Clinical QA

Clinical reports are often fragmented across healthcare institutions because privacy regulations and data silos limit direct information sharing. When patients seek care at a different hospital, they often carry paper or scanned reports from prior visits. This hinders EHR integration and longitudinal review, and downstream applications that depend on more complete patient records, such as patient management, follow-up care, real-world studies, and clinical-trial matching. Although OCR can digitize such reports, reliable extraction remains challenging because clinical documents are heterogeneous, OCR text is noisy, and many healthcare settings require low-cost on-premise deployment. We formulate this problem as canonical key-conditioned extractive question answering over OCR-derived clinical reports. Because the key fields are neither fixed nor known in advance, the key space is open. We maintain a canonical key inventory through iterative key mining, normalization, clustering, and lightweight human verification, and introduce key coverage as a metric to quantify inventory completeness. Using a 0.2B BERT-based model, experiments on real-world reports from more than 20 hospitals show performance improves monotonically with key coverage. The model achieves F1 scores of 0.839 and 0.893 under exact match and boundary-tolerant matching, respectively, once the Top-90 canonical keys are covered. These results show that key coverage is a dominant factor for end-to-end performance. At Top-90 coverage, our model outperforms a fine-tuned Qwen3-0.6B baseline under exact match. Although our annotated corpus is Chinese, the method relies on the language-agnostic key-value organization of semi-structured clinical reports and can be adapted to other settings given an appropriate canonical key inventory and alias mapping.

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.

Brazil's Unified Health System (SUS) relies on official clinical guidelines that define diagnostic criteria, treatments, dosages, and monitoring procedures for over 200 million citizens. Yet current LLMs perform poorly on this guideline-specific knowledge, and no benchmark evaluates clinical recall grounded in Brazilian Portuguese protocols. We address this gap by adapting Qwen2.5-14B-Instruct to the Brazilian clinical domain. From 178 official guidelines (~5.4M tokens), we generate ~70M tokens of synthetic data in three formats -- rephrases, wiki-style articles, and question-answer pairs -- using four generator LLMs. We then apply continual pre-training followed by Group Relative Policy Optimization (GRPO). We introduce HealthBench-BR, with 1,780 balanced true/false clinical assertions, and PCDT-QA, with 890 open-ended clinical questions scored by an LLM judge. Our best model achieves 83.9% on HealthBench-BR and 85.4% on PCDT-QA, outperforming GPT-5.2, Claude Sonnet 4.6, Gemini 3.1 Pro, and Google AI Overview's web-grounded RAG despite having only 14B parameters. Ablations show that generator diversity and reinforcement learning are critical to these gains. We release all datasets, benchmarks, and model weights to support reproducible clinical NLP research for Brazilian Portuguese. Code, data, and model weights are available at https://github.com/hugoabonizio/clinical-protocols-br

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

Multiple myeloma is managed through sequential lines of therapy over years to decades, with each decision depending on cumulative disease history distributed across dozens to hundreds of heterogeneous clinical documents. Whether LLM-based systems can synthesise this evidence at a level approaching expert agreement has not been established. A retrospective evaluation was conducted on longitudinal clinical records of 811 myeloma patients treated at a tertiary centre (2001-2026), covering 44,962 documents and 1,334,677 laboratory values, with external validation on MIMIC-IV. An agentic reasoning system was compared against single-pass retrieval-augmented generation (RAG), iterative RAG, and full-context input on 469 patient-question pairs from 48 templates at three complexity levels. Reference labels came from double annotation by four oncologists with senior haematologist adjudication. Iterative RAG and full-context input converged on a shared ceiling (75.4% vs 75.8%, p = 1.00). The agentic system reached 79.6% concordance (95% CI 76.4-82.8), exceeding both baselines (+3.8 and +4.2 pp; p = 0.006 and 0.007). Gains rose with question complexity, reaching +9.4 pp on criteria-based synthesis (p = 0.032), and with record length, reaching +13.5 pp in the top decile (n = 10). The system error rate (12.2%) was comparable to expert disagreement (13.6%), but severity was inverted: 57.8% of system errors were clinically significant versus 18.8% of expert disagreements. Agentic reasoning was the only approach to exceed the shared ceiling, with gains concentrated on the most complex questions and longest records. The greater clinical consequence of residual system errors indicates that prospective evaluation in routine care is required before these findings translate into patient benefit.

Knowledge graphs (KGs) are increasingly used to support large lan guage model (LLM) reasoning, but standard triplet-based KGs treat each relation as globally valid. In many settings, whether a relation should count as evidence depends on the context. We therefore formulate triplet validity as a triplet-specific function of context and refer to this formulation as a Quantum Knowledge Graph (QKG). We instantiate QKG in medicine using a diabetes-centered PrimeKG subgraph, whose 68,651 context-sensitive relations are further annotated with patient-group-specific constraints. We evaluate it in a reasoner--validator pipeline for medical question answering on a KG-grounded subset of MedReason containing 2,788 questions. With Haiku-4.5 as both the Reasoner and the Validator, KG-backed validation significantly improves over a no-validator baseline ($+0.61$ pp), and QKG with context matching yields the largest gain, outperforming both KG validation without context matching ($+0.79$ pp) and the no-validator baseline ($+1.40$ pp; paired McNemar, all $p<0.05$). Under a stronger validator (Qwen-3.6-Plus), the raw QKG gain over the no-validator baseline grows from $+1.40$ pp to $+5.96$ pp; the context-matching gap is non-significant ($p=0.73$) on the raw set but becomes borderline significant ($p=0.05$) after adjustment for knowledge leakage and suspicious questions, consistent with a benchmark-gold ceiling rather than a QKG limitation. Taken together, the results support the view that the value of a KG in LLM-based clinical reasoning lies not merely in storing medically related facts, but in representing whether those facts are applicable to the specific patient context. For reproducibility and further research, we release the curated QKG datasets and source code.\footnote{https://github.com/HKAI-Sci/QKG}

Electronic health record (EHR) question answering is often handled by LLM-based pipelines that are costly to deploy and do not explicitly leverage the hierarchical structure of clinical data. Motivated by evidence that medical ontologies and patient trajectories exhibit hyperbolic geometry, we propose HypEHR, a compact Lorentzian model that embeds codes, visits, and questions in hyperbolic space and answers queries via geometry-consistent cross-attention with type-specific pointer heads. HypEHR is pretrained with next-visit diagnosis prediction and hierarchy-aware regularization to align representations with the ICD ontology. On two MIMIC-IV-based EHR-QA benchmarks, HypEHR approaches LLM-based methods while using far fewer parameters. Our code is publicly available at https://github.com/yuyuliu11037/HypEHR.

In this paper, we propose a modified version of the MedQA-USMLE dataset, named MEDQA-OPEN, which contains open-ended medical questions without options to mimic clinical scenarios, along with clinician-approved reasoned answers. Additionally, we implement a prompt driven by Chain of Thought (CoT) reasoning, CLINICR, to mirror the prospective process of incremental reasoning, reaching a correct response to medical questions. We empirically demonstrate how CLINICR outperforms the state-of-the-art 5-shot CoT-based prompt (Liévin et al., 2022). We also present an approach that mirrors real-life clinical practice by first exploring multiple differential diagnoses through MCQ-CLINICR and subsequently narrowing down to a final diagnosis using MCQ-ELIMINATIVE. Finally, emphasizing the importance of response verification in medical settings, we utilize a reward model mechanism, replacing the elimination process performed by MCQ-ELIMINATIVE.