Differentiable Loop Extrusion Model

This package provides functions to train, predict, and evaluate Differentiable Loop Extrusion Model (DLEM) on HiC/Micro-C experiments formated as (m)cool files.

Installation:

Requires Python 3.11-3.13 pip install dlem-jax

Tutorials:

• CLI Usage
• Synthetic Data
• Train and use model w/ Python API

References:

• CLI Reference
• API Reference
• Core Reference

Contributing

Install dev environment w/ Pixi:

pixi install --environment dev

Contributing using Docker:

docker-compose build

docker-compose up dlem-dev --watch