Chia-Chun Chiang

Scott L. Fleming, Alejandro Lozano, William J. Haberkorn et al. · stanford

The ability of large language models (LLMs) to follow natural language instructions with human-level fluency suggests many opportunities in healthcare to reduce administrative burden and improve quality of care. However, evaluating LLMs on realistic text generation tasks for healthcare remains challenging. Existing question answering datasets for electronic health record (EHR) data fail to capture the complexity of information needs and documentation burdens experienced by clinicians. To address these challenges, we introduce MedAlign, a benchmark dataset of 983 natural language instructions for EHR data. MedAlign is curated by 15 clinicians (7 specialities), includes clinician-written reference responses for 303 instructions, and provides 276 longitudinal EHRs for grounding instruction-response pairs. We used MedAlign to evaluate 6 general domain LLMs, having clinicians rank the accuracy and quality of each LLM response. We found high error rates, ranging from 35% (GPT-4) to 68% (MPT-7B-Instruct), and an 8.3% drop in accuracy moving from 32k to 2k context lengths for GPT-4. Finally, we report correlations between clinician rankings and automated natural language generation metrics as a way to rank LLMs without human review. We make MedAlign available under a research data use agreement to enable LLM evaluations on tasks aligned with clinician needs and preferences.

Alejandro Lozano, Keiko Ihara, Ping-Hao Yang et al.

Summarizing the latest medical literature to guide clinical decision-making is essential for evidence-based medicine and high-quality patient care. Yet clinicians face increasing challenges due to limited time with patients and a rapidly growing volume of published articles. Although retrieval-augmented large language models (LLMs) have shown promise in clinical summarization, human evaluations of their effectiveness in synthesizing broader scientific literature and direct comparisons to expert-written syntheses remain scarce. We constructed a RAG-based agentic AI framework using three state-of-the-art LLMs: Sonnet, GPT-4o, and Llama 3.1. A headache specialist created 13 questions, three for prompt optimization and ten for evaluation. Ten headache specialists across the United States and Canada each wrote a summary for one question, yielding four summaries per question (expert, Sonnet, GPT-4o, and Llama). The experts, blinded to authorship, critically evaluated the summaries, excluding the topic for which they wrote a summary, based on correctness, completeness, conciseness, and clinical utility, scoring each from 1 to 10 using standardized rubrics. They also ranked the summaries by preference and indicated whether they believed each summary was written by an expert or an LLM. Our study, comparing LLM- and expert-written literature summaries evaluated by headache specialists, showed that expert-written summaries were preferred, although experts sometimes found it challenging to distinguish between human- and AI-generated summaries. We also identified key expert-valued features beyond standard evaluation metrics that can guide future refinement of both human and AI literature summarization pipelines.

Alejandro Lozano, Scott L Fleming, Chia-Chun Chiang et al.

The quickly-expanding nature of published medical literature makes it challenging for clinicians and researchers to keep up with and summarize recent, relevant findings in a timely manner. While several closed-source summarization tools based on large language models (LLMs) now exist, rigorous and systematic evaluations of their outputs are lacking. Furthermore, there is a paucity of high-quality datasets and appropriate benchmark tasks with which to evaluate these tools. We address these issues with four contributions: we release Clinfo.ai, an open-source WebApp that answers clinical questions based on dynamically retrieved scientific literature; we specify an information retrieval and abstractive summarization task to evaluate the performance of such retrieval-augmented LLM systems; we release a dataset of 200 questions and corresponding answers derived from published systematic reviews, which we name PubMed Retrieval and Synthesis (PubMedRS-200); and report benchmark results for Clinfo.ai and other publicly available OpenQA systems on PubMedRS-200.

Yuting Guo, Swati Rajwal, Sahithi Lakamana et al.

Migraine is a high-prevalence and disabling neurological disorder. However, information migraine management in real-world settings could be limited to traditional health information sources. In this paper, we (i) verify that there is substantial migraine-related chatter available on social media (Twitter and Reddit), self-reported by migraine sufferers; (ii) develop a platform-independent text classification system for automatically detecting self-reported migraine-related posts, and (iii) conduct analyses of the self-reported posts to assess the utility of social media for studying this problem. We manually annotated 5750 Twitter posts and 302 Reddit posts. Our system achieved an F1 score of 0.90 on Twitter and 0.93 on Reddit. Analysis of information posted by our 'migraine cohort' revealed the presence of a plethora of relevant information about migraine therapies and patient sentiments associated with them. Our study forms the foundation for conducting an in-depth analysis of migraine-related information using social media data.

Shih-Cheng Huang, Zepeng Huo, Ethan Steinberg et al.

Synthesizing information from multiple data sources plays a crucial role in the practice of modern medicine. Current applications of artificial intelligence in medicine often focus on single-modality data due to a lack of publicly available, multimodal medical datasets. To address this limitation, we introduce INSPECT, which contains de-identified longitudinal records from a large cohort of patients at risk for pulmonary embolism (PE), along with ground truth labels for multiple outcomes. INSPECT contains data from 19,402 patients, including CT images, radiology report impression sections, and structured electronic health record (EHR) data (i.e. demographics, diagnoses, procedures, vitals, and medications). Using INSPECT, we develop and release a benchmark for evaluating several baseline modeling approaches on a variety of important PE related tasks. We evaluate image-only, EHR-only, and multimodal fusion models. Trained models and the de-identified dataset are made available for non-commercial use under a data use agreement. To the best of our knowledge, INSPECT is the largest multimodal dataset integrating 3D medical imaging and EHR for reproducible methods evaluation and research.

Kihyuk Yoon, Lingchao Mao, Catherine Chong et al.

Temporal information in structured electronic health records (EHRs) is often lost in sparse one-hot or count-based representations, while sequence models can be costly and data-hungry. We propose PaReGTA, an LLM-based encoding framework that (i) converts longitudinal EHR events into visit-level templated text with explicit temporal cues, (ii) learns domain-adapted visit embeddings via lightweight contrastive fine-tuning of a sentence-embedding model, and (iii) aggregates visit embeddings into a fixed-dimensional patient representation using hybrid temporal pooling that captures both recency and globally informative visits. Because PaReGTA does not require training from scratch but instead utilizes a pre-trained LLM, it can perform well even in data-limited cohorts. Furthermore, PaReGTA is model-agnostic and can benefit from future EHR-specialized sentence-embedding models. For interpretability, we introduce PaReGTA-RSS (Representation Shift Score), which quantifies clinically defined factor importance by recomputing representations after targeted factor removal and projecting representation shifts through a machine learning model. On 39,088 migraine patients from the All of Us Research Program, PaReGTA outperforms sparse baselines for migraine type classification while deep sequential models were unstable in our cohort.