reproduce paper results

examples/citation_benchmark/build_model.py

@@ -4,7 +4,6 @@ from pgl import data_loader
 import paddle.fluid as fluid
 import numpy as np
 import time
-from optimization import AdamW 
 
 def build_model(dataset, config, phase, main_prog):
     gw = pgl.graph_wrapper.GraphWrapper(
@@ -15,6 +14,7 @@ def build_model(dataset, config, phase, main_prog):
     m = GraphModel(config=config, num_class=dataset.num_classes) 
     logits = m.forward(gw, gw.node_feat["words"], phase)
 
+    # Take the last
     node_index = fluid.layers.data(
             "node_index",
             shape=[None, 1],
@@ -33,10 +33,11 @@ def build_model(dataset, config, phase, main_prog):
     loss = fluid.layers.mean(loss)
 
     if phase == "train":
-        AdamW(loss=loss,
-              learning_rate=config.learning_rate,
-              weight_decay=config.weight_decay,
-              train_program=main_prog)
+        adam = fluid.optimizer.Adam(
+            learning_rate=config.learning_rate,
+            regularization=fluid.regularizer.L2DecayRegularizer(
+                regularization_coeff=config.weight_decay))
+        adam.minimize(loss)
     return gw, loss, acc
 
 

examples/citation_benchmark/config/appnp.yaml

@@ -6,4 +6,4 @@ learning_rate: 0.01
 dropout: 0.5
 hidden_size: 64
 weight_decay: 0.0005 
-edge_dropout: 0.00
+edge_dropout: 0.0

examples/citation_benchmark/config/sgc.yaml

@@ -2,3 +2,4 @@ model_name: SGC
 num_layers: 2
 learning_rate: 0.2
 weight_decay: 0.000005 
+feature_pre_normalize: False

examples/citation_benchmark/model.py

@@ -3,8 +3,9 @@ import paddle.fluid.layers as L
 import pgl.layers.conv as conv
 
 def get_norm(indegree):
-    norm = L.pow(L.cast(indegree, dtype="float32") + 1e-6, factor=-0.5) 
-    norm = norm * L.cast(indegree > 0, dtype="float32")
+    float_degree = L.cast(indegree, dtype="float32")
+    float_degree = L.clamp(float_degree, min=1.0)
+    norm = L.pow(float_degree, factor=-0.5) 
     return norm
     
 
@@ -29,10 +30,6 @@ class GCN(object):
                 ngw = graph_wrapper
                 norm = graph_wrapper.node_feat["norm"]
 
-            feature = L.dropout(
-                    feature,
-                    self.dropout,
-                    dropout_implementation='upscale_in_train')
 
             feature = pgl.layers.gcn(ngw,
                 feature,
@@ -41,7 +38,7 @@ class GCN(object):
                 norm=norm,
                 name="layer_%s" % i)
 
-        feature = L.dropout(
+            feature = L.dropout(
                     feature,
                     self.dropout,
                     dropout_implementation='upscale_in_train')
@@ -150,10 +147,10 @@ class SGC(object):
     def forward(self, graph_wrapper, feature, phase):
         feature = conv.appnp(graph_wrapper,
             feature=feature,
-            norm=graph_wrapper.node_feat["norm"],
+            edge_dropout=0,
             alpha=0,
             k_hop=self.num_layers)
         feature.stop_gradient=True
-        feature = L.fc(feature, self.num_class, act=None, name="output")
+        feature = L.fc(feature, self.num_class, act=None, bias_attr=False, name="output")
         return feature
 

examples/citation_benchmark/optimization.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.
-"""Optimization and learning rate scheduling."""
-
-from __future__ import absolute_import
-from __future__ import division
-from __future__ import print_function
-
-import numpy as np
-import paddle.fluid as fluid
-
-def AdamW(loss,
-          learning_rate,
-          train_program,
-          weight_decay):
-
-    optimizer = fluid.optimizer.Adam(learning_rate=learning_rate)
-
-    def exclude_from_weight_decay(name):
-        if name.find("layer_norm") > -1:
-            return True
-        bias_suffix = ["_bias", "_b", ".b_0"]
-        for suffix in bias_suffix:
-            if name.endswith(suffix):
-                return True
-        return False
-
-    param_list = dict()
-
-    for param in train_program.global_block().all_parameters():
-        param_list[param.name] = param * 1.0
-        param_list[param.name].stop_gradient = True
-
-    _, param_grads = optimizer.minimize(loss)
-
-    if weight_decay > 0:
-        for param, grad in param_grads:
-            if exclude_from_weight_decay(param.name):
-                continue
-            with param.block.program._optimized_guard(
-                [param, grad]), fluid.framework.name_scope("weight_decay"):
-                updated_param = param - param_list[
-                    param.name] * weight_decay * learning_rate 
-                fluid.layers.assign(output=param, input=updated_param)

examples/citation_benchmark/train.py

@@ -22,33 +22,35 @@ import argparse
 from build_model import build_model
 import yaml
 from easydict import EasyDict as edict
+import tqdm
 
