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
Pythonversion 3.7.2Numpyversion 1.18.5PyTorchversion 1.5.1DGLversion 0.5.2sklearnversion 0.21.3scipyversion 1.2.1torch-geometric1.6.1ogbversion 1.2.3
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 onntrials: number of runsepochs_adj: number of epochsepochs: number of epochs for GNN_C (used for knn_gcn and 2step learning of the model)lr_adj: learning rate of GNN_DAElr: learning rate of GNN_Cw_decay_adj: l2 regularization parameter for GNN_DAEw_decay: l2 regularization parameter for GNN_Cnlayers_adj: number of layers for GNN_DAEnlayers: number of layers for GNN_Chidden_adj: hidden size of GNN_DAEhidden: hidden size of GNN_Cdropout1: dropout rate for GNN_DAEdropout2: dropout rate for GNN_Cdropout_adj1: dropout rate on adjacency matrix for GNN_DAEdropout_adj2: dropout rate on adjacency matrix for GNN_Cdropout2: dropout rate for GNN_Ck: k for knn initialization with knnlambda_: weight of loss of GNN_DAEnr: ratio of zeros to ones to mask out for binary featuresratio: ratio of ones to mask out for binary features and ratio of features to mask out for real values featuresmodel: model to run (choices are end2end, knn_gcn, or 2step)sparse: whether to make the adjacency sparse and run operations on sparse modegen_mode: identifies the graph generatornon_linearity: non-linearity to apply on the adjacency matrixmlp_act: activation function to use for the mlp graph generatormlp_h: hidden size of the mlp graph generatornoise: 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_DAEhalf_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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