[Example][Refactor] Graphsage link prediction example refactor (#4526)

* Refactor link pred example for graphsage

* Use ogb evaluator + README update

* Update

* Add comments

examples/pytorch/graphsage/README.md

@@ -54,8 +54,13 @@ python3 lightning/node_classification.py
 
 ### Minibatch training for link prediction
 
-Train w/ mini-batch sampling for link prediction on OGB-Citation2:
+Train w/ mini-batch sampling for link prediction on OGB-citation2:
 
 ```bash
 python3 link_pred.py
 ```
+
+Results (10 epochs):
+```
+Test MRR: 0.7386
+```

examples/pytorch/graphsage/link_pred.py

-import argparse
 import torch
 import torch.nn as nn
 import torch.nn.functional as F
 import torchmetrics.functional as MF
 import dgl
 import dgl.nn as dglnn
-import time
-import numpy as np
+from dgl.dataloading import DataLoader, NeighborSampler, MultiLayerFullNeighborSampler, as_edge_prediction_sampler, negative_sampler
 import tqdm
-# OGB must follow DGL if both DGL and PyG are installed. Otherwise DataLoader will hang.
-# (This is a long-standing issue)
-from ogb.linkproppred import DglLinkPropPredDataset
-
-parser = argparse.ArgumentParser()
-parser.add_argument('--pure-gpu', action='store_true',
-                    help='Perform both sampling and training on GPU.')
-args = parser.parse_args()
-
-device = 'cuda'
+import argparse
+from ogb.linkproppred import DglLinkPropPredDataset, Evaluator
 
 def to_bidirected_with_reverse_mapping(g):
     """Makes a graph bidirectional, and returns a mapping array ``mapping`` where ``mapping[i]``
-    is the reverse edge of edge ID ``i``.
-    Does not work with graphs that have self-loops.
+    is the reverse edge of edge ID ``i``. Does not work with graphs that have self-loops.
     """
     g_simple, mapping = dgl.to_simple(
         dgl.add_reverse_edges(g), return_counts='count', writeback_mapping=True)
@@ -34,8 +23,7 @@ def to_bidirected_with_reverse_mapping(g):
     idx_uniq = idx[mapping_offset[:-1]]
     reverse_idx = torch.where(idx_uniq >= num_edges, idx_uniq - num_edges, idx_uniq + num_edges)
     reverse_mapping = mapping[reverse_idx]
-
-    # Correctness check
+    # sanity check
     src1, dst1 = g_simple.edges()
     src2, dst2 = g_simple.find_edges(reverse_mapping)
     assert torch.equal(src1, dst2)
@@ -43,22 +31,20 @@ def to_bidirected_with_reverse_mapping(g):
     return g_simple, reverse_mapping
 
 class SAGE(nn.Module):
-    def __init__(self, in_feats, n_hidden):
+    def __init__(self, in_size, hid_size):
         super().__init__()
-        self.n_hidden = n_hidden
         self.layers = nn.ModuleList()
-        self.layers.append(dglnn.SAGEConv(in_feats, n_hidden, 'mean'))
-        self.layers.append(dglnn.SAGEConv(n_hidden, n_hidden, 'mean'))
-        self.layers.append(dglnn.SAGEConv(n_hidden, n_hidden, 'mean'))
+        # three-layer GraphSAGE-mean
+        self.layers.append(dglnn.SAGEConv(in_size, hid_size, 'mean'))
+        self.layers.append(dglnn.SAGEConv(hid_size, hid_size, 'mean'))
+        self.layers.append(dglnn.SAGEConv(hid_size, hid_size, 'mean'))
+        self.hid_size = hid_size
         self.predictor = nn.Sequential(
-            nn.Linear(n_hidden, n_hidden),
+            nn.Linear(hid_size, hid_size),
             nn.ReLU(),
-            nn.Linear(n_hidden, n_hidden),
+            nn.Linear(hid_size, hid_size),
             nn.ReLU(),
-            nn.Linear(n_hidden, 1))
-
-    def predict(self, h_src, h_dst):
-        return self.predictor(h_src * h_dst)
+            nn.Linear(hid_size, 1))
 
     def forward(self, pair_graph, neg_pair_graph, blocks, x):
         h = x
@@ -68,27 +54,25 @@ class SAGE(nn.Module):
                 h = F.relu(h)
         pos_src, pos_dst = pair_graph.edges()
         neg_src, neg_dst = neg_pair_graph.edges()
-        h_pos = self.predict(h[pos_src], h[pos_dst])
-        h_neg = self.predict(h[neg_src], h[neg_dst])
+        h_pos = self.predictor(h[pos_src] * h[pos_dst])
+        h_neg = self.predictor(h[neg_src] * h[neg_dst])
         return h_pos, h_neg
 
