README.md

GemNet: Universal Directional Graph Neural Networks for Molecules

Reference implementation in PyTorch of the geometric message passing neural network (GemNet). You can find its original TensorFlow 2 implementation in another repository. GemNet is a model for predicting the overall energy and the forces acting on the atoms of a molecule. It was proposed in the paper:

GemNet: Universal Directional Graph Neural Networks for Molecules
by Johannes Klicpera, Florian Becker, Stephan Günnemann
Published at NeurIPS 2021.

Run the code

Adjust config.yaml (or config_seml.yaml) to your needs. This repository contains notebooks for training the model (train.ipynb) and for generating predictions on a molecule loaded from ASE (predict.ipynb). It also contains a script for training the model on a cluster with Sacred and SEML (train_seml.py).

Compute scaling factors

You can either use the precomputed scaling_factors (in scaling_factors.json) or compute them yourself by running fit_scaling.py. Scaling factors are used to ensure a consistent scale of activations at initialization. They are the same for all GemNet variants.

Contact

Please contact [email protected] if you have any questions.

Cite

Please cite our paper if you use the model or this code in your own work:

@inproceedings{klicpera_gemnet_2021,
  title = {GemNet: Universal Directional Graph Neural Networks for Molecules},
  author = {Klicpera, Johannes and Becker, Florian and G{\"u}nnemann, Stephan},
  booktitle={Conference on Neural Information Processing Systems (NeurIPS)},
  year = {2021}
}