def test_graph_norm(self):
graph_list = []
edges1 = [(0, 1), (1, 2)]
num_nodes1 = 3
g1 = pgl.Graph(edges=edges1, num_nodes=num_nodes1)
graph_list.append(g1)
edges2 = [(0, 2), (0, 3), (1, 2)]
num_nodes2 = 4
g2 = pgl.Graph(edges=edges2, num_nodes=num_nodes2)
graph_list.append(g2)
multi_graph = pgl.Graph.disjoint(graph_list)
multi_graph.tensor()
feat = np.repeat(np.arange(0, 7).reshape(-1, 1), 3,
axis=1).astype("float32")
tensor_feat = paddle.to_tensor(feat, dtype="float32")
feat[0:3] = feat[0:3] / np.sqrt(3)
feat[3:] = feat[3:] / np.sqrt(4)
norm_feat = F.graph_norm(multi_graph, tensor_feat)
self.assertEqual(feat.tolist(), norm_feat.numpy().tolist())
gn_layer = nn.GraphNorm()
norm_feat = gn_layer(multi_graph, tensor_feat)
self.assertEqual(feat.tolist(), norm_feat.numpy().tolist())
def __call__(self, data_list):
"""
Collate features about a sublist of graph data and return join_graph,
masked_node_indice and masked_node_labels.
Args:
data_list : the graph data in gen_features.for data in data_list,
create node features and edge features according to pgl graph,and then
use graph wrapper to feed join graph, then the label can be arrayed to batch label.
Returns:
The batch data contains finetune label and valid,which are
collected from batch_label and batch_valid.
"""
atom_bond_graph_list = []
bond_angle_graph_list = []
label_list = []
for data in data_list:
ab_g = pgl.Graph(num_nodes=len(data[self.atom_names[0]]),
edges=data['edges'],
node_feat={
name: data[name].reshape([-1, 1])
for name in self.atom_names
},
edge_feat={
name: data[name].reshape([-1, 1])
for name in self.bond_names +
self.bond_float_names
})
ba_g = pgl.Graph(num_nodes=len(data['edges']),
edges=data['BondAngleGraph_edges'],
node_feat={},
edge_feat={
name: data[name].reshape([-1, 1])
for name in self.bond_angle_float_names
})
atom_bond_graph_list.append(ab_g)
bond_angle_graph_list.append(ba_g)
if not self.is_inference:
label_list.append(data['label'])
atom_bond_graph = pgl.Graph.batch(atom_bond_graph_list)
bond_angle_graph = pgl.Graph.batch(bond_angle_graph_list)
# TODO: reshape due to pgl limitations on the shape
self._flat_shapes(atom_bond_graph.node_feat)
self._flat_shapes(atom_bond_graph.edge_feat)
self._flat_shapes(bond_angle_graph.node_feat)
self._flat_shapes(bond_angle_graph.edge_feat)
if not self.is_inference:
if self.task_type == 'class':
labels = np.array(label_list)
# label: -1 -> 0, 1 -> 1
labels = ((labels + 1.0) / 2)
valids = (labels != 0.5)
return [atom_bond_graph, bond_angle_graph, valids, labels]
else:
labels = np.array(label_list, 'float32')
return atom_bond_graph, bond_angle_graph, labels
else:
return atom_bond_graph, bond_angle_graph
def prepareGraphData(self):
self.buildUserItemEdges()
self.buildUserUserEdges()
info_graph = pgl.Graph(num_nodes=self.conf['num_users'] +
self.conf['num_items'],
edges=self.user_item_edges)
soc_graph = pgl.Graph(num_nodes=self.conf['num_users'],
edges=self.user_user_edges)
return info_graph, soc_graph
def __init__(self, args, dataset):
super(LightGCN, self).__init__()
self.args = args