-    def inference(self, g, device, batch_size, num_workers, buffer_device=None):
-        # The difference between this inference function and the one in the official
-        # example is that the intermediate results can also benefit from prefetching.
+    def inference(self, g, device, batch_size):
+        """Layer-wise inference algorithm to compute GNN node embeddings."""
         feat = g.ndata['feat']
-        sampler = dgl.dataloading.MultiLayerFullNeighborSampler(1, prefetch_node_feats=['feat'])
-        dataloader = dgl.dataloading.DataLoader(
-                g, torch.arange(g.num_nodes()).to(g.device), sampler, device=device,
-                batch_size=1000, shuffle=False, drop_last=False, num_workers=num_workers)
-        if buffer_device is None:
-            buffer_device = device
-
+        sampler = MultiLayerFullNeighborSampler(1, prefetch_node_feats=['feat'])
+        dataloader = DataLoader(
+            g, torch.arange(g.num_nodes()).to(g.device), sampler, device=device,
+            batch_size=batch_size, shuffle=False, drop_last=False,
+            num_workers=0)
+        buffer_device = torch.device('cpu')
+        pin_memory = (buffer_device != device)
         for l, layer in enumerate(self.layers):
-            y = torch.zeros(g.num_nodes(), self.n_hidden, device=buffer_device,
-                            pin_memory=args.pure_gpu)
+            y = torch.empty(g.num_nodes(), self.hid_size, device=buffer_device,
+                            pin_memory=pin_memory)
             feat = feat.to(device)
-
-            for input_nodes, output_nodes, blocks in tqdm.tqdm(dataloader):
+            for input_nodes, output_nodes, blocks in tqdm.tqdm(dataloader, desc='Inference'):
                 x = feat[input_nodes]
                 h = layer(blocks[0], x)
                 if l != len(self.layers) - 1:
@@ -97,78 +81,92 @@ class SAGE(nn.Module):
             feat = y
         return y
 
-
-def compute_mrr(model, node_emb, src, dst, neg_dst, device, batch_size=500):
+def compute_mrr(model, evaluator, node_emb, src, dst, neg_dst, device, batch_size=500):
+    """Compute Mean Reciprocal Rank (MRR) in batches."""
     rr = torch.zeros(src.shape[0])
-    for start in tqdm.trange(0, src.shape[0], batch_size):
+    for start in tqdm.trange(0, src.shape[0], batch_size, desc='Evaluate'):
         end = min(start + batch_size, src.shape[0])
         all_dst = torch.cat([dst[start:end, None], neg_dst[start:end]], 1)
         h_src = node_emb[src[start:end]][:, None, :].to(device)
         h_dst = node_emb[all_dst.view(-1)].view(*all_dst.shape, -1).to(device)
-        pred = model.predict(h_src, h_dst).squeeze(-1)
-        relevance = torch.zeros(*pred.shape, dtype=torch.bool).to(pred.device)
-        relevance[:, 0] = True
-        rr[start:end] = MF.retrieval_reciprocal_rank(pred, relevance)
+        pred = model.predictor(h_src*h_dst).squeeze(-1)
+        input_dict = {'y_pred_pos': pred[:,0], 'y_pred_neg': pred[:,1:]}
+        rr[start:end] = evaluator.eval(input_dict)['mrr_list']
     return rr.mean()
 
-
-def evaluate(model, edge_split, device, num_workers):
+def evaluate(device, graph, edge_split, model, batch_size):
+    model.eval()
+    evaluator = Evaluator(name='ogbl-citation2')
     with torch.no_grad():
-        node_emb = model.inference(graph, device, 4096, num_workers, 'cpu')
+        node_emb = model.inference(graph, device, batch_size)
         results = []
         for split in ['valid', 'test']:
             src = edge_split[split]['source_node'].to(node_emb.device)
             dst = edge_split[split]['target_node'].to(node_emb.device)
             neg_dst = edge_split[split]['target_node_neg'].to(node_emb.device)
-            results.append(compute_mrr(model, node_emb, src, dst, neg_dst, device))
+            results.append(compute_mrr(model, evaluator, node_emb, src, dst, neg_dst, device))
     return results
 
