Multimodal Medical Code Tokenizer

Foundation models trained on patient electronic health records (EHRs) require tokenizing medical data into sequences of discrete vocabulary items. Existing tokenizers treat medical codes from EHRs as isolated textual tokens. However, each medical code is defined by its textual description, its position in ontological hierarchies, and its relationships to other codes, such as disease co-occurrences and drug-treatment associations. Medical vocabularies contain more than 600,000 codes with critical information for clinical reasoning. We introduce MedTok, a multimodal medical code tokenizer that uses the text descriptions and relational context of codes. MedTok processes text using a language model encoder and encodes the relational structure with a graph encoder. It then quantizes both modalities into a unified token space, preserving modality-specific and cross-modality information. We integrate MedTok into five EHR models and evaluate it on operational and clinical tasks across in-patient and out-patient datasets, including outcome prediction, diagnosis classification, drug recommendation, and risk stratification. Swapping standard EHR tokenizers with MedTok improves AUPRC across all EHR models, by 4.10% on MIMIC-III, 4.78% on MIMIC-IV, and 11.30% on EHRShot, with the largest gains in drug recommendation. Beyond EHR modeling, we demonstrate using MedTok tokenizer with medical QA systems. Our results demonstrate the potential of MedTok as a unified tokenizer for medical codes, improving tokenization for medical foundation models.

Graph AI in Medicine

In clinical artificial intelligence (AI), graph representation learning, mainly through graph neural networks (GNNs), stands out for its capability to capture intricate relationships within structured clinical datasets. With diverse data -- from patient records to imaging -- GNNs process data holistically by viewing modalities as nodes interconnected by their relationships. Graph AI facilitates model transfer across clinical tasks, enabling models to generalize across patient populations without additional parameters or minimal re-training. However, the importance of human-centered design and model interpretability in clinical decision-making cannot be overstated. Since graph AI models capture information through localized neural transformations defined on graph relationships, they offer both an opportunity and a challenge in elucidating model rationale. Knowledge graphs can enhance interpretability by aligning model-driven insights with medical knowledge. Emerging graph models integrate diverse data modalities through pre-training, facilitate interactive feedback loops, and foster human-AI collaboration, paving the way to clinically meaningful predictions.