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Unverified Commit 3611a66e authored by xiang song(charlie.song)'s avatar xiang song(charlie.song) Committed by GitHub
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Remove duplicate code of deepwalk (#1965) 


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examples/pytorch/deepwalk/README.md
View file @ 3611a66e
# DeepWalk # DeepWalk
- Paper link: [here](https://arxiv.org/pdf/1403.6652.pdf) - Paper link: [here](https://arxiv.org/pdf/1403.6652.pdf)
- Other implementation: [gensim](https://github.com/phanein/deepwalk), [deepwalk-c](https://github.com/xgfs/deepwalk-c)
The implementation includes multi-processing training with CPU and mixed training with CPU and multi-GPU. The example code was moved to examples/pytorch/ogb/deepwalk.
## Dependencies
- PyTorch 1.0.1+
## Tested version
- PyTorch 1.5.0
- DGL 0.4.3
## Input data
Currently, we support two builtin dataset: youtube and blog. Use --data\_file youtube to select youtube dataset and --data\_file blog to select blog dataset.
The data is avaliable at https://data.dgl.ai/dataset/DeepWalk/youtube.zip and https://data.dgl.ai/dataset/DeepWalk/blog.zip
The youtube.zip includes both youtube-net.txt, youtube-vocab.txt and youtube-label.txt; The blog.zip includes both blog-net.txt, blog-vocab.txt and blog-label.txt.
For other datasets please pass the full path to the trainer through --data\_file and the format of a network file should follow:
```
1(node id) 2(node id)
1 3
1 4
2 4
...
```
## How to run the code
To run the code:
```
python3 deepwalk.py --data_file youtube --output_emb_file emb.txt --mix --lr 0.2 --gpus 0 1 2 3 --batch_size 100 --negative 5
```
## How to save the embedding
By default the trained embedding is saved under --output\_embe\_file FILE\_NAME as a numpy object.
To save the trained embedding in raw format(txt format), please use --save\_in\_txt argument.
## Evaluation
To evalutate embedding on multi-label classification, please refer to [here](https://github.com/ShawXh/Evaluate-Embedding)
YouTube (1M nodes).
| Implementation | Macro-F1 (%) <br> 1% &emsp;&emsp; 3% &emsp;&emsp; 5% &emsp;&emsp; 7% &emsp;&emsp; 9% | Micro-F1 (%) <br> 1% &emsp;&emsp; 3% &emsp;&emsp; 5% &emsp;&emsp; 7% &emsp;&emsp; 9% |
|----|----|----|
| gensim.word2vec(hs) | 28.73 &emsp; 32.51 &emsp; 33.67 &emsp; 34.28 &emsp; 34.79 | 35.73 &emsp; 38.34 &emsp; 39.37 &emsp; 40.08 &emsp; 40.77 |
| gensim.word2vec(ns) | 28.18 &emsp; 32.25 &emsp; 33.56 &emsp; 34.60 &emsp; 35.22 | 35.35 &emsp; 37.69 &emsp; 38.08 &emsp; 40.24 &emsp; 41.09 |
| ours | 24.58 &emsp; 31.23 &emsp; 33.97 &emsp; 35.41 &emsp; 36.48 | 38.93 &emsp; 43.17 &emsp; 44.73 &emsp; 45.42 &emsp; 45.92 |
The comparison between running time is shown as below, where the numbers in the brackets denote time used on random-walk.
| Implementation | gensim.word2vec(hs) | gensim.word2vec(ns) | Ours |
|----|----|----|----|
| Time (s) | 27119.6(1759.8) | 10580.3(1704.3) | 428.89 |
Parameters.
- walk_length = 80, number_walks = 10, window_size = 5
- Ours: 4GPU (Tesla V100), lr = 0.2, batchs_size = 128, neg_weight = 5, negative = 1, num_thread = 4
- Others: workers = 8, negative = 5
Speeding-up with mixed CPU & multi-GPU. The used parameters are the same as above.
| #GPUs | 1 | 2 | 4 |
|----------|-------|-------|-------|
| Time (s) |1419.64| 952.04|428.89 |
examples/pytorch/deepwalk/deepwalk.py deleted 100644 → 0
View file @ 22167f72
import torch
import argparse
import dgl
import torch.multiprocessing as mp
from torch.utils.data import DataLoader
import os
import random
import time
import numpy as np
from reading_data import DeepwalkDataset
from model import SkipGramModel
from utils import thread_wrapped_func, shuffle_walks, sum_up_params
class DeepwalkTrainer:
def __init__(self, args):
""" Initializing the trainer with the input arguments """
self.args = args
self.dataset = DeepwalkDataset(
net_file=args.data_file,
map_file=args.map_file,
walk_length=args.walk_length,
window_size=args.window_size,
num_walks=args.num_walks,
batch_size=args.batch_size,
negative=args.negative,
gpus=args.gpus,
fast_neg=args.fast_neg,
ogbl_name=args.ogbl_name,
load_from_ogbl=args.load_from_ogbl,
)
self.emb_size = self.dataset.G.number_of_nodes()
self.emb_model = None
def init_device_emb(self):
""" set the device before training
will be called once in fast_train_mp / fast_train
"""
choices = sum([self.args.only_gpu, self.args.only_cpu, self.args.mix])
assert choices == 1, "Must choose only *one* training mode in [only_cpu, only_gpu, mix]"
# initializing embedding on CPU
self.emb_model = SkipGramModel(
emb_size=self.emb_size,
emb_dimension=self.args.dim,
walk_length=self.args.walk_length,
window_size=self.args.window_size,
batch_size=self.args.batch_size,
only_cpu=self.args.only_cpu,
only_gpu=self.args.only_gpu,
mix=self.args.mix,
neg_weight=self.args.neg_weight,
negative=self.args.negative,
lr=self.args.lr,
lap_norm=self.args.lap_norm,
fast_neg=self.args.fast_neg,
record_loss=self.args.print_loss,
norm=self.args.norm,
use_context_weight=self.args.use_context_weight,
async_update=self.args.async_update,
num_threads=self.args.num_threads,
)
torch.set_num_threads(self.args.num_threads)
if self.args.only_gpu:
print("Run in 1 GPU")
assert self.args.gpus[0] >= 0
self.emb_model.all_to_device(self.args.gpus[0])
elif self.args.mix:
print("Mix CPU with %d GPU" % len(self.args.gpus))
if len(self.args.gpus) == 1:
