terms_%s.csv' % (dn, tn)
dc_fn = '%s/AD_discrimination_confusability_%s.csv' % (dn, tn)
with open(d_fn, 'a') as o:
if os.path.getsize(d_fn) == 0:
o.write('simulation,time,stimulus,term\n')
for i,t in enumerate(terms):
o.write('%d,%d,%d,%s\n' % (self.simulation, self.time, i, t))
with open(dc_fn, 'a') as o:
if os.path.getsize(dc_fn) == 0:
o.write('simulation,time,stimulus.1,stimulus.2,')
o.write('term.1,term.2,distance\n')
for i in range(distances.shape[0]):
for j in range(i+1, distances.shape[0]):
o.write('%d,%d,%d,%d,%s,%s,%.3f\n' %
(self.simulation, self.time, i, j, terms[i],
terms[j], distances[i,j]))
return
def rankInCluster(self,labels,centers_features,K,X,tweets=None):
clusters = dict((clusId,{'all':[],'best':"",'first':"",'words':"","n":0,'sentiment':0}) for clusId in range(K))
if not tweets:
tweets = self.tweets
# In each cluster, do the following :
# 1) sort tweets by created time in descending order
# 2) get the first tweet (in terms of time)
# 3) find the tweet that is closet to the cluster centroid (best tweet)
for i,label in enumerate(labels):
clusters[label]['all'].append(tweets[i])
clusters[label]['n'] += 1
for label in labels:
clusters[label]['all'] = sorted(clusters[label]['all'], key=lambda x:x.time, reverse=True)
clusters[label]['first'] = clusters[label]['all'][-1].printTweet()
# Find the best tweet and avg sentiment in each cluster
for clusId in xrange(K):
print "{} tweets in cluster {}".format(len(clusters[clusId]['all']), clusId)
tweetIdxInClus = np.where(labels == clusId)
clusters[clusId]['sentiment'] = np.mean(X[tweetIdxInClus,-1])
if not clusters[clusId]["n"]:
break
#print tweetIdxInClus
centerCoord = centers_features[clusId].reshape(1,-1)
distToCtr = pairwise_distances(X[tweetIdxInClus], centerCoord) # dimension: (n_tweets, 1)
# Calculate tweet popularity/quality feature
popularity = []
for i,t in enumerate(tweets):
if i in tweetIdxInClus[0]:
popularity.append([t.retweetCnt,t.favCnt,t.isRetweet,t.followers])
popularity = np.array(popularity) # n_tweet X 5
coef = np.array([.5,.5,-.8,.2]) # hard-coded coefficient
#print "popularity:{}".format(popularity.dot(coef).shape)
norm_popularity = normalize(popularity).dot(coef).reshape(-1,1)
#print norm_popularity
#print norm_popularity.shape
feat = np.add(distToCtr, norm_popularity)
bestTweetId = np.argmax(feat)
clusters[clusId]['best'] = tweets[tweetIdxInClus[0][bestTweetId]].printTweet()
# Get the top words in each cluster
sorted_centers_features = centers_features.argsort()[:, ::-1]
for ctr in xrange(K):
top3words = []
found = 0
for field in sorted_centers_features[ctr]: # Get the top 3 common words
try:
top3words.append(self.tfidfDict[field].encode('utf-8', 'ignore'))
if found == 2:
break
found +=1
except IndexError:
continue
clusters[ctr]['words'] = "/".join(top3words)
return clusters
def binned():
#reader, pointer, dialect = csvreader("german.embeddings",verbose=True)
#dialect.quoting = csv.QUOTE_NONE
global featureMatrix
global wordVector
wordVector = []
features = []
for record in reader("german.embeddings", verbose=True, delimeter="\t", nrows=2000):
word, featurelst = record[0], [float(f) for f in record[1:]]
if VERBOSE:
print >> sys.stderr, word
features.append(featurelst)
wordVector.append(word)
featureMatrix = np.array(features)
#featureMatrix = StandardScaler().fit_transform(featureMatrix)
#print featureMatrix
#print featureMatrix.shape
euclideandist = pairwise_distances(featureMatrix)
#print max(euclideandist.flatten())
#print euclideandist
if VERBOSE:
print >> sys.stderr, wordVector[1:10]
print >> sys.stderr, featureMatrix
print >> sys.stderr, featureMatrix.shape
from multiprocessing import Pool
#p = Pool(3)
#p.map(kmeans, range(8, 100, 2), 2)
def asymmetric_n(min, max):
next = min
while next < max:
yield next
next += int(math.log(next, 2)) - 1
#for n in range(16,23):
# docluster(n,algorithm='kmeans')
from itertools import product
results = []
for eps, MinPts in product([5.5], [8]):
sil, n = docluster(algorithm='AffinityPropagation', showClusters=True, eps_in=eps, MinPts_in=MinPts)
results.append((sil, n, eps, MinPts))
print sorted(results, key=lambda x: x[0], reverse=True)
def discriminate(self):
# calculates the between-cell map distance for the BMUs of an array of
# stimuli used in Beekhuizen & Stevenson 2016.
# only uses sinij/goluboj or blue
t_set = { '111' : ['BU'], '112' : ['sinij', 'goluboj'] }
lg = self.parameters['target language']
t_ix = [i for i,t in enumerate(self.data.terms) if t in t_set[lg]]
testset = A([ self.get_input_item(t) for t in
self.data.discrimination_stimuli ])
positions = A([ A(self.get_bmu_ix(t)) for t in testset ])
distances = pairwise_distances(positions, metric = 'euclidean')
dn, tn = self.data.dirname, self.data.discrimination_data
pt = self.predict_terms(self.data.discrimination_stimuli)
terms = [t_set[lg][t] for t in pt[:,t_ix].argmax(1)]
#print(terms)
d_fn = '%s/discrimination_terms_%s_bo.csv' % (dn, tn)
dc_fn = '%s/discrimination_confusability_%s_bo.csv' % (dn, tn)
with open(d_fn, 'a') as o:
if os.path.getsize(d_fn) == 0:
o.write('simulation,time,stimulus,term\n')
for i,t in enumerate(terms):
o.write('%d,%d,%d,%s\n' % (self.simulation, self.time, i, t))
with open(dc_fn, 'a') as o:
if os.path.getsize(dc_fn) == 0:
o.write('simulation,time,stimulus.1,stimulus.2,')
o.write('term.1,term.2,distance\n')
for i in range(distances.shape[0]):
for j in range(i+1, distances.shape[0]):
o.write('%d,%d,%d,%d,%s,%s,%.3f\n' %
(self.simulation, self.time, i, j, terms[i],
terms[j], distances[i,j]))
return
def train(self, reactions, predictor_headers, response_headers, filename):
print "Preparing arrays"
data, labels = self._prepareArrays(reactions, predictor_headers, response_headers)
old_settings = np.seterr(divide='raise') # we don't want division by zero to pass
# This is how metric learn determines bounds internally
# but the lower bound can be zero this way (especially for low-dimensional data)
# which causes divide by zero errors
print "Calculating bounds"
pair_dists = pairwise_distances(data)
bounds = np.percentile(pair_dists, (5, 95))
# the extra check ensures against divide-by-zero errors later
if bounds[0] == 0:
bounds[0] = min(pair_dists[np.nonzero(pair_dists)])
print "Lowerbound was 0. Set to {}".format(bounds[0])
print "Preparing {} constraints with bounds of ({}, {})".format(self.num_constraints, bounds[0], bounds[1])
constraints = self.metric_object.prepare_constraints(labels, data.shape[0], self.num_constraints)
print "Fitting"
self.metric_object.fit(data, constraints, bounds=bounds)
self.save(filename)
np.seterr(**old_settings)
print "Transforming training set"
return self.metric_object.transform()
def __init__(self, X, constraints, bounds=None, A0=None):
"""
X: (n x d) data matrix - each row corresponds to a single instance
A0: [optional] (d x d) initial regularization matrix, defaults to identity
constraints: tuple of arrays: (a,b,c,d) indices into X, such that:
d(X[a],X[b]) < d(X[c],X[d])
bounds: (pos,neg) pair of bounds on similarity, such that:
d(X[a],X[b]) < pos
d(X[c],X[d]) > neg
"""
self.X = X
# check to make sure that no two constrained vectors are identical
a,b,c,d = constraints
ident = _vector_norm(self.X[a] - self.X[b]) > 1e-9
a, b = a[ident], b[ident]
ident = _vector_norm(self.X[c] - self.X[d]) > 1e-9
c, d = c[ident], d[ident]
self.C = a,b,c,d
# init bounds
if bounds is None:
self.bounds = np.percentile(pairwise_distances(X), (5, 95))
else:
assert len(bounds) == 2
self.bounds = bounds
# intialize metric
if A0 is None:
self.A = np.identity(self.X.shape[1])
else:
self.A = A0
def compute_neighbors(
self,
n_neighbors: int = 30,
knn: bool = True,
n_pcs: Optional[int] = None,
use_rep: Optional[str] = None,
method: _Method = 'umap',
random_state: AnyRandom = 0,
write_knn_indices: bool = False,
metric: _Metric = 'euclidean',
metric_kwds: Mapping[str, Any] = MappingProxyType({}),
) -> None:
"""\
Compute distances and connectivities of neighbors.
