dimenet

DGL Implementation of DimeNet and DimeNet++

This DGL example implements the GNN model proposed in the paper Directional Message Passing for Molecular Graphs and Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules. For the original implementation, see here.

Contributor: xnuohz

• This example implements both DimeNet and DimeNet++.
• The advantages of DimeNet++ over DimeNet
  • Fast interactions: replacing bilinear layer with a simple Hadamard priduct
  • Embedding hierarchy: using a higher number of embeddings by reducing the embedding size in blocks via down- and up-projection layers
  • Other improvements: using less interaction blocks

Requirements

The codebase is implemented in Python 3.6. For version requirement of packages, see below.

click 7.1.2
dgl 0.6.0
logzero 1.6.3
numpy 1.19.5
ruamel.yaml 0.16.12
scikit-learn 0.24.1
scipy 1.5.4
sympy 1.7.1
torch 1.7.0
tqdm 4.56.0

The graph datasets used in this example

The DGL's built-in QM9 dataset. Dataset summary:

• Number of Molecular Graphs: 130,831
• Number of Tasks: 12

Usage

Note: DimeNet++ is recommended to use over DimeNet.

Examples

The following commands learn a neural network and predict on the test set. Training a DimeNet model on QM9 dataset.

python main.py --model-cnf config/dimenet.yaml

Training a DimeNet++ model on QM9 dataset.

python main.py --model-cnf config/dimenet_pp.yaml

For faster experimentation, you should first put the author's pretrained folder here, which contains pre-trained TensorFlow models. You can convert a TensorFlow model to a PyTorch model by using the following commands.

python convert_tf_ckpt_to_pytorch.py --model-cnf config/dimenet_pp.yaml --convert-cnf config/convert.yaml

Then you can set flag: True in dimenet_pp.yaml and run the above script, DimeNet++ will use the pretrained weights to predict on the test set.

Configuration

For more details, please see config/dimenet.yaml and config/dimenet_pp.yaml

Model options

// The following paramaters are only used in DimeNet++
out_emb_size      int    Output embedding size.                                         Default is 256
int_emb_size      int    Input embedding size.                                          Default is 64
basis_emb_size    int    Basis embedding size.                                          Default is 8
extensive         bool   Readout operator for generating a graph-level representation.  Default is True 

// The following paramater is only used in DimeNet
num_bilinear      int    Third dimension of the bilinear layer tensor in DimeNet.       Default is 8

// The following paramaters are used in both DimeNet and DimeNet++
emb_size          int    Embedding size used throughout the model.                              Default is 128
num_blocks        int    Number of building blocks to be stacked.                               Default is 6 in DimeNet and 4 in DimeNet++   
num_spherical     int    Number of spherical harmonics.                                         Default is 7   
num_radial        int    Number of radial basis functions.                                      Default is 6   
envelope_exponent int    Shape of the smooth cutoff.                                            Default is 5   
cutoff            float  Cutoff distance for interatomic interactions.                          Default is 5.0 
num_before_skip   int    Number of residual layers in interaction block before skip connection. Default is 1   
num_after_skip    int    Number of residual layers in interaction block after skip connection.  Default is 2   
num_dense_output  int    Number of dense layers for the output blocks.                          Default is 3   
targets           list   List of targets to predict.                                            Default is ['mu']
output_init       string Initial function name for output layer.                                Default is 'GlorotOrthogonal'

Training options

num_train         int   Number of training samples.                     Default is 110000
num_valid         int   Number of validation samples.                   Default is 10000
data_seed         int   Random seed.                                    Default is 42
lr                float Learning rate.                                  Default is 0.001
weight_decay      float Weight decay.                                   Default is 0.0001
ema_decay         float EMA decay.                                      Default is 0.
batch_size        int   Batch size.                                     Default is 100
epochs            int   Training epochs.                                Default is 300
early_stopping    int   Patient epochs to wait before early stopping.   Default is 20
num_workers       int   Number of subprocesses to use for data loading. Default is 18
gpu               int   GPU index.                                      Default is 0, using CUDA:0
interval          int   Time intervals for model evaluation.            Default is 50
step_size         int   Period of learning rate decay.                  Default is 100
gamma             float Factor of learning rate decay.                  Default is 0.3

Performance

• Batch size is different
• Linear learning rate warm-up is not used
• Exponential learning rate decay is not used
• Exponential moving average (EMA) is not used
• The values for tasks except mu, alpha, r2, Cv should be x 10^-3
• The author's code didn't provide the pretrained model for gap task
• MAE(DimeNet in Table 1) is from here
• MAE(DimeNet++ in Table 2) is from here

Target	mu	alpha	homo	lumo	gap	r2	zpve	U0	U	H	G	Cv
MAE(DimeNet in Table 1)	0.0286	0.0469	27.8	19.7	34.8	0.331	1.29	8.02	7.89	8.11	8.98	0.0249
MAE(DimeNet++ in Table 2)	0.0297	0.0435	24.6	19.5	32.6	0.331	1.21	6.32	6.28	6.53	7.56	0.0230
MAE(DimeNet++, TF, pretrain)	0.0297	0.0435	0.0246	0.0195	-	0.3312	0.00121	0.0063	0.00628	0.00653	0.00756	0.0230
MAE(DimeNet++, TF, scratch)	0.0330	0.0447	0.0251	0.0227	0.0486	0.3574	0.00123	0.0065	0.00635	0.00658	0.00747	0.0224
MAE(DimeNet++, DGL)	0.0326	0.0537	0.0311	0.0255	0.0490	0.4801	0.0043	0.0141	0.0109	0.0117	0.0150	0.0254

Speed

Model	Original Implementation	DGL Implementation	Improvement
DimeNet	2839	1345	2.1x
DimeNet++	624	238	2.6x