mlsanityData to 7 Oct 2026

SNOBERT: A Benchmark for clinical notes entity linking in the SNOMED CT clinical terminology

arXiv 2405.16115 ↗First posted 25 May 2024cs.CL cs.LGcited by 4

Not on the map. Why?

Abstract (arXiv)

The extraction and analysis of insights from medical data, primarily stored in free-text formats by healthcare workers, presents significant challenges due to its unstructured nature. Medical coding, a crucial process in healthcare, remains minimally automated due to the complexity of medical ontologies and restricted access to medical texts for training Natural Language Processing models. In this paper, we proposed a method, "SNOBERT," of linking text spans in clinical notes to specific concepts in the SNOMED CT using BERT-based models. The method consists of two stages: candidate selection and candidate matching. The models were trained on one of the largest publicly available dataset of labeled clinical notes. SNOBERT outperforms other classical methods based on deep learning, as confirmed by the results of a challenge in which it was applied.

Key facts. Cited by 4 papers in the map (data through 7 Oct 2026). Builds on 8 of its 19 references that are in the map. First posted on arXiv 25 May 2024.

Builds on

8 of 19 references.

References · 8

  1. 2020Domain-Specific Language Model Pretraining for Biomedical Natural Language Processingcited by 996
  2. 2018A Survey on Deep Learning for Named Entity Recognitioncited by 281
  3. 2020Self-Alignment Pretraining for Biomedical Entity Representationscited by 233
  4. 2023MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrievalcited by 182
  5. 2022ReFinED: An Efficient Zero-shot-capable Approach to End-to-End Entity Linkingcited by 74
  6. 2021Fine-Tuning Large Neural Language Models for Biomedical Natural Language Processingcited by 57
  7. 2023Publicly Shareable Clinical Large Language Model Built on Synthetic Clinical Notescited by 51
  8. 2020COMETA: A Corpus for Medical Entity Linking in the Social Mediacited by 49

Built on by

Cited by year

Citing papers per year: 2025: 4.

4 papers.

  1. 2025Evaluating Retrieval-Augmented Generation vs. Long-Context Input for Clinical Reasoning over EHRscited by 4
  2. 2025Automated SNOMED CT Concept Annotation in Clinical Text Using Bi-GRU Neural Networkscited by 2
  3. 2025CDE-Mapper: Using Retrieval-Augmented Language Models for Linking Clinical Data Elements to Controlled Vocabulariescited by 1
  4. 2025Hierarchical Retrieval with Out-Of-Vocabulary Queries: A Case Study on SNOMED CTcited by 0