CongWeilin / GraphMixer

Packages that are needed including pytorch-geometric, pytorch, and pybind11. The code are tested under cuda113 and cuda116 environment. Please consider download these packages with the following commands:

# pytorch
pip3 install torch torchvision torchaudio --extra-index-url https://download.pytorch.org/whl/cu116

# pytorch-geometric
pip install torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.12.0+cu116.html

# pybind11 (used for c++ sampler)
pip install pybind11

Run the code

Step 1: Compile C++ sampler (from https://github.com/amazon-science/tgl).

python setup.py build_ext --inplace

Step 2: Download data by using DATA/down.sh. To create the sub-sampled version of GDELT dataset, please use DATA/GDELT_lite/gen_dataset.py.

Step 3: Preprocess data (from https://github.com/amazon-research/tgl)

python gen_graph.py --data REDDIT

Please replace REDDIT to other datasets, e.g., WIKI, MOOC, LASTFM, and GDELT_lite.

Step 3: Run experiment

python train.py --data REDDIT     --num_neighbors 10 --use_cached_subgraph --use_onehot_node_feats
python train.py --data WIKI       --num_neighbors 30 --use_cached_subgraph --use_onehot_node_feats
python train.py --data MOOC       --num_neighbors 20 --use_cached_subgraph --use_onehot_node_feats
python train.py --data LASTFM     --num_neighbors 10 --use_cached_subgraph --use_onehot_node_feats
python train.py --data GDELT_lite --num_neighbors 30 --use_cached_subgraph --use_onehot_node_feats --ignore_edge_feats # GDELT_ne 
python train.py --data GDELT_lite --num_neighbors 30 --use_cached_subgraph --ignore_edge_feats                         # GDELT_e
python train.py --data GDELT_lite --num_neighbors 30 --use_cached_subgraph                                             # GDELT

If you are running this dataset for the first, it need to take sometime pre-processing the input data. But it will only do it once.

Neural architecture

Model arch with hyper-parameters including time_dims, hidden_dims, node_feat_dims, edge_feat_dims, where time_dims = hidden_dims = 100 are the same for all baselines.

Mixer_per_node(
  (base_model): MLPMixer(
    (feat_encoder): FeatEncode(
      (time_encoder): TimeEncode(
        (w): Linear(in_features=1, out_features=time_dims, bias=True)
      )
      (feat_encoder): Linear(in_features=time_dims+edge_feat_dims, out_features=hidden_dims, bias=True)
    )
    (layernorm): LayerNorm((hidden_dims,), eps=1e-05, elementwise_affine=True)
    (mlp_head): Linear(in_features=hidden_dims, out_features=hidden_dims, bias=True)
    (mixer_blocks): ModuleList(
      (0): MixerBlock(
        (token_layernorm): LayerNorm((hidden_dims,), eps=1e-05, elementwise_affine=True)
        (token_forward): FeedForward(
          (linear_0): Linear(in_features=hidden_dims, out_features=0.5 * hidden_dims, bias=True)
          (linear_1): Linear(in_features=0.5 * hidden_dims, out_features=hidden_dims, bias=True)
        )
        (channel_layernorm): LayerNorm((hidden_dims,), eps=1e-05, elementwise_affine=True)
        (channel_forward): FeedForward(
          (linear_0): Linear(in_features=hidden_dims, out_features=4 * hidden_dims, bias=True)
          (linear_1): Linear(in_features=4 * hidden_dims, out_features=hidden_dims, bias=True)
        )
      )
    )
  )
  (edge_predictor): EdgePredictor_per_node(
    (src_fc): Linear(in_features=node_feat_dims+hidden_dims, out_features=hidden_dims, bias=True)
    (dst_fc): Linear(in_features=node_feat_dims+hidden_dims, out_features=hidden_dims, bias=True)
    (out_fc): Linear(in_features=hidden_dims, out_features=1, bias=True)
  )
  (creterion): BCEWithLogitsLoss()
)

Comments

To double check and make sure no information leakage, we implement a function check_data_leakage(args, g, df) in data_process_utils.py to go through all the training data we used for GraphMixer. To enable this, please add --check_data_leakage to the command line.