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Unverified Commit 6124667f authored by Da Zheng's avatar Da Zheng Committed by GitHub
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[Model] Refactor the sampling examples (#498) 

* reorganize sampling code.

* speedup gcn_ns.

* speed up gcn_cv

* fix graphsage_cv.

* undo the modification.

* accel training.

* update readme.
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examples/mxnet/sampling/README.md
View file @ 6124667f
...@@ -15,44 +15,44 @@ pip install mxnet --pre ...@@ -15,44 +15,44 @@ pip install mxnet --pre
### Neighbor Sampling & Skip Connection ### Neighbor Sampling & Skip Connection
cora: test accuracy ~83% with `--num-neighbors 2`, ~84% by training on the full graph cora: test accuracy ~83% with `--num-neighbors 2`, ~84% by training on the full graph
``` ```
DGLBACKEND=mxnet python gcn_ns_sc.py --dataset cora --self-loop --num-neighbors 2 --batch-size 1000000 --test-batch-size 1000000 --gpu 0 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model gcn_ns --dataset cora --self-loop --num-neighbors 2 --batch-size 1000 --test-batch-size 5000
``` ```
citeseer: test accuracy ~69% with `--num-neighbors 2`, ~70% by training on the full graph citeseer: test accuracy ~69% with `--num-neighbors 2`, ~70% by training on the full graph
``` ```
DGLBACKEND=mxnet python gcn_ns_sc.py --dataset citeseer --self-loop --num-neighbors 2 --batch-size 1000000 --test-batch-size 1000000 --gpu 0 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model gcn_ns --dataset citeseer --self-loop --num-neighbors 2 --batch-size 1000 --test-batch-size 5000
``` ```
pubmed: test accuracy ~76% with `--num-neighbors 3`, ~77% by training on the full graph pubmed: test accuracy ~78% with `--num-neighbors 3`, ~77% by training on the full graph
``` ```
DGLBACKEND=mxnet python gcn_ns_sc.py --dataset pubmed --self-loop --num-neighbors 3 --batch-size 1000000 --test-batch-size 1000000 --gpu 0 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model gcn_ns --dataset pubmed --self-loop --num-neighbors 3 --batch-size 1000 --test-batch-size 5000
``` ```
reddit: test accuracy ~91% with `--num-neighbors 2` and `--batch-size 1000`, ~93% by training on the full graph reddit: test accuracy ~91% with `--num-neighbors 3` and `--batch-size 1000`, ~93% by training on the full graph
``` ```
DGLBACKEND=mxnet python gcn_ns_sc.py --dataset reddit-self-loop --num-neighbors 2 --batch-size 1000 --test-batch-size 500 --n-hidden 64 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model gcn_ns --dataset reddit-self-loop --num-neighbors 3 --batch-size 1000 --test-batch-size 5000 --n-hidden 64
``` ```
### Control Variate & Skip Connection ### Control Variate & Skip Connection
cora: test accuracy ~84% with `--num-neighbors 1`, ~84% by training on the full graph cora: test accuracy ~84% with `--num-neighbors 1`, ~84% by training on the full graph
``` ```
DGLBACKEND=mxnet python gcn_cv_sc.py --dataset cora --self-loop --num-neighbors 1 --batch-size 1000000 --test-batch-size 1000000 --gpu 0 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model gcn_cv --dataset cora --self-loop --num-neighbors 1 --batch-size 1000000 --test-batch-size 1000000
``` ```
citeseer: test accuracy ~69% with `--num-neighbors 1`, ~70% by training on the full graph citeseer: test accuracy ~69% with `--num-neighbors 1`, ~70% by training on the full graph
``` ```
DGLBACKEND=mxnet python gcn_cv_sc.py --dataset citeseer --self-loop --num-neighbors 1 --batch-size 1000000 --test-batch-size 1000000 --gpu 0 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model gcn_cv --dataset citeseer --self-loop --num-neighbors 1 --batch-size 1000000 --test-batch-size 1000000
``` ```
pubmed: test accuracy ~77% with `--num-neighbors 1`, ~77% by training on the full graph pubmed: test accuracy ~79% with `--num-neighbors 1`, ~77% by training on the full graph
``` ```
