modify GaAN

.gitignore

@@ -2,6 +2,8 @@
 /examples/GaAN/dataset/
 /examples/GaAN/log/
 /examples/GaAN/__pycache__/
+/examples/GaAN/params/
+/DoorGod
 # Virtualenv
 /.venv/
 /venv/

examples/GaAN/conv.py

+# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""This package implements common layers to help building
+graph neural networks.
+"""
+import paddle.fluid as fluid
+from pgl import graph_wrapper
+from pgl.utils import paddle_helper
+
+__all__ = ['gcn', 'gat', 'gin', 'gaan']
+
+
+def gcn(gw, feature, hidden_size, activation, name, norm=None):
+    """Implementation of graph convolutional neural networks (GCN)
+
+    This is an implementation of the paper SEMI-SUPERVISED CLASSIFICATION
+    WITH GRAPH CONVOLUTIONAL NETWORKS (https://arxiv.org/pdf/1609.02907.pdf).
+
+    Args:
+        gw: Graph wrapper object (:code:`StaticGraphWrapper` or :code:`GraphWrapper`)
+
+        feature: A tensor with shape (num_nodes, feature_size).
+
+        hidden_size: The hidden size for gcn.
+
+        activation: The activation for the output.
+
+        name: Gcn layer names.
+
+        norm: If :code:`norm` is not None, then the feature will be normalized. Norm must
+              be tensor with shape (num_nodes,) and dtype float32.
+
+    Return:
+        A tensor with shape (num_nodes, hidden_size)
+    """
+
+    def send_src_copy(src_feat, dst_feat, edge_feat):
+        return src_feat["h"]
+
+    size = feature.shape[-1]
+    if size > hidden_size:
+        feature = fluid.layers.fc(feature,
+                                  size=hidden_size,
+                                  bias_attr=False,
+                                  param_attr=fluid.ParamAttr(name=name))
+
+    if norm is not None:
+        feature = feature * norm
+
+    msg = gw.send(send_src_copy, nfeat_list=[("h", feature)])
+
+    if size > hidden_size:
+        output = gw.recv(msg, "sum")
+    else:
+        output = gw.recv(msg, "sum")
+        output = fluid.layers.fc(output,
+                                 size=hidden_size,
+                                 bias_attr=False,
+                                 param_attr=fluid.ParamAttr(name=name))
+
+    if norm is not None:
+        output = output * norm
+
+    bias = fluid.layers.create_parameter(
+        shape=[hidden_size],
+        dtype='float32',
+        is_bias=True,
+        name=name + '_bias')
+    output = fluid.layers.elementwise_add(output, bias, act=activation)
+    return output
+
+
+def gat(gw,
+        feature,
+        hidden_size,
+        activation,
+        name,
+        num_heads=8,
+        feat_drop=0.6,
+        attn_drop=0.6,
+        is_test=False):
+    """Implementation of graph attention networks (GAT)
+
+    This is an implementation of the paper GRAPH ATTENTION NETWORKS
+    (https://arxiv.org/abs/1710.10903).
+
+    Args:
+        gw: Graph wrapper object (:code:`StaticGraphWrapper` or :code:`GraphWrapper`)
+
+        feature: A tensor with shape (num_nodes, feature_size).
+
+        hidden_size: The hidden size for gat.
+
+        activation: The activation for the output.
+
+        name: Gat layer names.
+
+        num_heads: The head number in gat.
+
+        feat_drop: Dropout rate for feature.
+
+        attn_drop: Dropout rate for attention.
+
+        is_test: Whether in test phrase.
+
+    Return:
+        A tensor with shape (num_nodes, hidden_size * num_heads)
+    """
+
+    def send_attention(src_feat, dst_feat, edge_feat):
+        output = src_feat["left_a"] + dst_feat["right_a"]
+        output = fluid.layers.leaky_relu(
+            output, alpha=0.2)  # (num_edges, num_heads)
+        return {"alpha": output, "h": src_feat["h"]}
+
+    def reduce_attention(msg):
+        alpha = msg["alpha"]  # lod-tensor (batch_size, seq_len, num_heads)
+        h = msg["h"]
+        alpha = paddle_helper.sequence_softmax(alpha)
+        old_h = h
+        h = fluid.layers.reshape(h, [-1, num_heads, hidden_size])
+        alpha = fluid.layers.reshape(alpha, [-1, num_heads, 1])
+        if attn_drop > 1e-15:
+            alpha = fluid.layers.dropout(
+                alpha,