Parameters
----------
n_neighbors
Use this number of nearest neighbors.
knn
Restrict result to `n_neighbors` nearest neighbors.
{n_pcs}
{use_rep}
Returns
-------
Writes sparse graph attributes `.distances` and `.connectivities`.
Also writes `.knn_indices` and `.knn_distances` if
`write_knn_indices==True`.
"""
from sklearn.metrics import pairwise_distances
start_neighbors = logg.debug('computing neighbors')
if n_neighbors > self._adata.shape[0]: # very small datasets
n_neighbors = 1 + int(0.5 * self._adata.shape[0])
logg.warning(
f'n_obs too small: adjusting to `n_neighbors = {n_neighbors}`')
if method == 'umap' and not knn:
raise ValueError('`method = \'umap\' only with `knn = True`.')
if method == 'rapids' and metric != 'euclidean':
raise ValueError(
"`method` 'rapids' only supports the 'euclidean' `metric`.")
if method not in {'umap', 'gauss', 'rapids'}:
raise ValueError(
"`method` needs to be 'umap', 'gauss', or 'rapids'.")
if self._adata.shape[0] >= 10000 and not knn:
logg.warning(
'Using high n_obs without `knn=True` takes a lot of memory...')
# do not use the cached rp_forest
self._rp_forest = None
self.n_neighbors = n_neighbors
self.knn = knn
X = _choose_representation(self._adata, use_rep=use_rep, n_pcs=n_pcs)
# neighbor search
use_dense_distances = (metric == 'euclidean'
and X.shape[0] < 8192) or knn == False
if use_dense_distances:
_distances = pairwise_distances(X, metric=metric, **metric_kwds)
knn_indices, knn_distances = _get_indices_distances_from_dense_matrix(
_distances, n_neighbors)
if knn:
self._distances = _get_sparse_matrix_from_indices_distances_numpy(
knn_indices, knn_distances, X.shape[0], n_neighbors)
else:
self._distances = _distances
elif method == 'rapids':
knn_indices, knn_distances = compute_neighbors_rapids(
X, n_neighbors)
else:
# non-euclidean case and approx nearest neighbors
if X.shape[0] < 4096:
X = pairwise_distances(X, metric=metric, **metric_kwds)
metric = 'precomputed'
knn_indices, knn_distances, forest = compute_neighbors_umap(
X,
n_neighbors,
random_state,
metric=metric,
metric_kwds=metric_kwds)
# very cautious here
try:
if forest:
self._rp_forest = _make_forest_dict(forest)
except:
pass
# write indices as attributes
if write_knn_indices:
self.knn_indices = knn_indices
self.knn_distances = knn_distances
start_connect = logg.debug('computed neighbors', time=start_neighbors)
if not use_dense_distances or method in {'umap', 'rapids'}:
# we need self._distances also for method == 'gauss' if we didn't
# use dense distances
self._distances, self._connectivities = _compute_connectivities_umap(
knn_indices,
knn_distances,
self._adata.shape[0],
self.n_neighbors,
)
# overwrite the umap connectivities if method is 'gauss'
# self._distances is unaffected by this
if method == 'gauss':
self._compute_connectivities_diffmap()
logg.debug('computed connectivities', time=start_connect)
self._number_connected_components = 1
if issparse(self._connectivities):
from scipy.sparse.csgraph import connected_components
self._connected_components = connected_components(
self._connectivities)
self._number_connected_components = self._connected_components[0]
x = x.reshape((numSamples, -1)).astype(np.float) / 255.0
x_r = x_r.reshape((numSamples, -1))
x_nr = x_nr.reshape((numSamples, -1))
locations = [np.where(y == i)[0] for i in range(10)]
result = []
for i in range(10):
sampleMat = x[locations[i], ...]
sampleMat_r = x_r[locations[i], ...]
sampleMat_nr = x_nr[locations[i], ...]
toDelete = [j * j for j in range(sampleMat.shape[0])]
dist = np.delete(pairwise_distances(sampleMat).flatten(), toDelete)
mean_ = np.mean(dist)
std_ = np.std(dist)
norm_ = norm(mean_, std_)
dist_r = np.delete(pairwise_distances(sampleMat_r).flatten(), toDelete)
mean_r = np.mean(dist_r)
std_r = np.std(dist_r)
norm_r = norm(mean_r, std_r)
dist_nr = np.delete(pairwise_distances(sampleMat_nr).flatten(), toDelete)
mean_nr = np.mean(dist_nr)
std_nr = np.std(dist_nr)
norm_nr = norm(mean_nr, std_nr)
# show histogram
str(digInd))
# In[14]:
subset0 = X[y[:] == 0]
# In[15]:
subset1 = X[y[:] == 1]
# #### 1E -- Genuine vs. Imposter Calculations
# In[16]:
#create symetric matrices representing distances between all genuine zeros, where the diagonal is 0 (same value)
gen0 = pairwise_distances(subset0, subset0)
gen1 = pairwise_distances(subset1, subset1)
#create matrix representing the distance between all 1s and all 0s
imp = pairwise_distances(subset0, subset1)
# In[17]:
gen0DiffVals = []
#create an array of the lower triangle of the genuine 0 matrices
for i in range(len(gen0)):
for j in range(len(gen0)):
if j >= i:
continue
else:
gen0DiffVals.append(gen0[i][j])
def compute_fitness(self, X):
if len(X.shape) == 1:
X = X.reshape(1, -1)
distances = pairwise_distances(X, self.L, metric=self.distance)
membership = argmin(distances, axis=1)
return (-distances[range(distances.shape[0]), membership].sum())
def get_recommendations_system_collaborative():
# Key to works.
try:
wine_key = request.args.get('wine_key')
except KeyError:
return "Wine Key cannot be null"
# Get database connection
conn = get_database_connection()
# Prepare data frames.
df = load_database_with_wines_and_ratings_features(conn)
wines = load_database_with_wines_features(conn)
ratings = load_database_with_ratings_features(conn)
# Close connection.
close_database_connection(conn)
# Average wine ratings
wines_df_stats = df.groupby('wine_name').agg(
{'rating': [np.size, np.mean]})
# Filters the statistical dataset with wines that have more than x analyzes.
min_10 = wines_df_stats['rating']['size'] >= 3
wines_df_stats[min_10].sort_values([('rating', 'mean')], ascending=False)
# Pivot Table
matrix_df = ratings.pivot_table(index=['wine_id'],
columns=['user_id'],
values=['rating']).reset_index(drop=True)
matrix_df.fillna(0, inplace=True)
# Calculate Cosine Similarity.
wines_similarity = 1 - pairwise_distances(matrix_df.to_numpy(),
metric='cosine')
np.fill_diagonal(wines_similarity, 0)
# Set Similarities to Matrix data frame.
matrix_df = pd.DataFrame(wines_similarity)
# Recommendation System
try:
wine = wines[wines['wine_name'] == wine_key].index.tolist()
wine = wine[0]
wines['similarity'] = matrix_df.iloc[wine]
wines.drop_duplicates('wine_id')
wines.drop(columns=[
'alcohol_content', 'country', 'grape', 'harmonization', 'harvest',
'producer', 'region', 'service', 'type', 'volume'
],
axis=1,
inplace=True)
result = pd.DataFrame(
wines.sort_values(['similarity'], ascending=False))
return jsonify(json.loads(result[0:int(10)].to_json(orient='records')))
except:
return "Wine not found."