assert self.args.gpus[0] >= 0, 'mix CPU with GPU should have available GPU'
self.emb_model.set_device(self.args.gpus[0])
else:
print("Run in CPU process")
self.args.gpus = [torch.device('cpu')]
def train(self):
""" train the embedding """
if len(self.args.gpus) > 1:
self.fast_train_mp()
else:
self.fast_train()
def fast_train_mp(self):
""" multi-cpu-core or mix cpu & multi-gpu """
self.init_device_emb()
self.emb_model.share_memory()
if self.args.count_params:
sum_up_params(self.emb_model)
start_all = time.time()
ps = []
for i in range(len(self.args.gpus)):
p = mp.Process(target=self.fast_train_sp, args=(i, self.args.gpus[i]))
ps.append(p)
p.start()
for p in ps:
p.join()
print("Used time: %.2fs" % (time.time()-start_all))
if self.args.save_in_txt:
self.emb_model.save_embedding_txt(self.dataset, self.args.output_emb_file)
elif self.args.save_in_pt:
self.emb_model.save_embedding_pt(self.dataset, self.args.output_emb_file)
else:
self.emb_model.save_embedding(self.dataset, self.args.output_emb_file)
@thread_wrapped_func
def fast_train_sp(self, rank, gpu_id):
""" a subprocess for fast_train_mp """
if self.args.mix:
self.emb_model.set_device(gpu_id)
torch.set_num_threads(self.args.num_threads)
if self.args.async_update:
self.emb_model.create_async_update()
sampler = self.dataset.create_sampler(rank)
dataloader = DataLoader(
dataset=sampler.seeds,
batch_size=self.args.batch_size,
collate_fn=sampler.sample,
shuffle=False,
drop_last=False,
num_workers=self.args.num_sampler_threads,
)
num_batches = len(dataloader)
print("num batchs: %d in process [%d] GPU [%d]" % (num_batches, rank, gpu_id))
# number of positive node pairs in a sequence
num_pos = int(2 * self.args.walk_length * self.args.window_size\
- self.args.window_size * (self.args.window_size + 1))
start = time.time()
with torch.no_grad():
for i, walks in enumerate(dataloader):
if self.args.fast_neg:
self.emb_model.fast_learn(walks)
else:
# do negative sampling
bs = len(walks)
neg_nodes = torch.LongTensor(
np.random.choice(self.dataset.neg_table,
bs * num_pos * self.args.negative,
replace=True))
self.emb_model.fast_learn(walks, neg_nodes=neg_nodes)
if i > 0 and i % self.args.print_interval == 0:
if self.args.print_loss:
print("GPU-[%d] batch %d time: %.2fs loss: %.4f" \
% (gpu_id, i, time.time()-start, -sum(self.emb_model.loss)/self.args.print_interval))
self.emb_model.loss = []
else:
print("GPU-[%d] batch %d time: %.2fs" % (gpu_id, i, time.time()-start))
start = time.time()
if self.args.async_update:
self.emb_model.finish_async_update()
def fast_train(self):
""" fast train with dataloader with only gpu / only cpu"""
# the number of postive node pairs of a node sequence
num_pos = 2 * self.args.walk_length * self.args.window_size\
- self.args.window_size * (self.args.window_size + 1)
num_pos = int(num_pos)
self.init_device_emb()
if self.args.async_update:
self.emb_model.share_memory()
self.emb_model.create_async_update()
if self.args.count_params:
sum_up_params(self.emb_model)
sampler = self.dataset.create_sampler(0)
dataloader = DataLoader(
dataset=sampler.seeds,
batch_size=self.args.batch_size,
collate_fn=sampler.sample,
shuffle=False,
drop_last=False,
num_workers=self.args.num_sampler_threads,
)
num_batches = len(dataloader)
print("num batchs: %d\n" % num_batches)
start_all = time.time()
start = time.time()
with torch.no_grad():
max_i = num_batches
for i, walks in enumerate(dataloader):
if self.args.fast_neg:
self.emb_model.fast_learn(walks)
else:
# do negative sampling
bs = len(walks)
neg_nodes = torch.LongTensor(
np.random.choice(self.dataset.neg_table,
bs * num_pos * self.args.negative,
replace=True))
self.emb_model.fast_learn(walks, neg_nodes=neg_nodes)
if i > 0 and i % self.args.print_interval == 0:
if self.args.print_loss:
print("Batch %d training time: %.2fs loss: %.4f" \
% (i, time.time()-start, -sum(self.emb_model.loss)/self.args.print_interval))
self.emb_model.loss = []
else:
print("Batch %d, training time: %.2fs" % (i, time.time()-start))
start = time.time()
if self.args.async_update:
self.emb_model.finish_async_update()
print("Training used time: %.2fs" % (time.time()-start_all))
if self.args.save_in_txt:
self.emb_model.save_embedding_txt(self.dataset, self.args.output_emb_file)
elif self.args.save_in_pt:
self.emb_model.save_embedding_pt(self.dataset, self.args.output_emb_file)
else:
self.emb_model.save_embedding(self.dataset, self.args.output_emb_file)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="DeepWalk")
# input files
## personal datasets
parser.add_argument('--data_file', type=str,
help="path of the txt network file, builtin dataset include youtube-net and blog-net")
## ogbl datasets
parser.add_argument('--ogbl_name', type=str,
help="name of ogbl dataset, e.g. ogbl-ddi")
parser.add_argument('--load_from_ogbl', default=False, action="store_true",
help="whether load dataset from ogbl")
# output files
parser.add_argument('--save_in_txt', default=False, action="store_true",
help='Whether save dat in txt format or npy')
parser.add_argument('--save_in_pt', default=False, action="store_true",
help='Whether save dat in pt format or npy')
parser.add_argument('--output_emb_file', type=str, default="emb.npy",
help='path of the output npy embedding file')
parser.add_argument('--map_file', type=str, default="nodeid_to_index.pickle",
help='path of the mapping dict that maps node ids to embedding index')
parser.add_argument('--norm', default=False, action="store_true",
