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.

A long-standing ambition for artificial intelligence (AI) in biomedicine is the development of AI systems that could eventually make major scientific discoveries, with the potential to be worthy of a Nobel Prize--fulfilling the Nobel Turing Challenge [1]. While the concept of an "AI scientist" is aspirational, advances in agent-based AI pave the way to the development of AI agents as conversable systems capable of skeptical learning and reasoning that coordinate large language models (LLMs), machine learning (ML) tools, experimental platforms, or even combinations of them [2-5] (Figure 1). The complexity of biological problems requires a multistage approach, where decomposing complex questions into simpler tasks is necessary. AI agents can break down a problem into manageable subtasks, which can then be addressed by agents with specialized functions for targeted problem-solving and integration of scientific knowledge, paving the way toward a future in which a major biomedical discovery is made solely by AI [2, 6].