Dependencies

Please use the following command to install the requirements:

pip install -r requirements.txt

For molecule generation, additionally run the following command:

conda install -c conda-forge rdkit=2020.09.1.0
pip install git+https://github.com/fabriziocosta/EDeN.git

Preparations

To preprocess the molecular graph datasets for training models, run the following command:

python data/preprocess.py --dataset ${dataset_name}
python data/preprocess_for_nspdk.py --dataset ${dataset_name}

For the evaluation of generic graph generation tasks, run the following command to compile the ORCA program (see http://www.biolab.si/supp/orca/orca.html):

cd evaluation/orca 
g++ -O2 -std=c++11 -o orca orca.cpp

Configurations

The configurations are provided on the configs/ directory.

Pretrained checkpoints

We provide checkpoints of the pretrained models on the checkpoints/ directory, which are used in the experiments.

For the VAE checkpoints:

• ego_small/ae/ae.pth
• community_small/ae/ae.pth
• ENZYMES/ae/ae.pth
• grid/ae/ae.pth
• QM9/ae/ae.pth
• ZINC250k/ae/ae.pth

For the score model checkpoints:

• ego_small/score_model/score_model.pth
• community_small/score_model/score_model.pth
• ENZYMES/score_model/score_model.pth
• grid/score_model/score_model.pth
• QM9/score_model/score_model.pth
• ZINC250k/score_model/score_model.pth

Training

We provide the commands for training a hyperbolic score model on several datasets.

For example, to train a VAE on QM9

python qm9_autoencoder.py

and then train the score model,

python qm9.py

To train on generic graph datasets, please import the appropriate config and comment out unrelated configuration librariesin train_synthetic.py and train_synthetic_autoencoder.py.

For example:

# import configs.community_small_config as configs
import configs.ego_small_config as configs
# import configs.enzymes_config as configs
# import configs.grid_config as configs

Sampling scripts

We provide sampling scripts of our models on the script/ directory

• script/sample_community_small.sh
• script/sample_ego_small.sh
• script/sample_enzymes.sh
• script/sample_grid.sh
• script/sample_qm9.sh
• script/sample_zinc.sh

To sample on qm9:

sh script/sample_qm9.sh