self.dataset = dataset
self.num_users = self.dataset.n_users
self.num_items = self.dataset.m_items
num_nodes = self.dataset.n_users + self.dataset.m_items
self.latent_dim = self.args.recdim
self.n_layers = self.args.n_layers
self.lightgcn = LightGCN_Layer(self.n_layers)
# self.lightgcn = LightGCNonv(self.n_layers)
self.embedding_user = nn.Embedding(
num_embeddings=self.num_users, embedding_dim=self.latent_dim)
self.embedding_item = nn.Embedding(
num_embeddings=self.num_items, embedding_dim=self.latent_dim)
emb_item_weight = np.random.normal(
0, 0.1,
self.embedding_item.weight.numpy().shape).astype(np.float32)
emb_user_weight = np.random.normal(
0, 0.1,
self.embedding_user.weight.numpy().shape).astype(np.float32)
self.embedding_item.weight.set_value(emb_item_weight)
self.embedding_user.weight.set_value(emb_user_weight)
self.f = nn.Sigmoid()
edges = paddle.to_tensor(self.dataset.trainEdge, dtype='int64')
self.Graph = pgl.Graph(num_nodes=num_nodes, edges=edges)
self.lightgcn.train()
def test_dump_tensor_load_numpy(self):
path = './tmp'
glist = []
dim = 4
num_nodes = 10
edges = np.random.randint(low=1,
high=num_nodes,
size=[np.random.randint(low=2, high=10), 2])
nfeat = np.random.randn(num_nodes, dim)
efeat = np.random.randn(len(edges), dim)
g = pgl.Graph(edges=edges,
num_nodes=num_nodes,
node_feat={'nfeat': nfeat},
edge_feat={'efeat': efeat})
in_before = g.indegree()
g.outdegree()
g.tensor()
# Merge Graph
g.dump(path)
g2 = pgl.Graph.load(path)
in_after = g2.indegree()
for a, b in zip(in_before, in_after):
self.assertEqual(a, b)
del g2
del in_after
import shutil
shutil.rmtree(path)
def test_disjoint_graph(self):
glist = []
dim = 4
for i in range(5):
num_nodes = np.random.randint(low=2, high=10)
edges = np.random.randint(
low=1,
high=num_nodes,
size=[np.random.randint(low=1, high=10), 2])
nfeat = np.random.randn(num_nodes, dim)
efeat = np.random.randn(len(edges), dim)
g = pgl.Graph(edges=edges,
num_nodes=num_nodes,
node_feat={'nfeat': nfeat},
edge_feat={'efeat': efeat})
glist.append(g)
# Merge Graph
multi_graph = pgl.Graph.disjoint(glist)
# Check Graph Index
node_index = [np.ones(g.num_nodes) * n for n, g in enumerate(glist)]
edge_index = [np.ones(g.num_edges) * n for n, g in enumerate(glist)]
node_index = np.concatenate(node_index)
edge_index = np.concatenate(edge_index)
self.assertTrue(np.all(node_index == multi_graph.graph_node_id))
self.assertTrue(np.all(edge_index == multi_graph.graph_edge_id))
multi_graph.tensor()
self.assertTrue(
np.all(node_index == multi_graph.graph_node_id.numpy()))
self.assertTrue(
np.all(edge_index == multi_graph.graph_edge_id.numpy()))
def lod_prot_chain(self, prot_chain_name):
if prot_chain_name in self.cache:
return self.cache[prot_chain_name]
label_idx = self.labels[prot_chain_name].astype("int64")
labels = np.zeros(self.n_labels)
labels[label_idx] = 1.0
prot_chain = np.load(
os.path.join(self.prot_chain_data_dir + f"/{prot_chain_name}.npz"),
allow_pickle=True,
)
seq = prot_chain["seq"]
edges = prot_chain["n2n_edges"]
num_nodes = len(seq)