+                dropout_prob=attn_drop,
+                is_test=is_test,
+                dropout_implementation="upscale_in_train")
+        h = h * alpha
+        h = fluid.layers.reshape(h, [-1, num_heads * hidden_size])
+        h = fluid.layers.lod_reset(h, old_h)
+        return fluid.layers.sequence_pool(h, "sum")
+
+    if feat_drop > 1e-15:
+        feature = fluid.layers.dropout(
+            feature,
+            dropout_prob=feat_drop,
+            is_test=is_test,
+            dropout_implementation='upscale_in_train')
+
+    ft = fluid.layers.fc(feature,
+                         hidden_size * num_heads,
+                         bias_attr=False,
+                         param_attr=fluid.ParamAttr(name=name + '_weight'))
+    left_a = fluid.layers.create_parameter(
+        shape=[num_heads, hidden_size],
+        dtype='float32',
+        name=name + '_gat_l_A')
+    right_a = fluid.layers.create_parameter(
+        shape=[num_heads, hidden_size],
+        dtype='float32',
+        name=name + '_gat_r_A')
+    reshape_ft = fluid.layers.reshape(ft, [-1, num_heads, hidden_size])
+    left_a_value = fluid.layers.reduce_sum(reshape_ft * left_a, -1)
+    right_a_value = fluid.layers.reduce_sum(reshape_ft * right_a, -1)
+
+    msg = gw.send(
+        send_attention,
+        nfeat_list=[("h", ft), ("left_a", left_a_value),
+                    ("right_a", right_a_value)])
+    output = gw.recv(msg, reduce_attention)
+    bias = fluid.layers.create_parameter(
+        shape=[hidden_size * num_heads],
+        dtype='float32',
+        is_bias=True,
+        name=name + '_bias')
+    bias.stop_gradient = True
+    output = fluid.layers.elementwise_add(output, bias, act=activation)
+    return output
+
+
+def gin(gw,
+        feature,
+        hidden_size,
+        activation,
+        name,
+        init_eps=0.0,
+        train_eps=False):
+    """Implementation of Graph Isomorphism Network (GIN) layer.
+
+    This is an implementation of the paper How Powerful are Graph Neural Networks?
+    (https://arxiv.org/pdf/1810.00826.pdf).
+
+    In their implementation, all MLPs have 2 layers. Batch normalization is applied
+    on every hidden layer.
+
+    Args:
+        gw: Graph wrapper object (:code:`StaticGraphWrapper` or :code:`GraphWrapper`)
+
+        feature: A tensor with shape (num_nodes, feature_size).
+
+        name: GIN layer names.
+
+        hidden_size: The hidden size for gin.
+
+        activation: The activation for the output.
+
+        init_eps: float, optional
+            Initial :math:`\epsilon` value, default is 0.
+
+        train_eps: bool, optional
+            if True, :math:`\epsilon` will be a learnable parameter.
+
+    Return:
+        A tensor with shape (num_nodes, hidden_size).
+    """
+
+    def send_src_copy(src_feat, dst_feat, edge_feat):
+        return src_feat["h"]
+
+    epsilon = fluid.layers.create_parameter(
+        shape=[1, 1],
+        dtype="float32",
+        attr=fluid.ParamAttr(name="%s_eps" % name),
+        default_initializer=fluid.initializer.ConstantInitializer(
+            value=init_eps))
+
+    if not train_eps:
+        epsilon.stop_gradient = True
+
+    msg = gw.send(send_src_copy, nfeat_list=[("h", feature)])
+    output = gw.recv(msg, "sum") + feature * (epsilon + 1.0)
+
+    output = fluid.layers.fc(output,
+                             size=hidden_size,
+                             act=None,
+                             param_attr=fluid.ParamAttr(name="%s_w_0" % name),
+                             bias_attr=fluid.ParamAttr(name="%s_b_0" % name))
+
+    output = fluid.layers.layer_norm(
+        output,
+        begin_norm_axis=1,
+        param_attr=fluid.ParamAttr(
+            name="norm_scale_%s" % (name),
+            initializer=fluid.initializer.Constant(1.0)),
+        bias_attr=fluid.ParamAttr(
+            name="norm_bias_%s" % (name),
+            initializer=fluid.initializer.Constant(0.0)), )
+
+    if activation is not None:
+        output = getattr(fluid.layers, activation)(output)
+
+    output = fluid.layers.fc(output,