DGLBACKEND=mxnet python gcn_cv_sc.py --dataset pubmed --self-loop --num-neighbors 1 --batch-size 1000000 --test-batch-size 1000000 --gpu 0 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model gcn_cv --dataset pubmed --self-loop --num-neighbors 1 --batch-size 1000000 --test-batch-size 1000000
``` ```
reddit: test accuracy ~93% with `--num-neighbors 1` and `--batch-size 1000`, ~93% by training on the full graph reddit: test accuracy ~93% with `--num-neighbors 1` and `--batch-size 1000`, ~93% by training on the full graph
``` ```
DGLBACKEND=mxnet python gcn_cv_sc.py --dataset reddit-self-loop --num-neighbors 1 --batch-size 1000 --test-batch-size 500 --n-hidden 64 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model gcn_cv --dataset reddit-self-loop --num-neighbors 1 --batch-size 10000 --test-batch-size 5000 --n-hidden 64
``` ```
### Control Variate & GraphSAGE-mean ### Control Variate & GraphSAGE-mean
...@@ -61,6 +61,6 @@ Following [Control Variate](https://arxiv.org/abs/1710.10568), we use the mean p ...@@ -61,6 +61,6 @@ Following [Control Variate](https://arxiv.org/abs/1710.10568), we use the mean p
reddit: test accuracy 96.1% with `--num-neighbors 1` and `--batch-size 1000`, ~96.2% in [Control Variate](https://arxiv.org/abs/1710.10568) with `--num-neighbors 2` and `--batch-size 1000` reddit: test accuracy 96.1% with `--num-neighbors 1` and `--batch-size 1000`, ~96.2% in [Control Variate](https://arxiv.org/abs/1710.10568) with `--num-neighbors 2` and `--batch-size 1000`
``` ```
DGLBACKEND=mxnet python graphsage_cv.py --batch-size 1000 --test-batch-size 500 --n-epochs 50 --dataset reddit --num-neighbors 1 --n-hidden 128 --dropout 0.2 --weight-decay 0 DGLBACKEND=mxnet python examples/mxnet/sampling/train.py --model graphsage_cv --batch-size 1000 --test-batch-size 5000 --n-epochs 50 --dataset reddit --num-neighbors 1 --n-hidden 128 --dropout 0.2 --weight-decay 0
``` ```
examples/mxnet/sampling/gcn_cv_sc.py
View file @ 6124667f
...@@ -21,14 +21,15 @@ class NodeUpdate(gluon.Block): ...@@ -21,14 +21,15 @@ class NodeUpdate(gluon.Block):
def forward(self, node): def forward(self, node):
h = node.data['h'] h = node.data['h']
norm = node.data['norm']
if self.test: if self.test:
norm = node.data['norm']
h = h * norm h = h * norm
else: else:
agg_history_str = 'agg_h_{}'.format(self.layer_id-1) agg_history_str = 'agg_h_{}'.format(self.layer_id-1)
agg_history = node.data[agg_history_str] agg_history = node.data[agg_history_str]
subg_norm = node.data['subg_norm']
# control variate # control variate
h = h + agg_history h = h * subg_norm + agg_history * norm
if self.dropout: if self.dropout:
h = mx.nd.Dropout(h, p=self.dropout) h = mx.nd.Dropout(h, p=self.dropout)
h = self.dense(h) h = self.dense(h)
...@@ -39,7 +40,6 @@ class NodeUpdate(gluon.Block): ...@@ -39,7 +40,6 @@ class NodeUpdate(gluon.Block):
return {'activation': h} return {'activation': h}
class GCNSampling(gluon.Block): class GCNSampling(gluon.Block):
def __init__(self, def __init__(self,
in_feats, in_feats,
...@@ -85,7 +85,7 @@ class GCNSampling(gluon.Block): ...@@ -85,7 +85,7 @@ class GCNSampling(gluon.Block):
nf.layers[i].data['h'] = h nf.layers[i].data['h'] = h
nf.block_compute(i, nf.block_compute(i,
fn.copy_src(src='h', out='m'), fn.copy_src(src='h', out='m'),
lambda node : {'h': node.mailbox['m'].mean(axis=1)}, fn.sum(msg='m', out='h'),
layer) layer)
h = nf.layers[i+1].data.pop('activation') h = nf.layers[i+1].data.pop('activation')
# update history # update history
...@@ -139,63 +139,24 @@ class GCNInfer(gluon.Block): ...@@ -139,63 +139,24 @@ class GCNInfer(gluon.Block):
return h return h
def main(args): def gcn_cv_train(g, ctx, args, n_classes, train_nid, test_nid, n_test_samples):
# load and preprocess dataset features = g.ndata['features']
data = load_data(args) labels = g.ndata['labels']
if args.gpu >= 0:
ctx = mx.gpu(args.gpu)
else:
ctx = mx.cpu()
if args.self_loop and not args.dataset.startswith('reddit'):
data.graph.add_edges_from([(i,i) for i in range(len(data.graph))])