n_self_loops = np.sum(edges[:, 0] == edges[:, 1])
if n_self_loops == 0:
node_id = np.arange(num_nodes, dtype="int64")
self_loop = np.array([node_id, node_id]).T
edges = np.concatenate([edges, self_loop])
p_graph = pgl.Graph(
edges,
num_nodes=num_nodes,
node_feat={"seq": paddle.to_tensor(seq, dtype="int64")},
)
padded_features = np.zeros((self.padded_len, self.n_feats)).astype("float32")
seq_one_hot = self.one_hot[seq]
padded_features[: seq.shape[0]] = seq_one_hot
out = p_graph, padded_features, labels
if self.use_cache:
self.cache[prot_chain_name] = out
return out
def __init_weight(self):
self.num_users = self.dataset.n_users
self.num_items = self.dataset.m_items
self.latent_dim = self.config['latent_dim_rec']
self.n_layers = self.config['lightGCN_n_layers']
self.lgn = LightGCNonv(self.n_layers)
self.embedding_user = nn.Embedding(num_embeddings=self.num_users,
embedding_dim=self.latent_dim)
self.embedding_item = nn.Embedding(num_embeddings=self.num_items,
embedding_dim=self.latent_dim)
if self.config['pretrain'] == 0:
emb_item_weight = np.random.normal(
0, 0.1,
self.embedding_item.weight.numpy().shape).astype(np.float32)
emb_user_weight = np.random.normal(
0, 0.1,
self.embedding_user.weight.numpy().shape).astype(np.float32)
else:
emb_item_weight = np.load('item_embedding.npy').astype(np.float32)
emb_user_weight = np.load('item_embedding.npy').astype(np.float32)
self.embedding_item.weight.set_value(emb_item_weight)
self.embedding_user.weight.set_value(emb_user_weight)
self.f = nn.Sigmoid()
num_nodes = self.dataset.n_users + self.dataset.m_items
edges = paddle.to_tensor(self.dataset.trainEdge, dtype='int64')
self.Graph = pgl.Graph(num_nodes=num_nodes, edges=edges)
print(f"lgn is already to go(dropout:{self.config['dropout']})")
self.lgn.train()
def fp_collatefn(self, batch_data):
graph_list = []
labels = []
mgf_list = []
maccs_list = []
for gdata in batch_data:
g = pgl.Graph(edges=gdata['edge_index'].T,
num_nodes=gdata['num_nodes'],
node_feat={'feat': gdata['node_feat']},
edge_feat={'feat': gdata['edge_feat']})
graph_list.append(g)
labels.append(gdata['label'])
mgf_list.append(gdata['mgf'])
maccs_list.append(gdata['maccs'])
labels = np.array(labels, dtype="float32")
g = pgl.Graph.batch(graph_list)
mgf_feat = np.array(mgf_list, dtype="float32")
maccs_feat = np.array(maccs_list, dtype="float32")
others = {}
others['mgf'] = mgf_feat
others['maccs'] = maccs_feat
return {'graph': g, 'mgf': mgf_feat, 'maccs': maccs_feat}, labels
def smile_to_graph(smile):
"""set max atom number equals to 100"""
mol = Chem.MolFromSmiles(smile)
c_size = mol.GetNumAtoms()
#features = np.empty([c_size, 78])
mask = [0] * 100
features = np.zeros([100, 78])
for i, atom in enumerate(mol.GetAtoms()):
if atom.GetAtomicNum == 0:
return None
feature = atom_features(atom)
features[i, :] = feature / sum(feature)
mask[i] = 1
edges = []
for bond in mol.GetBonds():
i = bond.GetBeginAtomIdx()
j = bond.GetEndAtomIdx()
edges.append((i, j))
edges.append((j, i))
#g = nx.Graph(edges).to_directed()
g = pgl.Graph(num_nodes=100,
edges=edges,
