def linked_kernel_density_estimation(cls,
n_instances,
features,
node_dict=None,
alpha=0.1
# ,batch_size=1,
# sparse=False
):
"""
WRITEME
"""
n_features = len(features)
# the top one is a sum layer with a single node
root_node = SumNode()
root_layer = SumLayerLinked([root_node])
# second one is a product layer with n_instances nodes
product_nodes = [ProductNode() for i in range(n_instances)]
product_layer = ProductLayerLinked(product_nodes)
# linking them to the root node
for prod_node in product_nodes:
root_node.add_child(prod_node, 1. / n_instances)
# last layer can be a categorical smoothed input
# or sum_layer + categorical indicator input
input_layer = None
layers = None
n_leaf_nodes = n_features * n_instances
if node_dict is None:
# creating a sum_layer with n_leaf_nodes
sum_nodes = [SumNode() for i in range(n_leaf_nodes)]
# store them into a layer
sum_layer = SumLayerLinked(sum_nodes)
# linking them to the products above
for i, prod_node in enumerate(product_nodes):
for j in range(n_features):
# getting the next n_features nodes
prod_node.add_child(sum_nodes[i * n_features + j])
# now creating the indicator nodes
input_layer = \
CategoricalIndicatorLayerLinked(vars=features)
# linking the sum nodes to the indicator vars
for i, sum_node in enumerate(sum_nodes):
# getting the feature id
j = i % n_features
# and thus its number of values
n_values = features[j]
# getting the indices of indicators
start_index = sum(features[:j])
end_index = start_index + n_values
indicators = [node for node in input_layer.nodes()
][start_index:end_index]
for ind_node in indicators:
sum_node.add_child(ind_node, 1. / n_values)
# storing levels
layers = [sum_layer, product_layer, root_layer]
else:
# create a categorical smoothed layer
input_layer = \
CategoricalSmoothedLayerLinked(vars=features,
node_dicts=node_dict,
alpha=alpha)
# it shall contain n_leaf_nodes nodes
smooth_nodes = list(input_layer.nodes())
assert len(smooth_nodes) == n_leaf_nodes
# linking it
for i, prod_node in enumerate(product_nodes):
for j in range(n_features):
# getting the next n_features nodes
prod_node.add_child(smooth_nodes[i * n_features + j])
# setting the used levels
layers = [product_layer, root_layer]
# create the spn from levels
kern_spn = SpnLinked(input_layer, layers)
return kern_spn
def build_product_layer(parent_layer, parent_scope_list,
n_max_children, n_scope_children, input_layer,
rand_gen):
# grouping the scopes of the parents
scope_clusters = cluster_set_scope(parent_scope_list)
# for each scope add a fixed number of children
children_lists = {
scope: [
ProductNode(var_scope=scope)
for i in range(n_scope_children)
]
for scope in scope_clusters
}
# counting which node is used
children_counts = {
scope: [0 for i in range(n_scope_children)]
for scope in scope_clusters
}
# now link those randomly to their parent
for parent, scope in zip(parent_layer.nodes(), parent_scope_list):
# only for nodes not becoming leaves
if len(scope) > 1:
# sampling at most n_max_children from those in the same
# scope
children_scope_list = children_lists[scope]
sample_length = min(len(children_scope_list),
n_max_children)
sampled_ids = rand_gen.sample(range(n_scope_children),
sample_length)
sampled_children = [None for i in range(sample_length)]
for i, id in enumerate(sampled_ids):
# getting the sampled child
sampled_children[i] = children_scope_list[id]
# updating its counter
children_counts[scope][id] += 1
for child in sampled_children:
# parent is a sum layer, we must set a random weight
rand_weight = rand_gen.random()
parent.add_child(child, rand_weight)
# we can now normalize it
parent.normalize()
else:
# binding the node to the input layer
(scope_var, ) = scope
link_leaf_to_input_layer(parent, scope_var, input_layer,
rand_gen)
# pruning those children never used
for scope in children_lists.keys():
children_scope_list = children_lists[scope]
scope_counts = children_counts[scope]
used_children = [
child
for count, child in zip(scope_counts, children_scope_list)
if count > 0
]
children_lists[scope] = used_children
# creating the layer and new scopelist
# print('children list val', children_lists.values())
children_list = [
child for child in itertools.chain.from_iterable(
children_lists.values())
]
scope_list = [
key for key, child_list in children_lists.items()
for elem in child_list
]
# print('children list', children_list)
# print('scope list', scope_list)
prod_layer = ProductLayerLinked(children_list)
return prod_layer, scope_list
def layered_linked_spn(cls, root_node):
"""
Given a simple linked version (parent->children),
returns a layered one (linked + layers)
"""
layers = []
root_layer = None
input_nodes = []
layer_nodes = []
input_layer = None
# layers.append(root_layer)
previous_level = None
# collecting nodes to visit
open = deque()
next_open = deque()
closed = set()
open.append(root_node)
while open:
# getting a node
current_node = open.popleft()