train_nid = mx.nd.array(np.nonzero(data.train_mask)[0]).astype(np.int64)
test_nid = mx.nd.array(np.nonzero(data.test_mask)[0]).astype(np.int64)
num_neighbors = args.num_neighbors
n_layers = args.n_layers
features = mx.nd.array(data.features).as_in_context(ctx)
labels = mx.nd.array(data.labels).as_in_context(ctx)
train_mask = mx.nd.array(data.train_mask).as_in_context(ctx)
val_mask = mx.nd.array(data.val_mask).as_in_context(ctx)
test_mask = mx.nd.array(data.test_mask).as_in_context(ctx)
in_feats = features.shape[1] in_feats = features.shape[1]
n_classes = data.num_labels
n_edges = data.graph.number_of_edges()
n_train_samples = train_mask.sum().asscalar()
n_test_samples = test_mask.sum().asscalar()
n_val_samples = val_mask.sum().asscalar()
print("""----Data statistics------'
#Edges %d
#Classes %d
#Train samples %d
#Val samples %d
#Test samples %d""" %
(n_edges, n_classes,
n_train_samples,
n_val_samples,
n_test_samples))
# create GCN model
g = DGLGraph(data.graph, readonly=True)
g.ndata['features'] = features
norm = mx.nd.expand_dims(1./g.in_degrees().astype('float32'), 1) norm = mx.nd.expand_dims(1./g.in_degrees().astype('float32'), 1)
g.ndata['norm'] = norm.as_in_context(ctx) g.ndata['norm'] = norm.as_in_context(ctx)
degs = g.in_degrees().astype('float32').asnumpy()
degs[degs > args.num_neighbors] = args.num_neighbors
g.ndata['subg_norm'] = mx.nd.expand_dims(mx.nd.array(1./degs, ctx=ctx), 1)
g.update_all(fn.copy_src(src='features', out='m'), g.update_all(fn.copy_src(src='features', out='m'),
fn.sum(msg='m', out='preprocess'), fn.sum(msg='m', out='preprocess'),
lambda node : {'preprocess': node.data['preprocess'] * node.data['norm']}) lambda node : {'preprocess': node.data['preprocess'] * node.data['norm']})
n_layers = args.n_layers
for i in range(n_layers): for i in range(n_layers):
g.ndata['h_{}'.format(i)] = mx.nd.zeros((features.shape[0], args.n_hidden), ctx=ctx) g.ndata['h_{}'.format(i)] = mx.nd.zeros((features.shape[0], args.n_hidden), ctx=ctx)
g.ndata['h_{}'.format(n_layers-1)] = mx.nd.zeros((features.shape[0], 2*args.n_hidden), ctx=ctx) g.ndata['h_{}'.format(n_layers-1)] = mx.nd.zeros((features.shape[0], 2*args.n_hidden), ctx=ctx)
model = GCNSampling(in_feats, model = GCNSampling(in_feats,
...@@ -229,21 +190,21 @@ def main(args): ...@@ -229,21 +190,21 @@ def main(args):
dur = [] dur = []
for epoch in range(args.n_epochs): for epoch in range(args.n_epochs):
for nf in dgl.contrib.sampling.NeighborSampler(g, args.batch_size, for nf in dgl.contrib.sampling.NeighborSampler(g, args.batch_size,
num_neighbors, args.num_neighbors,
neighbor_type='in', neighbor_type='in',
num_workers=32,
shuffle=True, shuffle=True,
num_hops=n_layers, num_hops=n_layers,
seed_nodes=train_nid): seed_nodes=train_nid):
for i in range(n_layers): for i in range(n_layers):
agg_history_str = 'agg_h_{}'.format(i) agg_history_str = 'agg_h_{}'.format(i)
g.pull(nf.layer_parent_nid(i+1), fn.copy_src(src='h_{}'.format(i), out='m'), g.pull(nf.layer_parent_nid(i+1), fn.copy_src(src='h_{}'.format(i), out='m'),
fn.sum(msg='m', out=agg_history_str), fn.sum(msg='m', out=agg_history_str))
lambda node : {agg_history_str: node.data[agg_history_str] * node.data['norm']})
node_embed_names = [['preprocess', 'h_0']] node_embed_names = [['preprocess', 'h_0']]
for i in range(1, n_layers): for i in range(1, n_layers):
node_embed_names.append(['h_{}'.format(i), 'agg_h_{}'.format(i-1)]) node_embed_names.append(['h_{}'.format(i), 'agg_h_{}'.format(i-1), 'subg_norm', 'norm'])
node_embed_names.append(['agg_h_{}'.format(n_layers-1)]) node_embed_names.append(['agg_h_{}'.format(n_layers-1), 'subg_norm', 'norm'])
nf.copy_from_parent(node_embed_names=node_embed_names) nf.copy_from_parent(node_embed_names=node_embed_names)
# forward # forward
...@@ -269,6 +230,7 @@ def main(args): ...@@ -269,6 +230,7 @@ def main(args):
trainer._kvstore.pull(idx, out=infer_params[key].data()) trainer._kvstore.pull(idx, out=infer_params[key].data())
num_acc = 0. num_acc = 0.
