def forward(self, is_test=False):
"""
Build the network.
"""
substruct_graph_wrapper = GraphWrapper(
name="graph",
node_feat=[('atom_type', [None, 1], "int64"),
('chirality_tag', [None, 1], "int64")],
edge_feat=[('bond_type', [None, 1], "int64"),
('bond_direction', [None, 1], "int64")])
context_graph_wrapper = GraphWrapper(
name="context_graph",
node_feat=[('atom_type', [None, 1], "int64"),
('chirality_tag', [None, 1], "int64")],
edge_feat=[('bond_type', [None, 1], "int64"),
('bond_direction', [None, 1], "int64")])
substruct_center_idx = layers.data(name="substruct_center_idx",
shape=[-1, 1],
dtype="int64")
context_overlap_idx = layers.data(name="context_overlap_idx",
shape=[-1, 1],
dtype="int64")
context_overlap_lod = layers.data(name="context_overlap_lod",
shape=[1, -1],
dtype="int32")
context_cycle_index = layers.data(name="context_cycle_index",
shape=[-1, 1],
dtype="int64")
substruct_node_repr = self.substruct_model.forward(
substruct_graph_wrapper, is_test=is_test)
substruct_repr = layers.gather(substruct_node_repr,
substruct_center_idx)
context_node_repr = self.context_model.forward(context_graph_wrapper,
is_test=is_test)
context_overlap_repr = layers.gather(context_node_repr,
context_overlap_idx)
context_repr = layers.sequence_pool(
layers.lod_reset(context_overlap_repr, context_overlap_lod),
self.context_pooling)
neg_context_repr = layers.gather(context_repr, context_cycle_index)
pred_pos = layers.reduce_sum(substruct_repr * context_repr, 1)
pred_neg = layers.reduce_sum(substruct_repr * neg_context_repr, 1)
label_pos = pred_pos * 0.0 + 1.0
label_pos.stop_gradient = True
label_neg = pred_neg * 0.0
label_neg.stop_gradient = True
loss = layers.sigmoid_cross_entropy_with_logits(x=pred_pos, label=label_pos) \
+ layers.sigmoid_cross_entropy_with_logits(x=pred_neg, label=label_neg)
loss = layers.reduce_mean(loss)
self.substruct_graph_wrapper = substruct_graph_wrapper
self.context_graph_wrapper = context_graph_wrapper
self.loss = loss
def create_model(args, config, graph_label):
"""Create model for given model configuration."""
logging.info('building model')
graph_wrapper = GraphWrapper(name="graph",
node_feat=[('atom_type', [None, 1], "int64"),
('chirality_tag', [None,
1], "int64")],
edge_feat=[('bond_type', [None, 1], "int64"),
('bond_direction', [None,
1], "int64")])
encoder = GINEncoder(config)
global_repr, patch_summary = encoder.forward(graph_wrapper)
hid = L.fc(global_repr,
config['hidden_size'],
act='relu',
name='finetune_fc1')
hid = L.fc(hid, config['hidden_size'], act='relu', name='finetune_fc2')
logits = L.fc(global_repr, args.num_tasks, name="finetune_fc3")
loss = L.sigmoid_cross_entropy_with_logits(x=logits, label=graph_label)
loss = L.reduce_mean(loss)
pred = L.sigmoid(logits)
keys = ['loss', 'graph_wrapper', 'encoder', 'graph_emb', 'pred']
Agent = namedtuple('Agent', keys)
return Agent(loss=loss,
graph_wrapper=graph_wrapper,
encoder=encoder,
graph_emb=global_repr,
pred=pred)
def __init__(self,
model_config,
use_pretrained_compound_gnns=False):
self.model_config = model_config
self.use_pretrained_compound_gnns = use_pretrained_compound_gnns
dim = CompoundConstants.atomic_numeric_feat_dim
self.compound_graph_wrapper = GraphWrapper(
name="compound_graph",
node_feat=[
('atom_type', [None, 1], "int64"),
('chirality_tag', [None, 1], "int64"),
('atom_numeric_feat', [None, dim], "float32")],
edge_feat=[
('bond_type', [None, 1], "int64"),
('bond_direction', [None, 1], "int64")
])
protein_token = fluid.layers.data(name='protein_token', shape=[None, 1], dtype='int64')
protein_token_lod = fluid.layers.data(name='protein_token_lod', shape=[None], dtype='int32')
self.protein_token = fluid.layers.lod_reset(protein_token, y=protein_token_lod)
if use_pretrained_compound_gnns:
self.compound_model = PretrainGNNModel(model_config['compound'], name='gnn') # TODO: update the name to 'compound'
else:
self.compound_model = CompoundGNNModel(model_config['compound'], name='compound')
self.protein_model = ProteinSequenceModel(model_config['protein'], name='protein')
def forward(self, is_test=False):
"""
Build the network.