from sklearn.metrics import pairwise_distances from sklearn.datasets import load_digits import matplotlib.pyplot as plt # --- READING DATA --- digits = load_digits().data # --- BUILDING SIMILARITY MATRIX --- SMatrix = pairwise_distances(digits, metric='sqeuclidean')
np.random.seed(100)
# set the number of observed data points
n = 200
# draw random points from a log-normal and a gaussian distributions
Y = np.random.lognormal(mean=2, sigma=0.3, size=n)
X = np.random.normal(loc=np.exp(2.0 + 0.3**2 / 2.0),
scale=0.3 * np.exp(2.0),
size=n)
XX = X[:, np.newaxis]
YY = Y[:, np.newaxis]
# compute MMD/K-S two sample tests and their null distributions
sigma2 = np.median(pairwise_distances(XX, YY, metric='euclidean'))**2 * 2.0
mmd2u, mmd2u_null, p_value = two_sample_test(XX,
YY,
model='MMD',
kernel_function='rbf',
gamma=1.0 / sigma2,
iterations=5000,
verbose=True,
n_jobs=1)
ks, ks_null, ks_p_value = two_sample_test(XX,
YY,
model='KS',
iterations=5000,
verbose=True,
n_jobs=1)
def _test(self, args, epoch, disc, gen, test_loader, test_output_dir):
mse_criterion = nn.MSELoss()
cls_criterion = nn.CrossEntropyLoss()
_loss_g, _loss_cls_gen, _loss_adv_gen = 0., 0., 0.
_loss_d, _loss_cls, _loss_adv = 0., 0., 0.
_loss_recon, _loss_mse = 0., 0.
_loss = 0.
ypred, ypred_gen = [], []
ytrue, ytrue_gen = [], []
cls_count = [0] * 10
class_featmaps = np.zeros((10, 1000, 256 * 14 * 14))
class_featmaps_gen = np.zeros((10, 1000, 256 * 14 * 14))
class_idx = [0] * 10
for i, (inputs, featmaps, targets, indexes) in enumerate(test_loader):
inputs, featmaps, targets = inputs.to(args.device), featmaps.to(
args.device), targets.to(args.device)
feats, gen_targets = self._sample_vecs_index(inputs.shape[0])
feats, gen_targets = feats.to(args.device), gen_targets.to(
args.device)
gen_image = gen(feats.unsqueeze(2).unsqueeze(3).detach())
for j, target in enumerate(
targets.detach().cpu().numpy().astype(int)):
class_featmaps[target, class_idx[target]] = featmaps[j].view(
256 * 14 * 14).detach().cpu().numpy()
class_featmaps_gen[target,
class_idx[target]] = gen_image[j].view(
256 * 14 * 14).detach().cpu().numpy()
class_idx[target] += 1
print(class_idx)
plt.figure(figsize=(12, 12))
plt.imshow(
pairwise_distances(np.vstack(class_featmaps[0:10]), metric='l2'))
plt.colorbar()
plt.savefig("self.png")
plt.close()
print(class_idx)
plt.figure(figsize=(12, 12))
plt.imshow(
pairwise_distances(np.vstack(class_featmaps_gen[0:10]),
metric='l2'))
plt.colorbar()
plt.savefig("self_gen.png")
plt.close()
plt.figure(figsize=(12, 12))
plt.imshow(
pairwise_distances(np.vstack(class_featmaps[0:10]),
np.vstack(class_featmaps_gen[0:10]),
metric='l2'))
plt.colorbar()
plt.savefig("pair.png")
plt.close()
plt.figure(figsize=(12, 12))
plt.imshow(
pairwise_distances(np.vstack(class_featmaps[0:10]),
metric='cosine'))
plt.colorbar()
plt.savefig("self_cosine.png")
plt.close()
plt.figure(figsize=(12, 12))
plt.imshow(
pairwise_distances(np.vstack(class_featmaps_gen[0:10]),
metric='cosine'))
plt.colorbar()
plt.savefig("self_gen_cosine.png")
plt.close()
plt.figure(figsize=(12, 12))
plt.imshow(
pairwise_distances(np.vstack(class_featmaps[0:10]),
np.vstack(class_featmaps_gen[0:10]),
metric='cosine'))
plt.colorbar()
plt.savefig("pair_cosine.png")
plt.close()
for i, (images, featmaps, targets, indexes) in enumerate(test_loader):
loss = 0
images, featmaps, targets = images.to(args.device), featmaps.to(
args.device), targets.to(args.device)
if args.data == "image":
inputs = (images * 2) - 1
else:
inputs = featmaps
feats, logits_cls, logits_adv = disc(inputs)
loss_cls = cls_criterion(logits_cls, targets.long())
loss = loss_cls
_loss_cls += loss_cls.item()
preds = F.softmax(logits_cls,
dim=1).argmax(dim=1).cpu().numpy().tolist()
ypred.extend(preds)
ytrue.extend(targets)
feats, gen_targets = self._sample_vecs_index(inputs.shape[0])
feats, gen_targets = feats.to(args.device), gen_targets.to(
args.device)
gen_image = gen(feats.unsqueeze(2).unsqueeze(3).detach())
feats_gen, logits_cls_gen, logits_adv_gen = disc(gen_image)
loss_cls_gen = cls_criterion(logits_cls_gen, gen_targets.long())
loss += args.cls_w * loss_cls_gen
_loss_cls_gen += loss_cls_gen.item()
if args.adv:
loss_adv = (adversarial_loss(logits_adv,
is_real=True,
is_disc=True,
type_=args.adv_type) +
adversarial_loss(logits_adv_gen,
is_real=False,
is_disc=True,
type_=args.adv_type))
_loss_adv += loss_adv.item()
loss += args.adv_w * loss_adv.clone() / 2.
loss_adv_gen = adversarial_loss(logits_adv_gen,
is_real=True,
is_disc=False,
type_=args.adv_type)
_loss_adv_gen += loss_adv_gen.item()
loss += args.adv_w * loss_adv_gen.clone()
if args.recon:
loss_recon = (1 - nn.CosineSimilarity(dim=1, eps=1e-6)(
feats_gen, feats).mean())
loss += args.adv_r * loss_recon.clone()
_loss_recon += loss_recon.item()
if args.mse:
loss_mse = nn.MSELoss()(gen_image, inputs)
loss += args.mse_w * loss_mse.clone()
_loss_mse += args.mse_w * loss_mse.item()
preds_gen = F.softmax(logits_cls_gen,
dim=1).argmax(dim=1).cpu().numpy().tolist()
ypred_gen.extend(preds_gen)
ytrue_gen.extend(gen_targets)
_loss += loss.item()
if i % 10 == 0:
visualize(inputs[0],
gen_image[0],
out_dir=test_output_dir + str(epoch) + "_" + str(i) +
".jpg",
featmap=(args.data == "featmap"))
if sum(cls_count) < 50:
cls_count = visualize_classes(inputs, gen_image, gen_targets,
cls_count, test_output_dir,
args.data == "featmap")
acc = round((np.array(ypred) == np.array(ytrue)).sum() / len(ytrue), 4)
acc_gen = round((np.array(ypred_gen) == np.array(ytrue_gen)).sum() /
len(ytrue_gen), 4)
print("Test Set Epoch {}, Training Iteration {}".format(epoch, i))
print("Accuracy: {}, Accuracy gen: {}".format(acc, acc_gen))
print("Loss: {}, Loss_cls: {}, Loss_cls_gen: {}".format(
_loss / (i + 1), _loss_cls / (i + 1), _loss_cls_gen / (i + 1)))
if args.adv:
print("Loss_adv: {}, Loss_adv_gen: {}".format(
_loss_adv / (i + 1), _loss_adv_gen / (i + 1)))
if args.mse:
print("Loss_mse: {}".format(_loss_mse / (i + 1)))
return return_statement(i, acc, acc_gen, _loss_cls, _loss_cls_gen,
_loss_adv, _loss_adv_gen, _loss_recon,
_loss_mse)
def multi_component_layout(
data,
graph,
n_components,
component_labels,
dim,
random_state,
metric="euclidean",
metric_kwds={},
):
"""Specialised layout algorithm for dealing with graphs with many connected components.
This will first fid relative positions for the components by spectrally embedding
their centroids, then spectrally embed each individual connected component positioning
them according to the centroid embeddings. This provides a decent embedding of each
component while placing the components in good relative positions to one another.
