import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
import numpy as np
import math
import dgl
import random
import dgl.nn as dglnn
from . import BaseModel, register_model
from .CompGCN import CompGraphConvLayer
import os
def get_norm_id(id_map, some_id):
#如果不存在，返回一个id最大值
if some_id not in id_map:
id_map[some_id] = len(id_map)
return id_map[some_id]
def norm_graph(node_id_map, edge_id_map, edge_list):
norm_edge_list = []
for e in edge_list:
norm_edge_list.append(
(
get_norm_id(node_id_map, e[0]),
get_norm_id(node_id_map, e[1]),
get_norm_id(edge_id_map, e[2]),
)
)
return norm_edge_list
class NodeEncoder(torch.nn.Module):
def __init__(
self,
base_embedding_dim,
num_nodes,
pretrained_node_embedding_tensor,
is_pre_trained,
):
super().__init__()
self.pretrained_node_embedding_tensor = pretrained_node_embedding_tensor
self.base_embedding_dim = base_embedding_dim
if not is_pre_trained:
self.base_embedding_layer = torch.nn.Embedding(
num_nodes, base_embedding_dim
)#.cuda()
self.base_embedding_layer.weight.data.uniform_(-1, 1)
else:
self.base_embedding_layer = torch.nn.Embedding.from_pretrained(
pretrained_node_embedding_tensor
)#.cuda()
def forward(self, node_id):
node_id = torch.LongTensor([int(node_id)])#.cuda()
x_base = self.base_embedding_layer(node_id)
return x_base
class GCNGraphEncoder(torch.nn.Module):
def __init__(
self,
G,
pretrained_node_embedding_tensor,
is_pre_trained,
base_embedding_dim,
max_length,
):
super().__init__()
self.g = G
self.base_embedding_dim = base_embedding_dim
self.max_length = max_length
self.no_nodes = self.g.num_nodes() #用DGL的表示方式
self.no_relations = self.g.num_edges()
# print('check *************', self.no_relations)
self.node_embedding = NodeEncoder(
base_embedding_dim,
self.no_nodes,
pretrained_node_embedding_tensor,
is_pre_trained,
)
self.special_tokens = {"[PAD]": 0, "[MASK]": 1}
self.special_embed = torch.nn.Embedding(
len(self.special_tokens), base_embedding_dim
)
self.special_embed.weight.data.uniform_(-1, 1)
def forward(self, subgraphs_list, masked_nodes):
num_subgraphs = len(subgraphs_list)
node_emb = torch.zeros(
num_subgraphs, self.max_length + 1, self.base_embedding_dim#+1是因为包含
)
for ii,subgraph in enumerate(subgraphs_list):
#node_id_map = batch_id_maps[ii][0]
#edge_type_map = batch_id_maps[ii][1]
masked_set = masked_nodes[ii]
for node in subgraph.nodes():
node_id=subgraph.ndata[dgl.NID][int(node)]
if node_id not in masked_set: # used to ignore the masked nodes
node_emb[ii][node] = self.node_embedding(int(node_id))
# get embeddings for special tokens
# will be used for masking and padding before bert layer
special_tokens_embed = {}
for token in self.special_tokens:
node_id = Variable(torch.LongTensor([self.special_tokens[token]]))
tmp_embed = self.special_embed(node_id)
special_tokens_embed[self.special_tokens[token] + self.no_nodes] = {
"token": token,
"embed": tmp_embed,
}
return node_emb
def get_attn_pad_mask(subgraph_list, pad_id, max_len):
#seq_q and seq_k are both all_nodes, which is list(list(subgraph_nodes))
batch_size = len(subgraph_list)
len_q=max_len
# print(batch_size, len_q, len_k)
pad_attn_mask = []
for itm in subgraph_list:
tmp_mask = []
for sub in itm.ndata[dgl.NID]:
if sub == pad_id:
tmp_mask.append(True)
else:
tmp_mask.append(False)
if len(tmp_mask)<max_len:
tmp_mask=tmp_mask+[True]*(max_len-len(tmp_mask))
pad_attn_mask.append(tmp_mask)
# print(tmp_mask)
# print('mask', len(pad_attn_mask), len(pad_attn_mask[0]))
pad_attn_mask = Variable(torch.ByteTensor(pad_attn_mask)).unsqueeze(1)
pad_attn_mask = pad_attn_mask#.cuda()
return pad_attn_mask.expand(batch_size, len_q, len_q) # batch_size x len_q x len_k
def gelu(x):
""""Implementation of the gelu activation function by Hugging Face."""
