def main():
test_network = ["karate_club", "facebook"]
for net in test_network:
net_file = data_utils.get_data_path(net)
g = graph_utils.load_basic_network(net_file)
sir_file = net_file.split('.')[0] + '-sir.txt'
sir = {}
if os.path.exists(sir_file):
with open(sir_file, 'r') as f:
for l in f:
data = l.split()
id = int(data[0])
score = float(data[1])
sir[id] = score
else:
print("SIR Simulation start.")
sir = sir_ranking(g, gamma=1.0, num_epoch=100)
print("SIR Simulation end.")
centralities = [
nx.degree_centrality, nx.closeness_centrality,
nx.eigenvector_centrality, nx.pagerank, Local_gravity_model
]
for c in centralities:
if c.__name__ == 'pagerank':
res = c(g, alpha=0.95)
elif c.__name__ == 'Local_gravity_model':
res = c(g, depth=2)
else:
res = c(g)
tau, p = kendallTau(res, sir)
print("%s\t%s\t%f" % (net, c.__name__, tau))
def main():
for dataset_name in data_utils.data_file:
net_file = data_utils.get_data_path(dataset_name)
nx_adj = graph_utils.load_networkx_format(net_file)
g = nx.from_scipy_sparse_matrix(nx_adj)
train, test, val, train_neg, test_neg, val_neg = graph_utils.train_test_split(
nx_adj, pos_neg_ratio=0.5)
logger.info("[%s] train 1#%d 0#%d" %
(dataset_name, len(train), len(train_neg)))
logger.info("[%s] test 1#%d 0#%d" %
(dataset_name, len(test), len(test_neg)))
logger.info("[%s] valid 1#%d 0#%d" %
(dataset_name, len(val), len(val_neg)))
# Compute basic link prediction indexes from g_train
aa_matrix = np.zeros(nx_adj.shape)
g_train = nx.from_edgelist(train)
train_nodes = g_train.nodes
candidate_edges = []
for u, v in test:
if u in train_nodes and v in train_nodes:
candidate_edges.append((u, v))
for u, v in test_neg:
if u in train_nodes and v in train_nodes:
candidate_edges.append((u, v))
# Run Algos
lp_baselines = {
"Adamic-Adar": nx.adamic_adar_index,
"Resouce Allocation": nx.resource_allocation_index,
"Jaccard": nx.jaccard_coefficient,
"Preferential Attachment": nx.preferential_attachment
}
print("#============================")
print("Method\tAUC\tAP")
for baseline in lp_baselines:
for u, v, p in lp_baselines[baseline](g_train, candidate_edges):
aa_matrix[u][v] = p
aa_matrix[v][u] = p # make sure it's symmetric
# Calculate ROC AUC and Average Precision
roc, ap = get_roc_score(test, test_neg, aa_matrix)
print("%s\t%.6f\t%.6f" % (baseline, roc, ap))
logger.info("[%s]\t%s\t%.6f\t%.6f" %
(dataset_name, baseline, roc, ap))
print("#============================")
def explore_lyb():
net_file = data_utils.get_data_path("lyb")
g = graph_utils.load_basic_network(net_file)
n2v_emb = node2vec.node2vec_emb(g, p=0.5, q=2, out_dim=32, num_walks=20)
n2v_emb.learn_embedding()
# out_file = net_file.split('.')[0]+'-n2v_emb.txt'
# n2v_emb.output_embedding(out_file)
node_labels = graph_utils.load_node_labels(data_utils.get_node_path("lyb"))
sus_best = n2v_emb.model.most_similar(positive=['23'])
for item in sus_best:
print(node_labels[int(item[0])], item[1])
com = list(greedy_modularity_communities(g))
node_community = {}
for i, c in enumerate(com):
for node in c:
node_community[node_labels[node]] = i
print(node_community)
network_stats(g, 'BA-Network')
# WS-Network
k = 20
p = 0.01
g = nx.watts_strogatz_graph(n, k, p)
g = g.to_undirected()
draw_degree_dist(g, k, title='WS-Network Distribution')
network_stats(g, 'WS-Network')
# powerlaw_cluster network
m = 10
p = 1
g = nx.powerlaw_cluster_graph(n, m, p)
g = g.to_undirected()
draw_degree_dist(g, m, title='PC-Network Distribution')
network_stats(g, 'PC-Network')
# Facebook Network
import os, sys
projct_root_path = os.path.dirname(
os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(projct_root_path)
import common.graph_utils as graph_utils
import common.data_utils as data_utils
net_file = data_utils.get_data_path("facebook")
g = graph_utils.load_basic_network(net_file)
g = g.to_undirected()
draw_degree_dist(g, m, title='Facebook-Network Distribution')
network_stats(g, 'Facebook-Network')
print('%d ego graph saved to adjacency_matrix.npy.' % (len(self.ego_graphs)))
np.save(os.path.join(file_dir, "influence_feature.npy"),self.influence_features)
print('influence_feature.npy saved.')
