The increasing volume of patient messages via electronic health record (EHR) portals has contributed significantly to clinician workload. Automating responses to these messages can help alleviate this burden, but it is essential to ensure that the generated responses are grounded in accurate clinical evidence. As part of the ArchEHR-QA 2025 BioNLP ACL shared task, we explore unsupervised methods for generating patient question responses that are both contextually accurate and evidence-backed. We investigate three novel approaches: zero-shot prompting, clustering-based evidence selection, and attention-based evidence attribution, along with a hybrid model that combines clustering and attention. Our methods do not require model fine-tuning and leverage the inherent structure of the input data to identify the most relevant supporting evidence from clinical notes. Our best-performing approach, which integrates clustering and attention, demonstrates a substantial improvement in factuality over baseline zero-shot methods, highlighting the potential of unsupervised strategies for enhancing the clinical utility of large language models in EHR contexts.

Large language models (LLMs) often behave inconsistently across inputs, indicating uncertainty and motivating the need for its quantification in high-stakes settings. Prior work on calibration and uncertainty quantification often focuses on individual models, overlooking the potential of model diversity. We hypothesize that LLMs make complementary predictions due to differences in training and the Zipfian nature of language, and that aggregating their outputs leads to more reliable uncertainty estimates. To leverage this, we propose MUSE (Multi-LLM Uncertainty via Subset Ensembles), a simple information-theoretic method that uses Jensen-Shannon Divergence to identify and aggregate well-calibrated subsets of LLMs. Experiments on binary prediction tasks demonstrate improved calibration and predictive performance compared to single-model and naive ensemble baselines. In addition, we explore using MUSE as guided signals with chain-of-thought distillation to fine-tune LLMs for calibration. MUSE is available at: https://github.com/LARK-NLP-Lab/MUSE.

The introduction of Large Language Models (LLMs) has advanced data representation and analysis, bringing significant progress in their use for medical questions and answering. Despite these advancements, integrating tabular data, especially numerical data pivotal in clinical contexts, into LLM paradigms has not been thoroughly explored. In this study, we examine the effectiveness of vector representations from last hidden states of LLMs for medical diagnostics and prognostics using electronic health record (EHR) data. We compare the performance of these embeddings with that of raw numerical EHR data when used as feature inputs to traditional machine learning (ML) algorithms that excel at tabular data learning, such as eXtreme Gradient Boosting. We focus on instruction-tuned LLMs in a zero-shot setting to represent abnormal physiological data and evaluating their utilities as feature extractors to enhance ML classifiers for predicting diagnoses, length of stay, and mortality. Furthermore, we examine prompt engineering techniques on zero-shot and few-shot LLM embeddings to measure their impact comprehensively. Although findings suggest the raw data features still prevail in medical ML tasks, zero-shot LLM embeddings demonstrate competitive results, suggesting a promising avenue for future research in medical applications.

The BioNLP Workshop 2023 initiated the launch of a shared task on Problem List Summarization (ProbSum) in January 2023. The aim of this shared task is to attract future research efforts in building NLP models for real-world diagnostic decision support applications, where a system generating relevant and accurate diagnoses will augment the healthcare providers’ decision-making process and improve the quality of care for patients. The goal for participants is to develop models that generated a list of diagnoses and problems using input from the daily care notes collected from the hospitalization of critically ill patients. Eight teams submitted their final systems to the shared task leaderboard. In this paper, we describe the tasks, datasets, evaluation metrics, and baseline systems. Additionally, the techniques and results of the evaluation of the different approaches tried by the participating teams are summarized.

Generative artificial intelligence (AI) is a promising direction for augmenting clinical diagnostic decision support and reducing diagnostic errors, a leading contributor to medical errors. To further the development of clinical AI systems, the Diagnostic Reasoning Benchmark (DR.BENCH) was introduced as a comprehensive generative AI framework, comprised of six tasks representing key components in clinical reasoning. We present a comparative analysis of in-domain versus out-of-domain language models as well as multi-task versus single task training with a focus on the problem summarization task in DR.BENCH. We demonstrate that a multi-task, clinically-trained language model outperforms its general domain counterpart by a large margin, establishing a new state-of-the-art performance, with a ROUGE-L score of 28.55. This research underscores the value of domain-specific training for optimizing clinical diagnostic reasoning tasks.

Text in electronic health records is organized into sections, and classifying those sections into section categories is useful for downstream tasks. In this work, we attempt to improve the transferability of section classification models by combining the dataset-specific knowledge in supervised learning models with the world knowledge inside large language models (LLMs). Surprisingly, we find that zero-shot LLMs out-perform supervised BERT-based models applied to out-of-domain data. We also find that their strengths are synergistic, so that a simple ensemble technique leads to additional performance gains.

Automatically summarizing patients’ main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient’s daily care plan using input from the provider’s progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

Applying methods in natural language processing on electronic health records (EHR) data has attracted rising interests. Existing corpus and annotation focus on modeling textual features and relation prediction. However, there are a paucity of annotated corpus built to model clinical diagnostic thinking, a processing involving text understanding, domain knowledge abstraction and reasoning. In this work, we introduce a hierarchical annotation schema with three stages to address clinical text understanding, clinical reasoning and summarization. We create an annotated corpus based on a large collection of publicly available daily progress notes, a type of EHR that is time-sensitive, problem-oriented, and well-documented by the format of Subjective, Objective, Assessment and Plan (SOAP). We also define a new suite of tasks, Progress Note Understanding, with three tasks utilizing the three annotation stages. This new suite aims at training and evaluating future NLP models for clinical text understanding, clinical knowledge representation, inference and summarization.