Semantic Representation for Agentic Self-Play in Automated Laboratories

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.

Biological laboratory automation can reduce repetitive manual work and improve reproducibility, but reliable embodied execution in wet-lab environments remains challenging. Protocols are often unstructured, labware is frequently transparent or reflective, and multi-step procedures require state-aware execution beyond one-shot instruction following. Existing robotic systems often rely on costly hardware, fixed workflows, dedicated instruments, or robotics-oriented interfaces. Here, we introduce BioProVLA-Agent, an affordable, protocol-driven, vision-enhanced embodied multi-agent system enabled by Vision-Language-Action (VLA) models for biological manipulation. The system uses protocols as the task interface and integrates protocol parsing, visual state verification, and embodied execution in a closed-loop workflow. A Tailored LLM Protocol Agent converts protocols into verifiable subtasks; a VLM-RAG Verification Agent assesses readiness and completion using observations, robot states, retrieved knowledge, and success/failure examples; and a VLA Embodied Agent executes verified subtasks through a lightweight policy. To improve robustness under wet-lab visual perturbations, we develop AugSmolVLA, an online augmentation strategy targeting transparent labware, reflections, illumination shifts, and overexposure. We evaluate the system on a hierarchical benchmark covering 15 atomic tasks, 6 composite workflows, and 3 bimanual tasks, including tube loading, sorting, waste disposal, cap twisting, and liquid pouring. Across normal and high-exposure settings, AugSmolVLA improves execution stability over ACT, X-VLA, and the original SmolVLA, especially for precise placement, transparent-object manipulation, composite workflows, and visually degraded scenes. These results suggest a practical route toward accessible, protocol-centered, and verification-capable embodied AI for biological manipulation.

AI is evaluated through knowledge, reasoning and plan generation, yet scientific agency requires reliable physical action and adaptation to evidence. Here, we use a robotic chemistry laboratory as a physical-world testbed to make scientific agency measurable. Its 45 modular workstations exposed as machine-readable skills enabled 4,608 trials. Only 3.3% of trials produced expert-assessed executable workflows under laboratory constraints; even the best system achieved 28.1%. Long-horizon planning remained a challenge: only three executable workflows exceeded 30 operations, although the longest contained 44. Across five rounds, experimental feedback prompted local adjustments but no workflow-level replanning or analytical-method redesign. By making physical executability and evidence-driven replanning measurable, our study provides an evidence-based assessment of deployment readiness and a diagnostic framework to guide closed-loop improvements towards physically grounded autonomous research.