def factorize(self, show_progress=False, compute_w=True, compute_h=True,
compute_err=True, niter=1):
""" Factorize s.t. WH = data
Parameters
----------
show_progress : bool
print some extra information to stdout.
compute_h : bool
iteratively update values for H.
compute_w : bool
iteratively update values for W.
compute_err : bool
compute Frobenius norm |data-WH| after each update and store
it to .ferr[k].
Updated Values
--------------
.W : updated values for W.
.H : updated values for H.
.ferr : Frobenius norm |data-WH|.
"""
AA.factorize(self, niter=1, show_progress=show_progress,
compute_w=compute_w, compute_h=compute_h,
compute_err=compute_err)
def __init__(self, data, num_bases=4, dist_measure='l2', init='fastmap', **kwargs):
AA.__init__(self, data, num_bases=num_bases)
self._dist_measure = dist_measure
self._init = init
# assign the correct distance function
if self._dist_measure == 'l1':
self._distfunc = l1_distance
elif self._dist_measure == 'l2':
self._distfunc = l2_distance
elif self._dist_measure == 'cosine':
self._distfunc = cosine_distance
elif self._dist_measure == 'abs_cosine':
self._distfunc = abs_cosine_distance
elif self._dist_measure == 'weighted_abs_cosine':
self._distfunc = weighted_abs_cosine_distance
elif self._dist_measure == 'kl':
self._distfunc = kl_divergence
def factorize(self,
show_progress=False,
compute_w=True,
compute_h=True,
compute_err=True,
niter=1):
""" Factorize s.t. WH = data
Parameters
----------
show_progress : bool
print some extra information to stdout.
compute_h : bool
iteratively update values for H.
compute_w : bool
iteratively update values for W.
compute_err : bool
compute Frobenius norm |data-WH| after each update and store
it to .ferr[k].
Updated Values
--------------
.W : updated values for W.
.H : updated values for H.
.ferr : Frobenius norm |data-WH|.
"""
AA.factorize(self,
niter=1,
show_progress=show_progress,
compute_w=compute_w,
compute_h=compute_h,
compute_err=compute_err)
def __init__(self,
data,
num_bases=4,
dist_measure='l2',
init='fastmap',
**kwargs):
AA.__init__(self, data, num_bases=num_bases)
self._dist_measure = dist_measure
self._init = init
# assign the correct distance function
if self._dist_measure == 'l1':
self._distfunc = l1_distance
elif self._dist_measure == 'l2':
self._distfunc = l2_distance
elif self._dist_measure == 'cosine':
self._distfunc = cosine_distance
elif self._dist_measure == 'abs_cosine':
self._distfunc = abs_cosine_distance
elif self._dist_measure == 'weighted_abs_cosine':
self._distfunc = weighted_abs_cosine_distance
elif self._dist_measure == 'kl':
self._distfunc = kl_divergence
def __init__(self, data, num_bases=4, niter=100, show_progress=False, compW=True, compH=True, dist_measure='l2'): # call inherited method AA.__init__(self, data, num_bases=num_bases, niter=niter, show_progress=show_progress, compW=compW) self._dist_measure = dist_measure self._compH = compH # assign the correct distance function if self._dist_measure == 'l1': self._distfunc = l1_distance elif self._dist_measure == 'l2': self._distfunc = l2_distance elif self._dist_measure == 'cosine': self._distfunc = cosine_distance elif self._dist_measure == 'kl': self._distfunc = kl_divergence elif self._dist_measure == 'sparse_graph_l2': self._distfunc = sparse_graph_l2_distance
def __init__(self, data, num_bases=4, base_sel=3):
# call inherited method
AA.__init__(self, data, num_bases=num_bases)
# base sel should never be larger than the actual data dimension
self._base_sel = base_sel
if base_sel > self.data.shape[0]:
self._base_sel = self.data.shape[0]
def __init__(self, data, num_bases=4, base_sel=3):
# call inherited method
AA.__init__(self, data, num_bases=num_bases)
# base sel should never be larger than the actual data dimension
self._base_sel = base_sel
if base_sel > self.data.shape[0]:
self._base_sel = self.data.shape[0]
def factorize(self,
show_progress=False,
compute_w=True,
compute_h=True,
compute_err=True,
robust_cluster=3,
niter=1,
robust_nselect=-1):
""" Factorize s.t. WH = data
Parameters
----------
show_progress : bool
print some extra information to stdout.
False, default
compute_h : bool
iteratively update values for H.
True, default
compute_w : bool
iteratively update values for W.
default, True
compute_err : bool
compute Frobenius norm |data-WH| after each update and store
it to .ferr[k].
robust_cluster : int, optional
set the number of clusters for robust map selection.
3, default
robust_nselect : int, optional
set the number of samples to consider for robust map
selection.
