arXiv subjects

Skatje Myers

Publications and source records attributed to Skatje Myers.

4 recordsLinked to original sources

arXiv2026

Evaluating Retrieval-Augmented Generation vs. Long-Context Input for Clinical Reasoning over EHRs

Objective: To evaluate whether retrieval-augmented generation (RAG) can serve as an efficient alternative to long-context prompting for clinical reasoning over electronic health records (EHRs). Methods: We defined three EHR-based tasks that are replicable across health systems and vary in reasoning complexity: 1) extracting imaging procedures (modality, date, and anatomic site), 2) generating timelines of therapeutic antibiotic use, and 3) identifying the key diagnoses for a hospitalization. Using real inpatient clinical notes from a US academic health system, we evaluated three large language models (GPT-5.4-mini, Mistral Medium 3, DeepSeek V3.1) with varying amounts of provided context, comparing targeted retrieval to using the most recent clinical notes. Results: For Imaging Procedures, RAG strongly outperformed recent-note inputs and exceeded long-context performance (by 0.17-9.83 F1 across all models) using fewer than 8K tokens. Similar benefits were observed for Antibiotic Timelines, where <8K of retrieved tokens matched long-context recent-notes performance (between -3.26 to +3.24 Jaccard). Error analysis revealed that missing information in the clinical notes--often due to inter-hospital transfers--limited performance to some extent. However, performance on the Diagnosis Generation task remains largely static across methods and models. Discussion: RAG demonstrated strong token efficiency across tasks, with the clearest and most consistent gains observed for imaging extraction and antibiotic timeline reconstruction. Diagnosis generation proved the most challenging task, suggesting ceiling effects imposed by documentation variability and evaluation constraints. Conclusion: Our results suggest that RAG remains a competitive and efficient approach for clinical tasks over large amounts of EHR, even as newer models become capable of handling increasingly longer amounts of text.

cs.CL↗

arXiv2024

Position Paper On Diagnostic Uncertainty Estimation from Large Language Models: Next-Word Probability Is Not Pre-test Probability

Large language models (LLMs) are being explored for diagnostic decision support, yet their ability to estimate pre-test probabilities, vital for clinical decision-making, remains limited. This study evaluates two LLMs, Mistral-7B and Llama3-70B, using structured electronic health record data on three diagnosis tasks. We examined three current methods of extracting LLM probability estimations and revealed their limitations. We aim to highlight the need for improved techniques in LLM confidence estimation.

cs.AI↗

arXiv2024

Lessons Learned on Information Retrieval in Electronic Health Records: A Comparison of Embedding Models and Pooling Strategies

Objective: Applying large language models (LLMs) to the clinical domain is challenging due to the context-heavy nature of processing medical records. Retrieval-augmented generation (RAG) offers a solution by facilitating reasoning over large text sources. However, there are many parameters to optimize in just the retrieval system alone. This paper presents an ablation study exploring how different embedding models and pooling methods affect information retrieval for the clinical domain. Methods: Evaluating on three retrieval tasks on two electronic health record (EHR) data sources, we compared seven models, including medical- and general-domain models, specialized encoder embedding models, and off-the-shelf decoder LLMs. We also examine the choice of embedding pooling strategy for each model, independently on the query and the text to retrieve. Results: We found that the choice of embedding model significantly impacts retrieval performance, with BGE, a comparatively small general-domain model, consistently outperforming all others, including medical-specific models. However, our findings also revealed substantial variability across datasets and query text phrasings. We also determined the best pooling methods for each of these models to guide future design of retrieval systems. Discussion: The choice of embedding model, pooling strategy, and query formulation can significantly impact retrieval performance and the performance of these models on other public benchmarks does not necessarily transfer to new domains. Further studies such as this one are vital for guiding empirically-grounded development of retrieval frameworks, such as in the context of RAG, for the clinical domain.

cs.CL↗

arXiv2024

When Raw Data Prevails: Are Large Language Model Embeddings Effective in Numerical Data Representation for Medical Machine Learning Applications?

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 prevails in medical ML tasks, zero-shot LLM embeddings demonstrate competitive results, suggesting a promising avenue for future research in medical applications.

cs.CL↗