Parameters
----------
data: array of shape (n_samples, n_features)
The source data -- required so we can generate centroids for each
connected component of the graph.
graph: sparse matrix
The adjacency matrix of the graph to be emebdded.
n_components: int
The number of distinct components to be layed out.
component_labels: array of shape (n_samples)
For each vertex in the graph the label of the component to
which the vertex belongs.
dim: int
The chosen embedding dimension.
metric: string or callable (optional, default 'euclidean')
The metric used to measure distances among the source data points.
metric_kwds: dict (optional, default {})
Keyword arguments to be passed to the metric function.
Returns
-------
embedding: array of shape (n_samples, dim)
The initial embedding of ``graph``.
"""
result = np.empty((graph.shape[0], dim), dtype=np.float32)
if n_components > 2 * dim:
meta_embedding = component_layout(
data,
n_components,
component_labels,
dim,
random_state,
metric=metric,
metric_kwds=metric_kwds,
)
else:
k = int(np.ceil(n_components / 2.0))
base = np.hstack([np.eye(k), np.zeros((k, dim - k))])
meta_embedding = np.vstack([base, -base])[:n_components]
for label in range(n_components):
component_graph = graph.tocsr()[component_labels == label, :].tocsc()
component_graph = component_graph[:, component_labels == label].tocoo()
distances = pairwise_distances([meta_embedding[label]], meta_embedding)
data_range = distances[distances > 0.0].min() / 2.0
if component_graph.shape[0] < 2 * dim:
result[component_labels == label] = (random_state.uniform(
low=-data_range,
high=data_range,
size=(component_graph.shape[0], dim),
) + meta_embedding[label])
continue
diag_data = np.asarray(component_graph.sum(axis=0))
# standard Laplacian
# D = scipy.sparse.spdiags(diag_data, 0, graph.shape[0], graph.shape[0])
# L = D - graph
# Normalized Laplacian
I = scipy.sparse.identity(component_graph.shape[0], dtype=np.float64)
D = scipy.sparse.spdiags(
1.0 / np.sqrt(diag_data),
0,
component_graph.shape[0],
component_graph.shape[0],
)
L = I - D * component_graph * D
k = dim + 1
num_lanczos_vectors = max(2 * k + 1,
int(np.sqrt(component_graph.shape[0])))
try:
eigenvalues, eigenvectors = scipy.sparse.linalg.eigsh(
L,
k,
which="SM",
ncv=num_lanczos_vectors,
tol=1e-4,
v0=np.ones(L.shape[0]),
maxiter=graph.shape[0] * 5,
)
order = np.argsort(eigenvalues)[1:k]
component_embedding = eigenvectors[:, order]
expansion = data_range / np.max(np.abs(component_embedding))
component_embedding *= expansion
result[component_labels == label] = (component_embedding +
meta_embedding[label])
except scipy.sparse.linalg.ArpackError:
warn(
"WARNING: spectral initialisation failed! The eigenvector solver\n"
"failed. This is likely due to too small an eigengap. Consider\n"
"adding some noise or jitter to your data.\n\n"
"Falling back to random initialisation!")
result[component_labels == label] = (random_state.uniform(
low=-data_range,
high=data_range,
size=(component_graph.shape[0], dim),
) + meta_embedding[label])
return result
from io import BytesIO
import sframe as sf
?multivariate_normal.pdf
multivariate_normal.pdf(1,mean=0,cov=1)
print multivariate_normal.pdf([10,5],mean=[3,4],cov=3)
print norm.pdf(3)
data_pts=pd.DataFrame({'X':[10,2,3],'Y':[5,1,7]})
data_pts=np.array(data_pts)
clusters=np.array([[3,4],[6,3],[4,6]])
dist=pairwise_distances(data_pts,clusters,metric='euclidean')
?np.argmin
np.argmin(dist,axis=1)
l=list()
for i in clusters:
l.append(multivariate_normal.pdf(data_pts,mean=i,cov=[[3,0],[0,3]]))
?np.array
l=np.array(l,shape=[3,3])
c_wts=[1./3,1./3,1./3]
l=l*c_wts
l=l.T
?normalize
res=normalize(l,norm='l1',axis=1)
c_wts_1=np.sum(res,axis=0)/np.sum(res)
def _leastsq_patch(ayxyx, pa_thresholds, angles, metric, dist_threshold,
solver, tol):
""" Helper function for _leastsq_ann.
Parameters
----------
axyxy : tuple
This tuple contains all per-segment data.
pa_thresholds : list of list
This is a per-annulus list of thresholds.
angles, metric, dist_threshold, solver, tol
These parameters are the same for each annulus or segment.
"""
iann, yy, xx, yy_opt, xx_opt = ayxyx
pa_threshold = pa_thresholds[iann]
values = ARRAY[:, yy, xx] # n_frames x n_pxs_segment
values_opt = ARRAY[:, yy_opt, xx_opt]
n_frames = ARRAY.shape[0]
if dist_threshold < 100:
mat_dists_ann_full = pairwise_distances(values, metric=metric)
else:
mat_dists_ann_full = np.ones((values.shape[0], values.shape[0]))
if pa_threshold > 0:
mat_dists_ann = np.zeros_like(mat_dists_ann_full)
for i in range(n_frames):
ind_fr_i = _find_indices_adi(angles, i, pa_threshold, None, False)
mat_dists_ann[i][ind_fr_i] = mat_dists_ann_full[i][ind_fr_i]
else:
mat_dists_ann = mat_dists_ann_full
matrix_res = np.zeros((values.shape[0], yy.shape[0]))
for i in range(n_frames):
vector = pn.DataFrame(mat_dists_ann[i])
if vector.sum().values > 0:
ind_ref = np.where(~np.isnan(vector))[0]
A = values_opt[ind_ref]
b = values_opt[i]
if solver == 'lstsq':
coef = sp.linalg.lstsq(A.T, b, cond=tol)[0] # SVD method
elif solver == 'nnls':
coef = sp.optimize.nnls(A.T, b)[0]
elif solver == 'lsq': # TODO
coef = sp.optimize.lsq_linear(A.T, b, bounds=(0, 1),
method='trf',
lsq_solver='lsmr')['x']
else:
raise ValueError("`solver` not recognized")
else:
msg = "No frames left in the reference set. Try increasing "
msg += "`dist_threshold` or decreasing `delta_rot`."
