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| 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} | |
| } | |
| ``` |