"""
graph_wrapper = GraphWrapper(name="graph",
node_feat=[
('atom_type', [None, 1], "int64"),
('chirality_tag', [None, 1], "int64")],
edge_feat=[
('bond_type', [None, 1], "int64"),
('bond_direction', [None, 1], "int64")])
masked_node_indice = layers.data(name="masked_node_indice", shape=[-1, 1], dtype="int64")
masked_node_label = layers.data(name="masked_node_label", shape=[-1, 1], dtype="int64")
node_repr = self.gnn_model.forward(graph_wrapper, is_test=is_test)
masked_node_repr = layers.gather(node_repr, masked_node_indice)
logits = layers.fc(masked_node_repr,
size=len(CompoundConstants.atom_num_list),
name="masked_node_logits")
loss, pred = layers.softmax_with_cross_entropy(
logits, masked_node_label, return_softmax=True)
loss = layers.reduce_mean(loss)
acc = layers.accuracy(pred, masked_node_label)
self.graph_wrapper = graph_wrapper
self.loss = loss
def forward(self, is_test=False):
"""tbd"""
graph_wrapper = GraphWrapper(name="graph",
node_feat=[
('atom_type', [None, 1], "int64"),
('chirality_tag', [None, 1], "int64")
],
edge_feat=[
('bond_type', [None, 1], "int64"),
('bond_direction', [None, 1], "int64")
])
supervised_label = layers.data(name="supervised_label",
shape=[None, self.task_num],
dtype="float32")
valid = layers.data("valid",
shape=[None, self.task_num],
dtype="float32")
node_repr = self.gnn_model.forward(graph_wrapper, is_test=is_test)
graph_repr = pgl.layers.graph_pooling(graph_wrapper, node_repr,
self.pool_type)
logits = layers.fc(graph_repr,
size=self.task_num,
name="pretrain_supervised_fc")
loss = layers.sigmoid_cross_entropy_with_logits(x=logits,
label=supervised_label)
loss = layers.reduce_sum(loss * valid) / layers.reduce_sum(valid)
self.graph_wrapper = graph_wrapper
self.loss = loss
def create_model(args, config):
"""Create model for given model configuration."""
logging.info('building model')
graph_wrapper = GraphWrapper(name="graph",
node_feat=[('atom_type', [None, 1], "int64"),
('chirality_tag', [None,
1], "int64")],
edge_feat=[('bond_type', [None, 1], "int64"),
('bond_direction', [None,
1], "int64")])
# NOTE: [num_nodes, num_graphs], bs = num_graphs
pos_mask = L.data(name='pos_mask',
shape=[-1, args.batch_size],
dtype='float32')
neg_mask = L.data(name='neg_mask',
shape=[-1, args.batch_size],
dtype='float32')
encoder = GINEncoder(config)
global_repr, patch_summary = encoder.forward(graph_wrapper)
global_D = FF(encoder.embedding_dim)
local_D = FF(encoder.embedding_dim)
g_enc = global_D.forward(global_repr)
l_enc = local_D.forward(patch_summary)
res = L.matmul(l_enc, g_enc, transpose_y=True)
E_pos = get_positive_expectation(res * pos_mask,
config['measure'],
average=False)
E_pos = L.reduce_sum(E_pos) / graph_wrapper.num_nodes
E_neg = get_negative_expectation(res * neg_mask,
config['measure'],
average=False)
E_neg = L.reduce_sum(E_neg) / (graph_wrapper.num_nodes *
(graph_wrapper.num_graph - 1))
local_global_loss = E_neg - E_pos
if config['prior']:
prior_D = PriorDiscriminator(encoder.embedding_dim)
prior = L.uniform_random([args.batch_size, encoder.embedding_dim],
min=0.0,
max=1.0)
term_1 = L.reduce_mean(L.log(prior_D.forward(prior)))
term_2 = L.reduce_mean(L.log(1.0 - prior_D.forward(global_repr)))
prior_loss = -(term_1 + term_2) * config['gamma']
else:
prior_loss = 0
total_loss = local_global_loss + prior_loss
keys = ['loss', 'graph_wrapper', 'encoder', 'graph_emb']
Agent = namedtuple('Agent', keys)
return Agent(loss=total_loss,
graph_wrapper=graph_wrapper,
encoder=encoder,
graph_emb=global_repr)
def __init__(self, args, graph_wrapper=None):
self.hidden_size = args.hidden_size
self.num_nodes = args.num_nodes
self.drop_rate = args.drop_rate
node_feature = [('feat', [None, 128], "float32")]
if graph_wrapper is None:
self.graph_wrapper = GraphWrapper(
name="graph", place=F.CPUPlace(), node_feat=node_feature)
else:
self.graph_wrapper = graph_wrapper
self.build_model(args)
def forward(self, is_test=False):
"""
Define the forward function,set the parameter layer options.