node_feat={'node_feat': features})
return g, mask
def test_neighbors(self):
num_nodes = 5
edges = [(0, 1), (0, 2), (1, 2), (3, 4)]
g1 = pgl.Graph(edges=edges, num_nodes=num_nodes)
pred, pred_eid = g1.predecessor(return_eids=True)
self.assertEqual(len(pred), num_nodes)
self.assertEqual(len(pred_eid), num_nodes)
self.assertEqual(set(pred[0]), set([]))
self.assertEqual(set(pred[1]), set([0]))
self.assertEqual(set(pred[2]), set([0, 1]))
self.assertEqual(set(pred[3]), set([]))
self.assertEqual(set(pred[4]), set([3]))
succ, succ_eid = g1.successor(return_eids=True)
self.assertEqual(len(succ), num_nodes)
self.assertEqual(len(succ_eid), num_nodes)
self.assertEqual(set(succ[0]), set([1, 2]))
self.assertEqual(set(succ[1]), set([2]))
self.assertEqual(set(succ[2]), set([]))
self.assertEqual(set(succ[3]), set([4]))
self.assertEqual(set(succ[4]), set([]))
def coord3_junc_collatefn(self, batch_data):
graph_list = []
labels = []
junc_graph_list = []
mol2junc_list = []
g_offset = 0
junc_g_offset = 0
for gdata in batch_data:
g = pgl.Graph(edges=gdata['mol_graph']['edge_index'].T,
num_nodes=gdata['mol_graph']['num_nodes'],
node_feat={
'feat': gdata['mol_graph']['node_feat'],
'3d': gdata['mol_coord']
},
edge_feat={'feat': gdata['mol_graph']['edge_feat']})
num_nodes = gdata['junction_tree']['num_nodes']
if num_nodes > 0:
nfeat = np.array(gdata['junction_tree']['junc_dict'],
dtype="int64").reshape(-1, 1)
junc_g = pgl.Graph(
edges=gdata['junction_tree']['edge_index'].T,
num_nodes=num_nodes,
node_feat={'feat': nfeat})
offset = np.array([g_offset, junc_g_offset], dtype="int64")
mol2junc = gdata['mol2juct'] + offset
junc_g_offset += junc_g.num_nodes
junc_graph_list.append(junc_g)
mol2junc_list.append(mol2junc)
graph_list.append(g)
labels.append(gdata['label'])
g_offset += g.num_nodes
mol2junc = np.concatenate(mol2junc_list, axis=0)
labels = np.array(labels, dtype="float32")
g = pgl.Graph.batch(graph_list)
junc_g = pgl.Graph.batch(junc_graph_list)
return {'graph': g, 'junc_graph': junc_g, 'mol2junc': mol2junc}, labels
def get_subgraph_by_masked(self, graph, mask):
index = L.where(mask)
if index.shape[0] > 0:
edges = graph.edges
sub_edges = paddle.gather(edges, index, axis=0)
sg = pgl.Graph(sub_edges, num_nodes=graph.num_nodes)
return sg
else:
return None
def load_from_file(path):
edges = []
with open(path) as inf:
for line in inf:
u, t = line.strip("\n").split("\t")
u, t = int(u), int(t)
edges.append((u, t))
edges = np.array(edges)
graph = pgl.Graph(edges)
return graph
def test_build_graph(self):
num_nodes = 5
dim = 4
edges = [(0, 1), (1, 2), (3, 4)]
nfeat = np.random.randn(num_nodes, dim)
efeat = np.random.randn(len(edges), dim)
g1 = pgl.Graph(edges=edges,
num_nodes=num_nodes,
node_feat={'nfeat': nfeat},
edge_feat={'efeat': efeat})
def test_num_nodes_valid(self):
num_nodes = 3
dim = 4
edges = [(0, 1), (1, 2), (3, 4)]
nfeat = np.random.randn(num_nodes, dim)
efeat = np.random.randn(len(edges), dim)
with self.assertRaises(ValueError):
g1 = pgl.Graph(edges=edges,
num_nodes=num_nodes,
node_feat={'nfeat': nfeat},
