[Example] Experimental results of deepwalk on ogb datasets (#1729)

* ogb-deepwalk

* ?

* ?

* remove pyg

examples/pytorch/ogb/deepwalk/README.md

@@ -3,6 +3,11 @@ To load ogb dataset, you need to run the following command, which will output a
 ```
 python3 load_dataset.py --name ogbl-collab
 ```
+Or you can run the code directly with:
+```
+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.
 
 ## 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).
@@ -10,7 +15,7 @@ For evaluatation we follow the code mlp.py provided by ogb [here](https://github
 ## Used config
 ogbl-collab
 ```
-python3 deepwalk.py --data_file ogbl-collab-net.txt --save_in_pt --output_emb_file embedding.pt --num_walks 50 --window_size 20 --walk_length 40 --lr 0.1 --negative 1 --neg_weight 1 --lap_norm 0.005 --mix --adam --gpus 0 1 2 3 --num_threads 4 --print_interval 2000 --print_loss --batch_size 32
+python3 deepwalk.py --ogbl_name ogbl-collab --load_from_ogbl --save_in_pt --output_emb_file embedding.pt --num_walks 50 --window_size 20 --walk_length 40 --lr 0.1 --negative 1 --neg_weight 1 --lap_norm 0.005 --mix --adam --gpus 0 --num_threads 4 --print_interval 2000 --print_loss --batch_size 32
 cd ./ogb/blob/master/examples/linkproppred/collab/
 cp embedding_pt_file_path ./
 python3 mlp.py --device 0 --runs 10 --use_node_embedding
@@ -18,28 +23,29 @@ python3 mlp.py --device 0 --runs 10 --use_node_embedding
 
 ogbl-ddi
 ```
-python3 deepwalk.py --data_file ogbl-ddi-net.txt --save_in_pt --output_emb_file ddi-embedding.pt --num_walks 50 --window_size 2 --walk_length 80 --lr 0.1 --negative 1 --neg_weight 1 --lap_norm 0.05 --only_gpu --adam --gpus 0 --num_threads 4 --print_interval 2000 --print_loss --batch_size 16 --use_context_weight
+python3 deepwalk.py --ogbl_name ogbl-ddi --load_from_ogbl --save_in_pt --output_emb_file ddi-embedding.pt --num_walks 50 --window_size 2 --walk_length 80 --lr 0.1 --negative 1 --neg_weight 1 --lap_norm 0.05 --only_gpu --adam --gpus 0 --num_threads 4 --print_interval 2000 --print_loss --batch_size 16 --use_context_weight
 cd ./ogb/blob/master/examples/linkproppred/ddi/
 cp embedding_pt_file_path ./
-python3 mlp.py --device 0 --runs 5
+python3 mlp.py --device 0 --runs 10 --epochs 100
 ```
 
 ogbl-ppa
 ```
-python3 deepwalk.py --data_file ogbl-ppa-net.txt --save_in_pt --output_emb_file ppa-embedding.pt --negative 1 --neg_weight 1 --batch_size 64 --print_interval 2000 --print_loss --window_size 2 --num_walks 30 --walk_length 80 --lr 0.1 --lap_norm 0.02 --adam --mix --gpus 0 1 --use_context_weight --num_threads 4
+python3 deepwalk.py --ogbl_name ogbl-ppa --load_from_ogbl --save_in_pt --output_emb_file ppa-embedding.pt --negative 1 --neg_weight 1 --batch_size 64 --print_interval 2000 --print_loss --window_size 2 --num_walks 30 --walk_length 80 --lr 0.1 --lap_norm 0.02 --adam --mix --gpus 0 --use_context_weight --num_threads 4
 cp embedding_pt_file_path ./
 python3 mlp.py --device 2 --runs 10
 ```
 
 ogbl-citation
 ```
-python3 deepwalk.py --data_file ogbl-citation-net.txt --save_in_pt --output_emb_file embedding.pt --window_size 2 --num_walks 10 --negative 1 --neg_weight 1 --walk_length 80 --batch_size 128 --print_loss --print_interval 1000 --mix --adam --gpus 0 1 2 3 --use_context_weight --num_threads 4 --lap_norm 0.05 --lr 0.1
+python3 deepwalk.py --ogbl_name ogbl-citation --load_from_ogbl --save_in_pt --output_emb_file embedding.pt --window_size 2 --num_walks 10 --negative 1 --neg_weight 1 --walk_length 80 --batch_size 128 --print_loss --print_interval 1000 --mix --adam --gpus 0 --use_context_weight --num_threads 4 --lap_norm 0.05 --lr 0.1