current_id = current_node.id
# has this already been seen?
if current_id not in closed:
closed.add(current_id)
layer_nodes.append(current_node)
# print('CURRENT NODE')
# print(current_node)
# expand it
for child in current_node.children:
# only for non leaf nodes
if (isinstance(child, SumNode)
or isinstance(child, ProductNode)):
next_open.append(child)
else:
# it must be an input node
if child.id not in closed:
input_nodes.append(child)
closed.add(child.id)
# open is now empty, but new open not
if (not open):
# swap them
open = next_open
next_open = deque()
# and create a new level alternating type
if previous_level is None:
# it is the first level
if isinstance(root_node, SumNode):
previous_level = SumLayerLinked([root_node])
elif isinstance(root_node, ProductNode):
previous_level = ProductLayerLinked([root_node])
elif isinstance(previous_level, SumLayerLinked):
previous_level = ProductLayerLinked(layer_nodes)
elif isinstance(previous_level, ProductLayerLinked):
previous_level = SumLayerLinked(layer_nodes)
layer_nodes = []
layers.append(previous_level)
#
# finishing layers
#
#
# checking for CLTreeNodes
cltree_leaves = False
for node in input_nodes:
if isinstance(node, CLTreeNode):
cltree_leaves = True
break
if cltree_leaves:
input_layer = CategoricalCLInputLayerLinked(input_nodes)
else:
# otherwiise assuming all input nodes are homogeneous
if isinstance(input_nodes[0], CategoricalSmoothedNode):
# print('SMOOTH LAYER')
input_layer = CategoricalSmoothedLayerLinked(input_nodes)
elif isinstance(input_nodes[0], CategoricalIndicatorNode):
input_layer = CategoricalIndicatorLayerLinked(input_nodes)
spn = SpnLinked(input_layer=input_layer, layers=layers[::-1])
return spn
def linked_naive_factorization(cls, features, node_dict=None, alpha=0.1):
"""
WRITEME
"""
n_features = len(features)
# create an input layer
input_layer = None
layers = None
# first layer is a product layer with n_feature children
root_node = ProductNode()
root_layer = ProductLayerLinked([root_node])
# second is a sum node on an indicator layer
if node_dict is None:
# creating sum nodes
sum_nodes = [SumNode() for i in range(n_features)]
# linking to the root
for node in sum_nodes:
root_node.add_child(node)
# store into a level
sum_layer = SumLayerLinked(sum_nodes)
# now create an indicator layer
input_layer = CategoricalIndicatorLayerLinked(vars=features)
# and linking it
# TODO make this a function
for i, sum_node in enumerate(sum_nodes):
# getting the feature id
j = i % n_features
# and thus its number of values
n_values = features[j]
# getting the indices of indicators
start_index = sum(features[:j])
end_index = start_index + n_values
indicators = [node for node in input_layer.nodes()
][start_index:end_index]
for ind_node in indicators:
sum_node.add_child(ind_node, 1. / n_values)
# collecting layers
layers = [sum_layer, root_layer]
# or a categorical smoothed layer
else:
input_layer = CategoricalSmoothedLayerLinked(vars=features,
node_dicts=node_dict,
alpha=alpha)
# it shall contain n_features nodes
smooth_nodes = list(input_layer.nodes())
assert len(smooth_nodes) == n_features
for node in smooth_nodes:
root_node.add_child(node)
# set layers accordingly
layers = [root_layer]
# build the spn
naive_fact_spn = SpnLinked(input_layer, layers)
return naive_fact_spn
def layered_linked_spn(cls, root_node, data, config={}):
"""
Given a simple linked version (parent->children),
returns a layered one (linked + layers)
"""
layers = []
root_layer = None
input_nodes = []
layer_nodes = []
input_layer = None
# layers.append(root_layer)
previous_level = None
# collecting nodes to visit
open = deque()
next_open = deque()
closed = set()
open.append(root_node)
while open:
# getting a node
current_node = open.popleft()