edge_feat={'efeat': efeat})
def build_net(input_size, num_class, hidden_size, num_layers):
num_nodes = F.data("num_nodes", shape=[1], dtype="int32")
edges = F.data("edges", shape=[None, 2], dtype="int32")
sample_index = F.data("sample_index", shape=[None], dtype="int32")
index = F.data("index", shape=[None], dtype="int32")
label = F.data("label", shape=[None], dtype="int64")
label = paddle.reshape(label, [-1, 1])
graph = pgl.Graph(num_nodes=num_nodes, edges=edges)
feat = F.data("feature", shape=[None, input_size], dtype="float32")
model = GraphSage(
input_size=input_size,
num_class=num_class,
hidden_size=hidden_size,
num_layers=num_layers)
g = pgl.Graph(num_nodes=num_nodes, edges=edges)
pred = model(g, feat)
pred = paddle.gather(pred, index)
loss = paddle.nn.functional.cross_entropy(pred, label)
acc = paddle.metric.accuracy(input=pred, label=label, k=1)
return loss, acc
def test_random_walk(self):
num_nodes = 5
dim = 4
edges = [(0, 1), (1, 2), (3, 4), (1, 0), (2, 1), (4, 3)]
nfeat = np.random.randn(num_nodes, dim)
efeat = np.random.randn(len(edges), dim)
g1 = pgl.Graph(edges=edges,
num_nodes=num_nodes,
node_feat={'nfeat': nfeat},
edge_feat={'efeat': efeat})
walk_paths = random_walk(g1, [0, 1], 2)
def test_send_and_recv(self):
np.random.seed(0)
num_nodes = 5
dim = 4
edges = [(0, 1), (1, 2), (3, 4), (4, 1), (1, 0)]
nfeat = np.array([[1, 2, 3, 4], [2, 3, 4, 5], [3, 4, 5, 6],
[4, 5, 6, 7], [5, 6, 7, 8]],
dtype="float32")
ground = np.array([[1, 2, 3, 4], [2, 3, 4, 5], [4, 5, 6, 7],
[5, 6, 7, 8], [2, 3, 4, 5]],
dtype="float32")
recv_ground = np.array(
[[2., 3., 4., 5.], [6., 8., 10., 12.], [2., 3., 4., 5.],
[0., 0., 0., 0.], [4., 5., 6., 7.]],
dtype="float32")
g = pgl.Graph(edges=edges,
num_nodes=num_nodes,
node_feat={'nfeat': nfeat})
g.tensor()
def send_func1(src_feat, dst_feat, edge_feat):
return src_feat
def send_func2(src_feat, dst_feat, edge_feat):
return {'h': src_feat['h']}
def reduce_func(msg):
return msg.reduce_sum(msg['h'])
# test send_func1
msg1 = g.send(send_func1, src_feat={'h': g.node_feat['nfeat']})
_msg = msg1['h'].numpy()
self.assertTrue((ground == _msg).all())
output = g.recv(reduce_func, msg1)
output = output.numpy()
self.assertTrue((recv_ground == output).all())
# test send_func2
msg2 = g.send(send_func1, src_feat={'h': g.node_feat['nfeat']})
_msg = msg2['h'].numpy()
self.assertTrue((ground == _msg).all())
output = g.recv(reduce_func, msg2)
output = output.numpy()
self.assertTrue((recv_ground == output).all())
def __getitem__(self, idx):
num_nodes = self.graph._graph_node_index[
idx + 1] - self.graph._graph_node_index[idx]
node_shift = self.graph._graph_node_index[idx]
edges = self.graph.edges[self.graph._graph_edge_index[idx]:self.graph.
_graph_edge_index[idx + 1]]
edges = edges - node_shift
edge_feat = {}
for key, value in self.graph.edge_feat.items():
edge_feat[key] = value[self.graph._graph_edge_index[idx]:self.
graph._graph_edge_index[idx + 1]]
node_feat = {}
for key, value in self.graph.node_feat.items():
node_feat[key] = value[self.graph._graph_node_index[idx]:self.
