# From Prompts to Protocols: An AI Agent for Laboratory Automation

arXiv: https://arxiv.org/abs/2605.16552 · HTML: https://mlsanity.com/paper/2605.16552/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Placed in Web, search, and research agents, one of 16 directions in LLM agents and tool use.
- Builds on 3 of its 27 references that are in the map.
- First posted on arXiv 15 May 2026.

## Placed in

- LLM agents and tool use / [Web, search, and research agents](https://mlsanity.com/agents/web-search-and-research-agents/)

## Builds on (most cited first, 3 of 3)

- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [ORGANA: A Robotic Assistant for Automated Chemistry Experimentation and Characterization](https://mlsanity.com/paper/2401.06949/) (2024)
- [AlabOS: A Python-based Reconfigurable Workflow Management Framework for Autonomous Laboratories](https://mlsanity.com/paper/2405.13930/) (2024)

## Abstract (arXiv)

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.