raise RuntimeError(msg)
recon = np.dot(coef, values[ind_ref])
matrix_res[i] = values[i] - recon
return matrix_res, yy, xx
def myfunction():
#data from task 1
randomData, stratifiedData, anotherX, targetForStrat, targetForRand, targetForOrg, attributeNames, latitude,longitude, stratLat, stratLong, numberInEachState, avArray = Task1.task1()
#additional data
stateFinancesData = ReadCSVFiles.readStates()
energyData = ReadCSVFiles.statePopulation()
medianHouseholdIncomeData = ReadCSVFiles.medianHouseholdIncome()
unemploymentData = ReadCSVFiles.unemployment()
averageIQData = ReadCSVFiles.averageIQ()
educationData = ReadCSVFiles.educationLevel()
bigData, avArray = ReadCSVFiles.getAllArray(stateFinancesData, energyData, medianHouseholdIncomeData, unemploymentData,averageIQData, educationData)
# print(anotherX)
# print(len(anotherX))
# for i in range(0,20):
# print(anotherX[i])
superTempArray = [None]*997
#link state with other attributes
for i in range(0,999):
if(i<742):
tempArray = [None]*22
for j in range(0,9):
tempArray[j] = anotherX[i][j]
#get big Data items associated with state
# tempArray = [None]*12
tempNum = int(anotherX[i][9])-1
for j in range(1,14):
tempArray[j+8] = bigData[j][tempNum]
superTempArray[i] = tempArray
elif((i>742)and(i<923)):
tempArray = [None]*22
for j in range(0,9):
tempArray[j] = anotherX[i][j]
#get big Data items associated with state
# tempArray = [None]*12
tempNum = int(anotherX[i][9])-1
for j in range(1,14):
tempArray[j+8] = bigData[j][tempNum]
superTempArray[i-1] = tempArray
elif(i>923):
tempArray = [None]*22
for j in range(0,9):
tempArray[j] = anotherX[i][j]
#get big Data items associated with state
# tempArray = [None]*12
tempNum = int(anotherX[i][9])-1
for j in range(1,14):
tempArray[j+8] = bigData[j][tempNum]
superTempArray[i-2] = tempArray
anotherX = np.array(superTempArray)
orgData_std = StandardScaler().fit_transform(anotherX)
# print(orgData_std)
# for i in range(0,len(orgData_std)):
# for j in range(0, len(orgData_std[i])):
# if(math.isnan(orgData_std[i][j])==True):
# print("TRUEE")
# print(math.isnan(orgData_std))
#pca = decomposition.PCA(n_components=3)
pcaOrg = decomposition.PCA()
# I transform the data and get respective eigenvalues
sklearn_pcaOrg = pcaOrg.fit_transform(orgData_std)
orgEigVal = pcaOrg.explained_variance_
sumOfOrgEig =0
contSumOfOrgEig = [None]*22
#calculate sum of all eigenval
for i in range(0,22):
sumOfOrgEig = orgEigVal[i] + sumOfOrgEig
contSumOfOrgEig[i] = sumOfOrgEig
orgVarArray = [None]*22
#calculate variance array
for i in range(0,22):
orgVarArray[i] = orgEigVal[i]/sumOfOrgEig
sumOrgVar =0
#get the sum of variances (total variance)
for i in range(0,22):
sumOrgVar = sumOrgVar + orgVarArray[i]
tempOrgVarSum =0
orgIntrDimCount = 0
#get when 75% of the total variance occured
for i in range(0,22):
tempOrgVarSum = tempOrgVarSum + orgVarArray[i]
if((tempOrgVarSum >(sumOrgVar*.75))and(orgIntrDimCount==0)):
orgIntrDimCount = i
#calculate loading factors
pcaOrgNew = decomposition.PCA(n_components=orgIntrDimCount)
sklearn_pcaOrg = pcaOrgNew.fit_transform(orgData_std)
orgLoadFact = pcaOrgNew.components_.T * np.sqrt(pcaOrgNew.explained_variance_)
orgSumOfSquaredLoad = [[0 for i in range(0,2)] for j in range(0,22)]
#get attributes with highest PCA loading
for i in range(0,22):
for j in range(0, orgIntrDimCount):
orgSumOfSquaredLoad[i] = orgSumOfSquaredLoad[i] + (orgLoadFact[i][j])**2
orgSumOfSquaredLoad[i][1]= i
#I sort the arrays
orgSumOfSquaredLoad.sort(key=lambda x: x[0])
#I get the highest 3 attributes
orgThreeHighAttr = np.array(orgSumOfSquaredLoad[-3:])
orgThreeHighAttrData = [[0 for i in range(0,3)] for j in range(0,997)]
#I get the data associated with the three highest attribtues
for j in range(0,997):
for i in range(0,3):
orgThreeHighAttrData[j][i] = orgData_std[j][int(orgThreeHighAttr[i][1])]
#names of the three highest attributes
orgColumns = [None]*3
attributeNames = ['Change in Rank', 'Revenue', 'Revenue Change', 'Profit', 'Profit Change', 'Assets', 'Market Value', 'Employees', 'Years on Fortune 500 List',
'Total Revenue', 'Federal Revenue','State Revenue','Total Expenditure','Instruction Expenditure','GDP','Census','Median Household Income',
'Unemployment Rate','Average IQ','High School Graduate','Bachelors Graduate','Masters Graduate']
for i in range(0,3):
orgColumns[i] = (attributeNames[int(orgThreeHighAttr[i][1])])
org3Data = pd.DataFrame(data = orgThreeHighAttrData, columns = orgColumns)
targetForOrg2 = pd.DataFrame(data=targetForOrg, columns = ['Target'])
#create the array with data points for 3 attr and cluster associated with that
org3DataFinal = pd.concat([org3Data, targetForOrg2[['Target']]], axis=1)
#create an array with coordinates for 3 attr scatter plot
bigOrg3Array = [[0 for i in range(0,9)] for j in range (0,997)]
for m in range(0,997):
count =0
for j in range(0,3):
for i in range(0,3):
bigOrg3Array[m][count]=([org3DataFinal.values[m][i],org3DataFinal.values[m][j]])
count = count +1
# print(bigOrg3Array)
#to visualize data on top 2 pcaVectors
pcaVisOrg = decomposition.PCA(n_components=2)
principalDFOrg = pd.DataFrame(data = pcaVisOrg.fit_transform(orgData_std), columns = ['Principal Component 1', 'Principal Component 2'])
# targetForStrat2 = pd.DataFrame(data=targetForStrat, columns = ['Target'])
# targetForRand2 = pd.DataFrame(data=targetForRand, columns = ['Target'])
targetForOrg2 = pd.DataFrame(data=targetForOrg, columns = ['Target'])
#print(targetForStrat)
#last row will show the cluster associated w/ each data point
finalDFOrg = pd.concat([principalDFOrg, targetForOrg2[['Target']]], axis=1)
#mds
mds_dataOrg = manifold.MDS(n_components=2, dissimilarity='precomputed')
#mds with euclidean
orgSimEuc = pairwise_distances(orgData_std, metric= 'euclidean')
# print("printing org sim euc")
# print(orgSimEuc)
orgDEuc = mds_dataOrg.fit_transform(orgSimEuc)
orgMDSdatEuc = pd.DataFrame(orgDEuc)
finalMDSOrgDataEuc = pd.concat([orgMDSdatEuc, targetForOrg2[['Target']]], axis=1)
#mds with corr
orgSimCor = pairwise_distances(orgData_std, metric= 'correlation')
orgDCor = mds_dataOrg.fit_transform(orgSimCor)
orgMDSdatCor = pd.DataFrame(orgDCor)
finalMDSOrgDataCor = pd.concat([orgMDSdatCor, targetForOrg2[['Target']]], axis=1)
#json data --> to export to front end
data = {}
data['orgEigVal'] = orgEigVal.tolist()
data['orgLoadFact'] = orgLoadFact.tolist()
data['orgSigNum'] = orgIntrDimCount
data['sumOfOrgEig'] = contSumOfOrgEig
finalMDSOrgDataEuc = np.array(finalMDSOrgDataEuc).tolist()
finalMDSOrgDataCor= np.array(finalMDSOrgDataCor).tolist()
org3DataFinal = np.array(org3DataFinal).tolist()
finalDFOrg = np.array(finalDFOrg).tolist()
for i in range(0,2):
finalMDSOrgDataEuc.pop()
finalMDSOrgDataCor.pop()
org3DataFinal.pop()
finalDFOrg.pop()