current_id = current_node.id
# has this already been seen?
if current_id not in closed:
closed.add(current_id)
layer_nodes.append(current_node)
# print('CURRENT NODE')
# print(current_node)
# expand it
for child in current_node.children:
# only for non leaf nodes
if (isinstance(child, SumNode) or
isinstance(child, ProductNode)):
next_open.append(child)
else:
# it must be an input node
if child.id not in closed:
input_nodes.append(child)
closed.add(child.id)
# open is now empty, but new open not
if (not open):
# swap them
open = next_open
next_open = deque()
# and create a new level alternating type
if previous_level is None:
# it is the first level
if isinstance(root_node, SumNode):
previous_level = SumLayerLinked([root_node])
elif isinstance(root_node, ProductNode):
previous_level = ProductLayerLinked([root_node])
elif isinstance(previous_level, SumLayerLinked):
previous_level = ProductLayerLinked(layer_nodes)
elif isinstance(previous_level, ProductLayerLinked):
previous_level = SumLayerLinked(layer_nodes)
layer_nodes = []
layers.append(previous_level)
if isinstance(input_nodes[0], PoissonNode):
input_layer = PoissonLayer(input_nodes)
if isinstance(input_nodes[0], GaussianNode):
input_layer = GaussianLayer(input_nodes)
if isinstance(input_nodes[0], BernoulliNode):
input_layer = BernoulliLayer(input_nodes)
spn = SpnLinked(data, input_layer=input_layer, layers=layers[::-1], config=config)
return spn
def build_linked_layered_spn(print_spn=True):
#
# building an indicator layer
ind_x_00 = CategoricalIndicatorNode(0, 0)
ind_x_01 = CategoricalIndicatorNode(0, 1)
ind_x_10 = CategoricalIndicatorNode(1, 0)
ind_x_11 = CategoricalIndicatorNode(1, 1)
ind_x_20 = CategoricalIndicatorNode(2, 0)
ind_x_21 = CategoricalIndicatorNode(2, 1)
input_layer = CategoricalIndicatorLayer(
[ind_x_00, ind_x_01, ind_x_10, ind_x_11, ind_x_20, ind_x_21])
#
# sum layer
#
sum_node_1 = SumNode(frozenset([0]))
sum_node_1.add_child(ind_x_00, 0.1)
sum_node_1.add_child(ind_x_01, 0.9)
sum_node_2 = SumNode(frozenset([0]))
sum_node_2.add_child(ind_x_00, 0.4)
sum_node_2.add_child(ind_x_01, 0.6)
sum_node_3 = SumNode(frozenset([1]))
sum_node_3.add_child(ind_x_10, 0.3)
sum_node_3.add_child(ind_x_11, 0.7)
sum_node_4 = SumNode(frozenset([1]))
sum_node_4.add_child(ind_x_10, 0.6)
sum_node_4.add_child(ind_x_11, 0.4)
sum_node_5 = SumNode(frozenset([2]))
sum_node_5.add_child(ind_x_20, 0.5)
sum_node_5.add_child(ind_x_21, 0.5)
sum_node_6 = SumNode(frozenset([2]))
sum_node_6.add_child(ind_x_20, 0.2)
sum_node_6.add_child(ind_x_21, 0.8)
sum_layer_1 = SumLayerLinked([
sum_node_1, sum_node_2, sum_node_3, sum_node_4, sum_node_5, sum_node_6
])
#
# product nodes
#
# xy
prod_node_7 = ProductNode(frozenset([0, 1]))
prod_node_7.add_child(sum_node_1)
prod_node_7.add_child(sum_node_3)
prod_node_8 = ProductNode(frozenset([0, 1]))
prod_node_8.add_child(sum_node_2)
prod_node_8.add_child(sum_node_4)
prod_node_9 = ProductNode(frozenset([0, 1]))
prod_node_9.add_child(sum_node_1)