Graph wrapper creates a graph data holders that attributes and features
in the graph are :code:`fluid.layers.data`.And we provide interface :
code:`to_feed` to help converting :code:`Graph`data into :code:`feed_dict`.
Args:
name: The graph data prefix,here is graph
node_feat: A list of tuples that decribe the details of node
feature tenosr. Each tuple must be (name, shape, dtype)
and the first dimension of the shape must be set unknown
(-1 or None) or we can easily use :code:`Graph.node_feat_info()`
to get the node_feat settings.
edge_feat: A list of tuples that decribe the details of edge
feature tenosr. Each tuple mush be (name, shape, dtype)
and the first dimension of the shape must be set unknown
(-1 or None) or we can easily use :code:`Graph.edge_feat_info()`
to get the edge_feat settings.
"""
graph_wrapper = GraphWrapper(name="graph",
node_feat=[
('atom_type', [None, 1], "int64"),
('chirality_tag', [None, 1], "int64")
],
edge_feat=[
('bond_type', [None, 1], "int64"),
('bond_direction', [None, 1], "int64")
])
finetune_label = layers.data(name="finetune_label",
shape=[None, self.num_tasks],
dtype="float32")
valid = layers.data("valid",
shape=[None, self.num_tasks],
dtype="float32")
node_repr = self.gnn_model.forward(graph_wrapper, is_test=is_test)
graph_repr = pgl.layers.graph_pooling(graph_wrapper, node_repr,
self.pool_type)
logits = layers.fc(graph_repr, size=self.num_tasks, name="finetune_fc")
loss = layers.sigmoid_cross_entropy_with_logits(x=logits,
label=finetune_label)
loss = layers.reduce_sum(loss * valid) / layers.reduce_sum(valid)
pred = layers.sigmoid(logits)
self.graph_wrapper = graph_wrapper
self.loss = loss
self.pred = pred
self.finetune_label = finetune_label
def __init__(self, args, dataset):
self.args = args
self.dataset = dataset
self.hidden_size = args.hidden_size
self.num_classes = args.num_classes
self.num_features = args.num_features
self.pooling_ratio = args.pooling_ratio
self.dropout_ratio = args.dropout_ratio
self.batch_size = args.batch_size
graph_data = []
g, label = self.dataset[0]
graph_data.append(g)
g, label = self.dataset[1]
graph_data.append(g)
batch_graph = MultiGraph(graph_data)
indegree = batch_graph.indegree()
norm = np.zeros_like(indegree, dtype="float32")
norm[indegree > 0] = np.power(indegree[indegree > 0], -0.5)
batch_graph.node_feat["norm"] = np.expand_dims(norm, -1)
graph_data = batch_graph
self.graph_wrapper = GraphWrapper(
name="graph", node_feat=graph_data.node_feat_info())
self.labels = L.data("labels",
shape=[None, self.args.num_classes],
dtype="int32",
append_batch_size=False)
self.labels_1dim = L.data("labels_1dim",
shape=[None],
dtype="int32",
append_batch_size=False)
self.graph_id = L.data("graph_id",
shape=[None],
dtype="int32",
append_batch_size=False)
if self.args.dataset_name == "FRANKENSTEIN":
self.gcn = gcn
else:
self.gcn = norm_gcn
self.build_model()
def __init__(self, name, edge_types, node_feat={}, edge_feat={}, **kwargs):
self.__data_name_prefix = name
self._edge_types = edge_types
self._multi_gw = {}
for edge_type in self._edge_types:
type_name = self.__data_name_prefix + '/' + edge_type
if node_feat:
n_feat = node_feat
else:
n_feat = {}
if edge_feat:
e_feat = edge_feat[edge_type]
else:
e_feat = {}
self._multi_gw[edge_type] = GraphWrapper(
name=type_name,
node_feat=n_feat,
edge_feat=e_feat)
def __init__(self, args, dataset):
self.args = args
self.dataset = dataset
self.hidden_size = self.args.hidden_size
self.embed_dim = self.args.embed_dim
