Awesome
<div align="center">BootGen
Official code for BootGen: "Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences".
<a href="https://pytorch.org/get-started/locally/"><img alt="PyTorch" src="https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white"></a>
Dependencies
- Python==3.7
pip install flexs
conda install -c bioconda viennarna
pip install design-bench==2.0.20
pip install polyleven
Running BootGen
GFP
python train.py --DA --task gfp --lr 5e-5
UTR
python train.py --DA --task utr --lr 5e-5
TFbind 8
python train.py --DA --task tfbind
RNA-A
python train.py --DA --task rna1
RNA-B
python train.py --DA --task rna2
RNA-C
python train.py --DA --task rna3
To test BootGen without "diverse aggregation," simply remove the "--DA" flag.
Cite us
If you find this code useful, please cite our paper:
@article{kim2023bootstrapped,
title={Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences},
author={Kim, Minsu and Berto, Federico and Ahn, Sungsoo and Park, Jinkyoo},
journal={arXiv preprint arXiv:2306.03111},
year={2023}
}