From 93ecf6ad6fd1cc749e6a209a9ca32e1812fed3b5 Mon Sep 17 00:00:00 2001 From: e-yi Date: Wed, 16 Oct 2019 16:06:59 +0800 Subject: [PATCH] add demo usage --- README.md | 62 +- demo_data.csv | 37885 ++++++++++++++++++++++++++++++++++++++++++++++++ model.py | 50 +- walker.py | 36 +- 4 files changed, 38008 insertions(+), 25 deletions(-) create mode 100644 demo_data.csv diff --git a/README.md b/README.md index 6101675..0c51deb 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,64 @@ # HIN2vec_pytorch a pytorch implementation of [HIN2vec](https://github.com/csiesheep/hin2vec) -in progress \ No newline at end of file + +>*HIN2Vec* learns distributed representations of nodes in heterogeneous information networks (HINs) by capturing the distiguishing metapath relationships between nodes. +Please refer the paper [here](https://dl.acm.org/citation.cfm?doid=3132847.3132953). + + +### Usage +create your own edge.csv refer to `demo_data.csv` + +create a main.py in the project folder, copy the following code and modify it. +```python + import torch + import pandas as pd + import torch.nn as nn + import torch.optim as optim + from torch.utils.data import DataLoader + + from walker import load_a_HIN_from_pandas + from model import NSTrainSet, HIN2vec, train + + # set parameters + window = 4 + walk_length = 300 + embed_size = 100 + neg = 5 + device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu") + print(f'device = {device}') + + # set dataset [PLEASE USE YOUR OWN DATASET TO REPLACE THIS] + demo_edge = pd.read_csv('./demo_data.csv', index_col=0) + + edges = [demo_edge] + + print('finish loading edges') + + # init HIN + hin = load_a_HIN_from_pandas(edges) + hin.window = window + + dataset = NSTrainSet(hin.sample(walk_length), hin.path_size, neg=neg) + + hin2vec = HIN2vec(hin.node_size, hin.path_size, embed_size) + + # set parameters + n_epoch = 10 + batch_size = 20 + log_interval = 200 + + data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True) + optimizer = optim.Adam(hin2vec.parameters()) # 原作者使用的是SGD？ 这里使用Adam + loss_function = nn.BCELoss() + + for epoch in range(n_epoch): + train(log_interval, hin2vec, device, data_loader, optimizer, loss_function, epoch) + + torch.save(hin2vec, 'hin2vec.pt') + + hin2vec.output_embeddings('start_node_embed.txt', 'end_node_embed.txt', 'path_embed.txt') + +``` + +Some more details could be found in [the original repo](https://github.com/csiesheep/hin2vec) diff --git a/demo_data.csv b/demo_data.csv new file mode 100644 index 0000000..797b15b --- /dev/null +++ b/demo_data.csv @@ -0,0 +1,37885 @@ +,dest_node,source_node,weight,source_class,dest_class,edge_class +0,OMIM102300,OMIM102100,0.10395,Di,Di,Di-Di +1,OMIM102400,OMIM102100,0.29165,Di,Di,Di-Di +2,OMIM102400,OMIM102300,0.18205,Di,Di,Di-Di +3,OMIM102500,OMIM102100,0.28702,Di,Di,Di-Di +4,OMIM102500,OMIM102300,0.10492,Di,Di,Di-Di +5,OMIM102500,OMIM102400,0.31504,Di,Di,Di-Di +6,OMIM103100,OMIM102100,0.14587,Di,Di,Di-Di 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train(log_interval, model, device, train_loader: DataLoader, optimizer, loss_function, epoch): model.train() @@ -99,36 +98,43 @@ def __len__(self): import pandas as pd import torch.optim as optim - from utils import load_a_HIN_from_pandas, thFilter + from walker import load_a_HIN_from_pandas - # device = 'cpu' + # set parameters + window = 4 + walk_length = 300 + embed_size = 100 + neg = 5 device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu") print(f'device = {device}') - edgeDiDr = pd.read_csv('G:/_projects/Lab/edge/edgeDiDr.csv', index_col=0) - edgeDiSim = pd.read_csv('G:/_projects/Lab/edge/edgeDiSim.csv', index_col=0) - edgeDrSim = pd.read_csv('G:/_projects/Lab/edge/edgeDrSim.csv', index_col=0) + # set dataset [PLEASE USE YOUR OWN DATASET TO REPLACE THIS] + demo_edge = pd.read_csv('./demo_data.csv', index_col=0) - edgeDiSim_filtered = thFilter(edgeDiSim, th=0.7) - edgeDrSim_filtered = thFilter(edgeDrSim, th=0.8) + edges = [demo_edge] print('finish loading edges') - hin = load_a_HIN_from_pandas([edgeDiDr, edgeDiSim_filtered, edgeDrSim_filtered]) - hin.window = 4 - - dataset = NSTrainSet(hin.sample(300), hin.path_size, neg=5) + # init HIN + hin = load_a_HIN_from_pandas(edges) + hin.window = window - hin2vec = HIN2vec(hin.node_size, hin.path_size, 100) + dataset = NSTrainSet(hin.sample(walk_length), hin.path_size, neg=neg) - data_loader = DataLoader(dataset, batch_size=5, shuffle=True) - optimizer = optim.Adam(hin2vec.parameters()) # 原作者使用的是SGD？ - loss_function = nn.BCELoss() + hin2vec = HIN2vec(hin.node_size, hin.path_size, embed_size) - n_epoch = 5 + # set parameters + n_epoch = 10 + batch_size = 20 log_interval = 200 + data_loader = DataLoader(dataset, batch_size=batch_size, shuffle=True) + optimizer = optim.Adam(hin2vec.parameters()) # 原作者使用的是SGD？ 这里使用Adam + loss_function = nn.BCELoss() + for epoch in range(n_epoch): train(log_interval, hin2vec, device, data_loader, optimizer, loss_function, epoch) torch.save(hin2vec, 'hin2vec.pt') + + hin2vec.output_embeddings('start_node_embed.txt', 'end_node_embed.txt', 'path_embed.txt') diff --git a/walker.py b/walker.py index 1c0a866..a1cf533 100644 --- a/walker.py +++ b/walker.py @@ -1,6 +1,7 @@ -from itertools import product import random +import pandas as pd import networkx as nx +from itertools import product from collections import defaultdict @@ -104,6 +105,38 @@ def print_statistics(self): print(f'size = {self.node_size}') +def load_a_HIN_from_pandas(edges, print_graph=False): + """ + 单向边：edges = list(pd.df) + """ + + def reverse(df): + """ + reverse source & dest + """ + df = df.rename({'source_node': 'dest_node', 'dest_node': 'source_node', + 'source_class': 'dest_class', 'dest_class': 'source_class'}, + axis=1) + # reverse edge_class + df.edge_class = df.edge_class.map(lambda x: '-'.join(reversed(x.split('-')))) + return df + + print('load graph from edges...') + g = HIN() + if isinstance(edges, list): + edges = pd.concat(edges, sort=False) + edges = edges.append(reverse(edges), sort=False, ignore_index=True) + + for index, row in edges.iterrows(): + g.add_edge(row['source_node'], row['source_class'], + row['dest_node'], row['dest_class'], row['edge_class'], + row['weight']) + if print_graph: + g.print_statistics() + print('finish loading graph!') + return g + + if __name__ == '__main__': hin = HIN() hin.window = 4 @@ -131,4 +164,3 @@ def print_statistics(self): print(hin.graph.edges) - # print(list(format_data(hin.sample(3), hin.path_size)))