Code for our paper "Non-Autoregressive Electron Redistribution Modeling for Reaction Prediction" (ICML 2021)
This repository contains a legacy version of our implementation, which we used to produce the results in our paper. Although the code style may be improved, we leave it unchanged for reproducibility.
The code has been tested using the following environment:
- python 3.7.6
- numpy 1.18.5
- torch 1.8.1
- rdkit 2018.03.4
For each atom, we assume it has at most 6 bonds, and at most 4 bonds around it are broken/formed during reactions.
These constraints can be easily relaxed by changing the hyperparameters in preprocess.py, but we leave them unchanged for reproducibility.
Notice that about 0.3% of reactions in USPTO-MIT do not satisfy the criteria and we subtract all our accuracy by 0.3% for a fair comparison with other methods.
If the training set is in data/train.txt, call
process("data/train")
defined in preprocess.py.
tb_port=6018
port=1$tb_port
n_gpu=2
name=tmp
OMP_NUM_THREADS=8
CUDA_VISIBLE_DEVICES=0,1
python -m torch.distributed.launch --nproc_per_node=$n_gpu --master_port $port ./main.py --world_size $n_gpu --train \
--vae \
--batch_size 128 --dropout=0.1 --depth 6 --dim 256 \
--prefix data --name $name --epochs 250For top-k sampling, we use temperature = 0.7*1.3**n, n = 0, 1,...and use the first k different valid predictions at the lowest temperature as the top-k predictions.
tb_port=6018
port=1$tb_port
n_gpu=1
name=tmp
OMP_NUM_THREADS=8
CUDA_VISIBLE_DEVICES=0
python -m torch.distributed.launch --nproc_per_node=$n_gpu --master_port $port ./main.py --world_size $n_gpu --test \
--vae \
--batch_size 256 --dropout=0.1 --depth 6 --dim 256 \
--prefix data --name $name --epochs 100 --checkpoint tmp.pt --temperature 0.7