# print(finalMDSOrgDataCor)
# print(org3DataFinal)
# print(contSumOfOrgEig)
# print("\n\n")
# print(bigOrg3Array)
data['pca2OrgValues'] = np.array(finalDFOrg).tolist()
data['orgMDSDataEuc'] = finalMDSOrgDataEuc
data['orgMDSDataCor'] = finalMDSOrgDataCor
data['org3LoadData'] = org3DataFinal
data['org3AttrNames'] = orgColumns
data['bigOrg3Array'] = bigOrg3Array
# print(bigOrg3Array)
# print(data)
json_data2 = json.dumps(data)
# print(json_data2)
return json_data2
paths = new_paths
print(f"Number of paths after subsampling: {len(paths)}")
# %% [markdown]
# ##
embedder = AdjacencySpectralEmbed(n_components=None, n_elbows=2)
embed = embedder.fit_transform(pass_to_ranks(adj))
embed = np.concatenate(embed, axis=-1)
pairplot(embed, labels=labels)
# %% [markdown]
# ## Show 2 dimensions of pairwise cosine embedding
pdist = pairwise_distances(embed, metric="cosine")
# %% [markdown]
# ##
manifold = TSNE(metric="precomputed")
# manifold = ClassicalMDS(n_components=2, dissimilarity="precomputed")
cos_embed = manifold.fit_transform(pdist)
# %% [markdown]
# ##
plot_df = pd.DataFrame(data=cos_embed)
plot_df["labels"] = labels
fig, axs = plt.subplots(1, 2, figsize=(20, 10))
ax = axs[0]
sns.scatterplot(
def topic_result(tt):
predicted_topics=[np.argsort(each)[::-1][0] for each in tt]
if predicted_topics==[0]:
return 'Family House'
elif predicted_topics==[1]:
return 'Tourism and Event'
elif predicted_topics==[2]:
return 'Peaceful Vacation'
elif predicted_topics==[3]:
return 'Young Life Style'
else:
return 'Specialty Needs'
similar_indices=pairwise_distances(tt,doc_topic,metric='cosine').argsort()[0][0:num]
similar_id = [(listings['id'].iloc[i]) for i in similar_indices]
similar_name = [(listings['name'].iloc[i]) for i in similar_indices]
similar_desc = [(listings['description'].iloc[i][0:165]) for i in similar_indices]
similar_url = [(listings['host_url'].iloc[i]) for i in similar_indices]
similar_pic = [(listings['picture_url'].iloc[i]) for i in similar_indices]
# def recommend(text,num):
# a=('Recommending ' + str(num) + ' Airbnb products for ' + str(text))
# b=('------------------------------------')
# for i in list(range(0,num)):
def magnitude_and_difference(matrix):
magnitude = np.sqrt(matrix.multiply(matrix).sum(1))
magnitude_diff = pairwise_distances(magnitude, metric='manhattan')
return magnitude, magnitude_diff
def predict(self, X, categorical_mapping=None):
# Scale the test set. Select wether to use the reference or
# just the train set weights
doRefWeightsScaling = False
doSymmetricalWeights = True
#if self.is_fitted:
X_test = X.copy()
# Prepare for the Euclidean distance
r_test = X_test.shape[0]
t_test = self.X_train.shape[0]
X_temp = np.concatenate([X_test, self.X_train], axis=0)
# Normalisation. If not z-score, normalise from 0 to 1
if self.normalisation_type == 'z-score':
x_normed = StandardScaler().fit_transform(X_temp)
else:
x_normed = (X_temp - X_temp.min(0)) / np.maximum(X_temp.ptp(0), 1)
if doSymmetricalWeights:
print('...Symmetrical Weights')
# scale using Cholesky's so W = Q.T Q
V = np.diag(self.x_combined_weights)
try:
Q = np.linalg.cholesky(V)
weights_Q = np.diag(Q)
except np.linalg.LinAlgError as err:
print(err)
doSymmetricalWeights = False
if doRefWeightsScaling:
X_test_scaled = np.multiply(x_normed[0:r_test, :],
np.sqrt(self.x_ref_weights))
elif doSymmetricalWeights:
X_test_scaled = np.multiply(x_normed[0:r_test, :], weights_Q)
else:
X_test_scaled = np.multiply(x_normed[0:r_test, :],
np.sqrt(self.x_weights))
# Scale the training set
if doSymmetricalWeights:
X_train_scaled = np.multiply(x_normed[r_test:(r_test + t_test), :],
weights_Q)
else:
X_train_scaled = np.multiply(x_normed[r_test:(r_test + t_test), :],
np.sqrt(self.x_weights))
y_k_all_list = []
y_k_list = []
y_k_weighted_list = []
y_delta_list = []
y_idx_closest_promos = []
y_distances_closest_promos = []
y_weights = []
testSize = X_test.shape[0]
for idx_test in range(0, testSize):
# Select the closest promotions. Try scaling...
current_promo_scaled = X_test_scaled[idx_test].reshape(1, -1)
# >> Euclidean distances
euclidean = np.squeeze(
pairwise_distances(X_train_scaled, current_promo_scaled))
idxSorted = np.argsort(euclidean)[0:self.num_neighbours]
x_A = self.X_train[idxSorted]
x_B = np.tile(X_test[idx_test], (self.num_neighbours, 1))
X_AB_test = np.concatenate([x_A, x_B], axis=1)
# differences regarding the reference promotions
xgb_frc = self.regressor.predict(X_AB_test)
# Get the average
y_delta_list.append(xgb_frc)
y_k_hat_all = xgb_frc + self.y_train[idxSorted]
y_k_hat = np.mean(y_k_hat_all)
# Weighted by the Euclidean distances
w_distance = 1.0 / np.maximum(euclidean[idxSorted], 1e-3)
y_k_hat_distances = \
w_distance.dot(y_k_hat_all.T)/np.sum(w_distance)
y_k_weighted_list.append(y_k_hat_distances)
# Append to the list
y_k_all_list.append(y_k_hat_all)
y_k_list.append(y_k_hat)
y_idx_closest_promos.append(idxSorted)
y_distances_closest_promos.append(euclidean[idxSorted])
y_weights.append(w_distance)
# Arrange the forecast as np-arrays
y_hat = np.array(y_k_list)
y_hat_weighted = np.array(y_k_weighted_list)
# Arrange the outputs
self.results = {
'y_idx_closest_promos': y_idx_closest_promos,
'y_hat': y_hat,
'y_hat_weighted': y_hat_weighted,
'y_delta_list': y_delta_list,
'y_k_all_list': y_k_all_list,
'y_distances_closest_promos': y_distances_closest_promos,
'y_weights': y_weights,
'feat_importances': self.feat_importances,
'internal_var_names': self.int_vars
}
# Sort out feature importances
if not doRefWeightsScaling:
idx_importances = np.argsort(self.x_combined_weights)[::-1]
int_var_names = self.int_vars[0:self.numFeatures]
else:
idx_importances = np.argsort(self.feat_importances)[::-1]
int_var_names = self.int_vars
# If provided
if categorical_mapping:
'''
Get the feature importances as a DF
'''
inputVars_plain = [
categorical_mapping.get(iVar, iVar) for iVar in
[int_var_names[this_idx] for this_idx in idx_importances]
]
df_feat_importances = pd.DataFrame(
self.feat_importances[idx_importances], index=inputVars_plain)
else:
inputVars_plain = [
int_var_names[this_idx] for this_idx in idx_importances
]
df_feat_importances = pd.DataFrame(
self.x_combined_weights[idx_importances],
index=inputVars_plain)
self.results['df_feat_importances'] = df_feat_importances
self.valid_predictions = True
return y_hat_weighted
# Load table
disp('Loading table...')
df = pd.read_csv(inputpath, index_col=0)
disp('%s samples and %s features detected' % (df.shape[1], df.shape[0]))
samples = df.columns
# Compute pairwise distances
if 'unifrac' in args.m:
features = df.index
metric = setup_unifrac(args.d, df.index, args.m)
elif (args.m in _METRICS_NAMES) & (
args.m not in PAIRWISE_DISTANCE_FUNCTIONS.keys()):
import scipy.spatial.distance as sd
metric = getattr(sd, args.m)
else:
metric = args.m
disp('Calculating pairwise distances...')
