ProtFlow

Environment creation

conda env create -f environment.yaml

Ensure all paths and hyperparameters in this project are defined according to your specific tasks. Download facebook/esm2_t12_35M_UR50D, Rostlab/prot_t5_xl_uniref50 and Rostlab/prot_t5_xl_half_uniref50-enc from hunggingface and add them at the root folder.

Data Preparation

create a data folder and convert your specific protein sequences into fasta format, and split it into train.fasta and valid.fasta

Training

1. Compute statistics

python -m utils.get_statistics
python -m utils.stat

2. Decoder training

python train_decoder.py

3. Compression-decompression module training

python train_compressor.py

4. FM holder training

torchrun --nproc_per_node=1 --master_port=31345  train_flow_matching.py

Generation

torchrun --nproc_per_node=1 --master_port=31345  generation.py