amallia / DeepZip

DeepZip

Description

DNA_compression using neural networks

Requirements

0. GPU, nvidia-docker
1. python 2/3
2. numpy
3. sklearn
4. keras 2.2.2
5. tensorflow (cpu/gpu) 1.8

(nvidia-docker is currently required to run the code) A simple way to install and run is to use the docker files provided:

cd docker
make bash BACKEND=tensorflow GPU=0 DATA=/path/to/data/

Code

To run a compression experiment:

Data Preparation

1. Place all the data to be compressed in data/files_to_be_compressed
2. Run the parser

cd data
./run_parser.sh

Running models

1. All the models are listed in models.py
2. Pick a model, to run compression experiment on all the data files in the data/files_to_be_compressed directory

cd src
./run_experiments.sh biLSTM