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!2465 GCN rectification 

Merge pull request !2465 from chentingting/gcn_rectification
This commit is contained in:
mindspore-ci-bot 2020-06-23 10:40:11 +08:00 committed by Gitee
parent 106f798092 a733102db9
commit 14868eb2b0
12 changed files with 63 additions and 339 deletions
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8
model_zoo/gcn/README.md
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@ -36,9 +36,9 @@ sh run_process_data.sh [SRC_PATH] [DATASET_NAME]
>> Launch
```
#Generate dataset in mindrecord format for cora
sh run_process_data.sh cora
sh run_process_data.sh ./data cora
#Generate dataset in mindrecord format for citeseer
sh run_process_data.sh citeseer
sh run_process_data.sh ./data citeseer
```
## Structure
@ -110,4 +110,6 @@ Epoch: 0200 train_loss= 0.57948 train_acc= 0.96429 val_loss= 1.04753 val_acc= 0.
Optimization Finished!
Test set results: cost= 1.00983 accuracy= 0.81300 time= 0.39083
...
```
```

3
model_zoo/gcn/scripts/run_process_data.sh
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@ -40,7 +40,8 @@ else
fi
MINDRECORD_PATH=`pwd`/data_mr
rm -f $MINDRECORD_PATH/*
rm -f $MINDRECORD_PATH/$DATASET_NAME
rm -f $MINDRECORD_PATH/$DATASET_NAME.db
cd ../../../example/graph_to_mindrecord || exit

2
model_zoo/gcn/src/dataset.py
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@ -55,7 +55,7 @@ def get_adj_features_labels(data_dir):
adj = adj + adj.T.multiply(adj.T > adj) + sp.eye(nodes_num)
nor_adj = normalize_adj(adj)
nor_adj = np.array(nor_adj.todense())
return nor_adj, features, labels_onehot
return nor_adj, features, labels_onehot, labels
def get_mask(total, begin, end):

2
model_zoo/gcn/src/gcn.py
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@ -21,7 +21,7 @@ from mindspore.ops import functional as F
from mindspore.ops import operations as P
from mindspore import Tensor
from mindspore.nn.layer.activation import get_activation
from src.metrics import Loss, Accuracy
from model_zoo.gcn.src.metrics import Loss, Accuracy
def glorot(shape):

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model_zoo/gcn/t-SNE_visualization_on_Cora.gif Normal file
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52
model_zoo/gcn/train.py
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@ -21,11 +21,25 @@ import time
import argparse
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation
from sklearn import manifold
from mindspore import context
from src.gcn import GCN, LossAccuracyWrapper, TrainNetWrapper
from src.config import ConfigGCN
from src.dataset import get_adj_features_labels, get_mask
from model_zoo.gcn.src.gcn import GCN, LossAccuracyWrapper, TrainNetWrapper
from model_zoo.gcn.src.config import ConfigGCN
from model_zoo.gcn.src.dataset import get_adj_features_labels, get_mask
def t_SNE(out_feature, dim):
t_sne = manifold.TSNE(n_components=dim, init='pca', random_state=0)
return t_sne.fit_transform(out_feature)
def update_graph(i, data, scat, plot):
scat.set_offsets(data[i])
plt.title('t-SNE visualization of Epoch:{0}'.format(i))
return scat, plot
def train():
@ -36,28 +50,39 @@ def train():
parser.add_argument('--train_nodes_num', type=int, default=140, help='Nodes numbers for training')
parser.add_argument('--eval_nodes_num', type=int, default=500, help='Nodes numbers for evaluation')
parser.add_argument('--test_nodes_num', type=int, default=1000, help='Nodes numbers for test')
parser.add_argument('--save_TSNE', type=bool, default=False, help='Whether to save t-SNE graph')
args_opt = parser.parse_args()
np.random.seed(args_opt.seed)
context.set_context(mode=context.GRAPH_MODE,
device_target="Ascend", save_graphs=False)
config = ConfigGCN()
adj, feature, label = get_adj_features_labels(args_opt.data_dir)
adj, feature, label_onehot, label = get_adj_features_labels(args_opt.data_dir)
nodes_num = label.shape[0]
nodes_num = label_onehot.shape[0]
train_mask = get_mask(nodes_num, 0, args_opt.train_nodes_num)
eval_mask = get_mask(nodes_num, args_opt.train_nodes_num, args_opt.train_nodes_num + args_opt.eval_nodes_num)
test_mask = get_mask(nodes_num, nodes_num - args_opt.test_nodes_num, nodes_num)
class_num = label.shape[1]
class_num = label_onehot.shape[1]
gcn_net = GCN(config, adj, feature, class_num)
gcn_net.add_flags_recursive(fp16=True)
eval_net = LossAccuracyWrapper(gcn_net, label, eval_mask, config.weight_decay)
test_net = LossAccuracyWrapper(gcn_net, label, test_mask, config.weight_decay)
train_net = TrainNetWrapper(gcn_net, label, train_mask, config)
eval_net = LossAccuracyWrapper(gcn_net, label_onehot, eval_mask, config.weight_decay)
test_net = LossAccuracyWrapper(gcn_net, label_onehot, test_mask, config.weight_decay)
train_net = TrainNetWrapper(gcn_net, label_onehot, train_mask, config)
loss_list = []
if args_opt.save_TSNE:
out_feature = gcn_net()
tsne_result = t_SNE(out_feature.asnumpy(), 2)
graph_data = []
graph_data.append(tsne_result)
fig = plt.figure()
scat = plt.scatter(tsne_result[:, 0], tsne_result[:, 1], s=2, c=label, cmap='rainbow')
plt.title('t-SNE visualization of Epoch:0', fontsize='large', fontweight='bold', verticalalignment='center')
for epoch in range(config.epochs):
t = time.time()
@ -76,6 +101,11 @@ def train():
"train_acc=", "{:.5f}".format(train_accuracy), "val_loss=", "{:.5f}".format(eval_loss),
"val_acc=", "{:.5f}".format(eval_accuracy), "time=", "{:.5f}".format(time.time() - t))
if args_opt.save_TSNE:
out_feature = gcn_net()
tsne_result = t_SNE(out_feature.asnumpy(), 2)
graph_data.append(tsne_result)
if epoch > config.early_stopping and loss_list[-1] > np.mean(loss_list[-(config.early_stopping+1):-1]):
print("Early stopping...")
break
@ -88,6 +118,10 @@ def train():
print("Test set results:", "loss=", "{:.5f}".format(test_loss),
"accuracy=", "{:.5f}".format(test_accuracy), "time=", "{:.5f}".format(time.time() - t_test))
if args_opt.save_TSNE:
ani = animation.FuncAnimation(fig, update_graph, frames=range(config.epochs + 1), fargs=(graph_data, scat, plt))
ani.save('t-SNE_visualization.gif', writer='imagemagick')
if __name__ == '__main__':
train()

