metadata

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 library on GitHub.

Citation

@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}
}