Neural at ArchEHR-QA 2026: One Method Fits All: Unified Prompt Optimization for Clinical QA over EHRs

Patient portals now give individuals direct access to their electronic health records (EHRs), yet access alone does not ensure patients understand or act on the complex clinical information contained in these records. The ArchEHR-QA 2026 shared task addresses this challenge by focusing on grounded question answering over EHRs, and this paper presents the system developed by the HealthNLP_Retrievers team for this task. The proposed approach uses a multi-stage cascaded pipeline powered by the Gemini 2.5 Pro large language model to interpret patient-authored questions and retrieve relevant evidence from lengthy clinical notes. Our architecture comprises four integrated modules: (1) a few-shot query reformulation unit which summarizes verbose patient queries; (2) a heuristic-based evidence scorer which ranks clinical sentences to prioritize recall; (3) a grounded response generator which synthesizes professional-caliber answers restricted strictly to identified evidence; and (4) a high-precision many-to-many alignment framework which links generated answers to supporting clinical sentences. This cascaded approach achieved competitive results. Across the individual tracks, the system ranked 1st in question interpretation, 5th in answer generation, 7th in evidence identification, and 9th in answer-evidence alignment. These results show that integrating large language models within a structured multi-stage pipeline improves grounding, precision, and the professional quality of patient-oriented health communication. To support reproducibility, our source code is publicly available in our GitHub repository

This paper presents the joint participation of the BIT.UA and AAUBS groups in the ArchEHR-QA 2026 shared task, which focuses on clinical question answering and evidence grounding in a low-resource setting. Due to the absence of training data and the strict data privacy constraints inherent to the healthcare domain (e.g. GDPR), we investigate the capabilities of Large Language Models (LLMs) without weight updates. We evaluate several state-of-the-art proprietary models and locally deployable open-source alternatives using various prompt engineering strategies, including task decomposition, Chain-of-Thought, and in-context learning. Furthermore, we explore majority voting and LLM-as-a-judge ensembling techniques to maximize predictive robustness. Our results demonstrate that while proprietary models exhibit strong resilience to prompt variations, domain-adapted open-source models (such as MedGemma 3 27B) achieve highly competitive performance when paired with the right prompt. Overall, our prompt-based approach proved highly effective, securing 1st place in Subtask 4 (evidence citation alignment) and 3rd place in Subtask 3 (patient-friendly answer generation). All code, results, and prompts are available on our GitHub repository: https://github.com/bioinformatics-ua/ArchEHR-QA-2026.

Discharge summaries are crucial clinical documents containing the context of a patient's overall hospital stay, and are routinely reviewed by medical experts for patient readmission, ongoing care, and diagnostic decision-making. When reviewing them, medical experts often must iteratively synthesize information across multiple summaries while verifying the evidence supporting each answer. Although large language models (LLMs) are increasingly explored for clinical question answering, existing benchmarks do not sufficiently reflect this setting: they often evaluate exam-style medical knowledge or focus on single-turn question answering with limited evidence-grounding evaluation. We introduce EHRNote-ChatQA, the first benchmark for evidence-grounded multi-turn clinical question answering over patients' multiple discharge summaries. Built from de-identified MIMIC-IV discharge summaries, EHRNote-ChatQA contains 967 patient-level multi-turn samples spanning one to five notes and 16,072 medical-expert-verified QA pairs (8,036 content questions, each paired with an evidence-grounding question) across eight clinical categories. The benchmark is constructed through an expert-informed pipeline combining discharge-summary structuring schema, expert-curated multi-turn QA templates, and LLM-based generation, followed by review and revision of every single QA sample by 11 medical experts. Benchmarking 22 open- and closed-source LLMs reveals several challenges, including that LLMs struggle more with evidence grounding than content answering, multi-turn errors compound across turns, and single-turn clinical QA performance does not reliably transfer to this setting. These findings establish EHRNote-ChatQA as a rigorous and practical benchmark for evaluating clinical QA systems. The dataset will be made publicly available through PhysioNet credentialed access.