num_tests = 0
for nf in dgl.contrib.sampling.NeighborSampler(g, args.test_batch_size, for nf in dgl.contrib.sampling.NeighborSampler(g, args.test_batch_size,
g.number_of_nodes(), g.number_of_nodes(),
...@@ -284,38 +246,9 @@ def main(args): ...@@ -284,38 +246,9 @@ def main(args):
batch_nids = nf.layer_parent_nid(-1).as_in_context(ctx) batch_nids = nf.layer_parent_nid(-1).as_in_context(ctx)
batch_labels = labels[batch_nids] batch_labels = labels[batch_nids]
num_acc += (pred.argmax(axis=1) == batch_labels).sum().asscalar() num_acc += (pred.argmax(axis=1) == batch_labels).sum().asscalar()
num_tests += nf.layer_size(-1)
break
print("Test Accuracy {:.4f}". format(num_acc/num_tests))
print("Test Accuracy {:.4f}". format(num_acc/n_test_samples))
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='GCN')
register_data_args(parser)
parser.add_argument("--dropout", type=float, default=0.5,
help="dropout probability")
parser.add_argument("--gpu", type=int, default=-1,
help="gpu")
parser.add_argument("--lr", type=float, default=3e-2,
help="learning rate")
parser.add_argument("--n-epochs", type=int, default=200,
help="number of training epochs")
parser.add_argument("--batch-size", type=int, default=1000,
help="train batch size")
parser.add_argument("--test-batch-size", type=int, default=1000,
help="test batch size")
parser.add_argument("--num-neighbors", type=int, default=2,
help="number of neighbors to be sampled")
parser.add_argument("--n-hidden", type=int, default=16,
help="number of hidden gcn units")
parser.add_argument("--n-layers", type=int, default=1,
help="number of hidden gcn layers")
parser.add_argument("--self-loop", action='store_true',
help="graph self-loop (default=False)")
parser.add_argument("--weight-decay", type=float, default=5e-4,
help="Weight for L2 loss")
args = parser.parse_args()
print(args)
main(args)
examples/mxnet/sampling/gcn_ns_sc.py
View file @ 6124667f
...@@ -10,17 +10,15 @@ from dgl.data import register_data_args, load_data ...@@ -10,17 +10,15 @@ from dgl.data import register_data_args, load_data
class NodeUpdate(gluon.Block): class NodeUpdate(gluon.Block):
def __init__(self, in_feats, out_feats, activation=None, test=False, concat=False): def __init__(self, in_feats, out_feats, activation=None, concat=False):
super(NodeUpdate, self).__init__() super(NodeUpdate, self).__init__()
self.dense = gluon.nn.Dense(out_feats, in_units=in_feats) self.dense = gluon.nn.Dense(out_feats, in_units=in_feats)
self.activation = activation self.activation = activation
self.concat = concat self.concat = concat
self.test = test
def forward(self, node): def forward(self, node):
h = node.data['h'] h = node.data['h']
if self.test: h = h * node.data['norm']
h = h * node.data['norm']
h = self.dense(h) h = self.dense(h)
# skip connection # skip connection
if self.concat: if self.concat:
...@@ -63,9 +61,11 @@ class GCNSampling(gluon.Block): ...@@ -63,9 +61,11 @@ class GCNSampling(gluon.Block):
if self.dropout: if self.dropout:
h = mx.nd.Dropout(h, p=self.dropout) h = mx.nd.Dropout(h, p=self.dropout)
nf.layers[i].data['h'] = h nf.layers[i].data['h'] = h
degs = nf.layer_in_degree(i + 1).astype('float32').as_in_context(h.context)
nf.layers[i + 1].data['norm'] = mx.nd.expand_dims(1./degs, 1)
nf.block_compute(i, nf.block_compute(i,
fn.copy_src(src='h', out='m'), fn.copy_src(src='h', out='m'),
lambda node : {'h': node.mailbox['m'].mean(axis=1)}, fn.sum(msg='m', out='h'),
layer) layer)
h = nf.layers[-1].data.pop('activation') h = nf.layers[-1].data.pop('activation')
...@@ -86,13 +86,13 @@ class GCNInfer(gluon.Block): ...@@ -86,13 +86,13 @@ class GCNInfer(gluon.Block):
