GGBall

Environment installation

This code was tested with PyTorch 2.0.1, cuda 11.8 and torch_geometrics 2.3.1

• Download anaconda/miniconda if needed

• Create a rdkit environment that directly contains rdkit:

  conda create -c conda-forge -n ggball rdkit=2023.03.2 python=3.9

• conda activate ggball

• Check that this line does not return an error:

  python3 -c 'from rdkit import Chem'

• Install graph-tool (https://graph-tool.skewed.de/):

  conda install -c conda-forge graph-tool=2.45

• Check that this line does not return an error:

  python3 -c 'import graph_tool as gt'

• Install the nvcc drivers for your cuda version. For example:

  conda install -c "nvidia/label/cuda-11.8.0" cuda

• Install a corresponding version of pytorch, for example:

  pip3 install torch==2.0.1 --index-url https://download.pytorch.org/whl/cu118

• Install other packages using the requirement file:

  pip install -r requirements.txt

• Install Geoopt:

  pip install geoopt

• Install pyg:

  ''' pip install pyg_lib torch_scatter torch_sparse torch_cluster torch_spline_conv -f https://data.pyg.org/whl/torch-2.0.1+cu118.html'''

• Run:

  pip install -e .

• Navigate to the ./analysis/orca directory and compile orca.cpp:

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

Note: graph_tool and torch_geometric currently seem to conflict on MacOS, I have not solved this issue yet.

Run the code

• All code about HAE or HVQVAE is currently launched through python3 main.py. Check hydra documentation (https://hydra.cc/) for overriding default parameters.
• To run the debugging code: python3 main.py dataset.debug=true. We advise to try to run the debug mode first before launching full experiments.
• To run a code with poincare flow matching: python3 train_flow.py.
• You can specify the dataset with python3 main.py dataset=ego_small. Look at configs/dataset for the list of datasets that are currently available

Generated samples

We provide the generated samples for some of the models. If you have retrained a model from scratch for which the samples are not available yet, we would be very happy if you could send them to us!

Troubleshooting

PermissionError: [Errno 13] Permission denied: './GGBall/analysis/orca/orca': You probably did not compile orca.