+def normalize(feat):
+    return feat / np.maximum(np.sum(feat, -1, keepdims=True), 1)
 
 
-def load(name):
+def load(name, normalized_feature=True):
     if name == 'cora':
         dataset = data_loader.CoraDataset()
     elif name == "pubmed":
-        dataset = data_loader.CitationDataset("pubmed", symmetry_edges=False)
+        dataset = data_loader.CitationDataset("pubmed", symmetry_edges=True)
     elif name == "citeseer":
-        dataset = data_loader.CitationDataset("citeseer", symmetry_edges=False)
+        dataset = data_loader.CitationDataset("citeseer", symmetry_edges=True)
     else:
         raise ValueError(name + " dataset doesn't exists")
-    return dataset
-
-
-def main(args, config):
-    dataset = load(args.dataset)
 
     indegree = dataset.graph.indegree()
-    norm = np.zeros_like(indegree, dtype="float32")
-    norm[indegree > 0] = np.power(indegree[indegree > 0], -0.5)
+    norm = np.maximum(indegree.astype("float32"), 1)
+    norm = np.power(norm, -0.5)
     dataset.graph.node_feat["norm"] = np.expand_dims(norm, -1)
+    dataset.graph.node_feat["words"] =  normalize(dataset.graph.node_feat["words"])
+    return dataset
+
 
+def main(args, config):
+    dataset = load(args.dataset, args.feature_pre_normalize)
     place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace()
     train_program = fluid.default_main_program()
     startup_program = fluid.default_startup_program()
-
     with fluid.program_guard(train_program, startup_program):
         with fluid.unique_name.guard():
             gw, loss, acc = build_model(dataset,
@@ -67,13 +69,11 @@ def main(args, config):
     test_program = test_program.clone(for_test=True)
 
     exe = fluid.Executor(place)
-    exe.run(startup_program)
 
 
     train_index = dataset.train_index
     train_label = np.expand_dims(dataset.y[train_index], -1)
     train_index = np.expand_dims(train_index, -1)
-    log.info("Number of Train %s" % len(train_index))
 
     val_index = dataset.val_index
     val_label = np.expand_dims(dataset.y[val_index], -1)
@@ -84,54 +84,55 @@ def main(args, config):
     test_index = np.expand_dims(test_index, -1)
 
     dur = []
-    cal_val_acc = []
-    cal_test_acc = []
+
+    # Feed data
+    feed_dict = gw.to_feed(dataset.graph)
+
+
+    best_test = []
  
-    for epoch in range(args.epoch):
-        if epoch >= 3:
-            t0 = time.time()
-        feed_dict = gw.to_feed(dataset.graph)
-        feed_dict["node_index"] = np.array(train_index, dtype="int64")
-        feed_dict["node_label"] = np.array(train_label, dtype="int64")
-        train_loss, train_acc = exe.run(train_program,
+    for run in range(args.runs):
+        exe.run(startup_program)
+        cal_val_acc = []
+        cal_test_acc = []
+        cal_val_loss = []
+        cal_test_loss = []
+        for epoch in tqdm.tqdm(range(args.epoch)):
+            feed_dict["node_index"] = np.array(train_index, dtype="int64")
+            feed_dict["node_label"] = np.array(train_label, dtype="int64")
+            train_loss, train_acc = exe.run(train_program,
                                         feed=feed_dict,
                                         fetch_list=[loss, acc],
                                         return_numpy=True)
 
-        if epoch >= 3:
-            time_per_epoch = 1.0 * (time.time() - t0)
-            dur.append(time_per_epoch)
 
-        feed_dict = gw.to_feed(dataset.graph)
-        feed_dict["node_index"] = np.array(val_index, dtype="int64")
-        feed_dict["node_label"] = np.array(val_label, dtype="int64")
-        val_loss, val_acc = exe.run(test_program,
+            feed_dict["node_index"] = np.array(val_index, dtype="int64")
+            feed_dict["node_label"] = np.array(val_label, dtype="int64")
+            val_loss, val_acc = exe.run(test_program,
                                     feed=feed_dict,
                                     fetch_list=[v_loss, v_acc],
                                     return_numpy=True)
 
