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arXiv · 2609.17855

SNOMED CT Concept Recommendation from Masked Clinical Context

Ali Noori
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Abstract

Standardizing clinical language to SNOMED CT supports interoperability, analytics, and reusable phenotyping, but concept recommendation remains difficult when relevant concepts are rare or absent from training data. We present a masked-concept recommendation benchmark using the SNOMED CT Entity Linking Challenge v1.2.1 data derived from MIMIC-IV-Note. The dataset contains 75,491 annotations across 272 discharge summaries, with 204 notes used for training and 68 for historical testing. For each unique note-concept pair, the target mention is masked from a local clinical context and the system ranks SNOMED CT concepts observed during training. We compare a popularity baseline, sparse TF-IDF concept prototypes, dense latent semantic analysis embeddings, sparse-dense fusion, retrieved-note evidence, and a retrieval-augmented hybrid. Sparse TF-IDF performs best, achieving Recall@1 of 14.81%, Recall@10 of 33.43%, MRR of 0.2114, and nDCG@10 of 0.2297. Retrieval augmentation does not improve this baseline, with Recall@10 of 31.99% and MRR of 0.1937. Performance is strongly affected by concept frequency: Recall@10 is 7.74% for concepts appearing in only one or two training notes versus 43.90% for concepts appearing in more than ten. In addition, 9.66% of test note-concept pairs contain concepts unseen during training. These findings show that local lexical context and terminology coverage are major determinants of recommendation quality in low-resource settings and provide a reproducible baseline for future ontology-grounded and biomedical-encoder retrieval systems.

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Ali Noori. 2026-09-15. SNOMED CT Concept Recommendation from Masked Clinical Context. https://arxiv.org/abs/2609.17855

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