0
tests/st/gnn/gcn/src/__init__.py
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23
tests/st/gnn/gcn/src/config.py
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@ -1,23 +0,0 @@
# Copyright 2020 Huawei Technologies Co., Ltd
#
# 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.
# ============================================================================
class ConfigGCN():
learning_rate = 0.01
epochs = 200
hidden1 = 16
dropout = 0.0
weight_decay = 5e-4
early_stopping = 10

60
tests/st/gnn/gcn/src/dataset.py
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@ -1,60 +0,0 @@
# Copyright 2020 Huawei Technologies Co., Ltd
#
# 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.
# ============================================================================
import numpy as np
import scipy.sparse as sp
import mindspore.dataset as ds
def normalize_adj(adj):
rowsum = np.array(adj.sum(1))
d_inv_sqrt = np.power(rowsum, -0.5).flatten()
d_inv_sqrt[np.isinf(d_inv_sqrt)] = 0.
d_mat_inv_sqrt = sp.diags(d_inv_sqrt)
return adj.dot(d_mat_inv_sqrt).transpose().dot(d_mat_inv_sqrt).tocoo()
def get_adj_features_labels(data_dir):
g = ds.GraphData(data_dir)
nodes = g.get_all_nodes(0)
nodes_list = nodes.tolist()
row_tensor = g.get_node_feature(nodes_list, [1, 2])
features = row_tensor[0]
labels = row_tensor[1]
nodes_num = labels.shape[0]
class_num = labels.max() + 1
labels_onehot = np.eye(nodes_num, class_num)[labels].astype(np.float32)
neighbor = g.get_all_neighbors(nodes_list, 0)
node_map = {node_id: index for index, node_id in enumerate(nodes_list)}
adj = np.zeros([nodes_num, nodes_num], dtype=np.float32)
for index, value in np.ndenumerate(neighbor):
# The first column of neighbor is node_id, second column to last column are neighbors of the first column.
# So we only care index[1] > 1.
# If the node does not have that many neighbors, -1 is padded. So if value < 0, we will not deal with it.
if value >= 0 and index[1] > 0:
adj[node_map[neighbor[index[0], 0]], node_map[value]] = 1
adj = sp.coo_matrix(adj)
adj = adj + adj.T.multiply(adj.T > adj) + sp.eye(nodes_num)
nor_adj = normalize_adj(adj)
nor_adj = np.array(nor_adj.todense())
return nor_adj, features, labels_onehot
def get_mask(total, begin, end):
mask = np.zeros([total]).astype(np.float32)
mask[begin:end] = 1
return mask

