Rare Diseases, Common Dilemmas: LLMs Prioritize Equal Resource Distribution over Patient Benefit in Decision-Making

As large language models (LLMs) enter high-stakes domains such as healthcare, understanding their moral reasoning becomes essential. Decisions about scarce medical resources often hinge on judgments of responsibility, particularly when patients' own actions contribute to illness. We investigate how LLMs reason about responsibility and its consequences, tracing their judgments across successive levels, from the behavior, to the resulting illness, to the denial of care. We evaluate a wide range of LLMs, spanning different model families and capability levels, on various clinical vignettes adapted from prior studies. Our results identify a judgment-consequence gap: LLMs largely agree with humans that patients bear responsibility for health-harming behaviors, yet overwhelmingly refuse to let that judgment influence how they allocate scarce resources. Specifically, LLMs default to random allocation, whereas humans consistently favor the less-culpable patient. Compared to humans, LLMs also place greater emphasis on access to information, reducing responsibility judgments when health-risk knowledge is unavailable. These findings reveal that LLMs apply a systematically different moral framework than humans when responsibility and resource scarcity intersect, surprisingly often amplifying normative disagreement with humans as reasoning capability increases.

Rare diseases represent one of the most challenging settings for clinical decision-making, where heterogeneous presentations, sparse evidence and limited expertise create persistent uncertainty throughout the care pathway. Although artificial intelligence could help, existing systems largely address isolated tasks, particularly diagnosis, and usually rely on downstream investigations rather than information available at initial presentation. Here we show that clinical AI performance under uncertainty can be improved not by scaling a single model, but by exploiting the diversity of multiple imperfect reasoning systems. Across heterogeneous large language models, we identify divergent reasoning trajectories with complementary error patterns and develop RareLens, which learns to reconcile these perspectives into actionable decisions across four stages of rare disease care: risk screening, diagnosis, treatment planning and prognosis prediction. Built on RarelensBench, a real-world dataset of 157,525 cases spanning all 33 Orphanet categories and more than 7,000 conditions, RareLens outperformed every frontier model tested, including GPT-5, DeepSeek-R1, Claude-3.7-Sonnet and Gemini-2.5-Pro, across all stages. It achieved an area under the curve of 0.917 for screening and top-1 accuracies of 65.5% and 89.8% for diagnosis and treatment. In an external evaluation involving 1,287 cases and 23 physicians, autonomous RareLens and physicians assisted by RareLens both outperformed unaided physicians, while demonstrating that effective human-AI collaboration requires more than simply providing model outputs. These findings establish divergent model reasoning as an exploitable source of information and suggest a general strategy for building AI systems that operate reliably under high clinical uncertainty.

Medicine is inherently pluralistic. Principles such as autonomy, beneficence, nonmaleficence, and justice routinely conflict, and such ethical dilemmas often sharply divide reasonable physicians. Good clinical practice navigates these tensions in concert with each patient's values rather than imposing a single ethical stance. The ethical values that large language models bring to medical advice, however, have not been systematically examined. We present a framework for auditing value pluralism in medical AI, comprising a benchmark of clinician-verified dilemmas and an attribution method that recovers value priorities directly from decisions. The ecosystem of frontier models spans physician-level value heterogeneity, and models discuss competing values in their reasoning (Overton pluralism) before committing to a decision. However, individual model decisions are near-deterministic across repeated sampling and semantic variations, failing to reproduce the distributional pluralism of the physician panel. Across benchmark cases, these consistent decisions reflect committed, systematic value preferences. While most model priorities fall within the natural range of inter-physician variation, some significantly underweight patient autonomy. A single LLM deployed without regard for its value priorities could amplify those priorities at scale to every patient it serves. Without explicit efforts to balance ethical perspectives with one or multiple models, these tools risk replacing clinical pluralism with a deployment monoculture.