help="whether to do normalization over node embedding after training")
# model parameters
parser.add_argument('--dim', default=128, type=int,
help="embedding dimensions")
parser.add_argument('--window_size', default=5, type=int,
help="context window size")
parser.add_argument('--use_context_weight', default=False, action="store_true",
help="whether to add weights over nodes in the context window")
parser.add_argument('--num_walks', default=10, type=int,
help="number of walks for each node")
parser.add_argument('--negative', default=1, type=int,
help="negative samples for each positve node pair")
parser.add_argument('--batch_size', default=128, type=int,
help="number of node sequences in each batch")
parser.add_argument('--walk_length', default=80, type=int,
help="number of nodes in a sequence")
parser.add_argument('--neg_weight', default=1., type=float,
help="negative weight")
parser.add_argument('--lap_norm', default=0.01, type=float,
help="weight of laplacian normalization, recommend to set as 0.1 / windoe_size")
# training parameters
parser.add_argument('--print_interval', default=100, type=int,
help="number of batches between printing")
parser.add_argument('--print_loss', default=False, action="store_true",
help="whether print loss during training")
parser.add_argument('--lr', default=0.2, type=float,
help="learning rate")
# optimization settings
parser.add_argument('--mix', default=False, action="store_true",
help="mixed training with CPU and GPU")
parser.add_argument('--gpus', type=int, default=[-1], nargs='+',
help='a list of active gpu ids, e.g. 0, used with --mix')
parser.add_argument('--only_cpu', default=False, action="store_true",
help="training with CPU")
parser.add_argument('--only_gpu', default=False, action="store_true",
help="training with GPU")
parser.add_argument('--async_update', default=False, action="store_true",
help="mixed training asynchronously, not recommended")
parser.add_argument('--fast_neg', default=False, action="store_true",
help="do negative sampling inside a batch")
parser.add_argument('--num_threads', default=8, type=int,
help="number of threads used for each CPU-core/GPU")
parser.add_argument('--num_sampler_threads', default=2, type=int,
help="number of threads used for sampling")
parser.add_argument('--count_params', default=False, action="store_true",
help="count the params, exit once counting over")
args = parser.parse_args()
if args.async_update:
assert args.mix, "--async_update only with --mix"
start_time = time.time()
trainer = DeepwalkTrainer(args)
trainer.train()
print("Total used time: %.2f" % (time.time() - start_time))
examples/pytorch/deepwalk/load_dataset.py deleted 100644 → 0
View file @ 22167f72
""" load dataset from ogb """
import argparse
from ogb.linkproppred import DglLinkPropPredDataset
def load_from_ogbl_with_name(name):
choices = ['ogbl-collab', 'ogbl-ddi', 'ogbl-ppa', 'ogbl-citation']
assert name in choices, "name must be selected from " + str(choices)
dataset = DglLinkPropPredDataset(name)
return dataset[0]
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('--name', type=str,
choices=['ogbl-collab', 'ogbl-ddi', 'ogbl-ppa', 'ogbl-citation'],
default='ogbl-collab',
help="name of datasets by ogb")
args = parser.parse_args()
name = args.name
g = load_from_ogbl_with_name(name=name)
try:
w = g.edata['edge_weight']
weighted = True
except:
weighted = False
with open(name + "-net.txt", "w") as f:
for i in range(g.edges()[0].shape[0]):
if weighted:
f.write(str(g.edges()[0][i].item()) + " "\
+str(g.edges()[1][i].item()) + " "\
+str(g.edata['edge_weight'][i]) + "\n")
else:
f.write(str(g.edges()[0][i].item()) + " "\
+str(g.edges()[1][i].item()) + " "\
+"1\n")
\ No newline at end of file
examples/pytorch/deepwalk/model.py deleted 100644 → 0
View file @ 22167f72
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import init
import random
import numpy as np
import torch.multiprocessing as mp
from torch.multiprocessing import Queue
from utils import thread_wrapped_func
def init_emb2pos_index(walk_length, window_size, batch_size):
''' select embedding of positive nodes from a batch of node embeddings
Return
------
index_emb_posu torch.LongTensor : the indices of u_embeddings
index_emb_posv torch.LongTensor : the indices of v_embeddings
Usage
-----
# emb_u.shape: [batch_size * walk_length, dim]
batch_emb2posu = torch.index_select(emb_u, 0, index_emb_posu)
'''
idx_list_u = []
idx_list_v = []
for b in range(batch_size):
for i in range(walk_length):
for j in range(i-window_size, i):
if j >= 0:
idx_list_u.append(j + b * walk_length)
idx_list_v.append(i + b * walk_length)
for j in range(i + 1, i + 1 + window_size):
if j < walk_length:
idx_list_u.append(j + b * walk_length)
idx_list_v.append(i + b * walk_length)
# [num_pos * batch_size]
index_emb_posu = torch.LongTensor(idx_list_u)
index_emb_posv = torch.LongTensor(idx_list_v)
return index_emb_posu, index_emb_posv
def init_emb2neg_index(walk_length, window_size, negative, batch_size):
'''select embedding of negative nodes from a batch of node embeddings
for fast negative sampling
Return
------
index_emb_negu torch.LongTensor : the indices of u_embeddings
index_emb_negv torch.LongTensor : the indices of v_embeddings
Usage
-----
# emb_u.shape: [batch_size * walk_length, dim]
batch_emb2negu = torch.index_select(emb_u, 0, index_emb_negu)
'''
idx_list_u = []
for b in range(batch_size):
for i in range(walk_length):