163
tests/st/gnn/gcn/src/gcn.py
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@ -1,163 +0,0 @@
# Copyright 2020 Huawei Technologies Co., Ltd
#
# 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.
# ============================================================================
import numpy as np
from mindspore import nn
from mindspore.common.parameter import ParameterTuple
from mindspore.ops import composite as C
from mindspore.ops import functional as F
from mindspore.ops import operations as P
from mindspore import Tensor
from mindspore.nn.layer.activation import get_activation
from src.metrics import Loss, Accuracy
def glorot(shape):
init_range = np.sqrt(6.0/(shape[0]+shape[1]))
initial = np.random.uniform(-init_range, init_range, shape).astype(np.float32)
return Tensor(initial)
class GraphConvolution(nn.Cell):
def __init__(self,
feature_in_dim,
feature_out_dim,
dropout_ratio=None,
activation=None):
super(GraphConvolution, self).__init__()
self.in_dim = feature_in_dim
self.out_dim = feature_out_dim
self.weight_init = glorot([self.out_dim, self.in_dim])
self.fc = nn.Dense(self.in_dim,
self.out_dim,
weight_init=self.weight_init,
has_bias=False)
self.dropout_ratio = dropout_ratio
if self.dropout_ratio is not None:
self.dropout = nn.Dropout(keep_prob=1-self.dropout_ratio)
self.dropout_flag = self.dropout_ratio is not None
self.activation = get_activation(activation)
self.activation_flag = self.activation is not None
self.matmul = P.MatMul()
def construct(self, adj, input_feature):
dropout = input_feature
if self.dropout_flag:
dropout = self.dropout(dropout)
fc = self.fc(dropout)
output_feature = self.matmul(adj, fc)
if self.activation_flag:
output_feature = self.activation(output_feature)
return output_feature
class GCN(nn.Cell):
def __init__(self, config, adj, feature, output_dim):
super(GCN, self).__init__()
self.adj = Tensor(adj)
self.feature = Tensor(feature)
input_dim = feature.shape[1]
self.layer0 = GraphConvolution(input_dim, config.hidden1, activation="relu", dropout_ratio=config.dropout)
self.layer1 = GraphConvolution(config.hidden1, output_dim, dropout_ratio=None)
def construct(self):
output0 = self.layer0(self.adj, self.feature)
output1 = self.layer1(self.adj, output0)
return output1
class LossAccuracyWrapper(nn.Cell):
def __init__(self, network, label, mask, weight_decay):
super(LossAccuracyWrapper, self).__init__()
self.network = network
self.loss = Loss(label, mask, weight_decay, network.trainable_params()[0])
self.accuracy = Accuracy(label, mask)
def construct(self):
preds = self.network()
loss = self.loss(preds)
accuracy = self.accuracy(preds)
return loss, accuracy
class LossWrapper(nn.Cell):
def __init__(self, network, label, mask, weight_decay):
super(LossWrapper, self).__init__()
self.network = network
self.loss = Loss(label, mask, weight_decay, network.trainable_params()[0])
def construct(self):
preds = self.network()
loss = self.loss(preds)
return loss
class TrainOneStepCell(nn.Cell):
r"""
Network training package class.
Wraps the network with an optimizer. The resulting Cell be trained without inputs.
Backward graph will be created in the construct function to do parameter updating. Different
parallel modes are available to run the training.
Args:
network (Cell): The training network.
optimizer (Cell): Optimizer for updating the weights.
sens (Number): The scaling number to be filled as the input of backpropagation. Default value is 1.0.
Outputs:
Tensor, a scalar Tensor with shape :math:`()`.
Examples:
>>> net = Net()
>>> loss_fn = nn.SoftmaxCrossEntropyWithLogits()
>>> optim = nn.Momentum(net.trainable_params(), learning_rate=0.1, momentum=0.9)
>>> loss_net = nn.WithLossCell(net, loss_fn)
>>> train_net = nn.TrainOneStepCell(loss_net, optim)
"""
def __init__(self, network, optimizer, sens=1.0):
super(TrainOneStepCell, self).__init__(auto_prefix=False)
self.network = network
self.network.add_flags(defer_inline=True)
self.weights = ParameterTuple(network.trainable_params())
self.optimizer = optimizer
self.grad = C.GradOperation('grad', get_by_list=True, sens_param=True)
self.sens = sens
def construct(self):
weights = self.weights
loss = self.network()
sens = P.Fill()(P.DType()(loss), P.Shape()(loss), self.sens)
grads = self.grad(self.network, weights)(sens)
return F.depend(loss, self.optimizer(grads))
class TrainNetWrapper(nn.Cell):
def __init__(self, network, label, mask, config):
super(TrainNetWrapper, self).__init__(auto_prefix=True)
self.network = network
loss_net = LossWrapper(network, label, mask, config.weight_decay)
optimizer = nn.Adam(loss_net.trainable_params(),
learning_rate=config.learning_rate)
self.loss_train_net = TrainOneStepCell(loss_net, optimizer)
self.accuracy = Accuracy(label, mask)
def construct(self):
loss = self.loss_train_net()
accuracy = self.accuracy(self.network())
return loss, accuracy