np.save(os.path.join(file_dir,"label.npy"),self.graph_labels)
print('label.npy saved.')
np.save(os.path.join(file_dir, "vertex_id.npy"), self.ego_virtices)
print('vertex_id.npy saved.')
np.save(os.path.join(file_dir, "vertex_feature.npy"), self.graph_node_features)
print('vertex_feature.npy saved.')
np.save(os.path.join(file_dir, "embedding.npy"),self.embedding)
print('embedding.npy saved.')
def load(self, file_dir):
self.ego_graphs = np.load(os.path.join(file_dir, "adjacency_matrix.npy"))
self.influence_features = np.load(os.path.join(file_dir, "influence_feature.npy")).astype(np.float32)
self.graph_labels = np.load(os.path.join(file_dir, "label.npy"))
self.ego_virtices = np.load(os.path.join(file_dir, "vertex_id.npy"))
self.graph_node_features = torch.FloatTensor(np.load(os.path.join(file_dir, "vertex_feature.npy")))
self.embedding = torch.FloatTensor(np.load(os.path.join(file_dir, "embedding.npy")))
print("%s dataset loaded." % (file_dir))
if __name__ == '__main__':
network_name = 'facebook'
net_file = data_utils.get_data_path(network_name)
g = graph_utils.load_basic_network(net_file)
dataset = deepinf_dataset(g, sir_file=net_file.split('.')[0]+'-sir.txt')
target_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),network_name+"_preprocess")
dataset.make()
dataset.save(target_path)
# dataset.load(target_path)
def main():
net_file = data_utils.get_data_path("twitter")
adj = load_networkx_format(net_file)
def main():
# Training settings
# Note: Hyper-parameters need to be tuned in order to obtain results reported in the paper.
parser = argparse.ArgumentParser(
description=
'PyTorch graph convolutional neural net for whole-graph classification'
)
parser.add_argument('--dataset',
type=str,
default="IMDBBINARY",
help='name of dataset (default: MUTAG)')
parser.add_argument('--device',
type=int,
default=0,
help='which gpu to use if any (default: 0)')
parser.add_argument('--batch_size',
type=int,
default=32,
help='input batch size for training (default: 32)')
parser.add_argument(
'--iters_per_epoch',
type=int,
default=50,
help='number of iterations per each epoch (default: 50)')
parser.add_argument('--epochs',
type=int,
default=50,
help='number of epochs to train (default: 20)')
parser.add_argument('--lr',
type=float,
default=0.001,
help='learning rate (default: 0.01)')
parser.add_argument(
'--seed',
type=int,
default=0,
help='random seed for splitting the dataset into 10 (default: 0)')
parser.add_argument(
'--fold_idx',
type=int,
default=0,
help='the index of fold in 10-fold validation. Should be less then 10.'
)
parser.add_argument(
'--num_layers',
type=int,
default=5,
help='number of layers INCLUDING the input one (default: 5)')
parser.add_argument(
'--num_mlp_layers',
type=int,
default=2,
help=
'number of layers for MLP EXCLUDING the input one (default: 2). 1 means linear model.'
)
parser.add_argument('--hidden_dim',
type=int,
default=128,
help='number of hidden units (default: 64)')
parser.add_argument('--final_dropout',
type=float,
default=0.5,
help='final layer dropout (default: 0.5)')
parser.add_argument(
'--graph_pooling_type',
type=str,
default="sum",
choices=["sum", "average"],
help='Pooling for over nodes in a graph: sum or average')
parser.add_argument(
'--neighbor_pooling_type',
type=str,
default="sum",
choices=["sum", "average", "max"],
help='Pooling for over neighboring nodes: sum, average or max')
parser.add_argument(
'--learn_eps',
action="store_true",
help=
'Whether to learn the epsilon weighting for the center nodes. Does not affect training accuracy though.'