 cp embedding_pt_file_path ./
-python3 mlp.py --device 2 --runs 5 --use_node_embedding
+python3 mlp.py --device 2 --runs 10 --use_node_embedding
 ```
 
-## Score
+## Result
 ogbl-collab
+<br>#params: 61258346(model) + 131841(mlp) = 61390187
 <br>Hits@10
 <br>&emsp;Highest Train: 74.83 ± 4.79
 <br>&emsp;Highest Valid: 40.03 ± 2.98
@@ -57,24 +63,26 @@ ogbl-collab
 <br>&emsp;&emsp;Final Test: 56.88 ± 0.37
 
 <br>obgl-ddi
-<br>Hits@10
-<br>&emsp;Highest Train: 35.05 ± 3.68
-<br>&emsp;Highest Valid: 31.72 ± 3.52
-<br>&emsp;&emsp;Final Train: 35.05 ± 3.68
-<br>&emsp;&emsp;Final Test: 12.68 ± 3.19
-<br>Hits@20
-<br>&emsp;Highest Train: 44.85 ± 1.26
-<br>&emsp;Highest Valid: 41.20 ± 1.41
-<br>&emsp;&emsp;Final Train: 44.85 ± 1.26
-<br>&emsp;&emsp;Final Test: 21.69 ± 3.14
-<br>Hits@30
-<br>&emsp;Highest Train: 52.28 ± 1.21
-<br>&emsp;Highest Valid: 48.49 ± 1.09
-<br>&emsp;&emsp;Final Train: 52.28 ± 1.21
-<br>&emsp;&emsp;Final Test: 29.13 ± 3.46
+<br>#params: 1444840(model) + 99073(mlp) = 1543913
+<br>&emsp;Hits@10
+<br>&emsp;Highest Train: 36.09 ± 2.47
+<br>&emsp;Highest Valid: 32.83 ± 2.30
+<br>&emsp;&emsp;Final Train: 36.06 ± 2.45
+<br>&emsp;&emsp;Final Test: 11.76 ± 3.91
+<br>&emsp;Hits@20
+<br>&emsp;Highest Train: 45.59 ± 2.45
+<br>&emsp;Highest Valid: 42.00 ± 2.36
+<br>&emsp;&emsp;Final Train: 45.56 ± 2.50
+<br>&emsp;&emsp;Final Test: 22.46 ± 2.90
+<br>&emsp;Hits@30
+<br>&emsp;Highest Train: 51.58 ± 2.41
+<br>&emsp;Highest Valid: 47.82 ± 2.19
+<br>&emsp;&emsp;Final Train: 51.58 ± 2.42
+<br>&emsp;&emsp;Final Test: 30.17 ± 3.39
 
 
 <br>ogbl-ppa
+<br>#params: 150024820(model) + 113921(mlp) = 150138741
 <br>Hits@10
 <br>&emsp;Highest Train: 3.58 ± 0.90
 <br>&emsp;Highest Valid: 2.88 ± 0.76
@@ -92,8 +100,9 @@ ogbl-collab
 <br>&emsp;&emsp;Final Test: 23.02 ± 1.63
 
 <br>ogbl-citation
+<br>#params: 757811178(model) + 131841(mlp) = 757943019
 <br>MRR
-<br>&emsp;Highest Train: 0.8796 ± 0.0007
-<br>&emsp;Highest Valid: 0.8141 ± 0.0007
-<br>&emsp;&emsp;Final Train: 0.8793 ± 0.0008
-<br>&emsp;&emsp;Final Test: 0.8159 ± 0.0006
+<br>&emsp;Highest Train: 0.8797 ± 0.0007
+<br>&emsp;Highest Valid: 0.8139 ± 0.0005
+<br>&emsp;&emsp;Final Train: 0.8792 ± 0.0008
+<br>&emsp;&emsp;Final Test: 0.8148 ± 0.0004

examples/pytorch/ogb/deepwalk/deepwalk.py

@@ -10,7 +10,7 @@ import numpy as np
 
 from reading_data import DeepwalkDataset
 from model import SkipGramModel
-from utils import thread_wrapped_func, shuffle_walks
+from utils import thread_wrapped_func, shuffle_walks, sum_up_params
 
 class DeepwalkTrainer:
     def __init__(self, args):
@@ -26,8 +26,10 @@ class DeepwalkTrainer:
             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 = len(self.dataset.net)
+        self.emb_size = self.dataset.G.number_of_nodes()
         self.emb_model = None
 
     def init_device_emb(self):
@@ -71,7 +73,7 @@ class DeepwalkTrainer:
             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 abaliable GPU'
-                self.emb_model.set_device(self.args.gpus[0])
+                #self.emb_model.set_device(self.args.gpus[0])
         else:
             print("Run in CPU process")
             self.args.gpus = [torch.device('cpu')]
@@ -89,6 +91,9 @@ class DeepwalkTrainer:
         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 = []
 
@@ -170,6 +175,9 @@ class DeepwalkTrainer:
 