graph._graph_node_index[idx + 1]]
#pretrain information
pretrain_info = {}
cid = self.pretrain_info_list[idx]["context_id"]
edge_index = self.pretrain_info_list[idx]["edge_index"]
tid = self.pretrain_info_list[idx]["twohop_context"]
if num_nodes != len(tid):
print(
f"idx {idx} num_nodes is : {num_nodes} and len of tid is : {len(tid)}, they are not equal"
)
exit(0)
bond_angle_index = self.pretrain_info_list[idx]["bond_angle_index"]
bond_angle = self.pretrain_info_list[idx]["bond_angle"]
dft_success = self.pretrain_info_list[idx]["dft_success"]
bond_angle_mask = np.array(
self.pretrain_info_list[idx]["bond_angle"] * 0 + dft_success,
dtype=bool)
edge_attr_float = np.array(
self.pretrain_info_list[idx]["edge_feat_float"])
edge_attr_float_mask = np.array(
self.pretrain_info_list[idx]["edge_feat_float"].reshape(-1) * 0 +
dft_success,
dtype=bool)
pretrain_info["edge_index"] = np.array(edge_index)
pretrain_info["tid"] = np.array(tid, dtype=int)
pretrain_info["bond_angle_index"] = bond_angle_index
pretrain_info["bond_angle"] = bond_angle
pretrain_info["bond_angle_mask"] = bond_angle_mask
pretrain_info["edge_attr_float"] = edge_attr_float
pretrain_info["edge_attr_float_mask"] = edge_attr_float_mask
smiles, label = self.raw_dataset[idx]
return (pgl.Graph(num_nodes=num_nodes,
edges=edges,
node_feat=node_feat,
edge_feat=edge_feat), self.label[idx], smiles,
pretrain_info)
def __call__(self, batch_data):
graph_list = []
labels = []
for gdata in batch_data:
g = pgl.Graph(edges=gdata['edges'],
num_nodes=gdata['num_nodes'],
node_feat={'feat': gdata['node_feat']},
edge_feat={'feat': gdata['edge_feat']})
graph_list.append(g)
labels.append(gdata['label'])
labels = np.array(labels, dtype="float32")
g = pgl.Graph.batch(graph_list)
return g, labels
def __init__(self, args, dataset):
super(NGCF, self).__init__()
self.args = args
self.dataset = dataset
self.num_users = self.dataset.n_users
self.num_items = self.dataset.m_items
num_nodes = self.dataset.n_users + self.dataset.m_items
self.latent_dim = self.args.recdim
self.n_layers = self.args.n_layers
self.ngcf = NGCF_Layer(self.latent_dim, self.latent_dim, self.n_layers)
edges = paddle.to_tensor(self.dataset.trainEdge, dtype='int64')
self.Graph = pgl.Graph(num_nodes=num_nodes, edges=edges)
self.f = nn.Sigmoid()
self.__init_weight()
def quality_graph_collatefn(self, batch_data):
graph_list = []
labels = []
for gdata in batch_data:
g = pgl.Graph(edges=gdata['mol_graph']['edge_index'].T,
num_nodes=gdata['mol_graph']['num_nodes'],
node_feat={'feat': gdata['mol_graph']['node_feat']},
edge_feat={'feat': gdata['mol_graph']['edge_feat']})
graph_list.append(g)
labels.append(gdata['label'])
labels = np.array(labels, dtype="float32")
g = pgl.Graph.batch(graph_list)
return {'graph': g}, labels
def create_random_graph():
dim = 8
num_nodes = np.random.randint(low=8, high=16)
edges = np.random.randint(
low=0,
high=num_nodes,
size=[np.random.randint(low=num_nodes * 3, high=num_nodes * 4), 2])
nfeat = np.random.randn(num_nodes, dim)
efeat = np.random.randn(len(edges), dim)
g = pgl.Graph(edges=edges,
num_nodes=num_nodes,
node_feat={'nfeat': nfeat},
edge_feat={'efeat': efeat})
return g
def __call__(self, data_list):
"""
Collate features about a sublist of graph data and return join_graph,
masked_node_indice and masked_node_labels.
Args:
data_list : the graph data in AttrmaskCollateFn.for data in data_list,
create node features and edge features according to pgl graph,and then
use graph wrapper to feed join graph, then the label can be arrayed to batch label.
Returns:
The batch data contains finetune label and valid,which are
collected from batch_label and batch_valid.