return x * 0.5 * (1.0 + torch.erf(x / math.sqrt(2.0)))
class ScaledDotProductAttention(torch.nn.Module):
def __init__(self, d_k):
super(ScaledDotProductAttention, self).__init__()
self.d_k = d_k
def forward(self, Q, K, V, attn_mask=None):
# print('mask', attn_mask.size())
scores = torch.matmul(Q, K.transpose(-1, -2)) / np.sqrt(self.d_k)
scores.masked_fill_(attn_mask == True, -1e9)#change dropped softmax value into
attn = torch.nn.Softmax(dim=-1)(scores)
context = torch.matmul(attn, V)
return context, attn
class MultiHeadAttention(torch.nn.Module):
def __init__(self, d_model, d_k, d_v, n_heads):
super(MultiHeadAttention, self).__init__()
self.n_heads = n_heads
self.d_k = d_k #dimension of K and Q
self.d_v = d_v #dimension of V
self.d_model = d_model
self.W_Q = torch.nn.Linear(d_model, d_k * n_heads)
self.W_K = torch.nn.Linear(d_model, d_k * n_heads)
self.W_V = torch.nn.Linear(d_model, d_v * n_heads)
self.scaled_dot_prod_attn = ScaledDotProductAttention(d_k)
self.wrap = torch.nn.Linear(self.n_heads * self.d_v, self.d_model)
self.layerNorm = torch.nn.LayerNorm(self.d_model)
def forward(self, Q, K, V, attn_mask=None):
#This V is not the V matrix of dot attention.
residual, batch_size = Q, Q.size(0)
q_s = self.W_Q(Q).view(batch_size, -1, self.n_heads, self.d_k).transpose(1, 2)#128(batcch)*4(head)*7(n_nodes)*64(d_k)
k_s = self.W_K(K).view(batch_size, -1, self.n_heads, self.d_k).transpose(1, 2)
v_s = self.W_V(V).view(batch_size, -1, self.n_heads, self.d_v).transpose(1, 2)
if attn_mask is not None:
attn_mask = attn_mask.unsqueeze(1).repeat(1, self.n_heads, 1, 1)
context, attn = self.scaled_dot_prod_attn(q_s, k_s, v_s, attn_mask=attn_mask)#context is H*A
context = (
context.transpose(1, 2)
.contiguous()
.view(batch_size, -1, self.n_heads * self.d_v)
)
output = self.wrap(context)
return self.layerNorm(output + residual), attn
#fNN in the paper
class PoswiseFeedForwardNet(torch.nn.Module):
def __init__(self, d_model, d_ff):
super(PoswiseFeedForwardNet, self).__init__()
self.fc1 = torch.nn.Linear(d_model, d_ff)
self.fc2 = torch.nn.Linear(d_ff, d_model)
def forward(self, x):
return self.fc2(gelu(self.fc1(x)))
class EncoderLayer(torch.nn.Module):
def __init__(self, d_model, d_k, d_v, d_ff, n_heads):
super(EncoderLayer, self).__init__()
self.enc_self_attn = MultiHeadAttention(d_model, d_k, d_v, n_heads)
self.pos_ffn = PoswiseFeedForwardNet(d_model, d_ff)
def forward(self, enc_inputs, enc_self_attn_mask):
enc_outputs, attn = self.enc_self_attn(
enc_inputs, enc_inputs, enc_inputs, enc_self_attn_mask
) # enc_inputs to same Q,K,V
enc_outputs = self.pos_ffn(
enc_outputs
) # enc_outputs: [batch_size x len_q x d_model]
return enc_outputs, attn
[docs]
@register_model('SLiCE')
class SLiCE(BaseModel):
@classmethod
def build_model_from_args(cls, args, hg):
# if args.embed_dir:
# pretrained_node_embedding_tensor=load_pickle(args.embed_dir)
return cls(G=hg,pretrained_node_embedding_tensor=None,args=args)#to-do: 命令行解析
def load_pretrained_node2vec(self,filename, base_emb_dim):
"""
loads embeddings from node2vec style file, where each line is
nodeid node_embedding
returns tensor containing node_embeddings
for graph nodes 0 to n-1
"""
node_embeddings = torch.empty(self.g.num_nodes(), 100)
with open(filename, "r") as f:
header = f.readline()
emb_dim = int(header.strip().split()[1])
for line in f:
arr = line.strip().split()
graph_node_id = arr[0]
node_emb = [float(x) for x in arr[1:]]
vocab_id = int(graph_node_id)
if vocab_id >= 0:
node_embeddings[vocab_id] = torch.tensor(node_emb)
# print(torch.tensor(node_emb).size())
out = node_embeddings
print("node2vec tensor", out.size())
return out
#参数来自原论文默认参数
def __init__(self,
G, #G为DGLGraph
args,
pretrained_node_embedding_tensor,
num_layers=6,
d_model=200,
d_k=64,
d_v=64,
d_ff=200 * 4,
n_heads=4,
is_pre_trained=False,
base_embedding_dim=200,#dimension of base embedding
max_length=6,#max length of walks
num_gcn_layers=2,#number of gcn layers before bert
node_edge_composition_func="mult",#options for node and edge compostion, sub|circ_conv|mult|no_rel
get_embeddings=False,#indicate if need to get node vectors from BERT encoder output
fine_tuning_layer=False,):
super().__init__()
#initialize
self.g=G
self.num_layers = num_layers
self.d_model = d_model
self.max_length = max_length
self.get_embeddings = get_embeddings
self.node_edge_composition_func = node_edge_composition_func
self.fine_tuning_layer = fine_tuning_layer
self.no_nodes = G.num_nodes()
self.n_pred=args.n_pred
#pretraining use node2vec if not exist
if not os.path.exists(args.pretrained_embeddings):
print("Run Node2vec to obtain pre-trained node embeddings ...")
