Knowing When to Stop: Pertura for Graph-Enforced PI Gating in Perturb-seq Agents

Scientific LLM agents can execute analysis code, but may proceed past unresolved experimental-design assumptions in complex assays such as Perturb-seq. We present Pertura, a Perturb-seq analysis agent that represents workflows as stateful phases with declarative preconditions, blocking PI interactions, and durable structured state. Phase-entry gates constrain downstream interpretation until assumptions about perturbation modality, controls, and annotation policy are resolved. On Norman/Weissman GSE133344, Pertura performs matrix-level QC, guide/target audit, CRISPRa sanity checks, and direction-of-effect interpretation. A no-gate ablation logs the same failed prechecks but allows execution to continue, showing that graph enforcement prevents unresolved design-boundary crossings.