dists = pairwise_distances(df.T, metric=metric, n_jobs=args.t)
# Place into dataframe
dist_df = pd.DataFrame(dists, samples, samples)
# Save
disp('Saving pairwise distances to: %s' % outputpath)
# Create output directory if it doesn't exist
outdir = os.path.dirname(outputpath)
if not os.path.exists(outdir):
os.makedirs(outdir)
dist_df.to_csv(outputpath)
def rotate(X, angle):
theta = np.deg2rad(angle)
R = [[np.cos(theta), np.sin(theta)], [-np.sin(theta), np.cos(theta)]]
return np.dot(X, R)
X2 = rotate(X, 20) + 5
plt.scatter(X2[:, 0], X2[:, 1], **colorize)
plt.axis('equal')
plt.show()
# calculated distance matrix
from sklearn.metrics import pairwise_distances
D = pairwise_distances(X)
print(D.shape)
plt.imshow(D, zorder=2, cmap='Blues', interpolation='nearest')
plt.colorbar()
plt.show()
# MDS: distance matrix ---- coordinate representation
from sklearn.manifold import MDS
model = MDS(n_components=2, dissimilarity='precomputed', random_state=1)
out = model.fit_transform(D)
plt.scatter(out[:, 0], out[:, 1], **colorize)
plt.axis('equal')
plt.show()
def __getitem__(self, item):
if self.cache_data:
if item in self.data_dict.keys():
return self.data_dict[item]
else:
pass
pdbid, pose, affinity = self.data_list[item]
node_feats, coords = None, None
with h5py.File(self.data_file, "r") as f:
if (
not self.dataset_name
in f[
"{}/{}/{}".format(
pdbid, self.feature_type, self.preprocessing_type
)
].keys()
):
print(pdbid)
return None
if self.use_docking:
# TODO: the next line will cuase runtime error because not selelcting poses
data = f[
"{}/{}/{}/{}".format(
pdbid,
self.feature_type,
self.preprocessing_type,
self.dataset_name,
)
][pose]["data"]
vdw_radii = (
f[
"{}/{}/{}/{}".format(
pdbid,
self.feature_type,
self.preprocessing_type,
self.dataset_name,
)
][pose]
.attrs["van_der_waals"]
.reshape(-1, 1)
)
else:
data = f[
"{}/{}/{}/{}".format(
pdbid,
self.feature_type,
self.preprocessing_type,
self.dataset_name,
)
]["data"]
vdw_radii = (
f[
"{}/{}/{}/{}".format(
pdbid,
self.feature_type,
self.preprocessing_type,
self.dataset_name,
)
]
.attrs["van_der_waals"]
.reshape(-1, 1)
)
if self.feature_type == "pybel":
coords = data[:, 0:3]
node_feats = np.concatenate([vdw_radii, data[:, 3:22]], axis=1)
else:
raise NotImplementedError
# account for the vdw radii in distance cacluations (consider each atom as a sphere, distance between spheres)
dists = pairwise_distances(coords, metric="euclidean")
edge_index, edge_attr = dense_to_sparse(torch.from_numpy(dists).float())
x = torch.from_numpy(node_feats).float()
y = torch.FloatTensor(affinity).view(-1, 1)
data = Data(
x=x, edge_index=edge_index, edge_attr=edge_attr.view(-1, 1), y=y
)
if self.cache_data:
if self.output_info:
self.data_dict[item] = (pdbid, pose, data)
else:
self.data_dict[item] = data
return self.data_dict[item]
else:
if self.output_info:
return (pdbid, pose, data)
else:
return data
def get_distances_centers(centers):
return pairwise_distances(centers)
from sklearn.metrics import pairwise_distances from src.datasets.datasets import Spheres dataset = Spheres() dataset_l, labels_l = dataset.sample(n_samples=8) DD = pairwise_distances(dataset_l, dataset_l) print(DD.max())
def test_dunn():
kmeans = KMeans(n_clusters=2, random_state=0)
labels = kmeans.fit_predict(iris)
d_val = dunn(pairwise_distances(iris), labels)
assert .05 < d_val < .1
def get_cluster_diameter(cluster):
distance = pairwise_distances(cluster)
return max(map(lambda x: x[len(distance) - 1], distance))
user_book = user_book.replace(np.nan, 0) # In[29]: user_book # In[30]: #Calculating Cosine Similarity between Users from sklearn.metrics import pairwise_distances from scipy.spatial.distance import cosine, correlation # In[31]: user_sim = 1 - pairwise_distances(user_book.values, metric='cosine') # In[32]: user_sim # In[33]: #Store the results in a dataframe user_sim_df = pd.DataFrame(user_sim) # In[34]: #Set the index and column names to user ids user_sim_df.index = book_df["User.ID"].unique() user_sim_df.columns = book_df["User.ID"].unique()
def get_prediction(vecs, pics):
dists = pairwise_distances(vecs, pics, metric='cosine')
return dists.T.argsort(1)
# Generamos muestra estratificada
split = StratifiedShuffleSplit(n_splits=1, test_size=0.45, random_state=42)
for train_index, test_index in split.split(df_users_to_cluster, df_users_to_cluster['divisionGiro']):
strat_test_set = df_users_to_cluster.iloc[train_index]
users_clustered = df_users_to_cluster.iloc[test_index]
print('------------MUESTRA ESTRATIFICADA-----------')
print(users_clustered['divisionGiro'].value_counts() / len(users_clustered))
print('Tamaño de datos a procesar', len(users_clustered))
# Calculo de la matriz de distancias con metrica gower
start = time.time()
gower_mat = metrics.pairwise_distances(
gower.gower_matrix(users_clustered),
metric="precomputed")
end = time.time()
print('Tiempo de ejecución de la matriz de distancia',end - start)
# Comparación de matriz de distancia con el primer registro
first_row = gower_mat[0]
print('Registro base: ',users_clustered[:1], "\n")
print('Registro mas parecido: ',users_clustered[first_row == min(first_row[first_row != min(first_row)])])
print('Registro menos parecido: ',users_clustered[first_row == max(first_row)])
# Implementamos el modelo de DBSCAN con la matriz ya computada
start = time.time()
model = DBSCAN(eps=0.11, min_samples=40, metric="precomputed")
model.fit(gower_mat)
end = time.time()
def compute_neighbors(
self,
n_neighbors: int = 30,
knn: bool = True,
n_pcs: Optional[int] = None,
use_rep: Optional[str] = None,
method: str = 'umap',
random_state: Optional[Union[RandomState, int]] = 0,
write_knn_indices: bool = False,
metric: str = 'euclidean',
metric_kwds: Mapping[str, Any] = {}
) -> None:
"""\
Compute distances and connectivities of neighbors.
Parameters
----------
n_neighbors
Use this number of nearest neighbors.
knn
Restrict result to `n_neighbors` nearest neighbors.
{n_pcs}
{use_rep}
Returns
-------
Writes sparse graph attributes `.distances` and `.connectivities`.
Also writes `.knn_indices` and `.knn_distances` if
`write_knn_indices==True`.
"""
if n_neighbors > self._adata.shape[0]: # very small datasets
n_neighbors = 1 + int(0.5*self._adata.shape[0])
logg.warn('n_obs too small: adjusting to `n_neighbors = {}`'
.format(n_neighbors))
if method == 'umap' and not knn:
raise ValueError('`method = \'umap\' only with `knn = True`.')
if method not in {'umap', 'gauss'}:
raise ValueError('`method` needs to be \'umap\' or \'gauss\'.')
if self._adata.shape[0] >= 10000 and not knn:
logg.warn(
'Using high n_obs without `knn=True` takes a lot of memory...')
self.n_neighbors = n_neighbors
self.knn = knn
X = choose_representation(self._adata, use_rep=use_rep, n_pcs=n_pcs)
# neighbor search
use_dense_distances = (metric == 'euclidean' and X.shape[0] < 8192) or knn == False
if use_dense_distances:
# standard eulcidean case for relatively small matrices
self._distances, knn_indices, knn_distances = compute_neighbors_numpy(
X, n_neighbors, knn=knn)
else:
# non-euclidean case and approx nearest neighbors
if X.shape[0] < 4096:
X = pairwise_distances(X, metric=metric, **metric_kwds)
metric = 'precomputed'
knn_indices, knn_distances = compute_neighbors_umap(
X, n_neighbors, random_state, metric=metric, metric_kwds=metric_kwds)
# write indices as attributes
if write_knn_indices:
self.knn_indices = knn_indices
self.knn_distances = knn_distances
logg.msg('computed neighbors', t=True, v=4)
if not use_dense_distances or method == 'umap':
# we need self._distances also for method == 'gauss' if we didn't
# use dense distances
self._distances, self._connectivities = compute_connectivities_umap(
knn_indices, knn_distances, self._adata.shape[0], self.n_neighbors)
# overwrite the umap connectivities if method is 'gauss'
# self._distances is unaffected by this
if method == 'gauss':
self._compute_connectivities_diffmap()
logg.msg('computed connectivities', t=True, v=4)
self._number_connected_components = 1
if issparse(self._connectivities):
from scipy.sparse.csgraph import connected_components
self._connected_components = connected_components(self._connectivities)
self._number_connected_components = self._connected_components[0]
def calculate_distance_matrix(X,
Y=None,
dist_metric='haversine',
n_jobs=0,
**kwds):
"""
Calculate a distance matrix based on a specific distance metric.
If only X is given, the pair-wise distances between all elements in X are calculated. If X and Y are given, the
distances between all combinations of X and Y are calculated. Distances between elements of X and X, and distances
between elements of Y and Y are not calculated.
Parameters
----------
X : GeoDataFrame (as trackintel staypoints or triplegs)
Y : GeoDataFrame (as trackintel staypoints or triplegs), optional
dist_metric: {'haversine', 'euclidean', 'dtw', 'frechet'}
The distance metric to be used for calculating the matrix. This function wraps around the
``pairwise_distance`` function from scikit-learn if only `X` is given and wraps around the
``scipy.spatial.distance.cdist`` function if X and Y are given. Therefore the following metrics
are also accepted:
via ``scikit-learn``: `[‘cityblock’, ‘cosine’, ‘euclidean’, ‘l1’, ‘l2’, ‘manhattan’]`
via ``scipy.spatial.distance``: `[‘braycurtis’, ‘canberra’, ‘chebyshev’, ‘correlation’, ‘dice’, ‘hamming’, ‘jaccard’,
‘kulsinski’, ‘mahalanobis’, ‘minkowski’, ‘rogerstanimoto’, ‘russellrao’, ‘seuclidean’, ‘sokalmichener’,
‘sokalsneath’, ‘sqeuclidean’, ‘yule’]`
triplegs can only be used in combination with `['dtw', 'frechet']`.
n_jobs: int
Number of cores to use: 'dtw', 'frechet' and all distance metrics from `pairwise_distance` (only available
if only X is given) are parallelized.
