def _setup_ak(self, post, nn, n2):
# This is the equivalent of CalculateAk in Fabber
#
# Some of this could probably be better done using linalg
# operations but bear in mind this is one parameter only
self.sigmaK = self.log_tf(tf.matrix_diag_part(post.cov)[:, self.idx], name="sigmak") # [W]
self.wK = self.log_tf(post.mean[:, self.idx], name="wk") # [W]
self.num_nn = self.log_tf(tf.sparse_reduce_sum(self.nn, axis=1), name="num_nn") # [W]
# Sum over vertices of parameter variance multiplied by number of
# nearest neighbours for each vertex
trace_term = self.log_tf(tf.reduce_sum(self.sigmaK * self.num_nn), name="trace") # [1]
# Sum of nearest and next-nearest neighbour mean values
self.sum_means_nn = self.log_tf(tf.reshape(tf.sparse_tensor_dense_matmul(self.nn, tf.reshape(self.wK, (-1, 1))), (-1,)), name="wksum") # [W]
self.sum_means_n2 = self.log_tf(tf.reshape(tf.sparse_tensor_dense_matmul(self.n2, tf.reshape(self.wK, (-1, 1))), (-1,)), name="contrib8") # [W]
# vertex parameter mean multipled by number of nearest neighbours
wknn = self.log_tf(self.wK * self.num_nn, name="wknn") # [W]
swk = self.log_tf(wknn - self.sum_means_nn, name="swk") # [W]
term2 = self.log_tf(tf.reduce_sum(swk * self.wK), name="term2") # [1]
gk = 1 / (0.5 * trace_term + 0.5 * term2 + 0.1)
hk = tf.multiply(tf.to_float(self.nvertices), 0.5) + 1.0
self.ak = self.log_tf(tf.identity(gk * hk, name="ak"))
def mean_log_pdf(self, samples):
samples = tf.reshape(samples, (self.nvertices, -1)) # [W, N]
self.num_nn = self.log_tf(tf.sparse_reduce_sum(self.nn, axis=1), name="num_nn") # [W]
expanded_nn = tf.sparse_concat(2, [tf.sparse.reshape(self.nn, (self.nvertices, self.nvertices, 1))] * self.sample_size)
xj = expanded_nn * tf.reshape(samples, (self.nvertices, 1, -1))
#xi = tf.reshape(tf.sparse.to_dense(tf.sparse.reorder(self.nn)), (self.nvertices, self.nvertices, 1)) * tf.reshape(samples, (1, self.nvertices, -1))
xi = expanded_nn * tf.reshape(samples, (1, self.nvertices, -1))
#xi = tf.sparse.transpose(xj, perm=(1, 0, 2))
neg_xi = tf.SparseTensor(xi.indices, -xi.values, dense_shape=xi.dense_shape )
dx2 = tf.square(tf.sparse.add(xj, neg_xi), name="dx2")
sdx = tf.sparse.reduce_sum(dx2, axis=0) # [W, N]
term1 = tf.identity(0.5*self.logak, name="term1")
term2 = tf.identity(-self.ak * sdx / 4, name="term2")
log_pdf = term1 + term2 # [W, N]
mean_log_pdf = tf.reshape(tf.reduce_mean(log_pdf, axis=-1), [self.nvertices]) # [W]
return mean_log_pdf
def _post_setup(self):
self.E_predict = _tf.reduce_sum([
_tf.sparse_tensor_dense_matmul(self.atom_maps[t],
self.ANNs[t].output)
for t in self.atom_types
],
axis=[0, 2],
name="E_prediction")
# Tensorflow operation to initialize the variables of the atomic
# networks
# self.init_vars = [a.init_vars for a in self.ANNs.itervalues()]
self.num_atoms = _tf.reduce_sum([
_tf.sparse_reduce_sum(self.atom_maps[t], axis=1)
for t in self.atom_types
],
axis=0,
name="NumberOfAtoms")
# Tensorflow operation that calculates the sum squared error per atom.
# Note that the whole error per atom is squared.
with _tf.name_scope("RMSE"):
self.rmse_weights = _tf.placeholder(shape=(None, ),
dtype=precision,
name="weights")
self.rmse = self.error_scaling * _tf.sqrt(
_tf.reduce_mean(
(self.target - self.E_predict)**2 * self.rmse_weights))
# self.rmse = self.error_scaling*_tf.sqrt(
# _tf.losses.mean_squared_error(self.target,
# self.E_predict, weights = 1.0/self.num_atoms**2))
self.rmse_summ = _tf.summary.scalar("RMSE",
self.rmse,
family="performance")
self.variables = _tf.get_collection(
_tf.GraphKeys.MODEL_VARIABLES,
scope=_tf.get_default_graph().get_name_scope())
self.saver = _tf.train.Saver(self.variables,
max_to_keep=None,
save_relative_paths=True)
def mean_log_pdf(self, samples):
r"""
mean log PDF for the MRF spatial prior.