-
-dataset = DglLinkPropPredDataset('ogbl-citation2')
-graph = dataset[0]
-graph, reverse_eids = to_bidirected_with_reverse_mapping(graph)
-graph = graph.to('cuda' if args.pure_gpu else 'cpu')
-reverse_eids = reverse_eids.to(device)
-seed_edges = torch.arange(graph.num_edges()).to(device)
-edge_split = dataset.get_edge_split()
-
-model = SAGE(graph.ndata['feat'].shape[1], 256).to(device)
-opt = torch.optim.Adam(model.parameters(), lr=0.001, weight_decay=5e-4)
-
-sampler = dgl.dataloading.NeighborSampler([15, 10, 5], prefetch_node_feats=['feat'])
-sampler = dgl.dataloading.as_edge_prediction_sampler(
+def train(args, device, g, reverse_eids, seed_edges, model):
+    # create sampler & dataloader
+    sampler = NeighborSampler([15, 10, 5], prefetch_node_feats=['feat'])
+    sampler = as_edge_prediction_sampler(
         sampler, exclude='reverse_id', reverse_eids=reverse_eids,
-        negative_sampler=dgl.dataloading.negative_sampler.Uniform(1))
-dataloader = dgl.dataloading.DataLoader(
-        graph, seed_edges, sampler,
+        negative_sampler=negative_sampler.Uniform(1))
+    use_uva = (args.mode == 'mixed')
+    dataloader = DataLoader(
+        g, seed_edges, sampler,
         device=device, batch_size=512, shuffle=True,
-        drop_last=False, num_workers=0, use_uva=not args.pure_gpu)
-
-durations = []
-for epoch in range(10):
-    model.train()
-    t0 = time.time()
-    for it, (input_nodes, pair_graph, neg_pair_graph, blocks) in enumerate(dataloader):
-        x = blocks[0].srcdata['feat']
-        pos_score, neg_score = model(pair_graph, neg_pair_graph, blocks, x)
-        pos_label = torch.ones_like(pos_score)
-        neg_label = torch.zeros_like(neg_score)
-        score = torch.cat([pos_score, neg_score])
-        labels = torch.cat([pos_label, neg_label])
-        loss = F.binary_cross_entropy_with_logits(score, labels)
-        opt.zero_grad()
-        loss.backward()
-        opt.step()
-        if (it + 1) % 20 == 0:
-            mem = torch.cuda.max_memory_allocated() / 1000000
-            print('Loss', loss.item(), 'GPU Mem', mem, 'MB')
-            if (it + 1) == 1000:
-                tt = time.time()
-                print(tt - t0)
-                durations.append(tt - t0)
-                break
-    if epoch % 10 == 0:
-        model.eval()
-        valid_mrr, test_mrr = evaluate(model, edge_split, device, 0 if args.pure_gpu else 12)
-        print('Validation MRR:', valid_mrr.item(), 'Test MRR:', test_mrr.item())
-print(np.mean(durations[4:]), np.std(durations[4:]))
+        drop_last=False, num_workers=0, use_uva=use_uva)
+    opt = torch.optim.Adam(model.parameters(), lr=0.0005)
+    for epoch in range(10):
+        model.train()
+        total_loss = 0
+        for it, (input_nodes, pair_graph, neg_pair_graph, blocks) in enumerate(dataloader):
+            x = blocks[0].srcdata['feat']
+            pos_score, neg_score = model(pair_graph, neg_pair_graph, blocks, x)
+            score = torch.cat([pos_score, neg_score])
+            pos_label = torch.ones_like(pos_score)
+            neg_label = torch.zeros_like(neg_score)
+            labels = torch.cat([pos_label, neg_label])
+            loss = F.binary_cross_entropy_with_logits(score, labels)
+            opt.zero_grad()
+            loss.backward()
+            opt.step()
+            total_loss += loss.item()
+            if (it+1) == 1000: break
+        print("Epoch {:05d} | Loss {:.4f}".format(epoch, total_loss / (it+1)))
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--mode", default='mixed', choices=['cpu', 'mixed', 'puregpu'],
+                        help="Training mode. 'cpu' for CPU training, 'mixed' for CPU-GPU mixed training, "
+                             "'puregpu' for pure-GPU training.")
+    args = parser.parse_args()
+    if not torch.cuda.is_available():
+        args.mode = 'cpu'
+    print(f'Training in {args.mode} mode.')
+
+    # load and preprocess dataset
+    print('Loading data')
+    dataset = DglLinkPropPredDataset('ogbl-citation2')
+    g = dataset[0]
+    g = g.to('cuda' if args.mode == 'puregpu' else 'cpu')
+    device = torch.device('cpu' if args.mode == 'cpu' else 'cuda')
+    g, reverse_eids = to_bidirected_with_reverse_mapping(g)
+    reverse_eids = reverse_eids.to(device)
+    seed_edges = torch.arange(g.num_edges()).to(device)
+    edge_split = dataset.get_edge_split()
+
+    # create GraphSAGE model
+    in_size = g.ndata['feat'].shape[1]
+    model = SAGE(in_size, 256).to(device)
+
+    # model training
+    print('Training...')
+    train(args, device, g, reverse_eids, seed_edges, model)
+
+    # validate/test the model
+    print('Validation/Testing...')
+    valid_mrr, test_mrr = evaluate(device, g, edge_split, model, batch_size=1000)
+    print('Validation MRR {:.4f}, Test MRR {:.4f}'.format(valid_mrr.item(),test_mrr.item()))