wconnell/enformer-finetune

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EnformerTX

Description

Finetune Enformer on expression data.

How to run

First, install dependencies

# clone project   
git clone https://github.com/wconnell/enformer-finetune

# install project   
cd enformer-finetune
pip install -e .   
pip install -r requirements.txt

Next, download data and test finetuning. The module ships with testing data files under tests/data/{train,val}.bed.

# download
bash download-data.sh
# build dataset
cd eft; python preprocess.py
# modify options in `config.yaml`...
# launch training
python main.py fit --config config.yaml

Notes

• DDP OOM issues on 24GB machine set: export PYTORCH_CUDA_ALLOC_CONF=max_split_size_mb:128
• requires batch_size >=2
• must use full precision (32 bit)
• use num_workers = 0