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moflow

Please refer to our paper:

Zang, Chengxi, and Fei Wang. "MoFlow: an invertible flow model for generating molecular graphs." In Proceedings of the 26th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, pp. 617-626. 2020.

https://arxiv.org/abs/2006.10137
@inproceedings{zang2020moflow,
  title={MoFlow: an invertible flow model for generating molecular graphs},
  author={Zang, Chengxi and Wang, Fei},
  booktitle={Proceedings of the 26th ACM SIGKDD International Conference on Knowledge Discovery \& Data Mining},
  pages={617--626},
  year={2020}
}

0. Install Libs:

conda create --name moflow python pandas matplotlib    (conda 4.6.7, python 3.8.5, pandas 1.1.2, matplotlib  3.3.2)
conda activate moflow
conda install pytorch torchvision cudatoolkit=10.2 -c pytorch (pytorch 1.6.0, torchvision 0.7.0)
conda install rdkit  (rdkit 2020.03.6)
conda install orderedset  (orderset 2.0.3)
conda install tabulate  (tabulate 0.8.7)
conda install networkx  (networkx 2.5)
conda install scipy  (scipy 1.5.0)
conda install seaborn  (seaborn 0.11.0)
pip install cairosvg (cairosvg 2.4.2)
pip install tqdm  (tqdm 4.50.0)

To clone code from this project, say

git clone https://github.com/calvin-zcx/moflow.git moflow

1. Data Preprocessing

To generate molecular graphs from SMILES strings

cd data
python data_preprocess.py --data_name qm9
python data_preprocess.py --data_name zinc250k

2. Model Training

Training model for QM9 dataset:

cd mflow
python train_model.py --data_name qm9  --batch_size 256  --max_epochs 200 --gpu 0  --debug True  --save_dir=results/qm9_64gnn_128-64lin_1-1mask_0d6noise_convlu1  --b_n_flow 10  --b_hidden_ch 128,128  --a_n_flow 27 --a_hidden_gnn 64  --a_hidden_lin 128,64  --mask_row_size_list 1 --mask_row_stride_list 1 --noise_scale 0.6 --b_conv_lu 1  2>&1 | tee qm9_64gnn_128-64lin_1-1mask_0d6noise_convlu1.log

Training model for zinc250k dataset:

cd mflow
python train_model.py  --data_name zinc250k  --batch_size  256  --max_epochs 200 --gpu 0  --debug True  --save_dir=results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask   --b_n_flow 10  --b_hidden_ch 512,512  --a_n_flow 38  --a_hidden_gnn 256  --a_hidden_lin  512,64   --mask_row_size_list 1 --mask_row_stride_list 1  --noise_scale 0.6  --b_conv_lu 2  2>&1 | tee zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask.log

Or downloading and using our trained models in

https://drive.google.com/drive/folders/1runxQnF3K_VzzJeWQZUH8VRazAGjZFNF 

3. Model Testing

3.1-Experiment: reconstruction

To reconstruct QM9 dataset:

cd mflow
python generate.py --model_dir results/qm9_64gnn_128-64lin_1-1mask_0d6noise_convlu1 -snapshot model_snapshot_epoch_200 --gpu 0 --data_name qm9  --hyperparams-path moflow-params.json --batch-size 256 --reconstruct  2>&1 | tee qm9_reconstruct_results.txt
### Results
Tips:  results can be printed & dumped to a .txt file by  "2>&1 | tee qm9_reconstruct_results.txt"
133885 in total, 120803  training data, 13082  testing data, 256 batchsize, train/batchsize 471.88671875
...
iter/total: 468/472, reconstruction_rate:1.0
iter/total: 469/472, reconstruction_rate:1.0
iter/total: 470/472, reconstruction_rate:1.0
iter/total: 471/472, reconstruction_rate:1.0
reconstruction_rate for all the train data:1.0 in 120803
Invertible model! 100% reconstruction!

To reconstruct zinc250k dataset:

cd mflow
python generate.py --model_dir results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask  -snapshot model_snapshot_epoch_200 --gpu  0  --data_name zinc250k --hyperparams-path moflow-params.json --batch-size 256  --reconstruct   2>&1 | tee zinc250k_reconstruct_results.txt
Results:
249455 in total, 224568  training data, 24887  testing data, 256 batchsize, train/batchsize 877.21875
...
iter/total: 877/878, reconstruction_rate:1.0
reconstruction_rate for all the train data:1.0 in 224568
Invertible model! 100% reconstruction!