for j in range(i-window_size, i):
if j >= 0:
idx_list_u += [i + b * walk_length] * negative
for j in range(i+1, i+1+window_size):
if j < walk_length:
idx_list_u += [i + b * walk_length] * negative
idx_list_v = list(range(batch_size * walk_length))\
* negative * window_size * 2
random.shuffle(idx_list_v)
idx_list_v = idx_list_v[:len(idx_list_u)]
# [bs * walk_length * negative]
index_emb_negu = torch.LongTensor(idx_list_u)
index_emb_negv = torch.LongTensor(idx_list_v)
return index_emb_negu, index_emb_negv
def init_weight(walk_length, window_size, batch_size):
''' init context weight '''
weight = []
for b in range(batch_size):
for i in range(walk_length):
for j in range(i-window_size, i):
if j >= 0:
weight.append(1. - float(i - j - 1)/float(window_size))
for j in range(i + 1, i + 1 + window_size):
if j < walk_length:
weight.append(1. - float(j - i - 1)/float(window_size))
# [num_pos * batch_size]
return torch.Tensor(weight).unsqueeze(1)
def init_empty_grad(emb_dimension, walk_length, batch_size):
""" initialize gradient matrix """
grad_u = torch.zeros((batch_size * walk_length, emb_dimension))
grad_v = torch.zeros((batch_size * walk_length, emb_dimension))
return grad_u, grad_v
def adam(grad, state_sum, nodes, lr, device, only_gpu):
""" calculate gradients according to adam """
grad_sum = (grad * grad).mean(1)
if not only_gpu:
grad_sum = grad_sum.cpu()
state_sum.index_add_(0, nodes, grad_sum) # cpu
std = state_sum[nodes].to(device) # gpu
std_values = std.sqrt_().add_(1e-10).unsqueeze(1)
grad = (lr * grad / std_values) # gpu
return grad
@thread_wrapped_func
def async_update(num_threads, model, queue):
""" asynchronous embedding update """
torch.set_num_threads(num_threads)
while True:
(grad_u, grad_v, grad_v_neg, nodes, neg_nodes) = queue.get()
if grad_u is None:
return
with torch.no_grad():
model.u_embeddings.weight.data.index_add_(0, nodes.view(-1), grad_u)
model.v_embeddings.weight.data.index_add_(0, nodes.view(-1), grad_v)
if neg_nodes is not None:
model.v_embeddings.weight.data.index_add_(0, neg_nodes.view(-1), grad_v_neg)
class SkipGramModel(nn.Module):
""" Negative sampling based skip-gram """
def __init__(self,
emb_size,
emb_dimension,
walk_length,
window_size,
batch_size,
only_cpu,
only_gpu,
mix,
neg_weight,
negative,
lr,
lap_norm,
fast_neg,
record_loss,
norm,
use_context_weight,
async_update,
num_threads,
):
""" initialize embedding on CPU
Paremeters
----------
emb_size int : number of nodes
emb_dimension int : embedding dimension
walk_length int : number of nodes in a sequence
window_size int : context window size
batch_size int : number of node sequences in each batch
only_cpu bool : training with CPU
only_gpu bool : training with GPU
mix bool : mixed training with CPU and GPU
negative int : negative samples for each positve node pair
neg_weight float : negative weight
lr float : initial learning rate
lap_norm float : weight of laplacian normalization
fast_neg bool : do negative sampling inside a batch
record_loss bool : print the loss during training
norm bool : do normalizatin on the embedding after training
use_context_weight : give different weights to the nodes in a context window
async_update : asynchronous training
"""
super(SkipGramModel, self).__init__()
self.emb_size = emb_size
self.emb_dimension = emb_dimension
self.walk_length = walk_length
self.window_size = window_size
self.batch_size = batch_size
self.only_cpu = only_cpu
self.only_gpu = only_gpu
self.mixed_train = mix
self.neg_weight = neg_weight
self.negative = negative
self.lr = lr
self.lap_norm = lap_norm
self.fast_neg = fast_neg
self.record_loss = record_loss
self.norm = norm
self.use_context_weight = use_context_weight
self.async_update = async_update
self.num_threads = num_threads
# initialize the device as cpu
self.device = torch.device("cpu")
# content embedding
self.u_embeddings = nn.Embedding(
self.emb_size, self.emb_dimension, sparse=True)
# context embedding
self.v_embeddings = nn.Embedding(
self.emb_size, self.emb_dimension, sparse=True)
# initialze embedding
initrange = 1.0 / self.emb_dimension
init.uniform_(self.u_embeddings.weight.data, -initrange, initrange)
init.constant_(self.v_embeddings.weight.data, 0)
# lookup_table is used for fast sigmoid computing
self.lookup_table = torch.sigmoid(torch.arange(-6.01, 6.01, 0.01))
self.lookup_table[0] = 0.
self.lookup_table[-1] = 1.
if self.record_loss:
self.logsigmoid_table = torch.log(torch.sigmoid(torch.arange(-6.01, 6.01, 0.01)))
self.loss = []
# indexes to select positive/negative node pairs from batch_walks
self.index_emb_posu, self.index_emb_posv = init_emb2pos_index(
self.walk_length,
self.window_size,
self.batch_size)
self.index_emb_negu, self.index_emb_negv = init_emb2neg_index(
self.walk_length,
self.window_size,
self.negative,
self.batch_size)
if self.use_context_weight:
self.context_weight = init_weight(
self.walk_length,
self.window_size,
self.batch_size)
# adam
self.state_sum_u = torch.zeros(self.emb_size)
self.state_sum_v = torch.zeros(self.emb_size)
# gradients of nodes in batch_walks
self.grad_u, self.grad_v = init_empty_grad(
self.emb_dimension,
self.walk_length,
self.batch_size)
def create_async_update(self):
""" Set up the async update subprocess.
"""
self.async_q = Queue(1)
self.async_p = mp.Process(target=async_update, args=(self.num_threads, self, self.async_q))
self.async_p.start()
def finish_async_update(self):
""" Notify the async update subprocess to quit.
