[Example] Add GraphMAE2

cogdl/data/data.py

@@ -480,16 +480,17 @@ def __init__(self, x=None, y=None, **kwargs):
         self.x = x
         self.y = y
         self.grb_adj = None
+        num_nodes = x.shape[0] if x is not None else None
 
         for key, item in kwargs.items():
             if key == "num_nodes":
                 self.__num_nodes__ = item
+                num_nodes = item
             elif key == "grb_adj":
                 self.grb_adj = item
             elif not is_read_adj_key(key):
                 self[key] = item
 
-        num_nodes = x.shape[0] if x is not None else None
         if "edge_index_train" in kwargs:
             self._adj_train = Adjacency(num_nodes=num_nodes)
             for key, item in kwargs.items():
@@ -534,14 +535,17 @@ def add_remaining_self_loops(self):
         self._adj_full.add_remaining_self_loops()
         if self._adj_train is not None:
             self._adj_train.add_remaining_self_loops()
+        return self
 
     def padding_self_loops(self):
         self._adj.padding_self_loops()
+        return self
 
     def remove_self_loops(self):
         self._adj_full.remove_self_loops()
         if self._adj_train is not None:
             self._adj_train.remove_self_loops()
+        return self
 
     def row_norm(self):
         self._adj.row_norm()
@@ -790,7 +794,7 @@ def sample_adj(self, batch, size=-1, replace=True):
             if not torch.is_tensor(batch):
                 batch = torch.tensor(batch, dtype=torch.long)
             (row_ptr, col_indices, nodes, edges) = sample_adj_c(
-                self._adj.row_indptr, self.col_indices, batch, size, replace
+                self.row_indptr, self.col_indices, batch, size, replace
             )
         else:
             if torch.is_tensor(batch):
@@ -891,13 +895,18 @@ def subgraph(self, node_idx, keep_order=False):
                 val = self.edge_weight.numpy()
                 N = self.num_nodes
                 self[key] = sp.csr_matrix((val, (row, col)), shape=(N, N))
-            sub_adj = self[key][node_idx, :][:, node_idx]
+            sub_adj = self[key][node_idx, :][:, node_idx].tocoo()
             sub_g = Graph()
-            sub_g.row_indptr = torch.from_numpy(sub_adj.indptr).long()
-            sub_g.col_indices = torch.from_numpy(sub_adj.indices).long()
+            # sub_g.row_indptr = torch.from_numpy(sub_adj.indptr).long()
+            # sub_g.col_indices = torch.from_numpy(sub_adj.indices).long()
+            row = torch.from_numpy(sub_adj.row).long()
+            col = torch.from_numpy(sub_adj.col).long()
+            sub_g.edge_index = (row, col)
             sub_g.edge_weight = torch.from_numpy(sub_adj.data)
+            sub_g.num_nodes = len(node_idx)
             for key in self.__keys__():
                 sub_g[key] = self[key][node_idx]
+            sub_g._adj._to_csr()
             return sub_g.to(self._adj.device)
 
     def edge_subgraph(self, edge_idx, require_idx=True):

