Calibrated? Not for Everyone: How Sexual Orientation and Religious Markers Distort LLM Accuracy and Confidence in Medical QA

Large Language Models (LLMs) have achieved strong performance in medical question answering and clinical reasoning tasks. However, their reliability under uncertainty remains poorly understood which raises critical concerns for deployment in high-stakes clinical settings. In such environments, incorrect predictions are inherently risky, but confident incorrect predictions can be particularly harmful as they may mislead clinical decision-making. In this paper, we conduct a systematic behavioral analysis of LLMs under clinical information uncertainty. We propose an evaluation framework based on the MedMCQA dataset consisting of two complementary uncertainty settings. First, we introduce linguistic uncertainty cues through prompt modifications to simulate ambiguous clinical contexts. Second, we construct an answer removal setting, wherein the correct option is deliberately excluded mandating the model to recognize insufficient information and abstain. We analyze both model accuracy and confidence behavior using multiple calibration metrics including calibration gap, Expected Calibration Error (ECE), and Unsafe Confident Error Rate (UCER) across 500 medical questions. Our results reveal a consistent failure mode, i.e., although accuracy degrades under increasing uncertainty, model confidence remains misaligned with accuracy. This leads to a substantial increase in unsafe confident errors, indicating that model confidence remains largely insensitive to clinically meaningful information loss. Furthermore, we observe significant variation across models in their ability to abstain when the correct answer is unavailable, with some models persistently producing high confidence hallucinated answers. These findings expose critical limitations in the epistemic reliability of current LLMs and highlight the need for uncertainty aware evaluation methods prior to their deployment in clinical workflows.

LLMs' linguistically expressed confidence should faithfully reflect their intrinsic uncertainty. While recent work shows LLMs struggle to use epistemic markers (e.g., "it is likely...") in a human-aligned fashion, it remains unclear whether models can apply their own linguistic confidence framework to associate markers with specific confidence levels in a stable and generalizable way, and how contextual features impact this ability. We conduct the first systematic study of this question, formalizing marker internal confidence (MIC) as the estimated intrinsic confidence a model associates with a specific epistemic marker in a given task domain. We present 7 metrics to evaluate the stability of MICs within and across distributions. Applying our analysis framework to diverse models and tasks, we find that LLMs remain faithfully miscalibrated even under model-centric interpretation of marker meanings, struggling to differentiate markers by internal confidence across distributions despite preserving a somewhat consistent ranking order across tasks. This supplies critical, complementary evidence to existing work toward a holistic understanding of faithful calibration in LLMs, emphasizing the need for more aligned and stable marker use to improve trustworthiness and reliability.

Medical large language model (LLM) evaluations rely on simplified, exam-style benchmarks that rarely reflect the ambiguity of real-world medical inquiries. We introduce the CLinical Evaluation of Ambiguity and Reliability (CLEAR) framework, which assesses how decision-space presentation, ambiguity, and uncertainty affect LLMs' reasoning on medical benchmarks. CLEAR systematically perturbs (1) the number of plausible answer options, (2) the presence of a ground truth or abstention option, and (3) the semantic framing of answer options. Applying CLEAR on three benchmarks evaluated across 17 LLMs reveals three notable limitations of existing evaluation methods. First, increasing the number of plausible answers degrades a model's ability to identify the correct answer and abstain against incorrect ones. Second, this lack of caution intensifies as the framing of abstention shifts from assertive rejection like "None of the Above" to uncertainty admission like "I don't know" (IDK). Notably, just including IDK in the answer space increases incorrect answer selections. Lastly, we formalize the performance gap between identifying the correct answer and abstaining from incorrect ones as the humility deficit, which worsens with model scale. Our findings reveal limitations in standard medical benchmarks and underscore that scaling alone does not resolve LLM reliability issues.