"""
self.async_q.put((None, None, None, None, None))
self.async_p.join()
def share_memory(self):
""" share the parameters across subprocesses """
self.u_embeddings.weight.share_memory_()
self.v_embeddings.weight.share_memory_()
self.state_sum_u.share_memory_()
self.state_sum_v.share_memory_()
def set_device(self, gpu_id):
""" set gpu device """
self.device = torch.device("cuda:%d" % gpu_id)
print("The device is", self.device)
self.lookup_table = self.lookup_table.to(self.device)
if self.record_loss:
self.logsigmoid_table = self.logsigmoid_table.to(self.device)
self.index_emb_posu = self.index_emb_posu.to(self.device)
self.index_emb_posv = self.index_emb_posv.to(self.device)
self.index_emb_negu = self.index_emb_negu.to(self.device)
self.index_emb_negv = self.index_emb_negv.to(self.device)
self.grad_u = self.grad_u.to(self.device)
self.grad_v = self.grad_v.to(self.device)
if self.use_context_weight:
self.context_weight = self.context_weight.to(self.device)
def all_to_device(self, gpu_id):
""" move all of the parameters to a single GPU """
self.device = torch.device("cuda:%d" % gpu_id)
self.set_device(gpu_id)
self.u_embeddings = self.u_embeddings.cuda(gpu_id)
self.v_embeddings = self.v_embeddings.cuda(gpu_id)
self.state_sum_u = self.state_sum_u.to(self.device)
self.state_sum_v = self.state_sum_v.to(self.device)
def fast_sigmoid(self, score):
""" do fast sigmoid by looking up in a pre-defined table """
idx = torch.floor((score + 6.01) / 0.01).long()
return self.lookup_table[idx]
def fast_logsigmoid(self, score):
""" do fast logsigmoid by looking up in a pre-defined table """
idx = torch.floor((score + 6.01) / 0.01).long()
return self.logsigmoid_table[idx]
def fast_learn(self, batch_walks, neg_nodes=None):
""" Learn a batch of random walks in a fast way. It has the following features:
1. It calculating the gradients directly without the forward operation.
2. It does sigmoid by a looking up table.
Specifically, for each positive/negative node pair (i,j), the updating procedure is as following:
score = self.fast_sigmoid(u_embedding[i].dot(v_embedding[j]))
# label = 1 for positive samples; label = 0 for negative samples.
u_embedding[i] += (label - score) * v_embedding[j]
v_embedding[i] += (label - score) * u_embedding[j]
Parameters
----------
batch_walks list : a list of node sequnces
lr float : current learning rate
neg_nodes torch.LongTensor : a long tensor of sampled true negative nodes. If neg_nodes is None,
then do negative sampling randomly from the nodes in batch_walks as an alternative.
Usage example
-------------
batch_walks = [torch.LongTensor([1,2,3,4]),
torch.LongTensor([2,3,4,2])])
lr = 0.01
neg_nodes = None
"""
lr = self.lr
# [batch_size, walk_length]
if isinstance(batch_walks, list):
nodes = torch.stack(batch_walks)
elif isinstance(batch_walks, torch.LongTensor):
nodes = batch_walks
if self.only_gpu:
nodes = nodes.to(self.device)
if neg_nodes is not None:
neg_nodes = neg_nodes.to(self.device)
emb_u = self.u_embeddings(nodes).view(-1, self.emb_dimension).to(self.device)
emb_v = self.v_embeddings(nodes).view(-1, self.emb_dimension).to(self.device)
## Postive
bs = len(batch_walks)
if bs < self.batch_size:
index_emb_posu, index_emb_posv = init_emb2pos_index(
self.walk_length,
self.window_size,
bs)
index_emb_posu = index_emb_posu.to(self.device)
index_emb_posv = index_emb_posv.to(self.device)
else:
index_emb_posu = self.index_emb_posu
index_emb_posv = self.index_emb_posv
# num_pos: the number of positive node pairs generated by a single walk sequence
# [batch_size * num_pos, dim]
emb_pos_u = torch.index_select(emb_u, 0, index_emb_posu)
emb_pos_v = torch.index_select(emb_v, 0, index_emb_posv)
pos_score = torch.sum(torch.mul(emb_pos_u, emb_pos_v), dim=1)
pos_score = torch.clamp(pos_score, max=6, min=-6)
# [batch_size * num_pos, 1]
score = (1 - self.fast_sigmoid(pos_score)).unsqueeze(1)
if self.record_loss:
self.loss.append(torch.mean(self.fast_logsigmoid(pos_score)).item())
# [batch_size * num_pos, dim]
if self.lap_norm > 0:
grad_u_pos = score * emb_pos_v + self.lap_norm * (emb_pos_v - emb_pos_u)
grad_v_pos = score * emb_pos_u + self.lap_norm * (emb_pos_u - emb_pos_v)
else:
grad_u_pos = score * emb_pos_v
grad_v_pos = score * emb_pos_u
if self.use_context_weight:
if bs < self.batch_size:
context_weight = init_weight(
self.walk_length,
self.window_size,
bs).to(self.device)
else:
context_weight = self.context_weight
grad_u_pos *= context_weight
grad_v_pos *= context_weight
# [batch_size * walk_length, dim]
if bs < self.batch_size:
grad_u, grad_v = init_empty_grad(
self.emb_dimension,
self.walk_length,
bs)
grad_u = grad_u.to(self.device)
grad_v = grad_v.to(self.device)
else:
self.grad_u = self.grad_u.to(self.device)
self.grad_u.zero_()
self.grad_v = self.grad_v.to(self.device)
self.grad_v.zero_()
grad_u = self.grad_u
grad_v = self.grad_v
grad_u.index_add_(0, index_emb_posu, grad_u_pos)
grad_v.index_add_(0, index_emb_posv, grad_v_pos)
## Negative
if bs < self.batch_size:
index_emb_negu, index_emb_negv = init_emb2neg_index(
self.walk_length, self.window_size, self.negative, bs)
index_emb_negu = index_emb_negu.to(self.device)