self.layers = gluon.nn.Sequential() self.layers = gluon.nn.Sequential()
# input layer # input layer
skip_start = (0 == n_layers-1) skip_start = (0 == n_layers-1)
self.layers.add(NodeUpdate(in_feats, n_hidden, activation, test=True, concat=skip_start)) self.layers.add(NodeUpdate(in_feats, n_hidden, activation, concat=skip_start))
# hidden layers # hidden layers
for i in range(1, n_layers): for i in range(1, n_layers):
skip_start = (i == n_layers-1) skip_start = (i == n_layers-1)
self.layers.add(NodeUpdate(n_hidden, n_hidden, activation, test=True, concat=skip_start)) self.layers.add(NodeUpdate(n_hidden, n_hidden, activation, concat=skip_start))
# output layer # output layer
self.layers.add(NodeUpdate(2*n_hidden, n_classes, test=True)) self.layers.add(NodeUpdate(2*n_hidden, n_classes))
def forward(self, nf): def forward(self, nf):
...@@ -106,55 +106,12 @@ class GCNInfer(gluon.Block): ...@@ -106,55 +106,12 @@ class GCNInfer(gluon.Block):
fn.sum(msg='m', out='h'), fn.sum(msg='m', out='h'),
layer) layer)
h = nf.layers[-1].data.pop('activation') return nf.layers[-1].data.pop('activation')
return h
def main(args):
# load and preprocess dataset
data = load_data(args)
if args.gpu >= 0:
ctx = mx.gpu(args.gpu)
else:
ctx = mx.cpu()
if args.self_loop and not args.dataset.startswith('reddit'):
data.graph.add_edges_from([(i,i) for i in range(len(data.graph))])
train_nid = mx.nd.array(np.nonzero(data.train_mask)[0]).astype(np.int64).as_in_context(ctx)
test_nid = mx.nd.array(np.nonzero(data.test_mask)[0]).astype(np.int64).as_in_context(ctx)
features = mx.nd.array(data.features).as_in_context(ctx) def gcn_ns_train(g, ctx, args, n_classes, train_nid, test_nid, n_test_samples):
labels = mx.nd.array(data.labels).as_in_context(ctx) in_feats = g.ndata['features'].shape[1]
train_mask = mx.nd.array(data.train_mask).as_in_context(ctx) labels = g.ndata['labels']
val_mask = mx.nd.array(data.val_mask).as_in_context(ctx)
test_mask = mx.nd.array(data.test_mask).as_in_context(ctx)
in_feats = features.shape[1]
n_classes = data.num_labels
n_edges = data.graph.number_of_edges()
n_train_samples = train_mask.sum().asscalar()
n_val_samples = val_mask.sum().asscalar()
n_test_samples = test_mask.sum().asscalar()
print("""----Data statistics------'
#Edges %d
#Classes %d
#Train samples %d
#Val samples %d
#Test samples %d""" %
(n_edges, n_classes,
n_train_samples,
n_val_samples,
n_test_samples))
# create GCN model
g = DGLGraph(data.graph, readonly=True)
g.ndata['features'] = features
num_neighbors = args.num_neighbors
degs = g.in_degrees().astype('float32').as_in_context(ctx) degs = g.in_degrees().astype('float32').as_in_context(ctx)
norm = mx.nd.expand_dims(1./degs, 1) norm = mx.nd.expand_dims(1./degs, 1)
...@@ -189,15 +146,13 @@ def main(args): ...@@ -189,15 +146,13 @@ def main(args):
# initialize graph # initialize graph
dur = [] dur = []
for epoch in range(args.n_epochs): for epoch in range(args.n_epochs):
index = 0
for nf in dgl.contrib.sampling.NeighborSampler(g, args.batch_size, for nf in dgl.contrib.sampling.NeighborSampler(g, args.batch_size,
args.num_neighbors, args.num_neighbors,
neighbor_type='in', neighbor_type='in',
shuffle=True, shuffle=True,
num_workers=32,
num_hops=args.n_layers+1, num_hops=args.n_layers+1,
seed_nodes=train_nid): seed_nodes=train_nid):
print(index)
index = index + 1
nf.copy_from_parent() nf.copy_from_parent()
# forward # forward
with mx.autograd.record(): with mx.autograd.record():
...@@ -217,6 +172,7 @@ def main(args): ...@@ -217,6 +172,7 @@ def main(args):
trainer._kvstore.pull(idx, out=infer_params[key].data()) trainer._kvstore.pull(idx, out=infer_params[key].data())
num_acc = 0. num_acc = 0.
