PyTorch code of "SLAPS: Self-Supervision Improves Structure Learning for Graph Neural Networks"

Related tags

Deep Learning SLAPS-GNN
Overview

SLAPS-GNN

This repo contains the implementation of the model proposed in SLAPS: Self-Supervision Improves Structure Learning for Graph Neural Networks.

Datasets

ogbn-arxiv dataset will be loaded automatically, while Cora, Citeseer, and Pubmed are included in the GCN package, available here. Place the relevant files in the folder data_tf.

Dependencies

To train the models, you need a machine with a GPU.

To install the dependencies, it is recommended to use a virtual environment. You can create a virtual environment and install all the dependencies with the following command:

conda env create -f environment.yml

The file requirements.txt was written for CUDA 9.2 and Linux so you may need to adapt it to your infrastructure.

Usage

To run the model you should define the following parameters:

  • dataset: The dataset you want to run the model on
  • ntrials: number of runs
  • epochs_adj: number of epochs
  • epochs: number of epochs for GNN_C (used for knn_gcn and 2step learning of the model)
  • lr_adj: learning rate of GNN_DAE
  • lr: learning rate of GNN_C
  • w_decay_adj: l2 regularization parameter for GNN_DAE
  • w_decay: l2 regularization parameter for GNN_C
  • nlayers_adj: number of layers for GNN_DAE
  • nlayers: number of layers for GNN_C
  • hidden_adj: hidden size of GNN_DAE
  • hidden: hidden size of GNN_C
  • dropout1: dropout rate for GNN_DAE
  • dropout2: dropout rate for GNN_C
  • dropout_adj1: dropout rate on adjacency matrix for GNN_DAE
  • dropout_adj2: dropout rate on adjacency matrix for GNN_C
  • dropout2: dropout rate for GNN_C
  • k: k for knn initialization with knn
  • lambda_: weight of loss of GNN_DAE
  • nr: ratio of zeros to ones to mask out for binary features
  • ratio: ratio of ones to mask out for binary features and ratio of features to mask out for real values features
  • model: model to run (choices are end2end, knn_gcn, or 2step)
  • sparse: whether to make the adjacency sparse and run operations on sparse mode
  • gen_mode: identifies the graph generator
  • non_linearity: non-linearity to apply on the adjacency matrix
  • mlp_act: activation function to use for the mlp graph generator
  • mlp_h: hidden size of the mlp graph generator
  • noise: type of noise to add to features (mask or normal)
  • loss: type of GNN_DAE loss (mse or bce)
  • epoch_d: epochs_adj / epoch2 of the epochs will be used for training GNN_DAE
  • half_val_as_train: use half of validation for train to get Cora390 and Citeseer370

Reproducing the Results in the Paper

In order to reproduce the results presented in the paper, you should run the following commands:

Cora

FP

Run the following command:

python main.py -dataset cora -ntrials 10 -epochs_adj 2000 -lr 0.001 -lr_adj 0.01 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 512 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.5 -dropout_adj2 0.25 -k 30 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 0 -non_linearity elu -epoch_d 5

MLP

Run the following command:

python main.py -dataset cora -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.001 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 512 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 20 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 1 -non_linearity relu -mlp_h 1433 -mlp_act relu -epoch_d 5

MLP-D

Run the following command:

python main.py -dataset cora -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.001 -w_decay 0.05 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 512 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 15 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 2 -non_linearity relu -mlp_act relu -epoch_d 5

Citeseer

FP

Run the following command:

python main.py -dataset citeseer -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.01 -w_decay 0.05 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 1024 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.4 -dropout_adj2 0.4 -k 30 -lambda_ 1.0 -nr 1 -ratio 10 -model end2end -sparse 0 -gen_mode 0 -non_linearity elu -epoch_d 5

MLP

Run the following command:

python main.py -dataset citeseer -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.001 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 1024 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 30 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 1 -non_linearity relu -mlp_act relu -mlp_h 3703 -epoch_d 5

MLP-D

Run the following command:

python main.py -dataset citeseer -ntrials 10 -epochs_adj 2000 -lr 0.001 -lr_adj 0.01 -w_decay 0.05 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 1024 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.5 -dropout_adj2 0.5 -k 20 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 2 -non_linearity relu -mlp_act tanh -epoch_d 5

Cora390

FP

Run the following command:

python main.py -dataset cora -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.01 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 512 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 20 -lambda_ 100.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 0 -non_linearity elu -epoch_d 5 -half_val_as_train 1

