EHRNoteQA: A Patient-Specific Question Answering Benchmark for Evaluating Large Language Models in Clinical Settings

This study introduces EHRNoteQA, a novel patient-specific question answering benchmark tailored for evaluating Large Language Models (LLMs) in clinical environments. Based on MIMIC-IV Electronic Health Record (EHR), a team of three medical professionals has curated the dataset comprising 962 unique questions, each linked to a specific patient's EHR clinical notes. What makes EHRNoteQA distinct from existing EHR-based benchmarks is as follows: Firstly, it is the first dataset to adopt a multi-choice question answering format, a design choice that effectively evaluates LLMs with reliable scores in the context of automatic evaluation, compared to other formats. Secondly, it requires an analysis of multiple clinical notes to answer a single question, reflecting the complex nature of real-world clinical decision-making where clinicians review extensive records of patient histories. Our comprehensive evaluation on various large language models showed that their scores on EHRNoteQA correlate more closely with their performance in addressing real-world medical questions evaluated by clinicians than their scores from other LLM benchmarks. This underscores the significance of EHRNoteQA in evaluating LLMs for medical applications and highlights its crucial role in facilitating the integration of LLMs into healthcare systems. The dataset will be made available to the public under PhysioNet credential access, promoting further research in this vital field.

Publicly Shareable Clinical Large Language Model Built on Synthetic Clinical Notes

The development of large language models tailored for handling patients' clinical notes is often hindered by the limited accessibility and usability of these notes due to strict privacy regulations. To address these challenges, we first create synthetic large-scale clinical notes using publicly available case reports extracted from biomedical literature. We then use these synthetic notes to train our specialized clinical large language model, Asclepius. While Asclepius is trained on synthetic data, we assess its potential performance in real-world applications by evaluating it using real clinical notes. We benchmark Asclepius against several other large language models, including GPT-3.5-turbo and other open-source alternatives. To further validate our approach using synthetic notes, we also compare Asclepius with its variants trained on real clinical notes. Our findings convincingly demonstrate that synthetic clinical notes can serve as viable substitutes for real ones when constructing high-performing clinical language models. This conclusion is supported by detailed evaluations conducted by both GPT-4 and medical professionals. All resources including weights, codes, and data used in the development of Asclepius are made publicly accessible for future research.

Rediscovery of CNN's Versatility for Text-based Encoding of Raw Electronic Health Records

Making the most use of abundant information in electronic health records (EHR) is rapidly becoming an important topic in the medical domain. Recent work presented a promising framework that embeds entire features in raw EHR data regardless of its form and medical code standards. The framework, however, only focuses on encoding EHR with minimal preprocessing and fails to consider how to learn efficient EHR representation in terms of computation and memory usage. In this paper, we search for a versatile encoder not only reducing the large data into a manageable size but also well preserving the core information of patients to perform diverse clinical tasks. We found that hierarchically structured Convolutional Neural Network (CNN) often outperforms the state-of-the-art model on diverse tasks such as reconstruction, prediction, and generation, even with fewer parameters and less training time. Moreover, it turns out that making use of the inherent hierarchy of EHR data can boost the performance of any kind of backbone models and clinical tasks performed. Through extensive experiments, we present concrete evidence to generalize our research findings into real-world practice. We give a clear guideline on building the encoder based on the research findings captured while exploring numerous settings.

UniHPF : Universal Healthcare Predictive Framework with Zero Domain Knowledge

Despite the abundance of Electronic Healthcare Records (EHR), its heterogeneity restricts the utilization of medical data in building predictive models. To address this challenge, we propose Universal Healthcare Predictive Framework (UniHPF), which requires no medical domain knowledge and minimal pre-processing for multiple prediction tasks. Experimental results demonstrate that UniHPF is capable of building large-scale EHR models that can process any form of medical data from distinct EHR systems. We believe that our findings can provide helpful insights for further research on the multi-source learning of EHRs.