14th place in the Arc Virtual Cell Challenge

We got the 14th place in the Arc Virtual Cell Challenge!

The challenge, organized by the Arc Institute and presented at NeurIPS 2025, brought together more than 5,000 participants from 114 countries to develop models that predict cellular responses to genetic perturbations.

I teamed up with Philipp Sven Lars Schäfer and Martin Garrido Rodriguez-Cordoba at the Saez Lab, and we’re proud of what we achieved with very limited compute and no access to private data. Our ML model was very lightweight and trained in minutes, which gave us the flexibility to iterate very quickly to explore many ideas.

One important issue we encountered is the lack of biologically meaningful and robust metrics to quantify the impact of perturbations on cells. During the competition, we quickly realised that the proposed metrics, while well intentioned, still present significant limitations, making it difficult to reliably assess model performance. Here are two interesting blog posts about this:

• The state of research on virtual cells
• Virtual cell perturbation metrics

Thanks to Julio Saez Rodriguez for supporting and encouraging us during the challenge, and to the Arc Institute for organizing it.