An Empirical Study of Graphormer on Large-Scale Molecular Modeling Datasets

Abstract

This technical note describes the recent updates of Graphormer, including architecture design modifications, and the adaption to 3D molecular dynamics simulation. The "Graphormer-V2" could attain better results on large-scale molecular modeling datasets than the vanilla one, and the performance gain could be consistently obtained on downstream tasks. In addition, we show that with a global receptive field and an adaptive aggregation strategy, Graphormer is more powerful than classic message-passing-based GNNs. Graphormer-V2 achieves much less MAE than the vanilla Graphormer on the PCQM4M quantum chemistry dataset used in KDD Cup 2021, where the latter one won the first place in this competition. In the meanwhile, Graphormer-V2 greatly outperforms the competitors in the recent Open Catalyst Challenge, which is a competition track on NeurIPS 2021 workshop, and aims to model the catalyst-adsorbate reaction system with advanced AI models. All models could be found at \url{https://github.com/Microsoft/Graphormer}.