examples/graphmae2/README.md

@@ -0,0 +1,87 @@
+<h1> GraphMAE2: A Decoding-Enhanced Masked Self-Supervised
+Graph Learner </h1>
+
+[**CogDL**](/~https://github.com/THUDM/cogdl) Implementation for WWW'23 paper:  [GraphMAE2: A Decoding-Enhanced Masked Self-Supervised
+Graph Learner](https://arxiv.org/abs/2304.04779).
+<img src="assets/../asserts/overview.png">
+
+[GraphMAE] The predecessor of this work: [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://arxiv.org/abs/2205.10803) can be found [here](/~https://github.com/THUDM/cogdl/tree/master/examples/graphmae).
+
+<h2>Dependencies </h2>
+
+* Python >= 3.7
+* [Pytorch](https://pytorch.org/) >= 1.9.0 
+* [cogdl](/~https://github.com/THUDM/cogdl) >= 0.5.3
+* pyyaml == 5.4.1
+
+
+<h2>Quick Start </h2>
+
+For quick start, you could run the scripts: 
+
+**Node classification**
+
+```bash
+sh run_minibatch.sh <dataset_name> <gpu_id> # for mini batch node classification
+# example: sh run_minibatch.sh ogbn-arxiv 0
+sh run_fullbatch.sh <dataset_name> <gpu_id> # for full batch node classification
+# example: sh run_fullbatch.sh cora 0
+
+# Or you could run the code manually:
+# for mini batch node classification
+python main_large.py --dataset ogbn-arxiv --encoder gat --decoder gat --seed 0 --device 0
+# for full batch node classification
+python main_full_batch.py --dataset cora --encoder gat --decoder gat --seed 0 --device 0
+```
+
+Supported datasets:
+
+* mini batch node classification:  `ogbn-arxiv`, `ogbn-products`, `mag-scholar-f`, `ogbn-papers100M`
+* full batch node classification: `cora`, `citeseer`, `pubmed`
+
+Run the scripts provided or add `--use_cfg` in command to reproduce the reported results.
+
+**For Large scale graphs**
+Before starting mini-batch training, you'll need to generate local clusters if you want to use local-clustering for training. By default, the program will load dataset from `./data` and save the generated local clusters to `./lc_ego_graphs`. To generate a local cluster,  you should first install [localclustering](/~https://github.com/kfoynt/LocalGraphClustering) and then run the following command:
+
+```
+python ./datasets/localclustering.py --dataset <your_dataset> --data_dir <path_to_data>
+```
+And we also provide the pre-generated local clusters which can be downloaded [here](https://cloud.tsinghua.edu.cn/d/64f859f389ca43eda472/) and then put into `lc_ego_graphs` for usage.
+
+
+
+<h2> Datasets </h2>
+
+During the code's execution, the OGB and small-scale datasets (Cora, Citeseer, and PubMed) will be downloaded automatically. 
+
+<h2> Experimental Results </h2>
+
+Experimental results of node classification on large-scale datasets (Accuracy, %):
+
+|                    | Ogbn-arxiv         | Ogbn-products     | Mag-Scholar-F       | Ogbn-papers100M     | 
+| ------------------ | ------------ | ------------ | ------------ | -------------- |
+| MLP                | 55.50±0.23     | 61.06±0.08     | 39.11±0.21     | 47.24±0.31     | 
+| SGC              | 66.92±0.08     | 74.87±0.25     | 54.68±0.23     | 63.29±0.19        | 
+| Random-Init               | 68.14±0.02     | 74.04±0.06     | 56.57±0.03     | 61.55±0.12     | 
+| CCA-SSG            | 68.57±0.02     | 75.27±0.05     | 51.55±0.03     | 55.67±0.15     | 
+| GRACE            | 69.34±0.01     | 79.47±0.59     | 57.39±0.02     | 61.21±0.12     | 
+| BGRL            | 70.51±0.03     | 78.59±0.02     | 57.57±0.01     | 62.18±0.15     | 
+| GGD            | -     | 75.70±0.40     | -     | 63.50±0.50     | 
+| GraphMAE            | 71.03±0.02     | 78.89±0.01     | 58.75±0.03     | 62.54±0.09     | 
+| **GraphMAE2** | **71.89±0.03** | **81.59±0.02** | **59.24±0.01** | **64.89±0.04** |
+
+
+
+<h1> Citing </h1>
+
+If you find this work is helpful to your research, please consider citing our paper:
+
+```
+@inproceedings{hou2023graphmae2,
+  title={GraphMAE2: A Decoding-Enhanced Masked Self-Supervised Graph Learner},
+  author={Zhenyu Hou, Yufei He, Yukuo Cen, Xiao Liu, Yuxiao Dong, Evgeny Kharlamov, Jie Tang},
+  booktitle={Proceedings of the ACM Web Conference 2023 (WWW’23)},
+  year={2023}
+}
+```

examples/graphmae2/configs/citeseer.yaml

@@ -0,0 +1,27 @@
+lr: 0.0005 # 0.0005
+lr_f: 0.025
+num_hidden: 1024
+num_heads: 4
+num_out_heads: 1
+num_layers: 2
+weight_decay: 1e-4
+weight_decay_f: 1e-2
+max_epoch: 500
+max_epoch_f: 500
+mask_rate: 0.5
+num_layers: 2
+encoder: gat
+decoder: gat 
+activation: prelu
+attn_drop: 0.1
+linear_prob: True
+in_drop: 0.2
+loss_fn: sce 
+drop_edge_rate: 0.0
+optimizer: adam
+replace_rate: 0.0
+alpha_l: 1
+scheduler: True
+remask_method: fixed
+momentum: 1
+lam: 0.1

examples/graphmae2/configs/cora.yaml

@@ -0,0 +1,27 @@
+lr: 0.001
+lr_f: 0.025
+num_hidden: 1024
+num_heads: 8
+num_out_heads: 1
+num_layers: 2
+weight_decay: 2e-4
+weight_decay_f: 1e-4
+max_epoch: 2000 
+max_epoch_f: 300
+mask_rate: 0.5
+num_layers: 2
+encoder: gat
+decoder: gat 
+activation: prelu
+attn_drop: 0.1
+linear_prob: True
+in_drop: 0.2
+loss_fn: sce 
+drop_edge_rate: 0.0
+optimizer: adam
+replace_rate: 0.1
+alpha_l: 4
+scheduler: True
+remask_method: fixed
+momentum: 0
+lam: 0.1