num_tests = 0
for nf in dgl.contrib.sampling.NeighborSampler(g, args.test_batch_size, for nf in dgl.contrib.sampling.NeighborSampler(g, args.test_batch_size,
g.number_of_nodes(), g.number_of_nodes(),
...@@ -228,38 +184,7 @@ def main(args): ...@@ -228,38 +184,7 @@ def main(args):
batch_nids = nf.layer_parent_nid(-1).astype('int64').as_in_context(ctx) batch_nids = nf.layer_parent_nid(-1).astype('int64').as_in_context(ctx)
batch_labels = labels[batch_nids] batch_labels = labels[batch_nids]
num_acc += (pred.argmax(axis=1) == batch_labels).sum().asscalar() num_acc += (pred.argmax(axis=1) == batch_labels).sum().asscalar()
num_tests += nf.layer_size(-1)
break
print("Test Accuracy {:.4f}". format(num_acc/n_test_samples)) print("Test Accuracy {:.4f}". format(num_acc/num_tests))
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='GCN')
register_data_args(parser)
parser.add_argument("--dropout", type=float, default=0.5,
help="dropout probability")
parser.add_argument("--gpu", type=int, default=-1,
help="gpu")
parser.add_argument("--lr", type=float, default=3e-2,
help="learning rate")
parser.add_argument("--n-epochs", type=int, default=200,
help="number of training epochs")
parser.add_argument("--batch-size", type=int, default=1000,
help="batch size")
parser.add_argument("--test-batch-size", type=int, default=1000,
help="test batch size")
parser.add_argument("--num-neighbors", type=int, default=3,
help="number of neighbors to be sampled")
parser.add_argument("--n-hidden", type=int, default=16,
help="number of hidden gcn units")
parser.add_argument("--n-layers", type=int, default=1,
help="number of hidden gcn layers")
parser.add_argument("--self-loop", action='store_true',
help="graph self-loop (default=False)")
parser.add_argument("--weight-decay", type=float, default=5e-4,
help="Weight for L2 loss")
args = parser.parse_args()
print(args)
main(args)
examples/mxnet/sampling/graphsage_cv.py
View file @ 6124667f
...@@ -114,7 +114,7 @@ class GraphSAGETrain(gluon.Block): ...@@ -114,7 +114,7 @@ class GraphSAGETrain(gluon.Block):
for i, layer in enumerate(self.layers): for i, layer in enumerate(self.layers):
parent_nid = dgl.utils.toindex(nf.layer_parent_nid(i+1)) parent_nid = dgl.utils.toindex(nf.layer_parent_nid(i+1))
layer_nid = nf.map_from_parent_nid(i, parent_nid) layer_nid = nf.map_from_parent_nid(i, parent_nid).as_in_context(h.context)
self_h = h[layer_nid] self_h = h[layer_nid]
# activation from previous layer of myself, used in graphSAGE # activation from previous layer of myself, used in graphSAGE
nf.layers[i+1].data['self_h'] = self_h nf.layers[i+1].data['self_h'] = self_h
...@@ -168,7 +168,7 @@ class GraphSAGEInfer(gluon.Block): ...@@ -168,7 +168,7 @@ class GraphSAGEInfer(gluon.Block):
for i, layer in enumerate(self.layers): for i, layer in enumerate(self.layers):
nf.layers[i].data['h'] = h nf.layers[i].data['h'] = h
parent_nid = dgl.utils.toindex(nf.layer_parent_nid(i+1)) parent_nid = dgl.utils.toindex(nf.layer_parent_nid(i+1))
layer_nid = nf.map_from_parent_nid(i, parent_nid) layer_nid = nf.map_from_parent_nid(i, parent_nid).as_in_context(h.context)
# activation from previous layer of the nodes in (i+1)-th layer, used in graphSAGE # activation from previous layer of the nodes in (i+1)-th layer, used in graphSAGE
self_h = h[layer_nid] self_h = h[layer_nid]
nf.layers[i+1].data['self_h'] = self_h nf.layers[i+1].data['self_h'] = self_h