         self.init_device_emb()
 
+        if self.args.count_params:
+            sum_up_params(self.emb_model)
+
         sampler = self.dataset.create_sampler(0)
 
         dataloader = DataLoader(
@@ -227,8 +235,17 @@ class DeepwalkTrainer:
 
 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",
@@ -237,52 +254,63 @@ if __name__ == '__main__':
             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=5, type=int, 
             help="negative samples for each positve node pair")
-    parser.add_argument('--iterations', default=1, type=int, 
-            help="iterations")
     parser.add_argument('--batch_size', default=10, type=int, 
             help="number of node sequences in each batch")
-    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('--walk_length', default=80, type=int, 
             help="number of nodes in a sequence")
-    parser.add_argument('--lr', default=0.2, type=float, 
-            help="learning rate")
     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")
+    
+    # training parameters
+    parser.add_argument('--iterations', default=1, type=int, 
+            help="iterations")
+    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('--fast_neg', default=True, action="store_true", 
-            help="do negative sampling inside a batch")
+
     parser.add_argument('--adam', default=False, action="store_true", 
             help="use adam for embedding updation, recommended")
     parser.add_argument('--sgd', default=False, action="store_true", 
             help="use sgd for embedding updation")
     parser.add_argument('--avg_sgd', default=False, action="store_true", 
             help="average gradients of sgd for embedding updation")
-    parser.add_argument('--norm', default=False, action="store_true", 
-            help="whether to do normalization over node embedding after training")
-    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('--fast_neg', default=False, action="store_true", 
+            help="do negative sampling inside a batch")
     parser.add_argument('--num_threads', default=2, type=int, 
             help="number of threads used for each CPU-core/GPU")
-    parser.add_argument('--gpus', type=int, default=[-1], nargs='+', 
-            help='a list of active gpu ids, e.g. 0')
+    
+    parser.add_argument('--count_params', default=False, action="store_true", 
+            help="count the params, then exit")
+
     args = parser.parse_args()
 
     start_time = time.time()

examples/pytorch/ogb/deepwalk/load_dataset.py

 """ load dataset from ogb """
 
-from ogb.linkproppred import PygLinkPropPredDataset
 import argparse
+from ogb.linkproppred import DglLinkPropPredDataset
 
-parser = argparse.ArgumentParser()
-parser.add_argument('--name', type=str,
+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
+    args = parser.parse_args()
 
-dataset = PygLinkPropPredDataset(name=name)
-data = dataset[0]
+    name = args.name
+    g = load_from_ogbl_with_name(name=name)
 
-try:
-    weighted = data.edge_weight
+    try:
+        w = g.edata['edge_weight']
         weighted = True
-except:
+    except:
         weighted = False
 
-with open(name + "-net.txt", "w") as f:
-    for i in range(data.edge_index.shape[1]):
+    with open(name + "-net.txt", "w") as f:
+        for i in range(g.edges()[0].shape[0]):
             if weighted:
-            f.write(str(data.edge_index[0][i].item()) + " "\
-                +str(data.edge_index[1][i].item()) + " "\
