The advent of large language models (LLMs) has opened new avenues for analyzing complex, unstructured data, particularly within the medical domain. Electronic Health Records (EHRs) contain a wealth of information in various formats, including free text clinical notes, structured lab results, and diagnostic codes. This paper explores the application of advanced language models to leverage these diverse data sources for improved clinical decision support. We will discuss how text-based features, often overlooked in traditional high dimensional EHR analysis, can provide semantically rich representations and aid in harmonizing data across different institutions. Furthermore, we delve into the challenges and opportunities of incorporating medical codes and ensuring the generalizability and fairness of AI models in healthcare.

In this study, we introduce FEET, a standardized protocol designed to guide the development and benchmarking of foundation models. While numerous benchmark datasets exist for evaluating these models, we propose a structured evaluation protocol across three distinct scenarios to gain a comprehensive understanding of their practical performance. We define three primary use cases: frozen embeddings, few-shot embeddings, and fully fine-tuned embeddings. Each scenario is detailed and illustrated through two case studies: one in sentiment analysis and another in the medical domain, demonstrating how these evaluations provide a thorough assessment of foundation models' effectiveness in research applications. We recommend this protocol as a standard for future research aimed at advancing representation learning models.

The utilization of Electronic Health Records (EHRs) for clinical risk prediction is on the rise. However, strict privacy regulations limit access to comprehensive health records, making it challenging to apply standard machine learning algorithms in practical real-world scenarios. Previous research has addressed this data limitation by incorporating medical ontologies and employing transfer learning methods. In this study, we investigate the potential of leveraging language models (LMs) as a means to incorporate supplementary domain knowledge for improving the performance of various EHR-based risk prediction tasks. Unlike applying LMs to unstructured EHR data such as clinical notes, this study focuses on using textual descriptions within structured EHR to make predictions exclusively based on that information. We extensively compare against previous approaches across various data types and sizes. We find that employing LMs to represent structured EHRs, such as diagnostic histories, leads to improved or at least comparable performance in diverse risk prediction tasks. Furthermore, LM-based approaches offer numerous advantages, including few-shot learning, the capability to handle previously unseen medical concepts, and adaptability to various medical vocabularies. Nevertheless, we underscore, through various experiments, the importance of being cautious when employing such models, as concerns regarding the reliability of LMs persist.

This paper presents medBERTde, a pre-trained German BERT model specifically designed for the German medical domain. The model has been trained on a large corpus of 4.7 Million German medical documents and has been shown to achieve new state-of-the-art performance on eight different medical benchmarks covering a wide range of disciplines and medical document types. In addition to evaluating the overall performance of the model, this paper also conducts a more in-depth analysis of its capabilities. We investigate the impact of data deduplication on the model's performance, as well as the potential benefits of using more efficient tokenization methods. Our results indicate that domain-specific models such as medBERTde are particularly useful for longer texts, and that deduplication of training data does not necessarily lead to improved performance. Furthermore, we found that efficient tokenization plays only a minor role in improving model performance, and attribute most of the improved performance to the large amount of training data. To encourage further research, the pre-trained model weights and new benchmarks based on radiological data are made publicly available for use by the scientific community.