MLP

Run the following command:

python main.py -dataset cora -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.001 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 512 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 20 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 1 -non_linearity relu -mlp_h 1433 -mlp_act relu -epoch_d 5 -half_val_as_train 1

MLP-D

Run the following command:

python main.py -dataset cora -ntrials 10 -epochs_adj 2000 -lr 0.001 -lr_adj 0.001 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 512 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 20 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 2 -non_linearity relu -mlp_act relu -epoch_d 5 -half_val_as_train 1

Citeseer370

FP

Run the following command:

python main.py -dataset citeseer -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.01 -w_decay 0.05 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 1024 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.5 -dropout_adj2 0.5 -k 30 -lambda_ 1.0 -nr 1 -ratio 10 -model end2end -sparse 0 -gen_mode 0 -non_linearity elu -epoch_d 5 -half_val_as_train 1

MLP

Run the following command:

python main.py -dataset citeseer -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.001 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 1024 -dropout1 0.25 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 30 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 1 -non_linearity relu -mlp_act tanh -mlp_h 3703 -epoch_d 5 -half_val_as_train 1

MLP-D

Run the following command:

python main.py -dataset citeseer -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.01 -w_decay 0.05 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 1024 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 20 -lambda_ 10.0 -nr 5 -ratio 10 -model end2end -sparse 0 -gen_mode 2 -non_linearity relu -mlp_act tanh -epoch_d 5 -half_val_as_train 1

Pubmed

MLP

Run the following command:

python main.py -dataset pubmed -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.01 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 128 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.5 -dropout_adj2 0.5 -k 15 -lambda_ 10.0 -nr 5 -ratio 20 -model end2end -gen_mode 1 -non_linearity relu -mlp_h 500 -mlp_act relu -epoch_d 5 -sparse 1

MLP-D

Run the following command:

python main.py -dataset pubmed -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.01 -w_decay 0.0005 -nlayers 2 -nlayers_adj 2 -hidden 32 -hidden_adj 128 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.25 -k 15 -lambda_ 100.0 -nr 5 -ratio 20 -model end2end -sparse 0 -gen_mode 2 -non_linearity relu -mlp_act tanh -epoch_d 5 -sparse 1

ogbn-arxiv

MLP

Run the following command:

python main.py -dataset ogbn-arxiv -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.001 -w_decay 0.0 -nlayers 2 -nlayers_adj 2 -hidden 256 -hidden_adj 256 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.25 -dropout_adj2 0.5 -k 15 -lambda_ 10.0 -nr 5 -ratio 100 -model end2end -sparse 0 -gen_mode 1 -non_linearity relu -mlp_h 128 -mlp_act relu -epoch_d 2001 -sparse 1 -loss mse -noise mask

MLP-D

Run the following command:

python main.py -dataset ogbn-arxiv -ntrials 10 -epochs_adj 2000 -lr 0.01 -lr_adj 0.001 -w_decay 0.0 -nlayers 2 -nlayers_adj 2 -hidden 256 -hidden_adj 256 -dropout1 0.5 -dropout2 0.5 -dropout_adj1 0.5 -dropout_adj2 0.25 -k 15 -lambda_ 10.0 -nr 5 -ratio 100 -model end2end -sparse 0 -gen_mode 2 -non_linearity relu -mlp_act relu -epoch_d 2001 -sparse 1 -loss mse -noise normal

Cite SLAPS

If you use this package for published work, please cite the following:

@inproceedigs{fatemi2021slaps,
  title={SLAPS: Self-Supervision Improves Structure Learning for Graph Neural Networks},
  author={Fatemi, Bahare and Asri, Layla El and Kazemi, Seyed Mehran},
  booktitle={Advances in Neural Information Processing Systems},
  year={2021}
}
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Comments
  • Loss is nan when setting args.sparse=1 on Citeseer

    Loss is nan when setting args.sparse=1 on Citeseer

    When I run the code on Citeseer and set args.sparse=1, I got a nan loss. I debug the code and find that the values of edges calculated by function knn_fast() contain nan values. How could I fix this bug? Thank you for your attention for this issue!

    opened by ryy980622 2
  • issue with DAE

    issue with DAE

    compare the generated features with original features, the size must match. so at model.py line 30:
    self.layers.append(GCNConv_dense(hidden_dim, nclasses))

    think it should be self.layers.append(GCNConv_dense(hidden_dim, in_dim))

    opened by jingyonglin 1
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