Arbitrary Data as Images: Fusion of Patient Data Across Modalities and Irregular Intervals with Vision Transformers

A patient undergoes multiple examinations in each hospital stay, where each provides different facets of the health status. These assessments include temporal data with varying sampling rates, discrete single-point measurements, therapeutic interventions such as medication administration, and images. While physicians are able to process and integrate diverse modalities intuitively, neural networks need specific modeling for each modality complicating the training procedure. We demonstrate that this complexity can be significantly reduced by visualizing all information as images along with unstructured text and subsequently training a conventional vision-text transformer. Our approach, Vision Transformer for irregular sampled Multi-modal Measurements (ViTiMM), not only simplifies data preprocessing and modeling but also outperforms current state-of-the-art methods in predicting in-hospital mortality and phenotyping, as evaluated on 6,175 patients from the MIMIC-IV dataset. The modalities include patient's clinical measurements, medications, X-ray images, and electrocardiography scans. We hope our work inspires advancements in multi-modal medical AI by reducing the training complexity to (visual) prompt engineering, thus lowering entry barriers and enabling no-code solutions for training. The source code will be made publicly available.

Clinical information extraction for Low-resource languages with Few-shot learning using Pre-trained language models and Prompting

Automatic extraction of medical information from clinical documents poses several challenges: high costs of required clinical expertise, limited interpretability of model predictions, restricted computational resources and privacy regulations. Recent advances in domain-adaptation and prompting methods showed promising results with minimal training data using lightweight masked language models, which are suited for well-established interpretability methods. We are first to present a systematic evaluation of these methods in a low-resource setting, by performing multi-class section classification on German doctor's letters. We conduct extensive class-wise evaluations supported by Shapley values, to validate the quality of our small training data set and to ensure the interpretability of model predictions. We demonstrate that a lightweight, domain-adapted pretrained model, prompted with just 20 shots, outperforms a traditional classification model by 30.5% accuracy. Our results serve as a process-oriented guideline for clinical information extraction projects working with low-resource.