PantheonOS

PantheonOS: An Evolvable Multi-Agent Framework for Automatic Genomics Discovery biorxiv.org/content/10.648…

I believe this is an important update, and I hope to build Pantheon-Store into a vibrant Biomedical AI community!🔥

Come and try Pantheon-Store! Aiming to build an Agent community for the biomedical field! 💫💫💫 app.pantheonos.stanford.edu/#/store

It's really cool! Please check our manuscript! 😎

We are thrilled to share our preprint (tinyurl.com/3mtbtcwu) on PantheonOS, the first evolvable, privacy-preserving multi-agent operating system for automatic genomics discovery. 📄 Preprint: tinyurl.com/3mtbtcwu 🤖 Open-source App (free to all users): app.pantheonos.stanford.edu 🌐 More: 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 From uncovering asymmetric Cer1–Nodal inhibition in early mouse embryos to mapping spatial disease programs in the human heart, PantheonOS demonstrates a future where AI agents don’t just analyze biology — they drive discovery. This is a step toward self-evolving AI systems that accelerate science itself and push human civilization toward the singularity. This work is built over 2 years by an incredible team (Weize @Nanguage who led this project, and also to Erwin, Zhongquan @BAKEZQ, Chris @chriswzou , Zehua @starlitnightly, Yifan @YifanLu2024 , Xuehai, Zhongquan, and Miao, Cinlong's wetlab support and the entire Qiu lab. We are grateful for all our funders and industrial collaborators: @Lenovo @vizgen_inc We are excited to scale this work further and welcome philanthropic, industrial, and venture support. We invite the community (pantheonos.stanford.edu/ecosystem) to contribute, extend, and collectively reimagine the future of automated biological discovery. 🌐 More details below:

The first truly expert-level solution. Surpassing all existing automatic annotation methods. ✔️ Detecting and validating marker genes ✔️ Interpreting clusters through chat ✔️ Finalizing cell type with supporting evidence youtube.com/watch?v=Ox4xeP…

here is the detailed input: pantheon-cli-docs.netlify.app/cases/seurat-l…

Ever imagined running Seurat with natural language and exploring your data step by step? No code This Pantheon-CLI case study shows a full single-cell workflow—normalization, clustering, QC, marker detection, and cell type mapping—all through conversation. youtube.com/watch?v=z407b9…

🚀 Introducing PantheonOS (pantheonOS.stanford.edu): A Fully Open-Source Agent OS for Science PantheonOS began as a research project in my Stanford lab and has since evolved into a vision to redefine data science in the era of AI—starting with computational biology, especially single-cell and spatial genomics. PantheonOS is a general agent platform built from the ground up. It is arguably the first distributed agent framework designed for scientific data analysis. 🔑 Key Features 1. Multi-Agent Collaboration – Built-in paradigms for distributed, cross-machine cooperation among agents and toolsets. 2. Native Toolset Support – Python, R, Julia, LaTeX, and more—designed for real scientific workflows. 3. Modular & Extensible – Developer-friendly design with shallow wrappers, plus LLM-driven toolset generation. 4. Evolvable Agents – Capable of evolving large-scale code projects to achieve superhuman performance (e.g., evolving upon the original Harmony [I Korsunsky, 2019, Nature Biotechnology] and Scanorama [BL Hie, 2019, Nature Biotechnology] implementations), and even evolving the system itself to adapt to new fields. 🎉 Stepwise Release Strategy We’re releasing PantheonOS in stages: Pantheon-CLI (today!), followed by Pantheon-Lab, Pantheon-Notebook, Pantheon-Slack, and more. 🌟 Pantheon-CLI Highlights - We're not just building another CLI tool. We're defining how scientists will interact with data in the AI era. - Open, Powerful, Python-First – The first fully open-source, endlessly extendable scientific “vibe analysis” framework. - Mixed Programming Magic – Combine Python, natural language, R, or Julia—seamlessly in the same environment. - PhD-Level Assistant – A command-line agent for complex real-world genomics and beyond, handling workflows at the PhD level. - Privacy by Design – Run entirely offline with local LLMs—your data never leaves your computer. ✅ Proven Applications (10 Demonstrations) Computational biology: 1. ATAC-seq: From raw reads to peak matrix 2. RNA-seq: From raw reads to expression matrix 3. Complex single-cell workflows (PhD-level) 4. Hybrid natural language + R for Seurat annotation 5. Learning from web tutorials + invoking single-cell foundation models 6. Cell segmentation on 10x Genomics HD Visium data And beyond: 7. Mixed Python & R programming examples 8. Molecular docking & structural analysis 9. Exploratory factor analysis for behavioral survey data 10. Customer segmentation & finance analytics 🌐 Learn More & Get Started Website: pantheonOS.stanford.edu Pantheon-CLI Documentation: pantheon-cli-docs.netlify.app GitHub Repo: github.com/aristoteleo/pa… 💬 Join our community: PantheonOS Slack: pantheonos.slack.com/ssb/redirect PantheonOS Discord: discord.com/invite/74yzAGYW