...@@ -181,64 +181,23 @@ class GraphSAGEInfer(gluon.Block): ...@@ -181,64 +181,23 @@ class GraphSAGEInfer(gluon.Block):
return h return h
def main(args): def graphsage_cv_train(g, ctx, args, n_classes, train_nid, test_nid, n_test_samples):
# load and preprocess dataset features = g.ndata['features']
data = load_data(args) labels = g.ndata['labels']
in_feats = g.ndata['features'].shape[1]
if args.gpu >= 0:
ctx = mx.gpu(args.gpu)
else:
ctx = mx.cpu()
if args.self_loop and not args.dataset.startswith('reddit'):
data.graph.add_edges_from([(i,i) for i in range(len(data.graph))])
train_nid = mx.nd.array(np.nonzero(data.train_mask)[0]).astype(np.int64)
test_nid = mx.nd.array(np.nonzero(data.test_mask)[0]).astype(np.int64)
num_neighbors = args.num_neighbors
n_layers = args.n_layers
features = mx.nd.array(data.features).as_in_context(ctx)
labels = mx.nd.array(data.labels).as_in_context(ctx)
train_mask = mx.nd.array(data.train_mask).as_in_context(ctx)
val_mask = mx.nd.array(data.val_mask).as_in_context(ctx)
test_mask = mx.nd.array(data.test_mask).as_in_context(ctx)
in_feats = features.shape[1]
n_classes = data.num_labels
n_edges = data.graph.number_of_edges()
n_train_samples = train_mask.sum().asscalar()
n_test_samples = test_mask.sum().asscalar()
n_val_samples = val_mask.sum().asscalar()
print("""----Data statistics------'
#Edges %d
#Classes %d
#Train samples %d
#Val samples %d
#Test samples %d""" %
(n_edges, n_classes,
n_train_samples,
n_val_samples,
n_test_samples))
g = DGLGraph(data.graph, readonly=True)
g.ndata['features'] = features
norm = mx.nd.expand_dims(1./g.in_degrees().astype('float32'), 1) norm = mx.nd.expand_dims(1./g.in_degrees().astype('float32'), 1)
g.ndata['norm'] = norm.as_in_context(ctx) g.ndata['norm'] = norm.as_in_context(ctx)
degs = g.in_degrees().astype('float32').asnumpy() degs = g.in_degrees().astype('float32').asnumpy()
degs[degs > num_neighbors] = num_neighbors degs[degs > args.num_neighbors] = args.num_neighbors
g.ndata['subg_norm'] = mx.nd.expand_dims(mx.nd.array(1./degs, ctx=ctx), 1) g.ndata['subg_norm'] = mx.nd.expand_dims(mx.nd.array(1./degs, ctx=ctx), 1)
g.update_all(fn.copy_src(src='features', out='m'), g.update_all(fn.copy_src(src='features', out='m'),
fn.sum(msg='m', out='preprocess'), fn.sum(msg='m', out='preprocess'),
lambda node : {'preprocess': node.data['preprocess'] * node.data['norm']}) lambda node : {'preprocess': node.data['preprocess'] * node.data['norm']})
n_layers = args.n_layers
for i in range(n_layers): for i in range(n_layers):
g.ndata['h_{}'.format(i)] = mx.nd.zeros((features.shape[0], args.n_hidden), ctx=ctx) g.ndata['h_{}'.format(i)] = mx.nd.zeros((features.shape[0], args.n_hidden), ctx=ctx)
...@@ -271,9 +230,10 @@ def main(args): ...@@ -271,9 +230,10 @@ def main(args):
dur = [] dur = []
for epoch in range(args.n_epochs): for epoch in range(args.n_epochs):
for nf in dgl.contrib.sampling.NeighborSampler(g, args.batch_size, for nf in dgl.contrib.sampling.NeighborSampler(g, args.batch_size,
num_neighbors, args.num_neighbors,
neighbor_type='in', neighbor_type='in',
shuffle=True, shuffle=True,
num_workers=32,
num_hops=n_layers, num_hops=n_layers,
add_self_loop=True, add_self_loop=True,
seed_nodes=train_nid): seed_nodes=train_nid):
...@@ -311,6 +271,7 @@ def main(args): ...@@ -311,6 +271,7 @@ def main(args):
trainer._kvstore.pull(idx, out=infer_params[key].data()) trainer._kvstore.pull(idx, out=infer_params[key].data())
num_acc = 0. num_acc = 0.