prod_node_9.add_child(sum_node_3)
#
# yz
prod_node_10 = ProductNode(frozenset([1, 2]))
prod_node_10.add_child(sum_node_4)
prod_node_10.add_child(sum_node_5)
prod_node_11 = ProductNode(frozenset([1, 2]))
prod_node_11.add_child(sum_node_4)
prod_node_11.add_child(sum_node_6)
prod_layer_2 = ProductLayerLinked(
[prod_node_7, prod_node_8, prod_node_9, prod_node_10, prod_node_11])
#
# sum nodes
#
# xy
sum_node_12 = SumNode(frozenset([0, 1]))
sum_node_12.add_child(prod_node_7, 0.1)
sum_node_12.add_child(prod_node_8, 0.9)
sum_node_13 = SumNode(frozenset([0, 1]))
sum_node_13.add_child(prod_node_8, 0.7)
sum_node_13.add_child(prod_node_9, 0.3)
#
# yz
sum_node_14 = SumNode(frozenset([1, 2]))
sum_node_14.add_child(prod_node_10, 0.6)
sum_node_14.add_child(prod_node_11, 0.4)
sum_layer_3 = SumLayerLinked([sum_node_12, sum_node_13, sum_node_14])
#
# product nodes
prod_node_15 = ProductNode(frozenset([0, 1, 2]))
prod_node_15.add_child(sum_node_12)
prod_node_15.add_child(sum_node_6)
prod_node_16 = ProductNode(frozenset([0, 1, 2]))
prod_node_16.add_child(sum_node_13)
prod_node_16.add_child(sum_node_5)
prod_node_17 = ProductNode(frozenset([0, 1, 2]))
prod_node_17.add_child(sum_node_2)
prod_node_17.add_child(sum_node_14)
prod_layer_4 = ProductLayerLinked(
[prod_node_15, prod_node_16, prod_node_17])
#
# root
sum_node_18 = SumNode(frozenset([0, 1, 2]))
sum_node_18.add_child(prod_node_15, 0.2)
sum_node_18.add_child(prod_node_16, 0.2)
sum_node_18.add_child(prod_node_17, 0.6)
sum_layer_5 = SumLayerLinked([sum_node_18])
#
# creating the spn
layers = [
sum_layer_1, prod_layer_2, sum_layer_3, prod_layer_4, sum_layer_5
]
nodes = [node for layer in layers for node in layer.nodes()]
spn = SpnLinked(input_layer=input_layer, layers=layers)
if print_spn:
print(spn)
return spn, layers, nodes
def test_linked_to_theano_indicator():
# creating single nodes
root = SumNode()
prod1 = ProductNode()
prod2 = ProductNode()
prod3 = ProductNode()
sum1 = SumNode()
sum2 = SumNode()
sum3 = SumNode()
sum4 = SumNode()
ind1 = CategoricalIndicatorNode(var=0, var_val=0)
ind2 = CategoricalIndicatorNode(var=0, var_val=1)
ind3 = CategoricalIndicatorNode(var=1, var_val=0)
ind4 = CategoricalIndicatorNode(var=1, var_val=1)
ind5 = CategoricalIndicatorNode(var=2, var_val=0)
ind6 = CategoricalIndicatorNode(var=2, var_val=1)
ind7 = CategoricalIndicatorNode(var=2, var_val=2)
ind8 = CategoricalIndicatorNode(var=3, var_val=0)
ind9 = CategoricalIndicatorNode(var=3, var_val=1)
ind10 = CategoricalIndicatorNode(var=3, var_val=2)
ind11 = CategoricalIndicatorNode(var=3, var_val=3)
prod4 = ProductNode()
prod5 = ProductNode()
prod6 = ProductNode()
prod7 = ProductNode()
# linking nodes
root.add_child(prod1, 0.3)
root.add_child(prod2, 0.3)
root.add_child(prod3, 0.4)
prod1.add_child(sum1)
prod1.add_child(sum2)
prod2.add_child(ind7)
prod2.add_child(ind8)
prod2.add_child(ind11)
prod3.add_child(sum3)
prod3.add_child(sum4)
sum1.add_child(ind1, 0.3)
sum1.add_child(ind2, 0.3)
sum1.add_child(prod4, 0.4)
sum2.add_child(ind2, 0.5)