This is calculating:
:math:`\log P = \frac{1}{2} \log \phi - \frac{\phi}{2}\underline{x^T} D \underline{x}`
"""
samples = tf.reshape(samples, (self.nvertices, -1)) # [W, N]
self.num_nn = self.log_tf(tf.sparse_reduce_sum(self.nn, axis=1), name="num_nn") # [W]
dx_diag = self.log_tf(tf.reshape(self.num_nn, (self.nvertices, 1)) * samples, name="dx_diag") # [W, N]
dx_offdiag = self.log_tf(tf.sparse_tensor_dense_matmul(self.nn, samples), name="dx_offdiag") # [W, N]
self.dx = self.log_tf(dx_diag - dx_offdiag, name="dx") # [W, N]
self.xdx = self.log_tf(samples * self.dx, name="xdx") # [W, N]
term1 = tf.identity(0.5*self.logak, name="term1")
term2 = tf.identity(-0.5*self.ak*self.xdx, name="term2")
log_pdf = term1 + term2 # [W, N]
mean_log_pdf = tf.reshape(tf.reduce_mean(log_pdf, axis=-1), [self.nvertices]) # [W]
# Gamma prior if we care
#q1, q2 = 1, 100
#mean_log_pdf += (q1-1) * self.logak - self.ak / q2
return mean_log_pdf
def sparse_message_pass(node_states,
adjacency_matrices,
num_edge_types,
hidden_size,
use_bias=True,
average_aggregation=False,
name="sparse_ggnn"):
"""One message-passing step for a GNN with a sparse adjacency matrix.
Implements equation 2 (the message passing step) in
[Li et al. 2015](https://arxiv.org/abs/1511.05493).
N = The number of nodes in each batch.
H = The size of the hidden states.
T = The number of edge types.
Args:
node_states: Initial states of each node in the graph. Shape is [N, H].
adjacency_matrices: Adjacency matrix of directed edges for each edge
type. Shape is [N, N, T] (sparse tensor).
num_edge_types: The number of edge types. T.
hidden_size: The size of the hidden state. H.
use_bias: Whether to use bias in the hidden layer.
average_aggregation: How to aggregate the incoming node messages. If
average_aggregation is true, the messages are averaged. If it is false,
they are summed.
name: (optional) The scope within which tf variables should be created.
Returns:
The result of one step of Gated Graph Neural Network (GGNN) message passing.
Shape: [N, H]
"""
n = tf.shape(node_states)[0]
t = num_edge_types
incoming_edges_per_type = tf.sparse_reduce_sum(adjacency_matrices, axis=1)
# Convert the adjacency matrix into shape [T, N, N] - one [N, N] adjacency
# matrix for each edge type. Since sparse tensor multiplication only supports
# two-dimensional tensors, we actually convert the adjacency matrix into a
# [T * N, N] tensor.
adjacency_matrices = tf.sparse_transpose(adjacency_matrices, [2, 0, 1])
adjacency_matrices = tf.sparse_reshape(adjacency_matrices, [t * n, n])
# Multiply the adjacency matrix by the node states, producing a [T * N, H]
# tensor. For each (edge type, node) pair, this tensor stores the sum of
# the hidden states of the node's neighbors over incoming edges of that type.
messages = tf.sparse_tensor_dense_matmul(adjacency_matrices, node_states)
# Rearrange this tensor to have shape [N, T * H]. The incoming states of each
# nodes neighbors are summed by edge type and then concatenated together into
# a single T * H vector.
messages = tf.reshape(messages, [t, n, hidden_size])
messages = tf.transpose(messages, [1, 0, 2])
messages = tf.reshape(messages, [n, t * hidden_size])
# Run each of those T * H vectors through a linear layer that produces
# a vector of size H. This process is equivalent to running each H-sized
# vector through a separate linear layer for each edge type and then adding
# the results together.
#
# Note that, earlier on, we added together all of the states of neighbors
# that were connected by edges of the same edge type. Since addition and
# multiplying by a linear layer are commutative, this process was equivalent
# to running each incoming edge through a linear layer separately and then
# adding everything at the end.
with tf.variable_scope(name, default_name="sparse_ggnn"):
final_node_states = common_layers.dense(messages,
hidden_size,
use_bias=False)
# Multiply the bias by for each edge type by the number of incoming nodes
# of that edge type.
if use_bias:
bias = tf.get_variable("bias",
initializer=tf.zeros([t, hidden_size]))
final_node_states += tf.matmul(incoming_edges_per_type, bias)
if average_aggregation:
incoming_edges = tf.reduce_sum(incoming_edges_per_type,
-1,
keepdims=True)
incoming_edges = tf.tile(incoming_edges, [1, hidden_size])
final_node_states /= incoming_edges + 1e-7
return tf.reshape(final_node_states, [n, hidden_size])
import tensorflow.compat.v1 as tf
tf.disable_v2_behavior()
sp = tf.SparseTensor(indices=[[0,0],[0,2],[1,1]], values=[1,1,1], dense_shape=[2,3])
reduce_sum_sp = [tf.sparse_reduce_sum(sp),
tf.sparse_reduce_sum(sp, axis=1),
tf.sparse_reduce_sum(sp, axis=1, keep_dims=True),
tf.sparse_reduce_sum(sp, axis=0),
tf.sparse_reduce_sum(sp, axis=0, keep_dims=True)
]
with tf.Session() as sess:
print('***************************************')
print(sess.run(reduce_sum_sp))