-1, default (automatically determine suitable number)
Updated Values
--------------
.W : updated values for W.
.H : updated values for H.
.ferr : Frobenius norm |data-WH|.
"""
self._robust_cluster = robust_cluster
self._robust_nselect = robust_nselect
if self._robust_nselect == -1:
self._robust_nselect = np.round(np.log(self.data.shape[1]) * 2)
AA.factorize(self,
niter=1,
show_progress=show_progress,
compute_w=compute_w,
compute_h=compute_h,
compute_err=compute_err)
def initialization(self):
# Fastmap like initialization
# set the starting index for fastmap initialization
cur_p = 0
# after 3 iterations the first "real" index is found
for i in range(3):
d = self._distance(cur_p)
cur_p = np.argmax(d)
self.select = []
self.select.append(cur_p)
if self._compH:
self.H = np.zeros((self._num_bases, self._num_samples))
if self._compW:
AA.initialization(self)
def update_w(self):
""" compute new W """
def select_hull_points(data, n=3):
""" select data points for pairwise projections of the first n
dimensions """
# iterate over all projections and select data points
idx = np.array([])
# iterate over some pairwise combinations of dimensions
for i in combinations(range(n), 2):
# sample convex hull points in 2D projection
convex_hull_d = quickhull(data[i, :].T)
# get indices for convex hull data points
idx = np.append(idx, vq(data[i, :], convex_hull_d.T))
idx = np.unique(idx)
return np.int32(idx)
# determine convex hull data points using either PCA or random
# projections
method = 'randomprojection'
if method == 'pca':
pcamodel = PCA(self.data)
pcamodel.factorize(show_progress=False)
proj = pcamodel.H
else:
R = np.random.randn(self._base_sel, self._data_dimension)
proj = np.dot(R, self.data)
self._hull_idx = select_hull_points(proj, n=self._base_sel)
aa_mdl = AA(self.data[:, self._hull_idx], num_bases=self._num_bases)
# determine W
aa_mdl.factorize(niter=50,
compute_h=True,
compute_w=True,
compute_err=True,
show_progress=False)
self.W = aa_mdl.W
self._map_w_to_data()
def factorize(self, show_progress=False, compute_w=True, compute_h=True,
compute_err=True, robust_cluster=3, niter=1, robust_nselect=-1):
""" Factorize s.t. WH = data
Parameters
----------
show_progress : bool
print some extra information to stdout.
False, default
compute_h : bool
iteratively update values for H.
True, default
compute_w : bool
iteratively update values for W.
default, True
compute_err : bool
compute Frobenius norm |data-WH| after each update and store
it to .ferr[k].
robust_cluster : int, optional
set the number of clusters for robust map selection.
3, default
robust_nselect : int, optional
set the number of samples to consider for robust map
selection.
-1, default (automatically determine suitable number)
Updated Values
--------------
.W : updated values for W.
.H : updated values for H.
.ferr : Frobenius norm |data-WH|.
"""
self._robust_cluster = robust_cluster
self._robust_nselect = robust_nselect
if self._robust_nselect == -1:
self._robust_nselect = np.round(np.log(self.data.shape[1])*2)
AA.factorize(self, niter=1, show_progress=show_progress,
compute_w=compute_w, compute_h=compute_h,
compute_err=compute_err)
def update_w(self):
""" compute new W """
def select_hull_points(data, n=3):
""" select data points for pairwise projections of the first n
dimensions """
# iterate over all projections and select data points
idx = np.array([])
# iterate over some pairwise combinations of dimensions
for i in combinations(range(n), 2):
# sample convex hull points in 2D projection
convex_hull_d = quickhull(data[i, :].T)
# get indices for convex hull data points
idx = np.append(idx, vq(data[i, :], convex_hull_d.T))
idx = np.unique(idx)
return np.int32(idx)
# determine convex hull data points using either PCA or random
# projections
method = 'randomprojection'
if method == 'pca':
pcamodel = PCA(self.data)
pcamodel.factorize(show_progress=False)
proj = pcamodel.H
else:
R = np.random.randn(self._base_sel, self._data_dimension)
proj = np.dot(R, self.data)
self._hull_idx = select_hull_points(proj, n=self._base_sel)
aa_mdl = AA(self.data[:, self._hull_idx], num_bases=self._num_bases)
# determine W
aa_mdl.factorize(niter=50, compute_h=True, compute_w=True,
compute_err=True, show_progress=False)
self.W = aa_mdl.W
self._map_w_to_data()
def __init__(self,
data,
num_bases=4,
niter=100,
show_progress=False,