self.dropout_prob = self.args.dropout_rate
self.pool_type = self.args.pool_type
self._init_vars = []
graph_data = []
g, label = self.dataset[0]
graph_data.append(g)
g, label = self.dataset[1]
graph_data.append(g)
batch_graph = pgl.graph.MultiGraph(graph_data)
graph_data = batch_graph
graph_data.edge_feat["feat"] = graph_data.edge_feat["feat"].astype(
"int64")
graph_data.node_feat["feat"] = graph_data.node_feat["feat"].astype(
"int64")
self.graph_wrapper = GraphWrapper(
name="graph",
place=F.CPUPlace(),
node_feat=graph_data.node_feat_info(),
edge_feat=graph_data.edge_feat_info())
self.atom_encoder = AtomEncoder(name="atom", emb_dim=self.embed_dim)
self.bond_encoder = BondEncoder(name="bond", emb_dim=self.embed_dim)
self.labels = L.data("labels",
shape=[None, self.args.num_class],
dtype="float32",
append_batch_size=False)
self.unmask = L.data("unmask",
shape=[None, self.args.num_class],
dtype="float32",
append_batch_size=False)
self.build_model()
def forward(self, is_test=False):
"""
Define the forward function,set the parameter layer options.
Graph wrapper creates a graph data holders that attributes and features
in the graph are :code:`fluid.layers.data`.And we provide interface :
code:`to_feed` to help converting :code:`Graph`data into :code:`feed_dict`.
Args:
name: The graph data prefix,here is graph
node_feat: A list of tuples that decribe the details of node
feature tenosr. Each tuple must be (name, shape, dtype)
and the first dimension of the shape must be set unknown
(-1 or None) or we can easily use :code:`Graph.node_feat_info()`
to get the node_feat settings.
edge_feat: A list of tuples that decribe the details of edge
feature tenosr. Each tuple mush be (name, shape, dtype)
and the first dimension of the shape must be set unknown
(-1 or None) or we can easily use :code:`Graph.edge_feat_info()`
to get the edge_feat settings.
Returns:
logits: the model prediction.
"""
graph_wrapper = GraphWrapper(name="graph",
node_feat=[
('atom_type', [None, 1], "int64"),
('chirality_tag', [None, 1], "int64")
],
edge_feat=[
('bond_type', [None, 1], "int64"),
('bond_direction', [None, 1], "int64")
])
node_repr = self.gnn_model.forward(graph_wrapper, is_test=is_test)
graph_repr = pgl.layers.graph_pooling(graph_wrapper, node_repr,
self.pool_type)
logits = layers.fc(graph_repr, size=self.num_tasks, name="finetune_fc")
return graph_wrapper, logits
def __init__(self, args, task):
candi_tasks = [ "predict_query", "predict_poi",
"pointwise", "pairwise", "listwise", "listwise_hinge"]
if task not in candi_tasks:
raise ValueError("task %s not in %s" % (task, candi_tasks))
self.norm_score = args.norm_score
self.ernie_config = ErnieConfig(args.ernie_config_path)
self.ernie_config.print_config()
self.city_size = 20000
self.hidden_size = 64
self._holder_list = []
node_feature = [
('src_ids', [None, args.max_seq_len], "int64"),
('pos_ids', [None, args.max_seq_len], "int64"),
('sent_ids', [None, args.max_seq_len], "int64"),
('input_mask', [None, args.max_seq_len], "float32"),
('node_types', [None], "int32"),
]
if task != 'predict_query':
self.graph_wrapper = GraphWrapper(
name="graph", place=F.CPUPlace(), node_feat=node_feature)
self._holder_list.extend(self.graph_wrapper.holder_list)
elif task == "predict_query":
# This is for save_inference_mode for query
self.graph_wrapper = FakeGraphWrapper(
node_feat=node_feature)
self._holder_list.extend(self.graph_wrapper.holder_list)
self.build_model(args, task)