index_emb_negv = index_emb_negv.to(self.device)
else:
index_emb_negu = self.index_emb_negu
index_emb_negv = self.index_emb_negv
emb_neg_u = torch.index_select(emb_u, 0, index_emb_negu)
if neg_nodes is None:
emb_neg_v = torch.index_select(emb_v, 0, index_emb_negv)
else:
emb_neg_v = self.v_embeddings.weight[neg_nodes].to(self.device)
# [batch_size * walk_length * negative, dim]
neg_score = torch.sum(torch.mul(emb_neg_u, emb_neg_v), dim=1)
neg_score = torch.clamp(neg_score, max=6, min=-6)
# [batch_size * walk_length * negative, 1]
score = - self.fast_sigmoid(neg_score).unsqueeze(1)
if self.record_loss:
self.loss.append(self.negative * self.neg_weight * torch.mean(self.fast_logsigmoid(-neg_score)).item())
grad_u_neg = self.neg_weight * score * emb_neg_v
grad_v_neg = self.neg_weight * score * emb_neg_u
grad_u.index_add_(0, index_emb_negu, grad_u_neg)
if neg_nodes is None:
grad_v.index_add_(0, index_emb_negv, grad_v_neg)
## Update
nodes = nodes.view(-1)
# use adam optimizer
grad_u = adam(grad_u, self.state_sum_u, nodes, lr, self.device, self.only_gpu)
grad_v = adam(grad_v, self.state_sum_v, nodes, lr, self.device, self.only_gpu)
if neg_nodes is not None:
grad_v_neg = adam(grad_v_neg, self.state_sum_v, neg_nodes, lr, self.device, self.only_gpu)
if self.mixed_train:
grad_u = grad_u.cpu()
grad_v = grad_v.cpu()
if neg_nodes is not None:
grad_v_neg = grad_v_neg.cpu()
else:
grad_v_neg = None
if self.async_update:
grad_u.share_memory_()
grad_v.share_memory_()
nodes.share_memory_()
if neg_nodes is not None:
neg_nodes.share_memory_()
grad_v_neg.share_memory_()
self.async_q.put((grad_u, grad_v, grad_v_neg, nodes, neg_nodes))
if not self.async_update:
self.u_embeddings.weight.data.index_add_(0, nodes.view(-1), grad_u)
self.v_embeddings.weight.data.index_add_(0, nodes.view(-1), grad_v)
if neg_nodes is not None:
self.v_embeddings.weight.data.index_add_(0, neg_nodes.view(-1), grad_v_neg)
return
def forward(self, pos_u, pos_v, neg_v):
''' Do forward and backward. It is designed for future use. '''
emb_u = self.u_embeddings(pos_u)
emb_v = self.v_embeddings(pos_v)
emb_neg_v = self.v_embeddings(neg_v)
score = torch.sum(torch.mul(emb_u, emb_v), dim=1)
score = torch.clamp(score, max=6, min=-6)
score = -F.logsigmoid(score)
neg_score = torch.bmm(emb_neg_v, emb_u.unsqueeze(2)).squeeze()
neg_score = torch.clamp(neg_score, max=6, min=-6)
neg_score = -torch.sum(F.logsigmoid(-neg_score), dim=1)
#return torch.mean(score + neg_score)
return torch.sum(score), torch.sum(neg_score)
def save_embedding(self, dataset, file_name):
""" Write embedding to local file. Only used when node ids are numbers.
Parameter
---------
dataset DeepwalkDataset : the dataset
file_name str : the file name
"""
embedding = self.u_embeddings.weight.cpu().data.numpy()
if self.norm:
embedding /= np.sqrt(np.sum(embedding * embedding, 1)).reshape(-1, 1)
np.save(file_name, embedding)
def save_embedding_pt(self, dataset, file_name):
""" For ogb leaderboard.
"""
try:
max_node_id = max(dataset.node2id.keys())
if max_node_id + 1 != self.emb_size:
print("WARNING: The node ids are not serial.")
embedding = torch.zeros(max_node_id + 1, self.emb_dimension)
index = torch.LongTensor(list(map(lambda id: dataset.id2node[id], list(range(self.emb_size)))))
embedding.index_add_(0, index, self.u_embeddings.weight.cpu().data)
if self.norm:
embedding /= torch.sqrt(torch.sum(embedding.mul(embedding), 1) + 1e-6).unsqueeze(1)
torch.save(embedding, file_name)
except:
self.save_embedding_pt_dgl_graph(dataset, file_name)
def save_embedding_pt_dgl_graph(self, dataset, file_name):
""" For ogb leaderboard """
embedding = torch.zeros_like(self.u_embeddings.weight.cpu().data)
valid_seeds = torch.LongTensor(dataset.valid_seeds)
valid_embedding = self.u_embeddings.weight.cpu().data.index_select(0,
valid_seeds)
embedding.index_add_(0, valid_seeds, self.u_embeddings.weight.cpu().data)
if self.norm:
embedding /= torch.sqrt(torch.sum(embedding.mul(embedding), 1) + 1e-6).unsqueeze(1)
torch.save(embedding, file_name)
def save_embedding_txt(self, dataset, file_name):
""" Write embedding to local file. For future use.
Parameter
---------
dataset DeepwalkDataset : the dataset
file_name str : the file name
"""
embedding = self.u_embeddings.weight.cpu().data.numpy()
if self.norm:
embedding /= np.sqrt(np.sum(embedding * embedding, 1)).reshape(-1, 1)
with open(file_name, 'w') as f:
f.write('%d %d\n' % (self.emb_size, self.emb_dimension))
for wid in range(self.emb_size):
e = ' '.join(map(lambda x: str(x), embedding[wid]))
f.write('%s %s\n' % (str(dataset.id2node[wid]), e))
\ No newline at end of file
examples/pytorch/deepwalk/reading_data.py deleted 100644 → 0
View file @ 22167f72
import os
import numpy as np
import scipy.sparse as sp
import pickle
import torch
from torch.utils.data import DataLoader
from dgl.data.utils import download, _get_dgl_url, get_download_dir, extract_archive
import random
import time
import dgl
from utils import shuffle_walks
#np.random.seed(3141592653)
def ReadTxtNet(file_path="", undirected=True):
""" Read the txt network file.
Notations: The network is unweighted.