sum2.add_child(prod4, 0.2)
sum2.add_child(prod5, 0.3)
sum3.add_child(prod6, 0.5)
sum3.add_child(prod7, 0.5)
sum4.add_child(prod6, 0.5)
sum4.add_child(prod7, 0.5)
prod4.add_child(ind3)
prod4.add_child(ind4)
prod5.add_child(ind5)
prod5.add_child(ind6)
prod6.add_child(ind9)
prod6.add_child(ind10)
prod7.add_child(ind9)
prod7.add_child(ind10)
# building layers from nodes
root_layer = SumLayerLinked([root])
prod_layer = ProductLayerLinked([prod1, prod2, prod3])
sum_layer = SumLayerLinked([sum1, sum2, sum3, sum4])
aprod_layer = ProductLayerLinked([prod4, prod5, prod6, prod7])
ind_layer = CategoricalIndicatorLayer(nodes=[
ind1, ind2, ind3, ind4, ind5, ind6, ind7, ind8, ind9, ind10, ind11
])
# creating the linked spn
spn_linked = SpnLinked(
input_layer=ind_layer,
layers=[aprod_layer, sum_layer, prod_layer, root_layer])
print(spn_linked)
# converting to theano repr
spn_theano = SpnFactory.linked_to_theano(spn_linked)
print(spn_theano)
# time for some inference comparison
for instance in I:
print('linked')
res_l = spn_linked.eval(instance)
print(res_l)
print('theano')
res_t = spn_theano.eval(instance)
print(res_t)
assert_array_almost_equal(res_l, res_t)
def test_linked_to_theano_categorical():
vars = [2, 2, 3, 4]
freqs = [{
'var': 0,
'freqs': [1, 2]
}, {
'var': 1,
'freqs': [2, 2]
}, {
'var': 0,
'freqs': [3, 2]
}, {
'var': 1,
'freqs': [0, 3]
}, {
'var': 2,
'freqs': [1, 0, 2]
}, {
'var': 3,
'freqs': [1, 2, 1, 2]
}, {
'var': 3,
'freqs': [3, 4, 0, 1]
}]
# create input layer first
input_layer = CategoricalSmoothedLayer(vars=vars, node_dicts=freqs)
# get nodes
ind_nodes = [node for node in input_layer.nodes()]
root_node = ProductNode()
sum1 = SumNode()
sum2 = SumNode()
prod1 = ProductNode()
prod2 = ProductNode()
sum3 = SumNode()
sum4 = SumNode()
# linking
root_node.add_child(sum1)
root_node.add_child(sum2)
root_node.add_child(ind_nodes[0])
root_node.add_child(ind_nodes[1])
sum1.add_child(ind_nodes[2], 0.4)
sum1.add_child(ind_nodes[3], 0.6)
sum2.add_child(ind_nodes[3], 0.2)
sum2.add_child(prod1, 0.5)
sum2.add_child(prod2, 0.3)
prod1.add_child(ind_nodes[4])
prod1.add_child(sum3)
prod1.add_child(sum4)
prod2.add_child(sum3)
prod2.add_child(sum4)
sum3.add_child(ind_nodes[5], 0.5)
sum3.add_child(ind_nodes[6], 0.5)
sum4.add_child(ind_nodes[5], 0.4)
sum4.add_child(ind_nodes[6], 0.6)
# creating layers
root_layer = ProductLayerLinked([root_node])
sum_layer = SumLayerLinked([sum1, sum2])
prod_layer = ProductLayerLinked([prod1, prod2])
sum_layer2 = SumLayerLinked([sum3, sum4])
# create the linked spn
spn_linked = SpnLinked(
input_layer=input_layer,
layers=[sum_layer2, prod_layer, sum_layer, root_layer])
print(spn_linked)
# converting to theano repr
spn_theano = SpnFactory.linked_to_theano(spn_linked)
print(spn_theano)
# time for some inference comparison
for instance in I:
print('linked')
res_l = spn_linked.eval(instance)
print(res_l)
print('theano')
res_t = spn_theano.eval(instance)
print(res_t)
assert_array_almost_equal(res_l, res_t)