# Improving Extraction of Clinical Event Contextual Properties from Electronic Health Records: A Comparative Study

arXiv: https://arxiv.org/abs/2408.17181 · HTML: https://mlsanity.com/paper/2408.17181/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 32 references that are in the map.
- First posted on arXiv 30 Aug 2024.

## Builds on (most cited first, 12 of 12)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Mistral 7B](https://mlsanity.com/paper/2310.06825/) (2023)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://mlsanity.com/paper/1904.05342/) (2019)
- [A Systematic Survey of Prompt Engineering in Large Language Models: Techniques and Applications](https://mlsanity.com/paper/2402.07927/) (2024)
- [How to Fine-Tune BERT for Text Classification?](https://mlsanity.com/paper/1905.05583/) (2019)
- [Multi-domain Clinical Natural Language Processing with MedCAT: the Medical Concept Annotation Toolkit](https://mlsanity.com/paper/2010.01165/) (2020)
- [Enhancing Clinical Concept Extraction with Contextual Embeddings](https://mlsanity.com/paper/1902.08691/) (2019)
- [Comparative Analysis of Text Classification Approaches in Electronic Health Records](https://mlsanity.com/paper/2005.06624/) (2020)

## Abstract (arXiv)

Electronic Health Records are large repositories of valuable clinical data, with a significant portion stored in unstructured text format. This textual data includes clinical events (e.g., disorders, symptoms, findings, medications and procedures) in context that if extracted accurately at scale can unlock valuable downstream applications such as disease prediction. Using an existing Named Entity Recognition and Linking methodology, MedCAT, these identified concepts need to be further classified (contextualised) for their relevance to the patient, and their temporal and negated status for example, to be useful downstream. This study performs a comparative analysis of various natural language models for medical text classification. Extensive experimentation reveals the effectiveness of transformer-based language models, particularly BERT. When combined with class imbalance mitigation techniques, BERT outperforms Bi-LSTM models by up to 28% and the baseline BERT model by up to 16% for recall of the minority classes. The method has been implemented as part of CogStack/MedCAT framework and made available to the community for further research.