El Agente Gr'afico: A Semantic Execution Runtime for Scientific Agents

Large language models (LLMs) can plan scientific workflows and generate code, but these capabilities do not specify how scientific state is validated, transferred and recorded across heterogeneous computational and experimental operations. Here we present El Agente Gr'afico, a semantic execution runtime for scientific agents that uses typed execution graphs to enforce admissible scientific state transitions, record provenance and confine model judgement to explicit decision points. Using the same top-level LLM and task-specific rubrics on six university-level quantum chemistry exercises, El Agente Gr'afico improved performance while reducing model cost by approximately 80% and wall-clock time by more than fourfold relative to our previous multi-agent architecture. Across ensemble spectroscopy and metal-organic framework (MOF) design, the runtime supported typed-state transfer, parallel execution and cross-session persistence. Open-ended studies of a disulfide redox mechanism and the vibrational hypothesis of olfaction required the agent to define the chemical scope and computational pathway of each investigation. A graph-construction skill distilled from these studies then enabled coding agents to author typed execution graphs for MOF literature mining. Together, these results show how typed execution graphs turn reusable procedural knowledge into scientific protocols that can be inspected, revised and transferred across computational and physical systems.