Parameters
----------
file_path str : path of network file
undirected bool : whether the edges are undirected
Return
------
net dict : a dict recording the connections in the graph
node2id dict : a dict mapping the nodes to their embedding indices
id2node dict : a dict mapping nodes embedding indices to the nodes
"""
if file_path == 'youtube' or file_path == 'blog':
name = file_path
dir = get_download_dir()
zip_file_path='{}/{}.zip'.format(dir, name)
download(_get_dgl_url(os.path.join('dataset/DeepWalk/', '{}.zip'.format(file_path))), path=zip_file_path)
extract_archive(zip_file_path,
'{}/{}'.format(dir, name))
file_path = "{}/{}/{}-net.txt".format(dir, name, name)
node2id = {}
id2node = {}
cid = 0
src = []
dst = []
net = {}
with open(file_path, "r") as f:
for line in f.readlines():
n1, n2 = list(map(int, line.strip().split(" ")[:2]))
if n1 not in node2id:
node2id[n1] = cid
id2node[cid] = n1
cid += 1
if n2 not in node2id:
node2id[n2] = cid
id2node[cid] = n2
cid += 1
n1 = node2id[n1]
n2 = node2id[n2]
if n1 not in net:
net[n1] = {n2: 1}
src.append(n1)
dst.append(n2)
elif n2 not in net[n1]:
net[n1][n2] = 1
src.append(n1)
dst.append(n2)
if undirected:
if n2 not in net:
net[n2] = {n1: 1}
src.append(n2)
dst.append(n1)
elif n1 not in net[n2]:
net[n2][n1] = 1
src.append(n2)
dst.append(n1)
print("node num: %d" % len(net))
print("edge num: %d" % len(src))
assert max(net.keys()) == len(net) - 1, "error reading net, quit"
sm = sp.coo_matrix(
(np.ones(len(src)), (src, dst)),
dtype=np.float32)
return net, node2id, id2node, sm
def net2graph(net_sm):
""" Transform the network to DGL graph
Return
------
G DGLGraph : graph by DGL
"""
start = time.time()
G = dgl.DGLGraph(net_sm)
end = time.time()
t = end - start
print("Building DGLGraph in %.2fs" % t)
return G
class DeepwalkDataset:
def __init__(self,
net_file,
map_file,
walk_length=80,
window_size=5,
num_walks=10,
batch_size=32,
negative=5,
gpus=[0],
fast_neg=True,
):
""" This class has the following functions:
1. Transform the txt network file into DGL graph;
2. Generate random walk sequences for the trainer;
3. Provide the negative table if the user hopes to sample negative
nodes according to nodes' degrees;
Parameter
---------
net_file str : path of the txt network file
walk_length int : number of nodes in a sequence
window_size int : context window size
num_walks int : number of walks for each node
batch_size int : number of node sequences in each batch
negative int : negative samples for each positve node pair
fast_neg bool : whether do negative sampling inside a batch
"""
self.walk_length = walk_length
self.window_size = window_size
self.num_walks = num_walks
self.batch_size = batch_size
self.negative = negative
self.num_procs = len(gpus)
self.fast_neg = fast_neg
self.net, self.node2id, self.id2node, self.sm = ReadTxtNet(net_file)
self.save_mapping(map_file)
self.G = net2graph(self.sm)
# random walk seeds
start = time.time()
seeds = torch.cat([torch.LongTensor(self.G.nodes())] * num_walks)
self.seeds = torch.split(shuffle_walks(seeds), int(np.ceil(len(self.net) * self.num_walks / self.num_procs)), 0)
end = time.time()
t = end - start
print("%d seeds in %.2fs" % (len(seeds), t))
# negative table for true negative sampling
if not fast_neg:
node_degree = np.array(list(map(lambda x: len(self.net[x]), self.net.keys())))
node_degree = np.power(node_degree, 0.75)
node_degree /= np.sum(node_degree)
node_degree = np.array(node_degree * 1e8, dtype=np.int)
self.neg_table = []
for idx, node in enumerate(self.net.keys()):
self.neg_table += [node] * node_degree[idx]
self.neg_table_size = len(self.neg_table)
self.neg_table = np.array(self.neg_table, dtype=np.long)
del node_degree
def create_sampler(self, gpu_id):
""" Still in construction...
Several mode:
1. do true negative sampling.
1.1 from random walk sequence
1.2 from node degree distribution
return the sampled node ids
2. do false negative sampling from random walk sequence
save GPU, faster
return the node indices in the sequences
"""
return DeepwalkSampler(self.G, self.seeds[gpu_id], self.walk_length)
def save_mapping(self, map_file):
with open(map_file, "wb") as f:
pickle.dump(self.node2id, f)
class DeepwalkSampler(object):
def __init__(self, G, seeds, walk_length):
self.G = G
self.seeds = seeds
self.walk_length = walk_length
def sample(self, seeds):
walks, _ = dgl.sampling.random_walk(self.G, seeds,
length=self.walk_length-1)
return walks
examples/pytorch/deepwalk/utils.py deleted 100644 → 0
View file @ 22167f72
import torch
from functools import wraps
from _thread import start_new_thread
import torch.multiprocessing as mp
def thread_wrapped_func(func):
"""Wrapped func for torch.multiprocessing.Process.
With this wrapper we can use OMP threads in subprocesses
otherwise, OMP_NUM_THREADS=1 is mandatory.
How to use:
@thread_wrapped_func
def func_to_wrap(args ...):
"""
@wraps(func)
def decorated_function(*args, **kwargs):
queue = mp.Queue()
def _queue_result():
exception, trace, res = None, None, None
try:
res = func(*args, **kwargs)
except Exception as e:
exception = e
trace = traceback.format_exc()
queue.put((res, exception, trace))
start_new_thread(_queue_result, ())
result, exception, trace = queue.get()
if exception is None:
return result
else:
assert isinstance(exception, Exception)
raise exception.__class__(trace)
return decorated_function
def shuffle_walks(walks):
seeds = torch.randperm(walks.size()[0])
return walks[seeds]
def sum_up_params(model):
""" Count the model parameters """
n = []
n.append(model.u_embeddings.weight.cpu().data.numel() * 2)
n.append(model.lookup_table.cpu().numel())
n.append(model.index_emb_posu.cpu().numel() * 2)
n.append(model.grad_u.cpu().numel() * 2)
try:
n.append(model.index_emb_negu.cpu().numel() * 2)
except:
pass
try:
n.append(model.state_sum_u.cpu().numel() * 2)
except:
pass
try:
n.append(model.grad_avg.cpu().numel())
except:
pass
try:
n.append(model.context_weight.cpu().numel())
except:
pass
print("#params " + str(sum(n)))
exit()
\ No newline at end of file
examples/pytorch/ogb/deepwalk/README.md
View file @ 3611a66e
## How to load ogb data # DeepWalk Example
- Paper link: [here](https://arxiv.org/pdf/1403.6652.pdf)
- Other implementation: [gensim](https://github.com/phanein/deepwalk), [deepwalk-c](https://github.com/xgfs/deepwalk-c)
The implementation includes multi-processing training with CPU and mixed training with CPU and multi-GPU.
## Dependencies
- PyTorch 1.5.0+
## Tested version
- PyTorch 1.5.0
- DGL 0.5.0
## Input data
Currently, we support two builtin dataset: youtube and blog. Use --data\_file youtube to select youtube dataset and --data\_file blog to select blog dataset.