-        val_loss = val_loss[0]
-        val_acc = val_acc[0]
-        cal_val_acc.append(val_acc)
+            cal_val_acc.append(val_acc[0])
+            cal_val_loss.append(val_loss[0])
 
-        feed_dict["node_index"] = np.array(test_index, dtype="int64")
-        feed_dict["node_label"] = np.array(test_label, dtype="int64")
-        test_loss, test_acc = exe.run(test_program,
+            feed_dict["node_index"] = np.array(test_index, dtype="int64")
+            feed_dict["node_label"] = np.array(test_label, dtype="int64")
+            test_loss, test_acc = exe.run(test_program,
                                   feed=feed_dict,
                                   fetch_list=[v_loss, v_acc],
                                   return_numpy=True)
 
-        test_loss = test_loss[0]
-        test_acc = test_acc[0]
-        cal_test_acc.append(test_acc)
+            cal_test_acc.append(test_acc[0])
+            cal_test_loss.append(test_loss[0])
 
-        log.info("Epoch %d " % epoch +
-                 "Train Loss: %f " % train_loss + "Train Acc: %f " % train_acc
-                 + "Val Loss: %f " % val_loss + "Val Acc: %f " % val_acc)
      
-    cal_val_acc = np.array(cal_val_acc)
-    log.info("Model: %s Best Test Accuracy: %f" % (config.model_name,
-                  cal_test_acc[np.argmax(cal_val_acc)]))
+        log.info("Runs %s: Model: %s Best Test Accuracy: %f" % (run, config.model_name,
+                  cal_test_acc[np.argmin(cal_val_loss)]))
+
+        best_test.append(cal_test_acc[np.argmin(cal_val_loss)])
+    log.info("Best Test Accuracy: %f ( stddev: %f )" % (np.mean(best_test), np.std(best_test)))
+    
 
 
 if __name__ == '__main__':
@@ -141,6 +142,8 @@ if __name__ == '__main__':
     parser.add_argument("--use_cuda", action='store_true', help="use_cuda")
     parser.add_argument("--conf", type=str, help="config file for models")
     parser.add_argument("--epoch", type=int, default=200, help="Epoch")
+    parser.add_argument("--runs", type=int, default=5, help="runs")
+    parser.add_argument("--feature_pre_normalize", type=bool, default=True, help="pre_normalize feature")
     args = parser.parse_args()
     config = edict(yaml.load(open(args.conf), Loader=yaml.FullLoader))
     log.info(args)

pgl/graph_wrapper.py

@@ -735,7 +735,7 @@ def get_degree(edge, num_nodes):
 
 class DropEdgeWrapper(BaseGraphWrapper):
     """Implement of Edge Drop """
-    def __init__(self, graph_wrapper, dropout):
+    def __init__(self, graph_wrapper, dropout, keep_self_loop=True):
         super(DropEdgeWrapper, self).__init__()
 
         # Copy Node's information
@@ -750,12 +750,17 @@ class DropEdgeWrapper(BaseGraphWrapper):
         # Dropout Edges
         src, dst = graph_wrapper.edges
         u = L.uniform_random(shape=L.cast(L.shape(src), 'int64'), min=0., max=1.)
+        
 
         # Avoid Empty Edges
         keeped = L.cast(u > dropout, dtype="float32")
         self._num_edges = L.reduce_sum(L.cast(keeped, "int32"))
         keeped = keeped + L.cast(self._num_edges == 0, dtype="float32")
 
+        if keep_self_loop:
+            self_loop = L.cast(src == dst, dtype="float32")
+            keeped = keeped + self_loop
+
         keeped = (keeped > 0.5)
         src = paddle_helper.masked_select(src, keeped)
         dst = paddle_helper.masked_select(dst, keeped)

pgl/layers/conv.py

@@ -16,6 +16,7 @@ graph neural networks.
 """
 import pgl
 import paddle.fluid as fluid
+import paddle.fluid.layers as L
 from pgl.utils import paddle_helper
 from pgl import message_passing
 
