Hierarchical Modeling of ICD Codes in EHR Foundation Models

Electronic health record foundation models typically treat ICD diagnosis codes as flat tokens, overlooking the clinically meaningful hierarchical structure that captures disease families, subcategories, and fine-grained diagnostic detail. As a result, existing EHR representation learning methods do not explicitly exploit the hierarchical structure already present in the coding system. In this work, we study ICD-10-CM hierarchy as a general inductive bias for clinical representation learning. We investigate two complementary mechanisms for incorporating hierarchy: first, by augmenting diagnosis sequences in a BERT-style transformer with tokens corresponding to different levels of the ICD hierarchy, and second, by injecting hierarchy into graph-based code representations through hierarchy-aware edges combined with diagnosis co-occurrence structure. Across these settings, we evaluate whether explicit hierarchy improves downstream prediction, which levels of the hierarchy are most useful, whether hierarchy encoding improves transfer across datasets, and how hierarchy reshapes embedding similarity structure. We conduct experiments on two large-scale real-world clinical datasets: MIMIC-IV, used for pretraining and in-domain evaluation, and eICU, used to assess cross-dataset transfer via frozen encoder probing. Our findings show that explicitly encoding ICD hierarchy improves over flat code representations in both in-domain and cross-dataset settings, while revealing that the most useful level of hierarchy depends on both the task and the modeling approach. More broadly, we focus on hierarchy-aware EHR representation learning and show that the benefits of encoding hierarchy are generalizable across modeling settings and hierarchy levels.

Neural Field Tokenizations with Hierarchy and Spatial Locality Priors

Neural fields parameterize data as functions from coordinates to values, providing a unified framework for representation learning across modalities. Existing approaches are dominated by per-sample meta-learning, which scales poorly due to memory-intensive inner-loop optimization. The natural alternative -- feed-forward encoding -- typically introduces modality-specific assumptions, sacrificing the generality that makes learning with neural fields attractive. We argue that locality and hierarchy are useful priors for learning field representations that can be injected without compromising modality-agnosticism. We propose LH-NeF, a framework to learn general-purpose tokenized representations of continuous signals. A locality-preserving hierarchical encoder maps raw coordinate-value field observations to structured tokens, from which the field is reconstructed during training. By replacing meta-learning's inner loop with a single forward pass, LH-NeF uses 42$\times$ less memory and supports 133$\times$ larger batches than the strongest modality-agnostic baseline. Across images, 3D shapes, and climate fields, our learned representations match or exceed performance of modality-agnostic, modality-specific, and specialized generative neural field baselines on both reconstruction and downstream tasks.