README.md

---
title: Ume Sandbox
emoji: 🚀
colorFrom: blue
colorTo: pink
sdk: gradio
sdk_version: 5.39.0
app_file: app.py
pinned: false
---

# UME Explorer

An interactive Gradio Space for visualizing molecular embeddings using the UME model.

✨ Features:
- UME embedding generation
- 2D and 3D PCA visualization
- Cosine similarity matrix with heatmap

### Model, dataset, and training code
UME source code lives in the [LOBSTER](https://github.com/prescient-design/lobster/tree/main/src/lobster) library on GitHub.

### Citation
```bibtex
@article{ume2025,
  title={Universal Molecular Encoder: Towards a Unified Representation of the Contents of the Cell},
  author={Zadorozhny, Karina and Lisanza, Sidney and Joren, Taylor and Chennakesavalu, Shriram and Grambow, Colin and Kleinhenz, Joseph and Southern, Joshua and Choi, Keunwoo and Bonneau, Richard and Dwyer, Henri and Cho, Kyunghyun and Ra, Stephen and Frey, Nathan C.},
  year={2025},
  journal={Prescient Design, Genentech}
}
```