[Example] Experimental results over ogbl-ddi (#1707)

* ogb-deepwalk

* update readme

* update readme

* update readme

* update readme

* ogbl-ddi

* readme
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

examples/pytorch/ogb/deepwalk/README.md

@@ -6,20 +6,29 @@ python3 load_dataset.py --name ogbl-collab
 
 ## Evaluation
 For evaluatation we follow the code provided by ogb [here](https://github.com/snap-stanford/ogb/blob/master/examples/linkproppred/collab/mlp.py).
+
+## 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
+
 cd ./ogb/blob/master/examples/linkproppred/collab/
 cp embedding_pt_file_path ./
 python3 mlp.py --device 0 --runs 10 --use_node_embedding
 ```
 
-## Used config
+ogbl-ddi
 ```
-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 --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
+cd ./ogb/blob/master/examples/linkproppred/ddi/
+cp embedding_pt_file_path ./
+python3 mlp.py --device 0 --runs 5
 ```
 
 
 ## Score
-Hits@10
+ogbl-collab
+<br>Hits@10
 <br>&emsp;Highest Train: 74.83 ± 4.79
 <br>&emsp;Highest Valid: 40.03 ± 2.98
 <br>&emsp;&emsp;Final Train: 74.51 ± 4.92
@@ -33,4 +42,22 @@ Hits@10
 <br>&emsp;Highest Train: 99.86 ± 0.04
 <br>&emsp;Highest Valid: 66.64 ± 0.32
 <br>&emsp;&emsp;Final Train: 99.84 ± 0.06
-<br>&emsp;&emsp;Final Test: 56.88 ± 0.37
\ No newline at end of file
+<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
+

examples/pytorch/ogb/deepwalk/deepwalk.py

@@ -58,6 +58,8 @@ class DeepwalkTrainer:
             avg_sgd=self.args.avg_sgd,
             fast_neg=self.args.fast_neg,
             record_loss=self.args.print_loss,
+            norm=self.args.norm,
+            use_context_weight=self.args.use_context_weight,
             )
         
         torch.set_num_threads(self.args.num_threads)
@@ -153,7 +155,7 @@ class DeepwalkTrainer:
                 if i > 0 and i % self.args.print_interval == 0:
                     if self.args.print_loss:
                         print("Solver [%d] batch %d tt: %.2fs loss: %.4f" \
-                            % (gpu_id, i, time.time()-start, sum(self.emb_model.loss)/self.args.print_interval))
+                            % (gpu_id, i, time.time()-start, -sum(self.emb_model.loss)/self.args.print_interval))
                         self.emb_model.loss = []
                     else:
                         print("Solver [%d] batch %d tt: %.2fs" % (gpu_id, i, time.time()-start))
@@ -209,7 +211,7 @@ class DeepwalkTrainer:
                     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))
+                                % (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))
@@ -273,6 +275,10 @@ if __name__ == '__main__':
             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('--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='+', 

examples/pytorch/ogb/deepwalk/load_dataset.py

@@ -13,8 +13,20 @@ name = args.name
 dataset = PygLinkPropPredDataset(name=name)
 data = dataset[0]
 
+try:
+    weighted = data.edge_weight
+    weighted = True
+except:
+    weighted = False
+
+
 with open(name + "-net.txt", "w") as f:
     for i in range(data.edge_index.shape[1]):
-        f.write(str(data.edge_index[0][i].item()) + " "\
-            +str(data.edge_index[1][i].item()) + " "\
-            +str(data.edge_weight[i].item()) + "\n")
\ No newline at end of file
+        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")
+        else:
+            f.write(str(data.edge_index[0][i].item()) + " "\
+                +str(data.edge_index[1][i].item()) + " "\
+                +"1\n")

examples/pytorch/ogb/deepwalk/model.py

@@ -73,11 +73,7 @@ def init_emb2neg_index(walk_length, window_size, negative, batch_size):
     return index_emb_negu, index_emb_negv
 
 def init_grad_avg(walk_length, window_size, batch_size):
-    '''select nodes' gradients from gradient matrix
-
-    Usage
-    -----
-
+    ''' averaging graidents by specific weights
     '''
     grad_avg = []
     for b in range(batch_size):
@@ -92,6 +88,22 @@ def init_grad_avg(walk_length, window_size, batch_size):
     # [num_pos * batch_size]
     return torch.Tensor(grad_avg).unsqueeze(1)
 
+def init_weight(walk_length, window_size, batch_size):
+    ''' select nodes' gradients from gradient matrix
+    '''
+    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))
@@ -131,6 +143,8 @@ class SkipGramModel(nn.Module):
         avg_sgd,
         fast_neg,
         record_loss,
+        norm,
+        use_context_weight,
         ):
         """ initialize embedding on CPU 
 
@@ -171,6 +185,8 @@ class SkipGramModel(nn.Module):
         self.avg_sgd = avg_sgd
         self.fast_neg = fast_neg
         self.record_loss = record_loss
+        self.norm = norm
+        self.use_context_weight = use_context_weight
         
         # initialize the device as cpu
         self.device = torch.device("cpu")
@@ -206,6 +222,12 @@ class SkipGramModel(nn.Module):
                 self.negative,
                 self.batch_size)
 
+        if self.use_context_weight:
+            self.context_weight = init_weight(
+                self.walk_length,
+                self.window_size,
+                self.batch_size)
+
         # coefficients for averaging the gradients
         if self.avg_sgd:
             self.grad_avg = init_grad_avg(
@@ -247,6 +269,8 @@ class SkipGramModel(nn.Module):
         self.grad_v = self.grad_v.to(self.device)
         if self.avg_sgd:
             self.grad_avg = self.grad_avg.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 """
@@ -340,6 +364,18 @@ class SkipGramModel(nn.Module):
         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(
@@ -453,6 +489,8 @@ class SkipGramModel(nn.Module):
         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):
@@ -462,6 +500,8 @@ class SkipGramModel(nn.Module):
         assert max(dataset.node2id.keys()) == self.emb_size - 1, "The node id does not starts from 0, saving embedding failed."
         index = torch.LongTensor(list(map(lambda node: dataset.node2id[node], list(range(self.emb_size)))))
         embedding = torch.index_select(embedding, 0, index)
+        if self.norm:
+            embedding /= torch.sqrt(torch.sum(embedding.mul(embedding), 1)).unsqueeze(1)
         torch.save(embedding, file_name)
 
     def save_embedding_txt(self, dataset, file_name):
@@ -473,6 +513,8 @@ class SkipGramModel(nn.Module):
         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):