"""
g_list = []
for data in data_list:
g = pgl.Graph(num_nodes=len(data[self.atom_names[0]]),
edges=data['edges'],
node_feat={
name: data[name].reshape([-1, 1])
for name in self.atom_names
},
edge_feat={
name: data[name].reshape([-1, 1])
for name in self.bond_names
})
g_list.append(g)
join_graph = pgl.Graph.batch(g_list)
for name in join_graph.node_feat:
join_graph.node_feat[name] = join_graph.node_feat[name].reshape(
[-1])
for name in join_graph.edge_feat:
join_graph.edge_feat[name] = join_graph.edge_feat[name].reshape(
[-1])
### mask atom
N = join_graph.num_nodes
masked_size = int(N * self.mask_ratio)
masked_node_indice = np.random.choice(range(N),
size=masked_size,
replace=False)
masked_node_labels = join_graph.node_feat['atomic_num'][
masked_node_indice]
for name in join_graph.node_feat:
join_graph.node_feat[name][masked_node_indice] = 0 # 0: OOV
return join_graph, masked_node_indice, masked_node_labels
def gen_drug_graph(drug_feature, data_id):
"""
Construct graphs from current drug features
:param drug_feature: current drug features generated from preceding steps
:param data_id: sample index
:return: a list of pgl.graph
"""
graph_list = []
for i in data_id:
g = pgl.Graph(edges=drug_feature[i[1]][-1],
num_nodes=Max_atoms,
node_feat={'nfeat': drug_feature[i[1]][0].astype('float32')},
)
graph_list.append(g)
return graph_list
def create_feeds(name_data_pair):
edges = name_data_pair["node_feat"].numpy()
node_feat = name_data_pair["edge_feat"].numpy()
edge_feat = name_data_pair["segment_ids"].numpy()
graphs = []
for i in range(edges.shape[0]):
g = pgl.Graph(
edges=edges[i],
node_feat={"node_attr": node_feat[i]},
edge_feat={"edge_attr": edge_feat[i]})
graphs.append(g)
graphs = pgl.Graph.batch(graphs).tensor()
name_data_pair["edges"] = graphs.edges
name_data_pair["node_feat"] = graphs.node_feat["node_attr"]
name_data_pair["edge_feat"] = graphs.edge_feat["edge_attr"]
name_data_pair["segment_ids"] = graphs.graph_node_id
return name_data_pair
def construct(tensors):
""" tensor list to ([graph_tensor, graph_tensor, ...],
other tensor)
"""
graph_num = 1
start_len = 0
datas = []
graph_list = []
for graph in range(graph_num):
graph_list.append(
pgl.Graph(num_nodes=tensors[start_len],
edges=tensors[start_len + 1]))
start_len += 2
for i in range(start_len, len(tensors)):
datas.append(tensors[i])
return graph_list, datas
def __call__(self, batch_data_list):
"""
Function caller to convert a batch of data into a big batch feed dictionary.
Args:
batch_data_list: a batch of the compound graph data.
Returns:
feed_dict: a dictionary contains `graph/xxx` inputs for PGL.
"""
g_list, label_list = [], []
for data in batch_data_list:
g = pgl.Graph(
num_nodes=len(data[self.atom_names[0]]),
edges=data['edges'],
node_feat={name: data[name].reshape([-1, 1])
for name in self.atom_names},
edge_feat={name: data[name].reshape([-1, 1])
for name in self.bond_names})
g_list.append(g)
if self.with_graph_label:
label_list.append(data['label'])
join_graph = pgl.Graph.batch(g_list)
output = [join_graph]
if self.with_graph_label:
if self.task_type == 'cls':
batch_label = np.array(label_list).reshape(
-1, self.num_cls_tasks)
elif self.task_type == 'reg':
label_list = [label[self.reg_target_id]
for label in label_list]
batch_label = np.array(label_list).reshape(-1, 1)
# label: -1 -> 0, 1 -> 1
batch_label = ((batch_label + 1.0) / 2).astype('float32')
batch_valid = (batch_label != 0.5).astype("float32")
output.extend([batch_label, batch_valid])
if self.with_pos_neg_mask:
pos_mask, neg_mask = MoleculeCollateFunc.get_pos_neg_mask(g_list)
output.extend([pos_mask, neg_mask])
return output
def new_graph_collatefn(self, batch_data):
# for graph_data_additional_features_0424.pkl
# with graph_transform in mol_features_extract.py
graph_list = []
labels = []
for gdata in batch_data:
efeat = np.delete(gdata['edge_feat'], -1, axis=1) # remove 3d dist
g = pgl.Graph(edges=gdata['edge_index'].T,
num_nodes=gdata['num_nodes'],
node_feat={'feat': gdata['node_feat']},
edge_feat={'feat': efeat})
graph_list.append(g)
labels.append(gdata['label'])
labels = np.array(labels, dtype="float32")
g = pgl.Graph.batch(graph_list)
return {'graph': g}, labels