yevgenin/om2seq

OM2Seq

Code for the paper: OM2Seq: Learning retrieval embeddings for optical genome mapping

The data used in this paper is available as parquet files at: https://zenodo.org/records/11076514

Setup shell environment

Before running any of the commands below, you need to setup the shell environment:

. run.sh

Building the Docker container

docker-build

Training the model

train
docker-run-gpu

Running the Benchmark

benchmark
docker-run-gpu

Reproducing the figures from the paper

figures-all
docker-run