Do Transformers Really Perform Bad for Graph Representation?

Graphormer

By Chengxuan Ying, Tianle Cai, Shengjie Luo, Shuxin Zheng*, Guolin Ke, Di He*, Yanming Shen and Tie-Yan Liu.

This repo is the official implementation of "Do Transformers Really Perform Bad for Graph Representation?".

Introduction

Graphormer is initially described in arxiv, which is a standard Transformer architecture with several structural encodings, which could effectively encoding the structural information of a graph into the model.

Graphormer achieves strong performance on PCQM4M-LSC (0.1234 MAE on val), MolPCBA (31.39 AP(%) on test), MolHIV (80.51 AUC(%) on test) and ZINC (0.122 MAE on test), surpassing previous models by a large margin.

Main Results

PCQM4M-LSC

OGBG-MolPCBA

OGBG-MolHIV

ZINC-500K

Requirements and Installation

Setup with Conda

# create a new environment
conda create --name graphormer python=3.7
conda activate graphormer
# install requirements
pip install rdkit-pypi cython
pip install ogb==1.3.1 pytorch-lightning==1.3.0
pip install torch==1.7.1+cu110 torchvision==0.8.2+cu110 -f https://download.pytorch.org/whl/torch_stable.html
pip install torch-geometric==1.6.3 ogb==1.3.1 pytorch-lightning==1.3.1 tqdm torch-sparse==0.6.9 torch-scatter==2.0.6 -f https://pytorch-geometric.com/whl/torch-1.7.0+cu110.html

Citation

Please kindly cite this paper if you use the code:

@article{ying2021transformers,
  title={Do Transformers Really Perform Bad for Graph Representation?},
  author={Ying, Chengxuan and Cai, Tianle and Luo, Shengjie and Zheng, Shuxin and Ke, Guolin and He, Di and Shen, Yanming and Liu, Tie-Yan},
  journal={arXiv preprint arXiv:2106.05234},
  year={2021}
}

GitHub

https://github.com/Microsoft/Graphormer