The data is avaliable at https://data.dgl.ai/dataset/DeepWalk/youtube.zip and https://data.dgl.ai/dataset/DeepWalk/blog.zip
The youtube.zip includes both youtube-net.txt, youtube-vocab.txt and youtube-label.txt; The blog.zip includes both blog-net.txt, blog-vocab.txt and blog-label.txt.
For other datasets please pass the full path to the trainer through --data\_file and the format of a network file should follow:
```
1(node id) 2(node id)
1 3
1 4
2 4
...
```
### How to run the code
To run the code:
```
python3 deepwalk.py --data_file youtube --output_emb_file emb.txt --mix --lr 0.2 --gpus 0 1 2 3 --batch_size 100 --negative 5
```
### How to save the embedding
By default the trained embedding is saved under --output\_embe\_file FILE\_NAME as a numpy object.
To save the trained embedding in raw format(txt format), please use --save\_in\_txt argument.
### Evaluation
To evalutate embedding on multi-label classification, please refer to [here](https://github.com/ShawXh/Evaluate-Embedding)
YouTube (1M nodes).
| Implementation | Macro-F1 (%) <br> 1% &emsp;&emsp; 3% &emsp;&emsp; 5% &emsp;&emsp; 7% &emsp;&emsp; 9% | Micro-F1 (%) <br> 1% &emsp;&emsp; 3% &emsp;&emsp; 5% &emsp;&emsp; 7% &emsp;&emsp; 9% |
|----|----|----|
| gensim.word2vec(hs) | 28.73 &emsp; 32.51 &emsp; 33.67 &emsp; 34.28 &emsp; 34.79 | 35.73 &emsp; 38.34 &emsp; 39.37 &emsp; 40.08 &emsp; 40.77 |
| gensim.word2vec(ns) | 28.18 &emsp; 32.25 &emsp; 33.56 &emsp; 34.60 &emsp; 35.22 | 35.35 &emsp; 37.69 &emsp; 38.08 &emsp; 40.24 &emsp; 41.09 |
| ours | 24.58 &emsp; 31.23 &emsp; 33.97 &emsp; 35.41 &emsp; 36.48 | 38.93 &emsp; 43.17 &emsp; 44.73 &emsp; 45.42 &emsp; 45.92 |
The comparison between running time is shown as below, where the numbers in the brackets denote time used on random-walk.
| Implementation | gensim.word2vec(hs) | gensim.word2vec(ns) | Ours |
|----|----|----|----|
| Time (s) | 27119.6(1759.8) | 10580.3(1704.3) | 428.89 |
Parameters.
- walk_length = 80, number_walks = 10, window_size = 5
- Ours: 4GPU (Tesla V100), lr = 0.2, batchs_size = 128, neg_weight = 5, negative = 1, num_thread = 4
- Others: workers = 8, negative = 5
Speeding-up with mixed CPU & multi-GPU. The used parameters are the same as above.
| #GPUs | 1 | 2 | 4 |
|----------|-------|-------|-------|
| Time (s) |1419.64| 952.04|428.89 |
## OGB Dataset
### How to load ogb data
To load ogb dataset, you need to run the following command, which will output a network file, ogbl-collab-net.txt: To load ogb dataset, you need to run the following command, which will output a network file, ogbl-collab-net.txt:
``` ```
python3 load_dataset.py --name ogbl-collab python3 load_dataset.py --name ogbl-collab
...@@ -9,10 +76,10 @@ python3 deepwalk --ogbl_name xxx --load_from_ogbl ...@@ -9,10 +76,10 @@ python3 deepwalk --ogbl_name xxx --load_from_ogbl
``` ```
However, ogb.linkproppred might not be compatible with mixed training with multi-gpu. If you want to do mixed training, please use no more than 1 gpu by the command above. However, ogb.linkproppred might not be compatible with mixed training with multi-gpu. If you want to do mixed training, please use no more than 1 gpu by the command above.
## Evaluation ### Evaluation
For evaluatation we follow the code mlp.py provided by ogb [here](https://github.com/snap-stanford/ogb/blob/master/examples/linkproppred/collab/mlp.py). For evaluatation we follow the code mlp.py provided by ogb [here](https://github.com/snap-stanford/ogb/blob/master/examples/linkproppred/collab/mlp.py).
## Used config ### Used config
ogbl-collab ogbl-collab
``` ```
python3 deepwalk.py --ogbl_name ogbl-collab --load_from_ogbl --save_in_pt --output_emb_file collab-embedding.pt --num_walks 50 --window_size 2 --walk_length 40 --lr 0.1 --negative 1 --neg_weight 1 --lap_norm 0.01 --mix --gpus 0 --num_threads 4 --print_interval 2000 --print_loss --batch_size 128 --use_context_weight python3 deepwalk.py --ogbl_name ogbl-collab --load_from_ogbl --save_in_pt --output_emb_file collab-embedding.pt --num_walks 50 --window_size 2 --walk_length 40 --lr 0.1 --negative 1 --neg_weight 1 --lap_norm 0.01 --mix --gpus 0 --num_threads 4 --print_interval 2000 --print_loss --batch_size 128 --use_context_weight
...@@ -43,7 +110,7 @@ cp embedding_pt_file_path ./ ...@@ -43,7 +110,7 @@ cp embedding_pt_file_path ./
python3 mlp.py --device 2 --runs 10 --use_node_embedding python3 mlp.py --device 2 --runs 10 --use_node_embedding
``` ```
## Result ### OGBL Resuls
ogbl-collab ogbl-collab
<br>#params: 61258346(model) + 131841(mlp) = 61390187 <br>#params: 61258346(model) + 131841(mlp) = 61390187
<br>Hits@10 <br>Hits@10
...@@ -106,3 +173,4 @@ ogbl-collab ...@@ -106,3 +173,4 @@ ogbl-collab
<br>&emsp;Highest Valid: 0.8271 ± 0.0003 <br>&emsp;Highest Valid: 0.8271 ± 0.0003
<br>&emsp;&emsp;Final Train: 0.8991 ± 0.0007 <br>&emsp;&emsp;Final Train: 0.8991 ± 0.0007
<br>&emsp;&emsp;Final Test: 0.8284 ± 0.0005 <br>&emsp;&emsp;Final Test: 0.8284 ± 0.0005
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