walks=[]
for _ in range(10):
nodes=list(G.nodes())
random.shuffle(nodes)
walk = dgl.sampling.node2vec_random_walk(G, torch.tensor(nodes), 1, 1, walk_length=80-1).tolist()#len=walk_length+1
walks.extend(walk)
walks = [list(map(str, walk)) for walk in walks]
from gensim.models import Word2Vec
model = Word2Vec(
walks,
# size=base_embedding_dim,
window=10,
min_count=0,
sg=1,
workers=8,
# iter=1,
)
model.wv.save_word2vec_format(args.pretrained_embeddings)
pretrained_node_embedding_tensor = self.load_pretrained_node2vec(
args.pretrained_embeddings, base_embedding_dim
)# (n_nodes*d_model)
#FIXME 暂时是用随机初始化，pretrain tensor是None
self.gcn_graph_encoder = GCNGraphEncoder(
G,
pretrained_node_embedding_tensor,
is_pre_trained,
base_embedding_dim,
max_length,
)
self.layers = torch.nn.ModuleList(
[EncoderLayer(d_model, d_k, d_v, d_ff, n_heads) for _ in range(num_layers)]
)#.cuda()
self.linear = torch.nn.Linear(d_model, d_model)#.cuda()
self.norm = torch.nn.LayerNorm(d_model)#.cuda()
# decoder
self.decoder = torch.nn.Linear(self.d_model, self.no_nodes)#.cuda()
def set_fine_tuning(self):
self.fine_tuning_layer = True
def GCN_MaskGeneration(self,subgraph_sequences):
n_pred=self.n_pred
masked_nodes = []#node id masked
masked_position = []# node index masked
for subgraph in subgraph_sequences:
num_nodes = subgraph.num_nodes()
mask_index = random.sample(range(num_nodes), n_pred)
subgraph_masked_nodes = []
subgraph_masked_position = []
for i in range(num_nodes):
if i in mask_index:
subgraph_masked_nodes.append(subgraph.ndata[dgl.NID][i])
subgraph_masked_position.append(i)
masked_nodes.append(subgraph_masked_nodes)
masked_position.append(subgraph_masked_position)
return torch.tensor(masked_nodes), torch.tensor(masked_position)
def forward(self, subgraph_list):
#subgraph list is a list of node subgraphs sampled by slice_sampler
if self.fine_tuning_layer:
masked_nodes=Variable(torch.LongTensor([[] for ii in range(len(subgraph_list))]))
else:
masked_nodes,masked_pos=self.GCN_MaskGeneration(subgraph_list)
# 将节点embedding和关系的embedding初始化，并采样得到
# context generation
node_emb = self.gcn_graph_encoder(subgraph_list, masked_nodes)
output = node_emb#.cuda()
enc_self_attn_mask = get_attn_pad_mask(subgraph_list,self.no_nodes,self.max_length+1)
# contextual translation
for layer in self.layers:
output, enc_self_attn = layer(output, enc_self_attn_mask)
try:
layer_output = torch.cat((layer_output, output.unsqueeze(1)), 1)#output embedding of each layer
except NameError: # FIXME - replaced bare except
layer_output = output.unsqueeze(1)#.cuda()
if self.fine_tuning_layer:
try:
att_output = torch.cat((att_output, enc_self_attn.unsqueeze(0)), 0)#output attention of each layer
except NameError: # FIXME - replaced bare except
att_output = enc_self_attn.unsqueeze(0)
# new added for ablation study
if self.num_layers == 0:
layer_output = output.unsqueeze(1)
att_output = "NA"
if self.fine_tuning_layer:
# print(output.size(), layer_output.size(), att_output.size())
return output, layer_output, att_output
else:
masked_pos = masked_pos[:,:,None].expand(
-1, -1, output.size(-1)
) # [batch_size, maxlen, d_model]
h_masked = torch.gather(
output, 1, masked_pos#.cuda()
) # masking position [batch_size, len, d_model]
h_masked = self.norm(gelu(self.linear(h_masked)))