-                +str(data.edge_weight[i].item()) + "\n")
+                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(data.edge_index[0][i].item()) + " "\
-                +str(data.edge_index[1][i].item()) + " "\
+                f.write(str(g.edges()[0][i].item()) + " "\
+                    +str(g.edges()[1][i].item()) + " "\
                     +"1\n")
\ No newline at end of file

examples/pytorch/ogb/deepwalk/model.py

@@ -496,6 +496,7 @@ class SkipGramModel(nn.Module):
     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.")
@@ -504,6 +505,21 @@ class SkipGramModel(nn.Module):
             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)
 

examples/pytorch/ogb/deepwalk/reading_data.py

@@ -8,8 +8,8 @@ from dgl.data.utils import download, _get_dgl_url, get_download_dir, extract_arc
 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. 
@@ -110,17 +110,31 @@ def net2graph(net_sm):
     print("Building DGLGraph in %.2fs" % t)
     return G
 
+def make_undirected(G):
+    G.readonly(False)
+    G.add_edges(G.edges()[1], G.edges()[0])
+    return G
+
+def find_connected_nodes(G):
+    nodes = []
+    for n in G.nodes():
+        if G.out_degree(n) > 0:
+            nodes.append(n.item())
+    return nodes
+
 class DeepwalkDataset:
     def __init__(self, 
             net_file,
             map_file,
-            walk_length=80,
-            window_size=5,
-            num_walks=10,
-            batch_size=32,
+            walk_length,
+            window_size,
+            num_walks,
+            batch_size,
             negative=5,
             gpus=[0],
             fast_neg=True,
+            ogbl_name="",
+            load_from_ogbl=False,
             ):
         """ This class has the following functions:
         1. Transform the txt network file into DGL graph;
@@ -145,26 +159,42 @@ class DeepwalkDataset:
         self.negative = negative
         self.num_procs = len(gpus)
         self.fast_neg = fast_neg
+
+        if load_from_ogbl:
+            assert len(gpus) == 1, "ogb.linkproppred is not compatible with multi-gpu training."
+            from load_dataset import load_from_ogbl_with_name
+            self.G = load_from_ogbl_with_name(ogbl_name)
+            self.G = make_undirected(self.G)
+        else:
             self.net, self.node2id, self.id2node, self.sm = ReadTxtNet(net_file)
             self.save_mapping(map_file)
             self.G = net2graph(self.sm)
 
+        self.num_nodes = self.G.number_of_nodes()
+
         # 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)
+        self.valid_seeds = find_connected_nodes(self.G)
+        if len(self.valid_seeds) != self.num_nodes:
+            print("WARNING: The node ids are not serial. Some nodes are invalid.")
+        
+        seeds = torch.cat([torch.LongTensor(self.valid_seeds)] * num_walks)
+        self.seeds = torch.split(shuffle_walks(seeds), 
+            int(np.ceil(len(self.valid_seeds) * 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.array(list(map(lambda x: self.G.out_degree(x), self.valid_seeds)))
             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()):
+            
+            for idx, node in enumerate(self.valid_seeds):
                 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)

examples/pytorch/ogb/deepwalk/utils.py

@@ -35,3 +35,31 @@ def thread_wrapped_func(func):
 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