Conformal Prediction for Risk-Controlled Medical Entity Extraction Across Clinical Domains

Large language models (LLMs) are increasingly used for medical summarization, but their outputs can omit medically important information and introduce unsupported claims. Existing error-detection methods produce heuristic or uncalibrated scores, providing no formal control over missed errors and no principled way to trade off safety against clinician review burden. We introduce Conformal Assessment for Risk Evaluation (CARE), a post-hoc, model-agnostic safety layer that uses conformal risk control to overlay calibrated omission and hallucination flags onto summaries from any LLM without retraining. CARE provides finite-sample, distribution-free guarantees through two controllers: a hallucination controller that bounds the probability of a document containing any unflagged hallucinated sentence, and an omission controller that bounds the expected fraction of important omissions not surfaced for review. Unlike hallucination detection, omissions depend jointly on whether a source sentence is important and whether it is covered by the summary. We show that calibrating only one dimension can violate the target risk bound, while marginal decompositions remain valid but overly conservative. By jointly calibrating over the full $(τ,γ)$ threshold space, CARE preserves formal guarantees while surfacing up to 5$\times$ fewer sentences than alternative calibrated baselines. Across five medical summarization tasks, CARE satisfies the target risk bound at $α= 0.15$ with 95% confidence across 100 calibration/test resplits, using only ~100 labeled documents per domain. In a preliminary clinician study (75 document reviews), calibrated flags improved omission detection by 28.6 percentage points on average. These results show that sentence-level safety guarantees are feasible for LLM-assisted medical summarization and offer a tunable mechanism for balancing residual risk and review effort.

Large language models (LLMs) are prone to generating factually incorrect outputs. Recent work has applied conformal prediction to provide uncertainty estimates and statistical guarantees for the factuality of LLM generations. However, existing approaches are typically not prompt-adaptive, limiting their ability to capture input-dependent variability. As a result, they may filter out too few items (leading to over-coverage) or too many (under-coverage) for a given task or prompt. We propose an adaptive conformal prediction approach that extends conformal score transformation methods to LLMs, with applications to long-form generation and multiple-choice question answering. This enables prompt-dependent calibration, retaining marginal coverage guarantees while improving conditional coverage. In addition, the approach naturally supports selective prediction, allowing unreliable claims or answer choices to be filtered out in downstream applications. We evaluate our approach on multiple white-box models across diverse domains and show that it significantly outperforms existing baselines in terms of conditional coverage.

Large language models are increasingly deployed in settings where reliability matters, yet output-level uncertainty signals such as token probabilities, entropy, and self-consistency can become brittle under calibration--deployment mismatch. Conformal prediction provides finite-sample validity under exchangeability, but its practical usefulness depends on the quality of the nonconformity score. We propose a conformal framework for LLM question answering that uses internal representations rather than output-facing statistics: specifically, we introduce Layer-Wise Information (LI) scores, which measure how conditioning on the input reshapes predictive entropy across model depth, and use them as nonconformity scores within a standard split conformal pipeline. Across closed-ended and open-domain QA benchmarks, with the clearest gains under cross-domain shift, our method achieves a better validity--efficiency trade-off than strong text-level baselines while maintaining competitive in-domain reliability at the same nominal risk level. These results suggest that internal representations can provide more informative conformal scores when surface-level uncertainty is unstable under distribution shift.