@@ -51,7 +52,7 @@ def gcn(gw, feature, hidden_size, activation, name, norm=None):
 
     size = feature.shape[-1]
     if size > hidden_size:
-        feature = fluid.layers.fc(feature,
+        feature = L.fc(feature,
                                   size=hidden_size,
                                   bias_attr=False,
                                   param_attr=fluid.ParamAttr(name=name))
@@ -65,7 +66,7 @@ def gcn(gw, feature, hidden_size, activation, name, norm=None):
         output = gw.recv(msg, "sum")
     else:
         output = gw.recv(msg, "sum")
-        output = fluid.layers.fc(output,
+        output = L.fc(output,
                                  size=hidden_size,
                                  bias_attr=False,
                                  param_attr=fluid.ParamAttr(name=name))
@@ -73,12 +74,12 @@ def gcn(gw, feature, hidden_size, activation, name, norm=None):
     if norm is not None:
         output = output * norm
 
-    bias = fluid.layers.create_parameter(
+    bias = L.create_parameter(
         shape=[hidden_size],
         dtype='float32',
         is_bias=True,
         name=name + '_bias')
-    output = fluid.layers.elementwise_add(output, bias, act=activation)
+    output = L.elementwise_add(output, bias, act=activation)
     return output
 
 
@@ -121,7 +122,7 @@ def gat(gw,
 
     def send_attention(src_feat, dst_feat, edge_feat):
         output = src_feat["left_a"] + dst_feat["right_a"]
-        output = fluid.layers.leaky_relu(
+        output = L.leaky_relu(
             output, alpha=0.2)  # (num_edges, num_heads)
         return {"alpha": output, "h": src_feat["h"]}
 
@@ -130,54 +131,54 @@ def gat(gw,
         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])
+        h = L.reshape(h, [-1, num_heads, hidden_size])
+        alpha = L.reshape(alpha, [-1, num_heads, 1])
         if attn_drop > 1e-15:
-            alpha = fluid.layers.dropout(
+            alpha = L.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")
+        h = L.reshape(h, [-1, num_heads * hidden_size])
+        h = L.lod_reset(h, old_h)
+        return L.sequence_pool(h, "sum")
 
     if feat_drop > 1e-15:
-        feature = fluid.layers.dropout(
+        feature = L.dropout(
             feature,
             dropout_prob=feat_drop,
             is_test=is_test,
             dropout_implementation='upscale_in_train')
 
-    ft = fluid.layers.fc(feature,
+    ft = L.fc(feature,
                          hidden_size * num_heads,
                          bias_attr=False,
                          param_attr=fluid.ParamAttr(name=name + '_weight'))
-    left_a = fluid.layers.create_parameter(
+    left_a = L.create_parameter(
         shape=[num_heads, hidden_size],
         dtype='float32',
         name=name + '_gat_l_A')
-    right_a = fluid.layers.create_parameter(
+    right_a = L.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)
+    reshape_ft = L.reshape(ft, [-1, num_heads, hidden_size])
+    left_a_value = L.reduce_sum(reshape_ft * left_a, -1)
+    right_a_value = L.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(
+    bias = L.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)
+    output = L.elementwise_add(output, bias, act=activation)
     return output
 
 
@@ -220,7 +221,7 @@ def gin(gw,
     def send_src_copy(src_feat, dst_feat, edge_feat):
         return src_feat["h"]
 
-    epsilon = fluid.layers.create_parameter(
+    epsilon = L.create_parameter(
         shape=[1, 1],
         dtype="float32",
         attr=fluid.ParamAttr(name="%s_eps" % name),
@@ -233,13 +234,13 @@ def gin(gw,
     msg = gw.send(send_src_copy, nfeat_list=[("h", feature)])
     output = gw.recv(msg, "sum") + feature * (epsilon + 1.0)
 
-    output = fluid.layers.fc(output,
+    output = L.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 = L.layer_norm(
         output,
         begin_norm_axis=1,
         param_attr=fluid.ParamAttr(
@@ -250,9 +251,9 @@ def gin(gw,
             initializer=fluid.initializer.Constant(0.0)), )
 
     if activation is not None:
-        output = getattr(fluid.layers, activation)(output)
+        output = getattr(L, activation)(output)
 
-    output = fluid.layers.fc(output,
+    output = L.fc(output,
                              size=hidden_size,
                              act=activation,
                              param_attr=fluid.ParamAttr(name="%s_w_1" % name),
@@ -270,10 +271,10 @@ def gaan(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o
         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])
+        feat_query = L.reshape(feat_query, [-1, heads, hidden_size_a])
+        feat_key = L.reshape(feat_key, [-1, heads, hidden_size_a])
         # E * M
-        alpha = fluid.layers.reduce_sum(feat_key * feat_query, dim=-1)
+        alpha = L.reduce_sum(feat_key * feat_query, dim=-1)
 
         return {'dst_node_feat': dst_feat['node_feat'],
                 'src_node_feat': src_feat['node_feat'],
@@ -287,15 +288,15 @@ def gaan(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o
         # 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')
+        x = L.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')
+        z = L.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")
+        g_max = L.sequence_pool(feat_gate, 'max')
+        g = L.concat([x, g_max, z], axis=1)
+        g = L.fc(g, heads, bias_attr=False, act="sigmoid")
 