3.2-Experiment: Random generation

Random Generation from sampling from latent space, QM9 model

10000 samples * 5 times:

python generate.py --model_dir results/qm9_64gnn_128-64lin_1-1mask_0d6noise_convlu1 -snapshot model_snapshot_epoch_200 --gpu 0 --data_name qm9 --hyperparams-path moflow-params.json --batch-size 10000 --temperature 0.85 --delta 0.05 --n_experiments 5 --save_fig false --correct_validity true 2>&1 | tee qm9_random_generation.log
Results
validity: mean=100.00%, sd=0.00%, vals=[100.0, 100.0, 100.0, 100.0, 100.0]
novelty: mean=98.05%, sd=0.12%, vals=[98.07731024763439, 98.11472930738985, 97.88434414668548, 97.95239055880573, 98.21877830331086]
uniqueness: mean=99.26%, sd=0.09%, vals=[99.33999999999999, 99.19, 99.26, 99.14, 99.37]
abs_novelty: mean=97.32%, sd=0.18%, vals=[97.43, 97.32, 97.16, 97.11, 97.6]
abs_uniqueness: mean=99.26%, sd=0.09%, vals=[99.33999999999999, 99.19, 99.26, 99.14, 99.37]
Task random generation done! Time 185.09 seconds, Data: Tue Sep 29 11:20:15 2020
# Above is just one random result. Tuning:
    --batch-size for the number of  mols to be generated
    --temperature for different generation results, 
    --correct_validity false for results without correction
    --save_fig true for figures of generated mols, set batch-size a resoanble number for dump figures 
# more details see parameter configuration in generate.py
# Output details are in qm9_random_generation.log

Random Generation from sampling from latent space, zinc250k model

10000 samples * 5 times:

python generate.py --model_dir results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask  -snapshot model_snapshot_epoch_200 --gpu  0  --data_name zinc250k --hyperparams-path moflow-params.json   --temperature 0.85  --batch-size 10000 --n_experiments 5  --save_fig false --correct_validity true 2>&1 | tee zinc250k_random_generation.log
Results
validity: mean=100.00%, sd=0.00%, vals=[100.0, 100.0, 99.99, 100.0, 100.0]
novelty: mean=100.00%, sd=0.00%, vals=[100.0, 100.0, 100.0, 100.0, 100.0]
uniqueness: mean=99.99%, sd=0.01%, vals=[100.0, 99.98, 100.0, 99.99, 99.99]
abs_novelty: mean=99.99%, sd=0.01%, vals=[100.0, 99.98, 99.99, 99.99, 99.99]
abs_uniqueness: mean=99.99%, sd=0.01%, vals=[100.0, 99.98, 99.99, 99.99, 99.99]
Task1 random generation done! Time 537.13 seconds, Data: Tue Sep 29 11:36:12 2020
# Above is just one random result. Tuning:
    --batch-size for the number of  mols to be generated
    --temperature for different generation results, 
    --correct_validity false for results without correction
    --save_fig true for figures of generated mols, set batch-size a resoanble number for dump figures 
# more details see parameter configuration in generate.py
# Output details are in qm9_random_generation.log

3.3-Experiment: Interpolation generation & visualization

Interpolation in the latent space, QM9 model

interpolation between 2 molecules (molecular graphs)

python generate.py --model_dir results/qm9_64gnn_128-64lin_1-1mask_0d6noise_convlu1 -snapshot model_snapshot_epoch_200 --gpu 0 --data_name qm9  --hyperparams-path moflow-params.json --batch-size 1000  --temperature 0.65   --int2point --inter_times 50  --correct_validity true 2>&1 | tee qm9_visualization_int2point.log

interpolation in a grid of molecules (molecular graphs)

python generate.py --model_dir results/qm9_64gnn_128-64lin_1-1mask_0d6noise_convlu1 -snapshot model_snapshot_epoch_200 --gpu 0 --data_name qm9  --hyperparams-path moflow-params.json --batch-size 1000  --temperature 0.65 --delta 5  --intgrid  --inter_times 40  --correct_validity true 2>&1 | tee tee qm9_visualization_intgrid.log

Interpolation in the latent space, zinc250k model

interpolation between 2 molecules (molecular graphs)

python generate.py --model_dir results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask  -snapshot model_snapshot_epoch_200 --gpu  0  --data_name zinc250k --hyperparams-path moflow-params.json --batch-size 1000  --temperature 0.8 --delta 0.5  --n_experiments 0 --correct_validity true   --int2point  --inter_times 10  2>&1 | tee zinc250k_visualization_int2point.log

interpolation in a grid of molecules (molecular graphs)

python generate.py --model_dir results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask  -snapshot model_snapshot_epoch_200 --gpu  0  --data_name zinc250k --hyperparams-path moflow-params.json --batch-size 1000  --temperature 0.8 --delta 5  --n_experiments 0 --correct_validity true   --intgrid --inter_times 2  2>&1 | tee zinc250k_visualization_intgrid.log

Some illustrations

interpolation

interpolation

3.4-Experiment: Molecular optimization & constrained optimization

Optimizing zinc250k w.r.t QED property

Training an additional MLP from latent space to QED property

python optimize_property.py -snapshot model_snapshot_epoch_200  --hyperparams_path moflow-params.json --batch_size 256 --model_dir results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask   --gpu 0 --max_epochs 3  --weight_decay 1e-3  --data_name zinc250k  --hidden 16,  --temperature 1.0  --property_name qed 2>&1 | tee  training_optimize_zinc250k_qed.log
# Output: a molecular property prediction model for optimization, say named as qed_model.pt
# e.g. saving qed regression model to: results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask/qed_model.pt
# Train and save model done! Time 477.87 seconds 
# Can tune:
#         --max_epochs 3  
#         --weight_decay 1e-3  
#         --hidden 16
# etc.