examples/graphmae2/configs/mag-scholar-f.yaml

@@ -0,0 +1,30 @@
+lr: 0.001
+lr_f: 0.001
+num_hidden: 1024
+num_heads: 8
+num_out_heads: 1
+num_layers: 4
+weight_decay: 0.04
+weight_decay_f: 0
+max_epoch: 10 
+max_epoch_f: 1000
+batch_size: 512
+batch_size_f: 256
+mask_rate: 0.5
+num_layers: 4
+encoder: gat
+decoder: gat 
+activation: prelu
+attn_drop: 0.2
+linear_prob: True
+in_drop: 0.2
+loss_fn: sce 
+drop_edge_rate: 0.5
+optimizer: adamw
+alpha_l: 2
+scheduler: True
+remask_method: random
+momentum: 0.996
+lam: 0.1
+delayed_ema_epoch: 0
+num_remasking: 3

examples/graphmae2/configs/ogbn-arxiv.yaml

@@ -0,0 +1,30 @@
+lr: 0.0025
+lr_f: 0.005
+num_hidden: 1024
+num_heads: 8
+num_out_heads: 1
+num_layers: 4
+weight_decay: 0.06
+weight_decay_f: 1e-4
+max_epoch: 60 
+max_epoch_f: 1000
+batch_size: 512
+batch_size_f: 256
+mask_rate: 0.5
+num_layers: 4
+encoder: gat
+decoder: gat 
+activation: prelu
+attn_drop: 0.1
+linear_prob: True
+in_drop: 0.2
+loss_fn: sce 
+drop_edge_rate: 0.5
+optimizer: adamw
+alpha_l: 6
+scheduler: True
+remask_method: random
+momentum: 0.996
+lam: 10.0
+delayed_ema_epoch: 40
+num_remasking: 3

examples/graphmae2/configs/ogbn-papers100M.yaml

@@ -0,0 +1,30 @@
+lr: 0.001
+lr_f: 0.001
+num_hidden: 1024
+num_heads: 4
+num_out_heads: 1
+num_layers: 4
+weight_decay: 0.05
+weight_decay_f: 0
+max_epoch: 10 
+max_epoch_f: 1000
+batch_size: 512
+batch_size_f: 256
+mask_rate: 0.5
+num_layers: 4
+encoder: gat
+decoder: gat 
+activation: prelu
+attn_drop: 0.2
+linear_prob: True
+in_drop: 0.2
+loss_fn: sce 
+drop_edge_rate: 0.5
+optimizer: adamw
+alpha_l: 2
+scheduler: True
+remask_method: random
+momentum: 0.996
+lam: 10.0
+delayed_ema_epoch: 0
+num_remasking: 3

examples/graphmae2/configs/ogbn-products.yaml

@@ -0,0 +1,30 @@
+lr: 0.002
+lr_f: 0.001
+num_hidden: 1024
+num_heads: 4
+num_out_heads: 1
+num_layers: 4
+weight_decay: 0.04
+weight_decay_f: 0
+max_epoch: 20 
+max_epoch_f: 1000
+batch_size: 512
+batch_size_f: 256
+mask_rate: 0.5
+num_layers: 4
+encoder: gat
+decoder: gat 
+activation: prelu
+attn_drop: 0.2
+linear_prob: True
+in_drop: 0.2
+loss_fn: sce 
+drop_edge_rate: 0.5
+optimizer: adamw
+alpha_l: 3
+scheduler: True
+remask_method: random
+momentum: 0.996
+lam: 5.0
+delayed_ema_epoch: 0
+num_remasking: 3

examples/graphmae2/configs/pubmed.yaml

@@ -0,0 +1,27 @@
+lr: 0.005
+lr_f: 0.025
+num_hidden: 512
+num_heads: 2
+num_out_heads: 1
+num_layers: 2
+weight_decay: 1e-5
+weight_decay_f: 5e-4
+max_epoch: 2000 
+max_epoch_f: 500
+mask_rate: 0.9
+num_layers: 2
+encoder: gat
+decoder: gat 
+activation: prelu
+attn_drop: 0.1
+linear_prob: True
+in_drop: 0.2
+loss_fn: sce 
+drop_edge_rate: 0.0
+optimizer: adam
+replace_rate: 0.0
+alpha_l: 4
+scheduler: True
+remask_method: fixed
+momentum: 0.995
+lam: 1