CDE-Mapper: Using Retrieval-Augmented Language Models for Linking Clinical Data Elements to Controlled Vocabularies

The standardization of clinical data elements (CDEs) aims to ensure consistent and comprehensive patient information across various healthcare systems. Existing methods often falter when standardizing CDEs of varying representation and complex structure, impeding data integration and interoperability in clinical research. We introduce CDE-Mapper, an innovative framework that leverages Retrieval-Augmented Generation approach combined with Large Language Models to automate the linking of CDEs to controlled vocabularies. Our modular approach features query decomposition to manage varying levels of CDEs complexity, integrates expert-defined rules within prompt engineering, and employs in-context learning alongside multiple retriever components to resolve terminological ambiguities. In addition, we propose a knowledge reservoir validated by a human-in-loop approach, achieving accurate concept linking for future applications while minimizing computational costs. For four diverse datasets, CDE-Mapper achieved an average of 7.2\% higher accuracy improvement compared to baseline methods. This work highlights the potential of advanced language models in improving data harmonization and significantly advancing capabilities in clinical decision support systems and research.

Process-Aware Analysis of Treatment Paths in Heart Failure Patients: A Case Study

Process mining in healthcare presents a range of challenges when working with different types of data within the healthcare domain. There is high diversity considering the variety of data collected from healthcare processes: operational processes given by claims data, a collection of events during surgery, data related to pre-operative and post-operative care, and high-level data collections based on regular ambulant visits with no apparent events. In this case study, a data set from the last category is analyzed. We apply process-mining techniques on sparse patient heart failure data and investigate whether an information gain towards several research questions is achievable. Here, available data are transformed into an event log format, and process discovery and conformance checking are applied. Additionally, patients are split into different cohorts based on comorbidities, such as diabetes and chronic kidney disease, and multiple statistics are compared between the cohorts. Conclusively, we apply decision mining to determine whether a patient will have a cardiovascular outcome and whether a patient will die.