def test_bfs(index_dtype, n=100):
def _bfs_nx(g_nx, src):
edges = nx.bfs_edges(g_nx, src)
layers_nx = [set([src])]
edges_nx = []
frontier = set()
edge_frontier = set()
for u, v in edges:
if u in layers_nx[-1]:
frontier.add(v)
edge_frontier.add(g.edge_id(u, v))
else:
layers_nx.append(frontier)
edges_nx.append(edge_frontier)
frontier = set([v])
edge_frontier = set([g.edge_id(u, v)])
# avoids empty successors
if len(frontier) > 0 and len(edge_frontier) > 0:
layers_nx.append(frontier)
edges_nx.append(edge_frontier)
return layers_nx, edges_nx
g = dgl.DGLGraph()
a = sp.random(n, n, 3 / n, data_rvs=lambda n: np.ones(n))
g.from_scipy_sparse_matrix(a)
if index_dtype == 'int32':
g = dgl.graph(g.edges()).int()
else:
g = dgl.graph(g.edges()).long()
g_nx = g.to_networkx()
src = random.choice(range(n))
layers_nx, _ = _bfs_nx(g_nx, src)
layers_dgl = dgl.bfs_nodes_generator(g, src)
assert len(layers_dgl) == len(layers_nx)
assert all(toset(x) == y for x, y in zip(layers_dgl, layers_nx))
g_nx = nx.random_tree(n, seed=42)
g = dgl.DGLGraph()
g.from_networkx(g_nx)
if index_dtype == 'int32':
g = dgl.graph(g.edges()).int()
else:
g = dgl.graph(g.edges()).long()
src = 0
_, edges_nx = _bfs_nx(g_nx, src)
edges_dgl = dgl.bfs_edges_generator(g, src)
assert len(edges_dgl) == len(edges_nx)
assert all(toset(x) == y for x, y in zip(edges_dgl, edges_nx))
def get_perturbed_inputs(i):
g = dgl.DGLGraph()
g.add_nodes(len(init_nodes[i]))
edges = np.nonzero(init_edges[i]).T
g.add_edges(*edges)
all_radii_nbr_node_inds = dgl.bfs_nodes_generator(
g, corruption_indices[i])
flattened_d_hop_node_inds = torch.cat(all_radii_nbr_node_inds)
num_nodes_per_radius = [len(r) for r in all_radii_nbr_node_inds]
# get 3d tensor for one graph where each slice has one neighbouring node corrupted
d_init_nodes = torch.stack([init_nodes[i]] *
len(flattened_d_hop_node_inds))
d_node_target_types = torch.stack([node_target_types[i]] *
len(flattened_d_hop_node_inds))
d_node_target_inds_vector = torch.stack(
[node_target_inds_vector[i]] * len(flattened_d_hop_node_inds))
d_init_edges = torch.stack([init_edges[i]] *
len(flattened_d_hop_node_inds))
d_node_masks = torch.stack([node_masks[i]] *
len(flattened_d_hop_node_inds))
d_edge_masks = torch.stack([edge_masks[i]] *
len(flattened_d_hop_node_inds))
d_init_hydrogens = torch.stack([init_hydrogens[i]] *
len(flattened_d_hop_node_inds))
d_original_node_inds = torch.stack([original_node_inds[i]] *
len(flattened_d_hop_node_inds))
# Don't corrupt source node
for k, j in enumerate(flattened_d_hop_node_inds[1:], 1):
original_node = init_nodes[i][j]
valid_choices = np.setdiff1d(
np.arange(len(QM9_SYMBOL_LIST[:5])), original_node.cpu())
replacement_node = np.random.choice(valid_choices)
d_init_nodes[k][j] = float(replacement_node)
if replace_hs is True:
original_h = init_hydrogens[i][j]
valid_h_choices = np.setdiff1d(np.arange(max_hs + 2),
original_h.cpu())
replacement_h = np.random.choice(valid_h_choices)
d_init_hydrogens[k][j] = float(replacement_h)
return d_init_nodes, d_node_target_types, d_node_target_inds_vector, d_init_edges, d_node_masks,\
d_edge_masks, d_init_hydrogens, d_original_node_inds, num_nodes_per_radius