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