compW=True,
compH=True,
base_sel=3):
# call inherited method
AA.__init__(self,
data,
num_bases=num_bases,
niter=niter,
show_progress=show_progress,
compW=compW)
self._compH = compH
# base sel should never be larger than the actual
# data dimension
if base_sel < self.data.shape[0]:
self._base_sel = base_sel
else:
self._base_sel = self.data.shape[0]
def update_h(self):
print self._method
if self._method == 'pca':
self.H = np.dot(pinv(self.W), self.data)
if self._method == 'nmf':
mdl = NMF(self.data, num_bases=self._num_bases)
mdl.W = self.W
mdl.factorize(compute_w=False, niter=50)
self.H = mdl.H.copy()
if self._method == 'aa':
mdl = AA(self.data, num_bases=self._num_bases)
mdl.W = self.W
mdl.factorize(compute_w=False)
self.H = mdl.H.copy()
def updateW(self):
def selectHullPoints(data, n=3):
""" select data points for pairwise projections of the first n
dimensions """
# iterate over all projections and select data points
idx = np.array([])
# iterate over some pairwise combinations of dimensions
for i in combinations(range(n), 2):
# sample convex hull points in 2D projection
convex_hull_d = quickhull(data[i, :].T)
# get indices for convex hull data points
idx = np.append(idx, vq(data[i, :], convex_hull_d.T))
idx = np.unique(idx)
return np.int32(idx)
# determine convex hull data points only if the total
# amount of available data is >50
#if self.data.shape[1] > 50:
pcamodel = PCA(self.data, show_progress=self._show_progress)
pcamodel.factorize()
self._hull_idx = selectHullPoints(pcamodel.H, n=self._base_sel)
#else:
# self._hull_idx = range(self.data.shape[1])
aa_mdl = AA(self.data[:, self._hull_idx],
num_bases=self._num_bases,
niter=self._niter,
show_progress=self._show_progress,
compW=True)
# initialize W, H, and beta
aa_mdl.initialization()
# determine W
aa_mdl.factorize()
self.W = aa_mdl.W
def launch():
seed = 1234
np.random.seed(seed)
light = Light()
light.initials()
light.file_snapshot()
light.set_seed(seed)
w, h = 28, 28
fast_test = False
test_ratio = 0.25
valid_ratio = 0.25
light.set("w", w)
light.set("h", h)
light.set("test_ratio", test_ratio)
light.set("valid_ratio", valid_ratio)
images = load_images(w=w, h=h)
X = images.reshape((-1, w*h))
# prepare
X = shuffle(X)
if fast_test is True:
max_evaluations_hp = 1
default_params = dict(
max_epochs=2
)
X = X[0:100]
else:
default_params = dict()
max_evaluations_hp = 20
default_params["batch_size"] = 128
#default_params["nb_layers"] = 1
eval_function = lambda model, X_v, _: float(model.get_reconstruction_error(X_v))
X_train_full, X_test = train_test_split(X, test_size=test_ratio)
X_train, X_valid = train_test_split(X_train_full, test_size=valid_ratio)
# show original data
#X_ = X.reshape((X.shape[0], im[0], im[1]))
#X_ = X_[0:10]
#grid_plot(X_, imshow_options={"cmap": "gray"})
#plt.savefig(dirname+"/orig.png")
#plt.show()
all_hp, all_scores = find_all_hp(
AA,
minimize_fn_with_hyperopt,
X_train,
X_valid,
None,
None,
max_evaluations=max_evaluations_hp,
default_params=default_params,
not_allowed_params=["batch_size"],
eval_function=eval_function
)
argmin = min(range(len(all_hp)), key=lambda i:all_scores[i])
best_hp, best_score = all_hp[argmin], all_scores[argmin]
best_hp.update(default_params)
aa = AA(**best_hp)
aa.fit(X_train_full, X_test)
best_model = aa
light.set("best_hp", best_hp)
light.set("best_score", best_score)
light.set("all_hp", all_hp)
light.set("all_scores", all_scores)
#light.set("best_model", light.insert_blob(best_model))
names = best_model.capsule.batch_optimizer.stats[0].keys()
stats = dict()
for name in names:
stats[name] = get_stat(name, best_model.capsule.batch_optimizer.stats)
light.set("layer_weights", light.insert_blob([layer.W.get_value() for layer in (best_model.all_layers[1:-1])]))
light.set("best_model_stats", stats)
light.set("nb_layers", aa.nb_layers * 2 - 1)
# reconstructions
R = np.arange(20)
X_test_hat = best_model.capsule.predict(X_test[R]).tolist()
light.set("reconstructions", light.insert_blob(X_test_hat))
light.endings()
def __init__(self, data, num_bases=4, method='pca', robust_map=True):
AA.__init__(self, data, num_bases=num_bases)
self.sub = []
self._robust_map = robust_map
self._method = method
def __init__(self, data, num_bases=4, method='pca', robust_map=True):
AA.__init__(self, data, num_bases=num_bases)
self.sub = []
self._robust_map = robust_map
self._method = method