bmorphism / tokengt

[Preprint'22] Tokenized Graph Transformer (TokenGT), in PyTorch

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Tokenized Graph Transformer - Official PyTorch Implementation

Pure Transformers are Powerful Graph Learners
Jinwoo Kim, Tien Dat Nguyen, Seonwoo Min, Sungjun Cho, Moontae Lee, Honglak Lee, Seunghoon Hong
arXiv Preprint

image-tokengt

Setting up experiments

Using the provided Docker image (recommended)

docker pull jw9730/tokengt:latest
docker run -it --gpus=all --ipc=host --name=tokengt -v /home:/home jw9730/tokengt:latest bash
# upon completion, you should be at /tokengt inside the container

Using the provided Dockerfile

git clone --recursive https://github.com/jw9730/tokengt.git /tokengt
cd tokengt
docker build --no-cache --tag tokengt:latest .
docker run -it --gpus all --ipc=host --name=tokengt -v /home:/home tokengt:latest bash
# upon completion, you should be at /tokengt inside the container

Using pip

sudo apt-get update
sudo apt-get install python3.9
git clone --recursive https://github.com/jw9730/tokengt.git tokengt
cd tokengt
bash install.sh

Running experiments

PCQM4Mv2 large-scale graph regression

cd large-scale-regression/scripts

# TokenGT (ORF)
bash pcqv2-orf.sh

# TokenGT (Lap)
bash pcqv2-lap.sh

# TokenGT (Lap) + Performer
bash pcqv2-lap-performer-finetune.sh

# TokenGT (ablated)
bash pcqv2-ablated.sh

# Attention distance plot for TokenGT (ORF)
bash visualize-pcqv2-orf.sh

# Attention distance plot for TokenGT (Lap)
bash visualize-pcqv2-lap.sh

Pre-Trained Models

We provide checkpoints of TokenGT (ORF) and TokenGT (Lap), both trained with PCQM4Mv2. Please download ckpts.zip from this link. Then, unzip ckpts and place it in the large-scale-regression/scripts directory, so that each trained checkpoint is located at large-scale-regression/scripts/ckpts/pcqv2-tokengt-[NODE_IDENTIFIER]-trained/checkpoint_best.pt. After that, you can resume the training from these checkpoints by adding the option --pretrained-model-name pcqv2-tokengt-[NODE_IDENTIFIER]-trained to the training scripts.

References

Our implementation uses code from the following repositories:

Citation

If you find our work useful, please consider citing it:

@article{kim2021transformers,
  author    = {Jinwoo Kim and Tien Dat Nguyen and Seonwoo Min and Sungjun Cho and Moontae Lee and Honglak Lee and Seunghoon Hong},
  title     = {Pure Transformers are Powerful Graph Learners},
  journal   = {arXiv},
  volume    = {abs/2207.02505},
  year      = {2022},
  url       = {https://arxiv.org/abs/2207.02505}
}

About

[Preprint'22] Tokenized Graph Transformer (TokenGT), in PyTorch

License:MIT License


Languages

Language:Python 61.9%Language:Jupyter Notebook 32.6%Language:Shell 2.7%Language:Cython 2.2%Language:Dockerfile 0.5%