         # softmax
         alpha = message['alpha']
@@ -303,19 +304,19 @@ def gaan(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o
 
         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 = L.reshape(feat_value, [-1, heads, hidden_size_v]) # E * M * D2
+        feat_value = L.elementwise_mul(feat_value, alpha, axis=0)
+        feat_value = L.reshape(feat_value, [-1, heads*hidden_size_v]) # E * (M * D2)
+        feat_value = L.lod_reset(feat_value, old)
 
-        feat_value = fluid.layers.sequence_pool(feat_value, 'sum') # N * (M * D2)
+        feat_value = L.sequence_pool(feat_value, 'sum') # N * (M * D2)
 
-        feat_value = fluid.layers.reshape(feat_value, [-1, heads, hidden_size_v]) # N * M * D2
+        feat_value = L.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 = L.elementwise_mul(feat_value, g, axis=0)
+        output = L.reshape(output, [-1, heads * hidden_size_v]) # N * (M * D2)
 
-        output = fluid.layers.concat([x, output], axis=1)
+        output = L.concat([x, output], axis=1)
 
         return output
 
@@ -324,16 +325,16 @@ def gaan(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o
     # 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,
+    feat_key = L.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,
+    feat_value = L.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,
+    feat_query = L.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, 
+    feat_gate = L.fc(feature, hidden_size_m, bias_attr=False, 
                                 param_attr=fluid.ParamAttr(name=name + '_project_gate'))
 
     # send 阶段
@@ -347,10 +348,10 @@ def gaan(gw, feature, hidden_size_a, hidden_size_v, hidden_size_m, hidden_size_o
 
     # 聚合邻居特征
     output = gw.recv(message, recv_func)
-    output = fluid.layers.fc(output, hidden_size_o, bias_attr=False,
+    output = L.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)
+    output = L.leaky_relu(output, alpha=0.1)
+    output = L.dropout(output, dropout_prob=0.1)
 
     return output
 
@@ -377,7 +378,7 @@ def gen_conv(gw,
     """
    
     if beta == "dynamic":
-        beta = fluid.layers.create_parameter(
+        beta = L.create_parameter(
                 shape=[1],
                 dtype='float32',
                 default_initializer=
@@ -392,13 +393,13 @@ def gen_conv(gw,
     output = message_passing.msg_norm(feature, output, name)
     output = feature + output
     
-    output = fluid.layers.fc(output,
+    output = L.fc(output,
                      feature.shape[-1],
                      bias_attr=False,
                      act="relu",
                      param_attr=fluid.ParamAttr(name=name + '_weight1'))
     
-    output = fluid.layers.fc(output,
+    output = L.fc(output,
                      feature.shape[-1],
                      bias_attr=False,
                      param_attr=fluid.ParamAttr(name=name + '_weight2'))
@@ -407,9 +408,9 @@ def gen_conv(gw,
 
 def get_norm(indegree):
     """Get Laplacian Normalization"""
-    norm = fluid.layers.pow(fluid.layers.cast(indegree, dtype="float32") + 1e-6,
-                     factor=-0.5) 
-    norm = norm * fluid.layers.cast(indegree > 0, dtype="float32")
+    float_degree = L.cast(indegree, dtype="float32")
+    float_degree = L.clamp(float_degree, min=1.0)
+    norm = L.pow(float_degree, factor=-0.5) 
     return norm
 
 def appnp(gw, feature, edge_dropout=0, alpha=0.2, k_hop=10):

pgl/sample.py

@@ -518,8 +518,10 @@ def graph_saint_random_walk_sample(graph,
     return subgraph
 
 
-def edge_drop(graph_wrapper, dropout_rate):
+def edge_drop(graph_wrapper, dropout_rate, keep_self_loop=True):
     if dropout_rate < 1e-5:
         return graph_wrapper
     else:
-        return pgl.graph_wrapper.DropEdgeWrapper(graph_wrapper, dropout_rate)
+        return pgl.graph_wrapper.DropEdgeWrapper(graph_wrapper,
+                   dropout_rate,
+                   keep_self_loop)