From Prompts to Protocols: An AI Agent for Laboratory Automation

Computer Science > Artificial Intelligence [Submitted on 15 May 2026] From Prompts to Protocols: An AI Agent for Laboratory Automation Angelos Angelopoulos, James F. Cahoon, Ron Alterovitz Automating science laboratories enables faster, safer, more accurate, and more reproducible execution of protocols, accelerating the discovery and testing of new materials, drugs, and more. However, setting up and running autonomous labs requires coordinating numerous instruments and robots, forcing scientists to write code, manage configuration files, and navigate complex software infrastructure. We present an AI agent architecture that integrates large language models with laboratory orchestration, enabling scientists to interactively create and monitor automated lab protocols using natural language. Integrated into the Experiment Orchestration System (EOS), the AI agent operates under an agentic loop with automated validation and error correction, and supports the complete experimental lifecycle: creating protocols, running and monitoring both protocols and closed-loop optimization campaigns, and analyzing results. A visual graph editor renders protocols as interactive node-based diagrams synchronized with the AI agent's protocol representation, enabling seamless alternation between AI-assisted and manual protocol construction. Evaluated on three simulated automated labs spanning chemistry, biology, and materials science, the AI agent achieves a 97% first-attempt protocol generation success rate and an order of magnitude reduction in required interface actions. Subjects: Artificial Intelligence (cs.AI); Robotics (cs.RO) Cite as: arXiv:2605.16552 [cs.AI]   (or arXiv:2605.16552v1 [cs.AI] for this version)   https://doi.org/10.48550/arXiv.2605.16552 Focus to learn more Submission history From: Ron Alterovitz [view email] [v1] Fri, 15 May 2026 18:52:41 UTC (4,928 KB) Access Paper: HTML (experimental) view license Current browse context: cs.AI < prev   |   next > new | recent | 2026-05 Change to browse by: cs cs.RO References & Citations NASA ADS Google Scholar Semantic Scholar Export BibTeX Citation Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Demos Related Papers About arXivLabs Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)