+                             size=hidden_size,
+                             act=activation,
+                             param_attr=fluid.ParamAttr(name="%s_w_1" % name),
+                             bias_attr=fluid.ParamAttr(name="%s_b_1" % name))
+
+    return output
+
+
+def gaan(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o, heads, name):
+    """Implementation of GaAN"""
+
+    def send_func(src_feat, dst_feat, edge_feat):
+        # 计算每条边上的注意力分数
+        # E * (M * D1), 每个 dst 点都查询它的全部邻边的 src 点
+        feat_query, feat_key = dst_feat['feat_query'], src_feat['feat_key']
+        # E * M * D1
+        old = feat_query
+        feat_query = fluid.layers.reshape(feat_query, [-1, heads, hidden_size_a])
+        feat_key = fluid.layers.reshape(feat_key, [-1, heads, hidden_size_a])
+        # E * M
+        alpha = fluid.layers.reduce_sum(feat_key * feat_query, dim=-1)
+
+        return {'dst_node_feat': dst_feat['node_feat'],
+                'src_node_feat': src_feat['node_feat'],
+                'feat_value': src_feat['feat_value'],
+                'alpha': alpha,
+                'feat_gate': src_feat['feat_gate']}
+
+    def recv_func(message):
+        # 每条边的终点的特征
+        dst_feat = message['dst_node_feat']
+        # 每条边的出发点的特征
+        src_feat = message['src_node_feat']
+        # 每个中心点自己的特征
+        x = fluid.layers.sequence_pool(dst_feat, 'average')
+        # 每个中心点的邻居的特征的平均值
+        z = fluid.layers.sequence_pool(src_feat, 'average')
+
+        # 计算 gate
+        feat_gate = message['feat_gate']
+        g_max = fluid.layers.sequence_pool(feat_gate, 'max')
+        g = fluid.layers.concat([x, g_max, z], axis=1)
+        g = fluid.layers.fc(g, heads, bias_attr=False, act="sigmoid")
+
+        # softmax
+        alpha = message['alpha']
+        alpha = paddle_helper.sequence_softmax(alpha) # E * M
+
+        feat_value = message['feat_value'] # E * (M * D2)
+        old = feat_value
+        feat_value = fluid.layers.reshape(feat_value, [-1, heads, hidden_size_v]) # E * M * D2
+        feat_value = fluid.layers.elementwise_mul(feat_value, alpha, axis=0)
+        feat_value = fluid.layers.reshape(feat_value, [-1, heads*hidden_size_v]) # E * (M * D2)
+        feat_value = fluid.layers.lod_reset(feat_value, old)
+
+        feat_value = fluid.layers.sequence_pool(feat_value, 'sum') # N * (M * D2)
+
+        feat_value = fluid.layers.reshape(feat_value, [-1, heads, hidden_size_v]) # N * M * D2
+
+        output = fluid.layers.elementwise_mul(feat_value, g, axis=0)
+        output = fluid.layers.reshape(output, [-1, heads * hidden_size_v]) # N * (M * D2)
+
+        output = fluid.layers.concat([x, output], axis=1)
+
+        return output
+
+    # feature N * D
+
+    # 计算每个点自己需要发送出去的内容
+    # 投影后的特征向量
+    # N * (D1 * M)
+    feat_key = fluid.layers.fc(feature, hidden_size_a * heads, bias_attr=False,
+                     param_attr=fluid.ParamAttr(name=name + '_project_key'))
+    # N * (D2 * M)
+    feat_value = fluid.layers.fc(feature, hidden_size_v * heads, bias_attr=False,
+                     param_attr=fluid.ParamAttr(name=name + '_project_value'))
+    # N * (D1 * M)
+    feat_query = fluid.layers.fc(feature, hidden_size_a * heads, bias_attr=False,
+                     param_attr=fluid.ParamAttr(name=name + '_project_query'))
+    # N * Dm
+    feat_gate = fluid.layers.fc(feature, hidden_size_m, bias_attr=False, 
+                                param_attr=fluid.ParamAttr(name=name + '_project_gate'))
+
+    # send 阶段
+
+    message = gw.send(
+        send_func,
+        nfeat_list=[('node_feat', feature), ('feat_key', feat_key), ('feat_value', feat_value),
+                    ('feat_query', feat_query), ('feat_gate', feat_gate)],
+        efeat_list=None,
+    )
+
+    # 聚合邻居特征
+    output = gw.recv(message, recv_func)
+    output = fluid.layers.fc(output, hidden_size_o, bias_attr=False,
+                            param_attr=fluid.ParamAttr(name=name + '_project_output'))
+    output = fluid.layers.leaky_relu(output, alpha=0.1)
+    output = fluid.layers.dropout(output, dropout_prob=0.1)
+
+    return output

