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Life sciences · Preprint
arXiv · November 4, 2026
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Tool-using large language model (LLM) agents translate model outputs into consequential actions, turning indirect prompt injection into an execution-security problem. Existing defenses constrain tool calls, trajectories, or information flows, but often leave action semantics, state dependencies, and evidence relations implicit, limiting generalization across heterogeneous tools and complicating safe updates. We present \ours{}, a dynamic ontology-guided governance framework. \ours{} grounds heterogeneous calls in a shared semantic representation and combines an executable ontology with episode-level task state to derive deterministic ready, waiting, and forbidden decisions. A waiting decision identifies an unmet but recoverable obligation, enabling bounded replanning without expanding the agent's authorization boundary. \ours{} evolves its ontology offline from verified training executions. An offline LLM proposes instance-independent action--state axioms, which are accepted only if they address ontology errors exposed by training failures, preserve logical consistency and protected entailments, and pass held-out validation before the ontology is frozen. We evaluate \ours{} on AgentDojo, ASB, and AgentDyn under benign and indirect prompt-injection settings. \ours{} achieves a 0\% attack success rate (ASR) across all three benchmarks while improving task utility under attack compared with existing baselines. These results show that explicit semantic governance can strengthen execution security without indiscriminate blocking.