LabCompiler: A Framework for Verifiable Human-Machine Laboratory Execution from Imperfect Protocols

Jingyuan Li, Dongzhan Zhou, Minting Pan, Yujie Liu, Yuan Gao +8

Closing the loop of AI-driven science requires reliably translating natural-language protocols into executable laboratory workflows despite protocol defects and heterogeneous hardware. Existing approaches often couple scientific interpretation with device-specific code generation, making errors difficult to localize and limiting reuse across laboratory platforms. We introduce LabCompiler, a robust protocol-to-execution framework that transforms imperfect natural-language protocols into verifiable human-machine workflows. Its protocol firewall diagnoses and repairs defects before compilation while preserving unaffected content, guided by troubleshooting knowledge accumulated through perturbation-guided self-evolution. A two-level, device-agnostic graph representation separates experimental semantics from hardware-specific implementation and supports capability-based device assignment with coordinated human execution. We further introduce a protocol recovery benchmark covering four controlled perturbation types and naturally occurring errors collected from protocols written by iGEM participants. Experiments show that LabCompiler outperforms frontier LLMs in protocol error…