)
parser.add_argument(
'--degree_as_tag',
action="store_true",
help=
'let the input node features be the degree of nodes (heuristics for unlabeled graph)'
)
parser.add_argument('--filename', type=str, default="", help='output file')
args = parser.parse_args()
# set up seeds and gpu device
torch.manual_seed(0)
np.random.seed(0)
device = torch.device(
"cuda:" +
str(args.device)) if torch.cuda.is_available() else torch.device("cpu")
if torch.cuda.is_available():
torch.cuda.manual_seed_all(0)
graphs, num_classes = load_graphs(data_utils.get_data_path(args.dataset),
args.degree_as_tag)
# 10-fold cross validation. Conduct an experiment on the fold specified by args.fold_idx.
train_graphs, test_graphs = separate_graph_data(graphs, args.seed,
args.fold_idx)
model = GraphCNN(args.num_layers, args.num_mlp_layers,
train_graphs[0].node_features.shape[1], args.hidden_dim,
num_classes, args.final_dropout, args.learn_eps,
args.graph_pooling_type, args.neighbor_pooling_type,
device).to(device)
optimizer = optim.Adam(model.parameters(), lr=args.lr)
scheduler = optim.lr_scheduler.StepLR(optimizer, step_size=50, gamma=0.5)
for epoch in range(1, args.epochs + 1):
scheduler.step()
print("$epoch", epoch)
avg_loss = train(args, model, device, train_graphs, optimizer, epoch)
acc_train, acc_test = test(args, model, device, train_graphs,
test_graphs, epoch)
if not args.filename == "":
with open(args.filename, 'w') as f:
f.write("%f %f %f" % (avg_loss, acc_train, acc_test))
f.write("\n")
print()
cur_level = list(neighbors(node))
visited = set(cur_level)
while depth_now <= depth and len(cur_level) > 0:
next_level = set()
for target in cur_level:
if target not in candidates:
candidates[target] = depth_now
for child in neighbors(target):
if child not in visited:
visited.add(child)
next_level.add(child)
cur_level = next_level
depth_now += 1
gravity = 0
for target in candidates:
distance = candidates[target]
if target != node and distance <= depth:
partial_gravity = degrees[node] * degrees[target] / (distance**
2)
gravity += partial_gravity
lgm_results[node] = gravity
return lgm_results
if __name__ == '__main__':
# g = nx.karate_club_graph()
net_file = data_utils.get_data_path("lyb")
g = graph_utils.load_basic_network(net_file)
lgm = Local_gravity_model(g)
print("Local Gravity Model:")
print(sorted(lgm.items(), key=lambda v: v[1], reverse=True))
def main():
net_file = data_utils.get_data_path("lyb")
g = graph_utils.load_basic_network(net_file)
n2v_emb = node2vec.node2vec_emb(g, p=0.5, q=2, out_dim=64, num_walks=20)
n2v_emb.learn_embedding()
avg_node_inf = node_influence / num_epoch if num_epoch > 0 else 0.0
sir_score[node] = avg_node_inf
return sir_score
def opt_beta(g):
k1s = 0
k2s = 0
for node in g.nodes():
k1s += len(list(g.neighbors(node)))
k2s += len(list(nx.bfs_tree(g, source=node, depth_limit=2).edges()))
if k2s > k1s:
beta = k1s / (k2s - k1s)
else:
beta = 0.1
return beta
if __name__ == '__main__':
# g = nx.karate_club_graph()
# sir_score = sir_ranking(g,num_epoch=1000)
# print(sorted(sir_score.items(), key=lambda v: v[1], reverse=True))\
net_file = data_utils.get_data_path("BlogCatalog")
g = graph_utils.load_basic_network(net_file)
st = time.time()
sir = sir_ranking(g, beta=opt_beta(g), gamma=1.0, num_epoch=100)
out_file = net_file.split('.')[0] + '-sir.txt'
with open(out_file, 'w') as f:
for i, v in sir.items():
f.write(str(i) + '\t' + str(round(v, 6)) + '\n')
print('time used:', time.time() - st)