To unleash the full potential of AI for Science, we must untether the agents from a purely digital environment. The agent's ability to control and explore in real-world labs is essential because the physical lab remains foundational to scientific discovery. While some tasks can be performed on a computer (e.g., data analysis, running simulated experiments), Eureka moments could occur at any time while operating lab instruments (e.g., when a scientist notices unexpected clues, intuition may prompt a real-time course change). Although autonomous labs are on the rise, which expose programmable APIs to control scientific instruments via software, bridging the gap between increasingly powerful AI agents and automated lab equipment requires innovation that draws insights from computer systems. We propose a new paradigm called ``Experiment-as-Code (EaC) Labs,'' where a core concept is to encode experiments as declarative configurations that can be compiled down to device-level APIs. AI agents come up with hypotheses and experiments, written as an ensemble of declarative configurations. The systems layer performs program analysis, safety checks, resource assignment, and job orchestration. Finally, programmatic experimentation occurs via actuating the device APIs. This is a general stack that is science-, lab-, and instrument-independent, representing a novel synthesis across the physical, systems, and intelligence layers to unleash the next breakthrough in AI for Science.
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.
Angelos Angelopoulos, James F. Cahoon, Ron Alterovitz
Scientific code repositories encode decades of human knowledge in executable models, methods, and tools. Yet fragmented toolchains, implicit domain conventions, and specialized correctness criteria make this knowledge difficult to convert into reliable learning experience-a challenge we call the scientific experience bottleneck. We introduce ScienceIDE, infrastructure for turning the world's scientific code into programmable environments for scientific agents. Guided by expert-defined scientific cases and acceptance criteria, agents transform repositories into executable environments that support task generation, execution, and scientific verification. These environments provide a shared foundation for supervised fine-tuning, reinforcement learning, and evaluation. Using verified interaction trajectories, we train PhAI-IDE-72B, PhAI-IDE-9B, and PhAI-IDE-4B. The model family shows gains in held-out scientific-code repair and across selected general-purpose benchmarks in code, reasoning, and knowledge, providing evidence of positive transfer from scientific experience to broader capabilities. ScienceIDE lays the foundation for an integrated workspace for agent learning and scientific practice, making humanity's scientific software a shared substrate for developing scientific intelligence. Code: https://github.com/aitofound/ScienceIDE
Scientific discovery workflows rely heavily on lab notes, where researchers record observations, interpret uncertain results, and plan follow-up experiments. Unlike polished publications, lab notes preserve evolving scientific reasoning, tacit scientific knowledge, and author uncertainty, giving AI agents access to the process of science. However, most prior work on scientific text focuses on papers, protocols, or structured databases, leaving informal laboratory notes underexplored as inputs to AI agents for science. This gap matters because tacit knowledge in lab notes is not written as a clean set of instructions: validated observations, tentative judgments, and possible experimental next steps often appear in the same passage. If these signals are conflated, an AI agent may mistake uncertain scientific judgments for confirmed conclusions or executable actions. To this end, we present Notes2Skills, a two-stage framework for turning lab notebooks into verifiable skills for scientific AI agents while preserving the author's certainty. Across three wet-lab sessions and seven original downstream configurations, Notes2Skills is the only tested configuration that avoids both observed regime-level failures: over-acting on uncertain notes and missing firm directives. We show that certainty preservation is a key missing piece between lab notebooks and reliable agent skills, opening a path toward safer AI co-scientist systems.