Deep generative genomic offset

Conditional VAEs for computing genomic offset.

Set up

git clone git@github.com:israfelsr/cvae-genomic-offset.git
cd cvae-genomic-offset
python3 -m venv cvae-genomic-offset-venv
source cvae-genomic-offset-venv/bin/activate
pip install --upgrade pip
pip install -r requirements.txt
export PYTHONPATH=$(pwd)

Training a simple CVAE

# Change parameters and hyperparameters in the .sh file
sh sbatchTrainCVAE.sh

Available models

This repository includes several implemented models and it's build to easily incorporate new models. The name of the already implemented models are shown below.

model = 'autoencoder'
model = 'simple_vae'
model = 'prior_vae'