This repository contains a tensorflow implementation of GCNN models for node classification, link predicition and joint node classification and link prediction to supplement the survey paper by Chami et al.

NOTE: This is not an officially supported Google product.

• train.py: trains a model with FLAGS parameters. train --helpshort for more information. .

• launch.py: trains several model with varied combinations of parameters. Specify parameters in launch.py file. launch --helpshort for more information.

• best_model.py: Parse the logs for multiple training with launch.py and finds best model parameters based on validation accuracy. best_model --helpshort for more information.

• models/

  • base_models.py: base model functionnalities (data utils, loss function, metrics etc)

  • node_models.py: forward pass implementation of node classification models (including Gat, Gcn, Mlp and SemiEmb)

  • edge_models.py: forward pass implementation of link prediction models (including Gae and Vgae)

  • node_edge_models.py: forward pass implementation of joint node classification and link prediction

• utils/

  • model_utils.py: layers implementation.

  • link_prediction_utils.py: implementation of some link prediction heuristics such as common neighbours or adamic adar

  • data_utils.py: data processing utils functions

  • train_utils.py train utils functions

• data/: contains data files for citation data (cora, citeseer, pubmed) and PPI

0. Install required libraries.

1. Set environment variables GCNN_HOME=$(pwd) export PATH="$GCNN_HOME:$PATH"

2. Put datasets the data folder.

3. Train GAT on cora with default parameters

SAVE_DIRECTORY="/tmp/models/cora/Gat" python train.py --save_dir=$SAVE_DIRECTORY --dataset=cora --model_name=Gat

4. Check results

cat $SAVE_DIRECTORY/*.log

This model should give approximately 83% test accuracy.

5. Launch multiple experiments

To launch multiple experiments for hyper-parameter search use the launch.py script. Update the parameters to search over in the launch.py file. For instance to train Gcn on cora with multiple parameters:

LAUNCH_DIR="/tmp/launch"

python launch.py --launch_save_dir=$LAUNCH_DIR --launch_model_name=Gcn --launch_dataset=cora --launch_n_runs=3

This will create subdirectories $LAUNCH_DIR/dataset_name/prop_edges_removed where the log files will be saved.

6. Retrieve best model parameters

python best_model.py --dir=$LAUNCH_DIR --models=Gcn --target=node_acc --datasets=cora

This will create a best_params file in $LAUNCH_DIR with the best parameters for each (dataset-model-proportion_edges_dropped) combination based on validation metrics.

cat $LAUNCH_DIR/best_params

• Reproduce Gat results on cora (83.5% average test accuracy):

python train.py --model_name=Gat --lr=0.005 --node_l2_reg=0.0005 --dataset=cora --p_drop_node=0.6 --n_att_node=8,1 --n_hidden_node=8 --save_dir=/tmp/models/cora/gat --epochs=10000 --patience=100 --normalize_adj=False --sparse_features=True

• Reproduce Gcn results on cora (81.5% average test accuracy):

python train.py --model_name=Gcn --epochs=200 --patience=10 --lr=0.01 --node_l2_reg=0.0005 --dataset=cora --p_drop_node=0.5 --n_hidden_node=16 --save_dir=/tmp/models/cora/gcn --normalize_adj=True --sparse_features=True

• Better Gcn results on cora (83.1% average test accuracy):

python train.py --model_name=Gcn --epochs=10000 --patience=100 --lr=0.005 --node_l2_reg=0.0005 --dataset=cora --p_drop_node=0.6 --input_dim=1433 --n_hidden_node=128 --save_dir=/tmp/models/cora/gcn_best --normalize_adj=True --sparse_features=True

• Train Gae on Cora with 10% of edges removed

python train.py --model_name=Gae --epochs=10000 --patience=50 --lr=0.005 --p_drop_edge=0. --n_hidden_edge=256-128 --save_dir=/tmp/models/cora/Gae --edge_l2_reg=0 --att_mechanism=dot --normalize_adj=True --edge_loss=w_sigmoid_ce --dataset=cora --sparse_features=True --drop_edge_prop=10

To add a new model:

• Create a model class inheriting from one of the base class (NodeModel, EdgeModel or NodeEdgeModel) and implement the inference step in the correspoding file (node_models.py, edge_models.py or node_edge_models.py)

• Add the model name to the list of models in train.py

To add another dataset:

• Write a load_${dataset_str}_data() function and add it to the load_data(dataset_str, data_path) function. the dataset_str will be the FLAG for this dataset.

• Save the data files in the data/ folder.

GAT original code

GCN original code

GAE original code