num_tests = 0
for nf in dgl.contrib.sampling.NeighborSampler(g, args.test_batch_size, for nf in dgl.contrib.sampling.NeighborSampler(g, args.test_batch_size,
g.number_of_nodes(), g.number_of_nodes(),
...@@ -327,38 +288,7 @@ def main(args): ...@@ -327,38 +288,7 @@ def main(args):
batch_nids = nf.layer_parent_nid(-1).as_in_context(ctx) batch_nids = nf.layer_parent_nid(-1).as_in_context(ctx)
batch_labels = labels[batch_nids] batch_labels = labels[batch_nids]
num_acc += (pred.argmax(axis=1) == batch_labels).sum().asscalar() num_acc += (pred.argmax(axis=1) == batch_labels).sum().asscalar()
num_tests += nf.layer_size(-1)
break
print("Test Accuracy {:.4f}". format(num_acc/n_test_samples)) print("Test Accuracy {:.4f}". format(num_acc/num_tests))
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='GraphSAGE with Control Variate')
register_data_args(parser)
parser.add_argument("--dropout", type=float, default=0.5,
help="dropout probability")
parser.add_argument("--gpu", type=int, default=-1,
help="gpu")
parser.add_argument("--lr", type=float, default=3e-2,
help="learning rate")
parser.add_argument("--n-epochs", type=int, default=200,
help="number of training epochs")
parser.add_argument("--batch-size", type=int, default=1000,
help="train batch size")
parser.add_argument("--test-batch-size", type=int, default=1000,
help="test batch size")
parser.add_argument("--num-neighbors", type=int, default=3,
help="number of neighbors to be sampled")
parser.add_argument("--n-hidden", type=int, default=16,
help="number of hidden GraphSAGE units")
parser.add_argument("--n-layers", type=int, default=1,
help="number of hidden GraphSAGE layers")
parser.add_argument("--self-loop", action='store_true',
help="graph self-loop (default=False)")
parser.add_argument("--weight-decay", type=float, default=5e-4,
help="Weight for L2 loss")
args = parser.parse_args()
print(args)
main(args)
examples/mxnet/sampling/train.py 0 → 100644
View file @ 6124667f
import argparse, time, math
import numpy as np
import mxnet as mx
from mxnet import gluon
from functools import partial
import dgl
import dgl.function as fn
from dgl import DGLGraph
from dgl.data import register_data_args, load_data
from gcn_ns_sc import gcn_ns_train
from gcn_cv_sc import gcn_cv_train
from graphsage_cv import graphsage_cv_train
def main(args):
# load and preprocess dataset
data = load_data(args)
if args.gpu >= 0:
ctx = mx.gpu(args.gpu)
else:
ctx = mx.cpu()
if args.self_loop and not args.dataset.startswith('reddit'):
data.graph.add_edges_from([(i,i) for i in range(len(data.graph))])
train_nid = mx.nd.array(np.nonzero(data.train_mask)[0]).astype(np.int64).as_in_context(ctx)
test_nid = mx.nd.array(np.nonzero(data.test_mask)[0]).astype(np.int64).as_in_context(ctx)
features = mx.nd.array(data.features).as_in_context(ctx)
labels = mx.nd.array(data.labels).as_in_context(ctx)
train_mask = mx.nd.array(data.train_mask).as_in_context(ctx)
val_mask = mx.nd.array(data.val_mask).as_in_context(ctx)
test_mask = mx.nd.array(data.test_mask).as_in_context(ctx)
in_feats = features.shape[1]
n_classes = data.num_labels
n_edges = data.graph.number_of_edges()
n_train_samples = train_mask.sum().asscalar()
n_val_samples = val_mask.sum().asscalar()
n_test_samples = test_mask.sum().asscalar()
print("""----Data statistics------'
#Edges %d
#Classes %d
#Train samples %d
#Val samples %d
#Test samples %d""" %
(n_edges, n_classes,
n_train_samples,
n_val_samples,
n_test_samples))
# create GCN model
g = DGLGraph(data.graph, readonly=True)
g.ndata['features'] = features
g.ndata['labels'] = labels
if args.model == "gcn_ns":
gcn_ns_train(g, ctx, args, n_classes, train_nid, test_nid, n_test_samples)
elif args.model == "gcn_cv":
gcn_cv_train(g, ctx, args, n_classes, train_nid, test_nid, n_test_samples)
elif args.model == "graphsage_cv":
graphsage_cv_train(g, ctx, args, n_classes, train_nid, test_nid, n_test_samples)
else:
print("unknown model. Please choose from gcn_ns, gcn_cv, graphsage_cv")
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='GCN')
register_data_args(parser)
parser.add_argument("--model", type=str,
help="select a model. Valid models: gcn_ns, gcn_cv, graphsage_cv")
parser.add_argument("--dropout", type=float, default=0.5,
help="dropout probability")
parser.add_argument("--gpu", type=int, default=-1,
help="gpu")
parser.add_argument("--lr", type=float, default=3e-2,
help="learning rate")
parser.add_argument("--n-epochs", type=int, default=200,
help="number of training epochs")
parser.add_argument("--batch-size", type=int, default=1000,
help="batch size")
parser.add_argument("--test-batch-size", type=int, default=1000,
help="test batch size")
parser.add_argument("--num-neighbors", type=int, default=3,
help="number of neighbors to be sampled")
parser.add_argument("--n-hidden", type=int, default=16,
help="number of hidden gcn units")
parser.add_argument("--n-layers", type=int, default=1,
help="number of hidden gcn layers")
parser.add_argument("--self-loop", action='store_true',
help="graph self-loop (default=False)")
parser.add_argument("--weight-decay", type=float, default=5e-4,
help="Weight for L2 loss")
parser.add_argument("--nworkers", type=int, default=1,
help="number of workers")
args = parser.parse_args()
print(args)
main(args)
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