arXiv:2509.02401v1 Announce Type: new Abstract: Large language model (LLM) agents are increasingly deployed in structured biomedical data environments, yet they often produce fluent but overconfident outputs when reasoning over complex multi-table data. We introduce an uncertainty-aware agent for query-conditioned multi-table summarization that leverages two complementary signals: (i) retrieval uncertainty--entropy over multiple table-selection rollouts--and (ii) summary uncertainty--combining self-consistency and perplexity. Summary uncertainty is incorporated into reinforcement learning (RL) with Group Relative Policy Optimization (GRPO), while both retrieval and summary uncertainty guide inference-time filtering and support the construction of higher-quality synthetic datasets. On multi-omics benchmarks, our approach improves factuality and calibration, nearly tripling correct and useful claims per summary (3.0(\rightarrow)8.4 internal; 3.6(\rightarrow)9.9 cancer multi-omics) and substantially improving downstream survival prediction (C-index 0.32(\rightarrow)0.63). These results demonstrate that uncertainty can serve as a control signal--enabling agents to abstain, communicate confidence, and become more reliable tools for complex structured-data environments.
