We are thrilled to share our preprint on PantheonOS, the first evolvable, privacy-preserving multi-agent operating system for automatic genomics discovery.

• Preprint: https://www.biorxiv.org/content/10.64898/2026.02.26.707870v1
• Website(online platform free to everyone): https://pantheonos.stanford.edu

PantheonOS unites LLM-powered agents, reinforcement learning, and agentic code evolution to push beyond routine analysis — evolving state-of-the-art algorithms to super-human performance.

• Evolved batch correction (Harmony, Scanorama, BBKNN) and Reinforcement learning or RL agumented algorithms
• RL–augmented gene panel design
• Intelligent routing across 22+ virtual cell foundation models
• Autonomous discovery from newly generated 3D early mouse embryo data
• Integrated human fetal heart multi-omics with 3D whole-heart spatial data

Pantheon is highly extensible, although it is currently showcased with applications in genomics, the architecture is very general. The code has now been open-sourced, and we hope to build a new-generation AI data science ecosystem. https://github.com/aristoteleo/PantheonOS