Or downloading and using our trained models in

https://drive.google.com/drive/folders/1runxQnF3K_VzzJeWQZUH8VRazAGjZFNF 

To optimize existing molecules to get novel molecules with optimized QED scores

python optimize_property.py -snapshot model_snapshot_epoch_200  --hyperparams_path moflow-params.json --batch_size 256 --model_dir results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask   --gpu 0   --data_name zinc250k   --property_name qed --topk 2000  --property_model_path qed_model.pt --debug false  --topscore 2>&1 | tee  zinc250k_top_qed_optimized.log
# Input: --property_model_path qed_model.pt is the regression model
# Output: dump a ranked list of generated optimized and novel molecules w.r.t qed

Illustrations of molecules with top QED

Optimization

Constrained Optimizing zinc250k w.r.t plogp(or qed) + similarity property

to train an additional MLP from latent space to plogp property

python optimize_property.py -snapshot model_snapshot_epoch_200  --hyperparams_path moflow-params.json --batch_size 256 --model_dir results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask   --gpu 0  --max_epochs 3  --weight_decay 1e-2  --data_name zinc250k  --hidden 16,  --temperature 1.0  --property_name plogp 2>&1 | tee training_optimize_zinc250k_plogp.log
# Output: a molecular property prediction model for optimization, say named as plogp_model.pt
# e.g. saving plogp  regression model to: results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask/plogp_model.pt
# Train and save model done! Time 473.74 seconds
# Can tune:
#         --max_epochs 3  
#         --weight_decay 1e-2  
#        --hidden 16
#etc.

To optimize existing molecules to get novel molecules with optimized plogp scores and constrained similarity

python optimize_property.py -snapshot model_snapshot_epoch_200  --hyperparams_path moflow-params.json --batch_size 256 --model_dir results/zinc250k_512t2cnn_256gnn_512-64lin_10flow_19fold_convlu2_38af-1-1mask   --gpu 0    --data_name zinc250k    --property_name plogp --topk 800 --property_model_path qed_model.pt   --consopt  --sim_cutoff 0 2>&1 | tee  zinc250k_constrain_optimize_plogp.log
# Input: --property_model_path qed_model.pt or plogp_model.pt is the regression model
         --sim_cutoff 0 (or 0.2, 0.4 etc for similarity)
         --topk 800 (choose first 800 molecules with worset property values for improving)
# Output: 
# Using qed_model.pt for optimizing plogp with 
# Because qed and plogp have some correlations, here we use both qed/plogp model for 2 optimization tasks
# --sim_cutoff 0:
#   similarity: 0.300610 +/- 0.201674 
#   Improvement:  8.612461 +/- 5.436995
#   success rate: 0.98875
# --sim_cutoff 0.2:
#   similarity:  0.434700 +/-  0.196490 
#   Improvement:  7.057115 +/-  5.041250
#   success rate: 0.9675
# --sim_cutoff 0.4:
#   similarity:  0.608440 +/-   0.177670 
#   Improvement:  4.712418 +/-   4.549682
#   success rate: 0.8575
# --sim_cutoff 0.6:
#   similarity:   0.792550 +/- 0.144577   
#   Improvement:   2.095266 +/-   2.858545  
#   success rate:  0.5825

# Using plogp_model.pt for optimizing plogp with 
# --sim_cutoff 0:
#    similarity:  0.260503 +/- 0.195945
#   Improvement:  9.238813 +/-  6.279859
#   success rate: 0.9925
# --sim_cutoff 0.2:
#    similarity:  0.425541 +/- 0.198020
#    Improvement:  7.246221 +/-  5.325543
#    success rate: 0.9575
# --sim_cutoff 0.4:
#    similarity:   0.625976 +/- 0.189293
#    Improvement:  4.504411 +/-  4.712031
#    success rate: 0.8425
# --sim_cutoff 0.6:
#    similarity:   0.810805 +/- 0.146080
#    Improvement:  1.820525 +/-  2.595302
#    success rate: 0.565

More configurations please refer to our codes optimize_property.py and the optimization chapter in our paper.

One illustration of optimizing plogp

optimiation plogp

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