Locality-Aware Graph-Rewiring in GNNs

In this repository, we release the code required to replicate and expand upon our results in our work: Locality-Aware Graph-Rewiring in GNNs. We release our work under the MIT license.

DISCLAIMER: The baseline results on LRGB are outdated as others has found that the original models were heavily undertuned. Please see this work for more details. As a consequence, we heavily encourage not using this repository as is, but rather running using the updated version of LRGB. As the main author is now working on different research, this repository is now not maintained anymore.

The core of the functionality of LASER may be found in the laser/rewiring directory, with the details being described in the paper and in the docs within the code.

Environment for LASER with Conda

We recommend building the environment through Conda.

conda create -n laser python=3.9
conda activate laser

conda install pytorch=1.9 torchvision torchaudio -c pytorch -c nvidia
conda install pyg=2.0.2 -c pyg -c conda-forge
conda install pandas scikit-learn

# RDKit is required for OGB-LSC PCQM4Mv2 and datasets derived from it.  
conda install openbabel fsspec rdkit -c conda-forge

# Check https://www.dgl.ai/pages/start.html to install DGL based on your CUDA requirements
pip install dgl-cu111 dglgo -f https://data.dgl.ai/wheels/repo.html

pip install performer-pytorch
pip install torchmetrics==0.7.2
pip install ogb
pip install wandb
pip install torch_geometric=2.0.2 pytorch_lightning yacs torch_scatter torch_sparse numba pytest

conda clean --all

Running LASER

The configuration files may be found in /configs, while utility running scripts may be found in /run. Here are some examples:

conda activate laser

# Run automated tests
pytest . 

# Running LASER on PCQM-Contact
python main.py --cfg configs/Contact-laser/pcqm-contact-GCN-laserglobal.yaml wandb.use False

# Running the LASER ablation study on Peptides-func
bash run/run_peptides_laser_ablation_func.sh

# Running the SAGE results on Peptides
bash run/run_sage_lrgb.sh

# Running the LASER TUDatasets results (warning that there is some stochasticity in the results)
bash run/run_tudataset_baselines.sh
bash run/run_tudataset_laser.sh

We note that for the TUDatasets experiments, as discussed in the paper, there is a lot of stochasticity which makes reproducing the results less reliable. This is instead not the case for the LRGB experiments.

Acknowledgments

In order to accurately replicate part of the baseline results, our code builds upon the Long-Range Graph Benchmark (LRGB) repository. We additionally borrow the implementations of First Order Spectral Rewiring (FOSR) and Stochastic Discrete Ricci Flow (SDRF) from their respective authors.