Medical code embeddings from claims-based co-occurrences: a unified semantic space for ICD-10 diagnoses and ATC medications

OBJECTIVE: The analysis of care trajectories derived from electronic health records and claims data has become increasingly common in biomedical informatics. This has enabled large-scale studies of care processes, yet widely used binary code representations result in high-dimensional, sparse data that fail to capture semantic relationships between medical concepts. Learning dense vector representations (embeddings) has emerged as a promising approach to address these limitations. We aimed to construct and share joint embeddings for the International Classification of Diseases (ICD-10) and the Anatomical Therapeutic Chemical (ATC) classification system, providing reusable semantic representations of diagnoses and treatments from real-world claims data. MATERIALS AND METHODS: Using claims records from 1.5 million patients, we defined code co-occurrences within temporal windows and constructed a Positive Pointwise Mutual Information (PPMI) matrix spanning ICD-10 and ATC codes. Singular Value Decomposition (SVD) was applied to derive a low-dimensional embedding space. Evaluation combined UMAP visualization, nearest-neighbor retrieval, and a code-level classification task based on ICD chapters and ATC classes. RESULTS: The embeddings reflected the hierarchical organization of ICD-10 and ATC and revealed associations across coding systems, including clinically relevant diagnosis-treatment relationships. The classification task achieved mean AUCs of 0.93 for ICD-10 and 0.90 for ATC, indicating strong grouping of semantically related codes. DISCUSSION: The embeddings provide a reusable, code-level semantic representation that can support code retrieval, reduce manual code grouping, and be aggregated into patient-level features without training a task-specific model. CONCLUSION: We release the first openly available joint ICD-10-ATC embedding space derived from real-world claims data, providing a reusable resource for biomedical informatics research.