examples/GaAN/main.sh

+python3 train.py --epochs 100 --lr 1e-2 --rc 0 --batch_size 1024 --gpu_id 4 --exp_id 39
\ No newline at end of file

examples/GaAN/model.py

 from paddle import fluid
 from pgl.utils import paddle_helper
-from pgl.layers import GaAN
+
+# from pgl.layers import gaan
+from conv import gaan
 
 class GaANModel(object):
     def __init__(self, num_class, num_layers, hidden_size_a=24, 
@@ -19,7 +21,7 @@ class GaANModel(object):
     def forward(self, gw):
         feature = gw.node_feat['node_feat']
         for i in range(self.num_layers):
-            feature = GaAN(gw, feature, self.hidden_size_a, self.hidden_size_v,
+            feature = gaan(gw, feature, self.hidden_size_a, self.hidden_size_v,
                            self.hidden_size_m, self.hidden_size_o, self.heads, 
                            self.name+'_'+str(i))
         

examples/GaAN/train.py

@@ -119,14 +119,6 @@ if __name__ == "__main__":
     val_program = train_program.clone(for_test=True)
 
     with fluid.program_guard(train_program, startup_program):
-    #     adam = fluid.optimizer.Adam(
-    #         learning_rate=1e-2,
-    #         regularization=fluid.regularizer.L2DecayRegularizer(
-    #             regularization_coeff=0.0005))
-#         lr = fluid.layers.natural_exp_decay(learning_rate=args.lr,
-#                                            decay_steps=1000,
-#                                            decay_rate=0.5,
-#                                            )
         lr = args.lr
         adam = fluid.optimizer.Adam(
             learning_rate=lr,
@@ -171,6 +163,7 @@ if __name__ == "__main__":
     start = time.time()
     print("Training Begin".center(50, "="))
     log_text.add_record(0, "Training Begin".center(50, "="))
+    best_valid = -1.0
     for epoch in range(args.epochs):
         start_e = time.time()
 #         print("Train Epoch {}".format(epoch).center(50, "="))
@@ -197,9 +190,22 @@ if __name__ == "__main__":
         log_valid_rocauc_epoch.add_record(epoch, valid_rocauc)
         log_time.add_record(epoch, end_e-start_e)
         
+        if valid_rocauc > best_valid:
+            print("Update: new {}, old {}".format(valid_rocauc, best_valid))
+            best_valid = valid_rocauc
+            
+#             fluid.io.save_vars(executor=exe, dirname='./vars/'+str(args.exp_id), main_program=val_program,
+#                               predicate=lambda x: True)
+            fluid.io.save_params(executor=exe, dirname='./params/'+str(args.exp_id), main_program=val_program)
+            
 
     print("Test Stage".center(50, "="))
     log_text.add_record(args.epochs+1, "Test Stage".center(50, "="))
+    
+#     fluid.io.load_vars(executor=exe, dirname='./params/'+str(args.exp_id), main_program=val_program,
+#                       predicate=lambda x: True)
+    fluid.io.load_params(executor=exe, dirname='./params/'+str(args.exp_id), main_program=val_program)
+    
     test_loss, test_rocauc = valid_epoch(
         test_iter, program=val_program, exe=exe, loss=loss, score=score,
         evaluator=evaluator, epoch=epoch)

pgl/layers/conv.py

@@ -18,7 +18,7 @@ import paddle.fluid as fluid
 from pgl import graph_wrapper
 from pgl.utils import paddle_helper
 
