def run_steps(node_embeddings):
"""Runs propagation and updates."""
if model_type == "ggnn":
final_embeddings = ggnn_steps(node_embeddings, edge_embeddings)
elif model_type == "transformer":
neighbor_mask = graph_layers.edge_mask(
edges=example.edges,
num_nodes=graph_metadata.num_nodes,
num_edge_types=num_edge_types,
forward_edge_type_indices=forward_edge_type_indices,
reverse_edge_type_indices=reverse_edge_type_indices)
# Allow nodes to attend to themselves
neighbor_mask = jnp.maximum(neighbor_mask,
jnp.eye(graph_metadata.num_nodes))
final_embeddings = transformer_steps(
node_embeddings,
edge_embeddings,
neighbor_mask,
num_real_nodes_per_graph=example.graph_metadata.num_nodes)
elif model_type == "nri_encoder":
final_embeddings = nri_steps(
node_embeddings,
edge_embeddings,
num_real_nodes_per_graph=example.graph_metadata.num_nodes)
return final_embeddings
def test_edge_nonzeros(self, which):
(edges, forward_edge_type_indices,
reverse_edge_type_indices) = self._setup_edges()
if which == "edge_mask":
nonzeros = graph_layers.edge_mask(
edges,
num_nodes=4,
num_edge_types=3,
forward_edge_type_indices=forward_edge_type_indices,
reverse_edge_type_indices=reverse_edge_type_indices)
elif which == "LearnableEdgeEmbeddings":
embeddings, _ = graph_layers.LearnableEdgeEmbeddings.init(
jax.random.PRNGKey(0),
edges=edges,
num_nodes=4,
num_edge_types=3,
forward_edge_type_indices=forward_edge_type_indices,
reverse_edge_type_indices=reverse_edge_type_indices,
embedding_dim=EDGE_EMBEDDING_DIM)
nonzeros = jnp.any(embeddings != 0, axis=-1).astype(jnp.float32)
expected = np.zeros([4, 4], np.float32)
expected[2, 0] = 1
expected[0, 1] = 1
expected[1, 2] = 1
expected[0, 2] = 1
expected[1, 0] = 1
expected[2, 1] = 1
np.testing.assert_allclose(nonzeros, expected)
def apply(
self,
graph_context,
node_embeddings,
edge_embeddings,
forward_edge_types=gin.REQUIRED,
reverse_edge_types=gin.REQUIRED,
walk_length_log2=gin.REQUIRED,
):
"""Modifies edge embeddings using a uniform random walk.
Uses an efficient repeated-squaring technique to compute the absorbing
distribution.
Args:
graph_context: Input graph for this example.
node_embeddings: Current node embeddings, as <float32[num_nodes,
node_embedding_dim]>
edge_embeddings: Current edge embeddings, as <float32[num_nodes,
num_nodes, edge_embedding_dim]>
forward_edge_types: Edge types to use in the forward direction. As a list
of lists to allow configuring groups of edges in config files; this will
be flattened before use.
reverse_edge_types: Edge types to use in the reverse direction. Note that
reversed edge types are given a separate embedding from forward edge
types; undirected edges should be represented by adding two edges in
opposite directions and then only using `forward_edge_types`. Also a
list of lists, as above.
walk_length_log2: Base-2 logarithm of maximum walk length; this determines
how many times we will square the transition matrix (doubling the walk
length).
Returns:
New node and edge embeddings. Node embeddings will not be modified. Edge
embeddings will be modified by adding a new edge type (either embedded or
concatenated based on graph_context.edges_are_embedded).
"""
num_nodes = node_embeddings.shape[0]
# pylint: disable=g-complex-comprehension
forward_edge_type_indices = [
graph_context.edge_types_to_indices[type_str]
for group in forward_edge_types for type_str in group
]
reverse_edge_type_indices = [
graph_context.edge_types_to_indices[type_str]
for group in reverse_edge_types for type_str in group
]
# pylint: enable=g-complex-comprehension
adjacency = graph_layers.edge_mask(
edges=graph_context.bundle.edges,
num_nodes=num_nodes,
num_edge_types=len(graph_context.edge_types_to_indices),
forward_edge_type_indices=forward_edge_type_indices,
reverse_edge_type_indices=reverse_edge_type_indices)
adjacency = jnp.maximum(adjacency, jnp.eye(num_nodes))
absorbing_logit = self.param(
"absorbing_logit",
shape=(),
initializer=lambda *_: jax.scipy.special.logit(0.1))
absorbing_prob = jax.nn.sigmoid(absorbing_logit)
nonabsorbing_prob = jax.nn.sigmoid(-absorbing_logit)
walk_matrix = nonabsorbing_prob * adjacency / jnp.sum(
adjacency, axis=1, keepdims=True)
# A, I
# A^2, A + I
# (A^2)^2 = A^4, (A + I)A^2 + (A + I) = A^3 + A^2 + A + I
# ...
def step(state, _):
nth_power, nth_partial_sum = state
return (nth_power @ nth_power,
nth_power @ nth_partial_sum + nth_partial_sum), None
(_, partial_sum), _ = jax.lax.scan(step,
(walk_matrix, jnp.eye(num_nodes)),
None,
length=walk_length_log2)
approx_visits = absorbing_prob * partial_sum
logits = model_util.safe_logit(approx_visits)
logits = model_util.ScaleAndShift(logits)
edge_weights = jax.nn.sigmoid(logits)
return (node_embeddings,
_add_edges(edge_embeddings, edge_weights[:, :, None],
graph_context.edges_are_embedded))