def test_kmeans_expr(self):
ctx = spartan.blob_ctx.get()
pts = expr.rand(N_PTS, N_DIM,
tile_hint=(divup(N_PTS, ctx.num_workers), N_DIM)).force()
k = KMeans(N_CENTERS, ITER)
k.fit(pts)
def benchmark_kmeans(ctx, timer): print "#worker:", ctx.num_workers N_PTS = 1000 * 256 N_CENTERS = 10 N_DIM = 512 ITER = 1 pts = expr.rand(N_PTS, N_DIM) k = KMeans(N_CENTERS, ITER) t1 = datetime.now() k.fit(pts) t2 = datetime.now() cost_time = millis(t1, t2) print "total cost time:%s ms, per iter cost time:%s ms" % (cost_time, cost_time/ITER)
def benchmark_kmeans(ctx, timer):
print "#worker:", ctx.num_workers
N_PTS = 1000 * 256
N_CENTERS = 10
N_DIM = 512
ITER = 1
pts = expr.rand(N_PTS, N_DIM)
k = KMeans(N_CENTERS, ITER)
t1 = datetime.now()
k.fit(pts)
t2 = datetime.now()
cost_time = millis(t1, t2)
print "total cost time:%s ms, per iter cost time:%s ms" % (
cost_time, cost_time / ITER)
def test_kmeans(self):
_skip_if_travis()
N_PTS = 1000 * 1000 * self.ctx.num_workers
ITER = 5
N_DIM = 10
N_CENTERS = 10
start = time.time()
pts = expr.rand(N_PTS, N_DIM).force()
k = KMeans(N_CENTERS, ITER)
k.fit(pts)
cost = time.time() - start
self._verify_cost("kmeans", cost)
def test_kmeans(self):
_skip_if_travis()
N_PTS = 1000 * 1000 * self.ctx.num_workers
ITER = 5
N_DIM = 10
N_CENTERS = 10
start = time.time()
pts = expr.rand(N_PTS, N_DIM).evaluate()
k = KMeans(N_CENTERS, ITER)
k.fit(pts)
cost = time.time() - start
self._verify_cost("kmeans", cost)
def spectral_cluster(points, k=10, num_iter=10, similarity_measurement='rbf'):
'''
clustering data points using kmeans spectral clustering method.
Args:
points(Expr or DistArray): the data points to be clustered.
k(int): the number of clusters we need to generate.
num_iter(int): the max number of iterations that kmeans clustering method runs.
similarity_measurement(str): distance method used to measure similarity between two points.
'''
# calculate similarity for each pair of points to generate the adjacency matrix A
A = expr.shuffle(points,
_row_similarity_mapper,
kw={'similarity_measurement': similarity_measurement},
shape_hint=(points.shape[0], points.shape[0]))
num_dims = A.shape[1]
# Construct the diagonal matrix D
D = expr.sum(A, axis=1, tile_hint=(A.shape[0], ))
# Calculate the normalized Laplacian of the form: L = D^(-0.5)AD^(-0.5)
L = expr.shuffle(A, _laplacian_mapper, kw={'D': D}, shape_hint=A.shape)
# Perform eigen-decomposition using Lanczos solver
overshoot = min(k * 2, num_dims)
d, U = lanczos.solve(L, L, overshoot, True)
U = U[:, 0:k]
# Generate initial clusters which picks rows as centers if that row contains max eigen
# value in that column
init_clusters = U[np.argmax(U, axis=0)]
# Run kmeans clustering with init_clusters
kmeans = KMeans(k, num_iter)
U = expr.from_numpy(U)
centers, labels = kmeans.fit(U, init_clusters)
return labels
def spectral_cluster(points, k=10, num_iter=10, similarity_measurement='rbf'):
'''
clustering data points using kmeans spectral clustering method.
Args:
points(Expr or DistArray): the data points to be clustered.
k(int): the number of clusters we need to generate.
num_iter(int): the max number of iterations that kmeans clustering method runs.
similarity_measurement(str): distance method used to measure similarity between two points.
'''
# calculate similarity for each pair of points to generate the adjacency matrix A
A = expr.shuffle(points, _row_similarity_mapper, kw={'similarity_measurement': similarity_measurement})
num_dims = A.shape[1]
# Construct the diagonal matrix D
D = expr.sum(A, axis=1, tile_hint=(A.shape[0],))
# Calculate the normalized Laplacian of the form: L = D^(-0.5)AD^(-0.5)
L = expr.shuffle(A, _laplacian_mapper, kw={'D': D})
# Perform eigen-decomposition using Lanczos solver
overshoot = min(k * 2, num_dims)
d, U = lanczos.solve(L, L, overshoot, True)
U = U[:, 0:k]
# Generate initial clusters which picks rows as centers if that row contains max eigen
# value in that column
init_clusters = U[np.argmax(U, axis=0)]
# Run kmeans clustering with init_clusters
kmeans = KMeans(k, num_iter)
U = expr.from_numpy(U)
centers, labels = kmeans.fit(U, init_clusters)
return labels
def test_kmeans_expr(self):
FLAGS.opt_parakeet_gen = 0
pts = expr.rand(N_PTS, N_DIM)
k = KMeans(N_CENTERS, ITER)
k.fit(pts)
def test_kmeans_expr(self): FLAGS.opt_parakeet_gen = 0 pts = expr.rand(N_PTS, N_DIM) k = KMeans(N_CENTERS, ITER) k.fit(pts)