# Specialty-Specific Medical Language Model for Immune-Mediated Diseases

arXiv: https://arxiv.org/abs/2605.28838 · HTML: https://mlsanity.com/paper/2605.28838/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 16 references that are in the map.
- First posted on arXiv 12 Apr 2026.

## Builds on (most cited first, 4 of 4)

- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Neural Natural Language Processing for Unstructured Data in Electronic Health Records: a Review](https://mlsanity.com/paper/2107.02975/) (2021)
- [Biomedical Named Entity Recognition at Scale](https://mlsanity.com/paper/2011.06315/) (2020)

## Abstract (arXiv)

Extracting detailed clinical information from free-text medical narratives remains a practical challenge for researchers and healthcare systems. Terminology for immune-mediated and infectious diseases is especially inconsistent across sources, which often limits the ability of general-purpose Natural Language Processing (NLP) systems to capture the relevant biomedical concepts with sufficient granularity. We developed a domain-specific Named Entity Recognition (NER) model tailored to identify disease-related entities occurring in immunology and infectious disease contexts. We assembled and manually annotated a dataset of 371 case reports in collaboration with two clinical specialists, defining twelve entity classes covering immune-mediated and infectious conditions as well as related symptoms and clinical descriptors. We evaluated several modeling strategies, including the MedicalNER architecture with multiple healthcare-specific embeddings, a BERT-based token classification model, and zero-shot NER systems. The strongest performance was obtained with a transformer-based model trained on clinical-domain embeddings, which reached an F1 score of 0.89, consistently outperforming baseline and zero-shot approaches. The combination of specialized embeddings and expert annotation proved particularly valuable for capturing nuanced disease terminology and improving generalization across heterogeneous biomedical text. The prompted LLM baseline achieved substantially lower performance under the same evaluation protocol, reflecting difficulties in producing span-consistent outputs for fine-grained entity boundaries despite detailed prompting. The resulting model provides a structured way to analyze case reports and can support downstream tasks such as cohort identification, disease monitoring, and clinical decision support.