pred_score = self.decoder(h_masked) # [batch_size, maxlen, n_vocab]
# print('check====', pred_score.size())
if self.get_embeddings:
return pred_score, masked_nodes, output
else:
return pred_score, masked_nodes
class SLiCEFinetuneLayer(torch.nn.Module):
@classmethod
def build_model_from_args(cls, args):
return cls(d_model=args.d_model,ft_d_ff=args.ft_d_ff,
ft_layer=args.ft_layer,ft_drop_rate=args.ft_drop_rate,
ft_input_option=args.ft_input_option, num_layers=args.num_layers)
def __init__(
self,
d_model,
ft_d_ff,
ft_layer,
ft_drop_rate,
ft_input_option,
num_layers,
):
super().__init__()
self.d_model = d_model
self.ft_layer = ft_layer
self.ft_input_option = ft_input_option
self.num_layers = num_layers
if ft_input_option in ["last", "last4_sum"]:
cnt_layers = 1
elif ft_input_option in ["last4_cat"]:
cnt_layers = 4
if self.num_layers == 0:
cnt_layers = 1
if self.ft_layer == "linear":
self.ft_decoder = torch.nn.Linear(d_model * cnt_layers, d_model)#.cuda()
elif self.ft_layer == "ffn":
self.ffn1 = torch.nn.Linear(d_model * cnt_layers, ft_d_ff)#.cuda()
print(self.num_layers, cnt_layers, self.ffn1)
self.dropout = torch.nn.Dropout(ft_drop_rate)#.cuda()
self.ffn2 = torch.nn.Linear(ft_d_ff, d_model)#.cuda()
def forward(self, graphbert_layer_output):
"""
graphbert_output = batch_sz * [CLS, source, target, relation, SEP] *
[emb_size]
"""
if self.ft_input_option == "last":
# use the output from laster layer of graphbert
graphbert_output = graphbert_layer_output[:, -1, :, :].squeeze(1)
source_embedding = graphbert_output[:, 0, :].unsqueeze(1)
destination_embedding = graphbert_output[:, 1, :].unsqueeze(1)
else:
# concatenate the output from the last four last four layers
# add for ablation study
no_layers = graphbert_layer_output.size(1)
if no_layers == 1:
start_layer = 0
else:
start_layer = no_layers - 4
for ii in range(start_layer, no_layers):
source_embed = graphbert_layer_output[:, ii, 0, :].unsqueeze(1)
destination_embed = graphbert_layer_output[:, ii, 1, :].unsqueeze(1)
if self.ft_input_option == "last4_cat":
try:
source_embedding = torch.cat(
(source_embedding, source_embed), 2
)
destination_embedding = torch.cat(
(destination_embedding, destination_embed), 2
)
except:
source_embedding = source_embed
destination_embedding = destination_embed
elif self.ft_input_option == "last4_sum":
try:
source_embedding = torch.add(source_embedding, 1, source_embed)
destination_embedding = torch.add(
destination_embedding, 1, destination_embed
)
except:
source_embedding = source_embed
destination_embedding = destination_embed
# print(source_embedding.size(), destination_embedding.size())
if self.ft_layer == "linear":
src_embedding = self.ft_decoder(source_embedding)
dst_embedding = self.ft_decoder(destination_embedding)
elif self.ft_layer == "ffn":
src_embedding = torch.relu(self.dropout(self.ffn1(source_embedding)))
src_embedding = self.ffn2(src_embedding)
dst_embedding = torch.relu(self.dropout(self.ffn1(destination_embedding)))
dst_embedding = self.ffn2(dst_embedding)
dst_embedding = dst_embedding.transpose(1, 2)
pred_score = torch.bmm(src_embedding, dst_embedding).squeeze(1)
pred_score = torch.sigmoid(pred_score)
# print('check+++++', pred_score.size())
return pred_score, src_embedding, dst_embedding.transpose(1, 2)