Official implementation (Pytorch 1.7.1) of:
E(n) Equivariant Normalizing Flows
Victor Garcia Satorras*, Emiel Hogeboom*, Fabian Fuchs, Ingmar Posner, Max Welling
https://arxiv.org/abs/2105.09016
Abstract: This paper introduces a generative model equivariant to Euclidean symmetries: E(n) Equivariant Normalizing Flows (E-NFs). To construct E-NFs, we take the discriminative E(n) graph neural networks and integrate them as a differential equation to obtain an invertible equivariant function: a continuous-time normalizing flow. We demonstrate that E-NFs considerably outperform baselines and existing methods from the literature on particle systems such as DW4 and LJ13, and on molecules from QM9 in terms of log-likelihood. To the best of our knowledge, this is the first flow that jointly generates molecule features and positions in 3D.
- Pytorch 1.7.1
- wandb (Weights and Biases)
- rdkit-pypi (Only for evaluation scripts)
You can use your Weights & Biases username by adding --wandb_usr <your username> to the experiments
GNN
EXP_NAME=exp_dw4_gnn_noatt_noaug python -u main_dw4_lj13.py --exp_name $EXP_NAME --data dw4 --model gnn_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation False --attention False
GNN attention
EXP_NAME=exp_dw4_gnn_att_noaug python -u main_dw4_lj13.py --exp_name $EXP_NAME --data dw4 --model gnn_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation False
GNN attention and augmentation
EXP_NAME=exp_dw4_gnn_att_aug python -u main_dw4_lj13.py --exp_name $EXP_NAME --data dw4 --model gnn_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation True
Simple dynamics.
EXP_NAME=exp_dw4_simple_dynamics python -u main_dw4_lj13.py --exp_name $EXP_NAME --data dw4 --model simple_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation False
Kernel dynamics
EXP_NAME=exp_dw4_kernel_dynamics python -u main_dw4_lj13.py --exp_name $EXP_NAME --data dw4 --model kernel_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation False
E-NF
EXP_NAME=exp_dw4_egnn python -u main_dw4_lj13.py --exp_name $EXP_NAME --data dw4 --model egnn_dynamics --sweep_n_data True --lr 5e-4 --n_layers 3 --nf 32
GNN
EXP_NAME=exp_lj13_gnn_noatt_noaug python -u main_dw4_lj13.py --exp_name $EXP_NAME --data lj13 --model gnn_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation False --attention False
GNN attention
EXP_NAME=exp_lj13_gnn_att python -u main_dw4_lj13.py --exp_name $EXP_NAME --data lj13 --model gnn_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation False
GNN attention and augmentation
EXP_NAME=exp_lj13_gnn_att_aug_a python -u main_dw4_lj13.py --exp_name $EXP_NAME --data lj13 --model gnn_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation True
Simple dynamics
EXP_NAME=exp_lj13_simple_dynamics python -u main_dw4_lj13.py --exp_name $EXP_NAME --data lj13 --model simple_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation False
Kernel dynamics
EXP_NAME=exp_lj13_kernel_dynamics python -u main_dw4_lj13.py --exp_name $EXP_NAME --data lj13 --model kernel_dynamics --sweep_n_data True --lr 1e-3 --n_layers 3 --nf 32 --data_augmentation False
EGNN
EXP_NAME=exp_lj13_egnn python -u main_dw4_lj13.py --exp_name $EXP_NAME --data lj13 --model egnn_dynamics --sweep_n_data True --lr 5e-4 --n_layers 3 --nf 32
E-NF
EXP_NAME=qm9pos_exp_27_egnn_nf64 python -u main_qm9_pos.py --exp_name $EXP_NAME --model egnn_dynamics --nf 64
GNN
EXP_NAME=qm9pos_exp_27_gnn_noatt_nf64 python -u main_qm9_pos.py --exp_name $EXP_NAME --model gnn_dynamics --nf 64 --lr 5e-4 --attention False
GNN attention
EXP_NAME=qm9pos_exp_27_gnn_att_nf64 python -u main_qm9_pos.py --exp_name $EXP_NAME --model gnn_dynamics --nf 64 --lr 5e-4 --save_model True
GNN attention and augmentation
EXP_NAME=qm9pos_exp_27_gnn_att_aug_nf64 python -u main_qm9_pos.py --exp_name $EXP_NAME --model gnn_dynamics --nf 64 --lr 5e-4 --save_model True
Kernel dynamics
EXP_NAME=qm9pos_exp_27_kernel_dynamics python -u main_qm9_pos.py --exp_name $EXP_NAME --model kernel_dynamics --lr 5e-4
Simple dynamics
EXP_NAME=qm9pos_exp_27_simple_dynamics_lr2e4 python -u main_qm9_pos.py --exp_name $EXP_NAME --model simple_dynamics --lr 2e-4
To train E-NF on QM9
python main_qm9.py --nf 64 --ode_regularization 0.001 --batch_size 128 --dequantizer argmax_variational --lr 5e-4 --exp_name qm9_enf --model egnn_dynamics
To train the best baseline on QM9 (GNN attention and augmentation)
python main_qm9.py --nf 64 --ode_regularization 0.001 --batch_size 128 --dequantizer argmax_variational --lr 5e-4 --exp_name qm9_baseline_augmentation --model gnn_dynamics --data_augmentation True
To resume the training on qm9 in case it diverges, you can use the same commands as before but adding two argumens. You will get experiments/<exp_name>_resume_resume
--resume experiments/<exp_name> --start_epoch <last_saved_epoch>
To evaluate a pre-trained model on QM9 (n_samples=10000 for the reported numbers in the paper)
python -u eval_analyze_qm9.py --model_path outputs/en_flows_pretrained --n_samples 1000 --val_novel_unique False
To generate samples from a pre-trained model run
python -u eval_sample_qm9.py --model_path outputs/en_flows_pretrained
The Robert Bosch GmbH is acknowledged for financial support.
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