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sdne.py
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sdne.py
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# -*- coding:utf-8 -*-
"""
Author:
Weichen Shen,weichenswc@163.com
Reference:
[1] Wang D, Cui P, Zhu W. Structural deep network embedding[C]//Proceedings of the 22nd ACM SIGKDD international conference on Knowledge discovery and data mining. ACM, 2016: 1225-1234.(https://www.kdd.org/kdd2016/papers/files/rfp0191-wangAemb.pdf)
"""
import time
import numpy as np
import scipy.sparse as sp
import tensorflow as tf
from tensorflow.python.keras import backend as K
from tensorflow.python.keras.callbacks import History
from tensorflow.python.keras.layers import Dense, Input
from tensorflow.python.keras.models import Model
from tensorflow.python.keras.regularizers import l1_l2
from ..utils import preprocess_nxgraph
def l_2nd(beta):
def loss_2nd(y_true, y_pred):
b_ = np.ones_like(y_true)
b_[y_true != 0] = beta
x = K.square((y_true - y_pred) * b_)
t = K.sum(x, axis=-1, )
return K.mean(t)
return loss_2nd
def l_1st(alpha):
def loss_1st(y_true, y_pred):
L = y_true
Y = y_pred
batch_size = tf.to_float(K.shape(L)[0])
return alpha * 2 * tf.linalg.trace(tf.matmul(tf.matmul(Y, L, transpose_a=True), Y)) / batch_size
return loss_1st
def create_model(node_size, hidden_size=[256, 128], l1=1e-5, l2=1e-4):
A = Input(shape=(node_size,))
L = Input(shape=(None,))
fc = A
for i in range(len(hidden_size)):
if i == len(hidden_size) - 1:
fc = Dense(hidden_size[i], activation='relu',
kernel_regularizer=l1_l2(l1, l2), name='1st')(fc)
else:
fc = Dense(hidden_size[i], activation='relu',
kernel_regularizer=l1_l2(l1, l2))(fc)
Y = fc
for i in reversed(range(len(hidden_size) - 1)):
fc = Dense(hidden_size[i], activation='relu',
kernel_regularizer=l1_l2(l1, l2))(fc)
A_ = Dense(node_size, 'relu', name='2nd')(fc)
model = Model(inputs=[A, L], outputs=[A_, Y])
emb = Model(inputs=A, outputs=Y)
return model, emb
class SDNE(object):
def __init__(self, graph, hidden_size=[32, 16], alpha=1e-6, beta=5., nu1=1e-5, nu2=1e-4, ):
self.graph = graph
# self.g.remove_edges_from(self.g.selfloop_edges())
self.idx2node, self.node2idx = preprocess_nxgraph(self.graph)
self.node_size = self.graph.number_of_nodes()
self.hidden_size = hidden_size
self.alpha = alpha
self.beta = beta
self.nu1 = nu1
self.nu2 = nu2
self.A, self.L = _create_A_L(self.graph, self.node2idx) # Adj Matrix,L Matrix
self.reset_model()
self.inputs = [self.A, self.L]
self._embeddings = {}
def reset_model(self, opt='adam'):
self.model, self.emb_model = create_model(self.node_size, hidden_size=self.hidden_size, l1=self.nu1,
l2=self.nu2)
self.model.compile(opt, [l_2nd(self.beta), l_1st(self.alpha)])
self.get_embeddings()
def train(self, batch_size=1024, epochs=1, initial_epoch=0, verbose=1):
if batch_size >= self.node_size:
if batch_size > self.node_size:
print('batch_size({0}) > node_size({1}),set batch_size = {1}'.format(
batch_size, self.node_size))
batch_size = self.node_size
return self.model.fit([self.A.todense(), self.L.todense()], [self.A.todense(), self.L.todense()],
batch_size=batch_size, epochs=epochs, initial_epoch=initial_epoch, verbose=verbose,
shuffle=False, )
else:
steps_per_epoch = (self.node_size - 1) // batch_size + 1
hist = History()
hist.on_train_begin()
logs = {}
for epoch in range(initial_epoch, epochs):
start_time = time.time()
losses = np.zeros(3)
for i in range(steps_per_epoch):
index = np.arange(
i * batch_size, min((i + 1) * batch_size, self.node_size))
A_train = self.A[index, :].todense()
L_mat_train = self.L[index][:, index].todense()
inp = [A_train, L_mat_train]
batch_losses = self.model.train_on_batch(inp, inp)
losses += batch_losses
losses = losses / steps_per_epoch
logs['loss'] = losses[0]
logs['2nd_loss'] = losses[1]
logs['1st_loss'] = losses[2]
epoch_time = int(time.time() - start_time)
hist.on_epoch_end(epoch, logs)
if verbose > 0:
print('Epoch {0}/{1}'.format(epoch + 1, epochs))
print('{0}s - loss: {1: .4f} - 2nd_loss: {2: .4f} - 1st_loss: {3: .4f}'.format(
epoch_time, losses[0], losses[1], losses[2]))
return hist
def evaluate(self, ):
return self.model.evaluate(x=self.inputs, y=self.inputs, batch_size=self.node_size)
def get_embeddings(self):
self._embeddings = {}
embeddings = self.emb_model.predict(self.A.todense(), batch_size=self.node_size)
look_back = self.idx2node
for i, embedding in enumerate(embeddings):
self._embeddings[look_back[i]] = embedding
return self._embeddings
def _create_A_L(graph, node2idx):
node_size = graph.number_of_nodes()
A_data = []
A_row_index = []
A_col_index = []
for edge in graph.edges():
v1, v2 = edge
edge_weight = graph[v1][v2].get('weight', 1)
A_data.append(edge_weight)
A_row_index.append(node2idx[v1])
A_col_index.append(node2idx[v2])
A = sp.csr_matrix((A_data, (A_row_index, A_col_index)), shape=(node_size, node_size))
A_ = sp.csr_matrix((A_data + A_data, (A_row_index + A_col_index, A_col_index + A_row_index)),
shape=(node_size, node_size))
D = sp.diags(A_.sum(axis=1).flatten().tolist()[0])
L = D - A_
return A, L