68
tests/st/gnn/gcn/src/metrics.py
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@ -1,68 +0,0 @@
# Copyright 2020 Huawei Technologies Co., Ltd
#
# 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.
# ============================================================================
from mindspore import nn
from mindspore import Tensor
from mindspore.common import dtype as mstype
from mindspore.ops import operations as P
class Loss(nn.Cell):
def __init__(self, label, mask, weight_decay, param):
super(Loss, self).__init__()
self.label = Tensor(label)
self.mask = Tensor(mask)
self.loss = P.SoftmaxCrossEntropyWithLogits()
self.one = Tensor(1.0, mstype.float32)
self.zero = Tensor(0.0, mstype.float32)
self.mean = P.ReduceMean()
self.cast = P.Cast()
self.l2_loss = P.L2Loss()
self.reduce_sum = P.ReduceSum()
self.weight_decay = weight_decay
self.param = param
def construct(self, preds):
param = self.l2_loss(self.param)
loss = self.weight_decay * param
preds = self.cast(preds, mstype.float32)
loss = loss + self.loss(preds, self.label)[0]
mask = self.cast(self.mask, mstype.float32)
mask_reduce = self.mean(mask)
mask = mask / mask_reduce
loss = loss * mask
loss = self.mean(loss)
return loss
class Accuracy(nn.Cell):
def __init__(self, label, mask):
super(Accuracy, self).__init__()
self.label = Tensor(label)
self.mask = Tensor(mask)
self.equal = P.Equal()
self.argmax = P.Argmax()
self.cast = P.Cast()
self.mean = P.ReduceMean()
def construct(self, preds):
preds = self.cast(preds, mstype.float32)
correct_prediction = self.equal(self.argmax(preds), self.argmax(self.label))
accuracy_all = self.cast(correct_prediction, mstype.float32)
mask = self.cast(self.mask, mstype.float32)
mask_reduce = self.mean(mask)
mask = mask / mask_reduce
accuracy_all *= mask
return self.mean(accuracy_all)

21
tests/st/gnn/gcn/test_gcn.py
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@ -17,9 +17,9 @@ import time
import pytest
import numpy as np
from mindspore import context
from src.gcn import GCN, LossAccuracyWrapper, TrainNetWrapper
from src.config import ConfigGCN
from src.dataset import get_adj_features_labels, get_mask
from model_zoo.gcn.src.gcn import GCN, LossAccuracyWrapper, TrainNetWrapper
from model_zoo.gcn.src.config import ConfigGCN
from model_zoo.gcn.src.dataset import get_adj_features_labels, get_mask
DATA_DIR = '/home/workspace/mindspore_dataset/cora/cora_mr/cora_mr'
@ -37,22 +37,23 @@ def test_gcn():
print("test_gcn begin")
np.random.seed(SEED)
context.set_context(mode=context.GRAPH_MODE,
device_target="Ascend", save_graphs=True)
device_target="Ascend", save_graphs=False)
config = ConfigGCN()
adj, feature, label = get_adj_features_labels(DATA_DIR)
config.dropout = 0.0
adj, feature, label_onehot, _ = get_adj_features_labels(DATA_DIR)
nodes_num = label.shape[0]
nodes_num = label_onehot.shape[0]
train_mask = get_mask(nodes_num, 0, TRAIN_NODE_NUM)
eval_mask = get_mask(nodes_num, TRAIN_NODE_NUM, TRAIN_NODE_NUM + EVAL_NODE_NUM)
test_mask = get_mask(nodes_num, nodes_num - TEST_NODE_NUM, nodes_num)
class_num = label.shape[1]
class_num = label_onehot.shape[1]
gcn_net = GCN(config, adj, feature, class_num)
gcn_net.add_flags_recursive(fp16=True)
eval_net = LossAccuracyWrapper(gcn_net, label, eval_mask, config.weight_decay)
test_net = LossAccuracyWrapper(gcn_net, label, test_mask, config.weight_decay)
train_net = TrainNetWrapper(gcn_net, label, train_mask, config)
eval_net = LossAccuracyWrapper(gcn_net, label_onehot, eval_mask, config.weight_decay)
test_net = LossAccuracyWrapper(gcn_net, label_onehot, test_mask, config.weight_decay)
train_net = TrainNetWrapper(gcn_net, label_onehot, train_mask, config)
loss_list = []
for epoch in range(config.epochs):