**kwds:
optional keywords passed to the distance functions.
Returns
-------
np.array
matrix of shape (len(X), len(X)) or of shape (len(X), len(Y))
"""
geom_type = X.geometry.iat[0].geom_type
if Y is None:
Y = X
assert Y.geometry.iat[0].geom_type == Y.geometry.iat[0].geom_type, "x and y need same geometry type " \
"(only first column checked)"
if geom_type == 'Point':
x1 = X.geometry.x.values
y1 = X.geometry.y.values
x2 = Y.geometry.x.values
y2 = Y.geometry.y.values
if dist_metric == 'haversine':
# create point pairs for distance calculation
nx = len(X)
ny = len(Y)
# if y != x they could have different dimensions
if ny >= nx:
ix_1, ix_2 = np.triu_indices(nx, k=1, m=ny)
trilix = np.tril_indices(nx, k=-1, m=ny)
else:
ix_1, ix_2 = np.tril_indices(nx, k=-1, m=ny)
trilix = np.triu_indices(nx, k=1, m=ny)
x1 = x1[ix_1]
y1 = y1[ix_1]
x2 = x2[ix_2]
y2 = y2[ix_2]
d = haversine_dist(x1, y1, x2, y2)
D = np.zeros((nx, ny))
D[(ix_1, ix_2)] = d
# mirror triangle matrix to be conform with scikit-learn format and to
# allow for non-symmetric distances in the future
D[trilix] = D.T[trilix]
else:
xy1 = np.concatenate((x1.reshape(-1, 1), y1.reshape(-1, 1)),
axis=1)
if Y is not None:
xy2 = np.concatenate((x2.reshape(-1, 1), y2.reshape(-1, 1)),
axis=1)
D = cdist(xy1, xy2, metric=dist_metric, **kwds)
else:
D = pairwise_distances(xy1, metric=dist_metric, n_jobs=n_jobs)
return D
elif geom_type == 'LineString':
if dist_metric in ['dtw', 'frechet']:
# these are the preparation steps for all distance functions based only on coordinates
if dist_metric == 'dtw':
d_fun = partial(dtw, **kwds)
elif dist_metric == 'frechet':
d_fun = partial(frechet_dist, **kwds)
# get combinations of distances that have to be calculated
nx = len(X)
ny = len(Y)
if ny >= nx:
ix_1, ix_2 = np.triu_indices(nx, k=1, m=ny)
trilix = np.tril_indices(nx, k=-1, m=ny)
else:
ix_1, ix_2 = np.tril_indices(nx, k=-1, m=ny)
trilix = np.triu_indices(nx, k=1, m=ny)
left = list(X.iloc[ix_1].geometry)
right = list(Y.iloc[ix_2].geometry)
# map the combinations to the distance function
if n_jobs == -1 or n_jobs > 1:
if n_jobs == -1:
n_jobs = multiprocessing.cpu_count()
with multiprocessing.Pool(processes=n_jobs) as pool:
left_right = list(zip(left, right))
d = np.array(list(pool.starmap(d_fun, left_right)))
else:
d = np.array(list(map(d_fun, left, right)))
# write results to (symmetric) distance matrix
D = np.zeros((nx, ny))
D[(ix_1, ix_2)] = d
D[trilix] = D.T[trilix]
return D
else:
raise AttributeError(
"Metric unknown. We only support ['dtw', 'frechet'] for LineStrings. "
f"You passed {dist_metric}")
else:
raise AttributeError(
f"We only support 'Point' and 'LineString'. Your geometry is {geom_type}"
)
def component_layout(
data,
n_components,
component_labels,
dim,
random_state,
metric="euclidean",
metric_kwds={},
):
"""Provide a layout relating the separate connected components. This is done
by taking the centroid of each component and then performing a spectral embedding
of the centroids.
Parameters
----------
data: array of shape (n_samples, n_features)
The source data -- required so we can generate centroids for each
connected component of the graph.
n_components: int
The number of distinct components to be layed out.
component_labels: array of shape (n_samples)
For each vertex in the graph the label of the component to
which the vertex belongs.
dim: int
The chosen embedding dimension.
metric: string or callable (optional, default 'euclidean')
The metric used to measure distances among the source data points.
metric_kwds: dict (optional, default {})
Keyword arguments to be passed to the metric function.
If metric is 'precomputed', 'linkage' keyword can be used to specify
'average', 'complete', or 'single' linkage. Default is 'average'
Returns
-------
component_embedding: array of shape (n_components, dim)
The ``dim``-dimensional embedding of the ``n_components``-many
connected components.
"""
if data is None:
# We don't have data to work with; just guess
return np.random.random(size=(n_components, dim)) * 10.0
component_centroids = np.empty((n_components, data.shape[1]),
dtype=np.float64)
if metric == "precomputed":
# cannot compute centroids from precomputed distances
# instead, compute centroid distances using linkage
distance_matrix = np.zeros((n_components, n_components),
dtype=np.float64)
linkage = metric_kwds.get("linkage", "average")
if linkage == "average":
linkage = np.mean
elif linkage == "complete":
linkage = np.max
elif linkage == "single":
linkage = np.min
else:
raise ValueError("Unrecognized linkage '%s'. Please choose from "
"'average', 'complete', or 'single'" % linkage)
for c_i in range(n_components):
dm_i = data[component_labels == c_i]
for c_j in range(c_i + 1, n_components):
dist = linkage(dm_i[:, component_labels == c_j])
distance_matrix[c_i, c_j] = dist
distance_matrix[c_j, c_i] = dist
else:
for label in range(n_components):
component_centroids[label] = data[component_labels == label].mean(
axis=0)
if scipy.sparse.isspmatrix(component_centroids):
warn(
"Forcing component centroids to dense; if you are running out of "
"memory then consider increasing n_neighbors.")
component_centroids = component_centroids.toarray()
if metric in SPECIAL_METRICS:
distance_matrix = pairwise_special_metric(
component_centroids,
metric=metric,
kwds=metric_kwds,
)
elif metric in SPARSE_SPECIAL_METRICS:
distance_matrix = pairwise_special_metric(
component_centroids,
metric=SPARSE_SPECIAL_METRICS[metric],
kwds=metric_kwds,
)
else:
if callable(metric) and scipy.sparse.isspmatrix(data):
function_to_name_mapping = {
v: k
for k, v in sparse_named_distances.items()
}
try:
metric_name = function_to_name_mapping[metric]
except KeyError:
raise NotImplementedError(
"Multicomponent layout for custom "
"sparse metrics is not implemented at "
"this time.")
distance_matrix = pairwise_distances(component_centroids,
metric=metric_name,
**metric_kwds)
else:
distance_matrix = pairwise_distances(component_centroids,
metric=metric,
**metric_kwds)
affinity_matrix = np.exp(-(distance_matrix**2))
component_embedding = SpectralEmbedding(
n_components=dim, affinity="precomputed",
random_state=random_state).fit_transform(affinity_matrix)
component_embedding /= component_embedding.max()
return component_embedding
len(book.User_ID.unique())
len(book.Book_Title.unique())
# convert data into n * p matrix
Book_pivot = book.pivot_table(index='User_ID',
columns='Book_Title',
values='Book_Rating').reset_index(drop=True)
# replace index of pivot with user id values
Book_pivot.index = book.User_ID.unique()
#Impute NaNs with 0 values
Book_pivot.fillna(0, inplace=True)
# calculate distance
# pairwise gives (1-cos(A,B)) so to negate that we are using 1- ahead of that
user_distance = 1 - pairwise_distances(Book_pivot.values, metric='cosine')
distance_matrix = pd.DataFrame(user_distance)
#Set the index and column names to user ids
distance_matrix.index = book.User_ID.unique()
distance_matrix.columns = book.User_ID.unique()
# fill diagnols with 0s as diagnol has all 1
np.fill_diagonal(distance_matrix.values, 0)
#Most Similar Users
distance_matrix.idxmax(axis=1)[0:5]