Reverse Probing: Supervised Token-level Uncertainty Quantification for Large Language Models in Clinical Text

Large language models (LLMs) are increasingly used for clinical text tasks such as summarization and revision. While most studies evaluate the fluency and coherence of LLM-generated text, whether LLMs correctly preserve diagnostic uncertainty remains underexplored. In clinical practice, phrases such as ``possible pneumonia'' communicate the strength of available evidence and directly guide decisions about follow-up testing and treatment. Altering these uncertainty expressions can change the clinical meaning entirely. In this paper, we systematically evaluated this problem in two steps. First, we constructed a benchmark of 1,200 clinical documents with 9,184 uncertainty annotations across five levels. Second, we evaluated three LLMs on this benchmark. Our results show that (1) LLMs preserve the original uncertainty cues poorly, often less than half the time; (2) LLMs struggle with nuanced distinctions between adjacent levels. This work reveals a failure mode not captured by standard evaluation metrics and provides implications for the safe deployment of LLMs in clinical workflows.

Clinical language models often assign high confidence to incorrect predictions, particularly in high-severity and out-of-distribution cases. We present MedBayes-Lite, a retraining-free uncertainty governance layer for transformer-based clinical predictors. It combines Monte Carlo dropout, predictive calibration, and confidence-guided abstention to defer low-confidence predictions for human review, adding no trainable parameters. Evaluated on MedMCQA and MedQA-USMLE, MedBayes-Lite reduces expected calibration error by 0.23 to 0.33 and drives harmful overconfident errors (confident, incorrect, high-severity predictions) toward zero. Under domain shift from MedMCQA to MedQA-USMLE, it reduces confident high-severity errors from about 21% to near zero while roughly halving calibration drift. We also introduce the Clinical Uncertainty Score (CUS), which strongly correlates with harmful overconfidence (r approximately 0.88). Although the framework does not improve risk-coverage ranking, and temperature scaling or deep ensembles may provide advantages in calibration cost or risk ranking, MedBayes-Lite offers a practical calibration-and-abstention layer that reduces confident high-severity errors in clinical question-answering benchmarks.

The maximum softmax probability (MSP) represents a default approach when evaluating uncertainty quantification for language model generation with structured output. Although cheap, it is often miscalibrated. Methods that probe the model's internal activations feed raw hidden states into opaque classifiers, reading activations as static snapshots and leaving implicit the layer-wise trajectory by which a representation is formed. Yet, similar endpoints can arise from very different paths, and how evidence accumulates, reinforces, or reverses across depth might reveal uncertainty that final probabilities obscure. We extract eleven scale-invariant geometric features, tracing the cumulative path of per-layer MLP updates, and feed them to a sparse linear probe. The probe outperforms MSP under selective abstention, with gains scaling with baseline miscalibration up to 21 AURC points. Because every feature has a closed-form geometric meaning, the probe's coefficients trace how and where along depth errors take shape -- which layers commit prematurely, which contradict the running state, where trajectories drift away from their endpoint.