-__all__ = ['gcn', 'gat', 'gin', 'GaAN']
+__all__ = ['gcn', 'gat', 'gin', 'gaan']
 
 
 def gcn(gw, feature, hidden_size, activation, name, norm=None):
@@ -259,87 +259,9 @@ def gin(gw,
 
     return output
 
-# def GaAN(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o, heads,
-#         name):
-#     """
-#     This is an implementation of the paper GaAN: Gated Attention Networks for Learning 
-#     on Large and Spatiotemporal Graphs(https://arxiv.org/abs/1803.07294)
-#     """
-#     # send function
-#     def send_func(src_feat, dst_feat, edge_feat):
-#         print("heads: {}, hidden_size_a: {}".format(heads, hidden_size_a))
-#         feat_query, feat_key = dst_feat['feat_query'], src_feat['feat_key']
-#         feat_query = fluid.layers.reshape(feat_query, [-1, heads, hidden_size_a])
-#         feat_key = fluid.layers.reshape(feat_key, [-1, heads, hidden_size_a])
-#         alpha = fluid.layers.reduce_sum(feat_key * feat_query, dim=-1)
-
-#         return {'dst_node_feat': dst_feat['node_feat'],
-#                 'src_node_feat': src_feat['node_feat'],
-#                 'feat_value': src_feat['feat_value'],
-#                 'alpha': alpha,
-#                 'feat_gate': src_feat['feat_gate']}
-    
-#     # recv function
-#     def recv_func(message):
-#         dst_feat = message['dst_node_feat'] # feature of dst nodes on each edge
-#         src_feat = message['src_node_feat'] # feature of src nodes on each edge
-#         x = fluid.layers.sequence_pool(dst_feat, 'average') # feature of center nodes
-#         z = fluid.layers.sequence_pool(src_feat, 'average') # mean feature of neighbors
-
-#         # compute gate
-#         feat_gate = message['feat_gate']
-#         g_max = fluid.layers.sequence_pool(feat_gate, 'max')
-#         g = fluid.layers.concat([x, g_max, z], axis=1)
-#         g = fluid.layers.fc(g, heads, bias_attr=False, act='sigmoid')
-
-#         # softmax of attention coefficient
-#         alpha = message['alpha']
-#         alpha = paddle_helper.sequence_softmax(alpha)
-
-#         feat_value = message['feat_value']
-#         old = feat_value
-#         feat_value = fluid.layers.reshape(feat_value, [-1, heads, hidden_size_v])
-#         feat_value = fluid.layers.elementwise_mul(feat_value, alpha, axis=0)
-#         feat_value = fluid.layers.reshape(feat_value, [-1, heads * hidden_size_v])
-#         feat_value = fluid.layers.lod_reset(feat_value, old)
-        
-#         feat_value = fluid.layers.sequence_pool(feat_value, 'sum')
-#         feat_value = fluid.layers.reshape(feat_value, [-1, heads, hidden_size_v])
-#         output = fluid.layers.elementwise_mul(feat_value, g, axis=0)
-#         output = fluid.layers.reshape(output, [-1, heads*hidden_size_v])
-#         output = fluid.layers.concat([x, output], axis=1)
-
-#         return output
-    
-#     # project the feature of nodes into new vector spaces
-#     feat_key = fluid.layers.fc(feature, hidden_size_a * heads, bias_attr=False,
-#                     param_attr=fluid.ParamAttr(name=name + '_project_key'))
-#     feat_value = fluid.layers.fc(feature, hidden_size_v * heads, bias_attr=False,
-#                     param_attr=fluid.ParamAttr(name=name + '_project_value'))
-#     feat_query = fluid.layers.fc(feature, hidden_size_a * heads, bias_attr=False,
-#                     param_attr=fluid.ParamAttr(name=name + '_project_query'))
-#     feat_gate = fluid.layers.fc(feature, hidden_size_m, bias_attr=False,
-#                     param_attr=fluid.ParamAttr(name=name + '_project_gate'))
-    
-#     # send stage
-#     msg = gw.send(send_func, nfeat_list=[('node_feat', feature),
-#                 ('feat_key', feat_key), ('feat_value', feat_value),
-#                 ('feat_query', feat_query), ('feat_gate', feat_gate)],
-#                 efeat_list=None,
-#                 )
-
-#     # recv stage
-#     output = gw.recv(msg, recv_func)
-    
-#     # output
-#     output = fluid.layers.fc(output, hidden_size_o, bias_attr=False,
-#                     param_attr=fluid.ParamAttr(name=name+'_project_output'))
-#     outout = fluid.layers.leaky_relu(output, alpha=0.1)
-#     output = fluid.layers.dropout(output, dropout_prob=0.1)
-
-#     return output
-
-def GaAN(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o, heads, name):
+
+def gaan(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o, heads, name):
+    """Implementation of GaAN"""
 
     def send_func(src_feat, dst_feat, edge_feat):
         # 计算每条边上的注意力分数