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

Tianyi Wang

Keywords: LLM agents, scientific workflows, Perturb-seq, single-cell genomics, computational biology

TL;DR: Pertura turns PI supervision into graph-enforced phase-entry control for Perturb-seq analysis agents.

Abstract: 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.

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Submission Number: 116