Combining Token Classification With Large Language Model Revision for Age-Friendly 4M Entity Recognition From Nursing Home Text Messages: Development and Evaluation Study

Background: obility, yet, this information is not captured in any structured form, making it unavailable for systematic monitoring or quality reporting. Automatically extracting 4M information accurately and efficiently from these messages could enable several downstream applications within long term care settings. This task, however, is challenging because of the fragmented syntax, brevity, abbreviations, and informality of TMs. Objective: This study aimed to develop and evaluate a multi-stage 4M Entity Recognition (4M-ER) pipeline that combines a fine-tuned token classifier with large language model (LLM) revision, using only locally deployed open-source models, to improve 4M information extraction from clinical TMs. Methods: We used an expert-annotated dataset of 1,169 TMs representing conversations between interdisciplinary care teams across 16 Midwest NHs. The pipeline first identifies candidate text spans using a fine-tuned Bio-ClinicalBERT token classifier. A semantic similarity retriever then selects in-context exemplars to guide an LLM revision in which the LLM (Gemma, Phi, Qwen, or Mistral) performs boundary correction, label evaluation, and selective acceptance or rejection of candidate spans. Baselines for comparison included single-stage zero-shot LLMs, single-stage fine-tuned Bio-ClinicalBERT, and a fine-tuned LLM (Gemma) from a prior study. Ablation studies assessed the contribution of each pipeline stage and the effect of message filtering. Robustness was evaluated across 5 repeated runs. Results: from 0.59 to 0.67 and Mobility from 0.64 to 0.67. Ablation studies confirmed that restricting LLMs to revision only yielded optimal accuracy and efficiency. Conclusions: The 4M-ER pipeline enables accurate and scalable extraction of 4M entities from clinical TMs by combining fine-tuned Bio-ClinicalBERT with LLM revision using only locally deployed open-source models. The structured 4M data produced by the pipeline can support 4M taxonomy and ontology construction, as demonstrated in the prior work, and provides a foundation for downstream applications including real-time clinical surveillance, compliance with emerging age-friendly quality measures, and predictive modeling in long-term care settings.

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Publication Details

Journal
medRxiv
Published
2026-04-01
DOI
https://doi.org/10.64898/2026.03.31.26349861
Primary Topic
Electronic Health Records Systems
Type
article
Field-Weighted Citation Impact
0.00

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article

Combining Token Classification With Large Language Model Revision for Age-Friendly 4M Entity Recognition From Nursing Home Text Messages: Development and Evaluation Study

Matthew Farmer, Kimberly Powell, Mihail Popescu, Philip Amewudah
medRxiv
Electronic Health Records Systems
article

Combining Token Classification With Large Language Model Revision for Age-Friendly 4M Entity Recognition From Nursing Home Text Messages: Development and Evaluation Study

Matthew Farmer, Kimberly Powell, Mihail Popescu, Philip Amewudah
article en

Abstract

Background: obility, yet, this information is not captured in any structured form, making it unavailable for systematic monitoring or quality reporting. Automatically extracting 4M information accurately and efficiently from these messages could enable several downstream applications within long term care settings. This task, however, is challenging because of the fragmented syntax, brevity, abbreviations, and informality of TMs. Objective: This study aimed to develop and evaluate a multi-stage 4M Entity Recognition (4M-ER) pipeline that combines a fine-tuned token classifier with large language model (LLM) revision, using only locally deployed open-source models, to improve 4M information extraction from clinical TMs. Methods: We used an expert-annotated dataset of 1,169 TMs representing conversations between interdisciplinary care teams across 16 Midwest NHs. The pipeline first identifies candidate text spans using a fine-tuned Bio-ClinicalBERT token classifier. A semantic similarity retriever then selects in-context exemplars to guide an LLM revision in which the LLM (Gemma, Phi, Qwen, or Mistral) performs boundary correction, label evaluation, and selective acceptance or rejection of candidate spans. Baselines for comparison included single-stage zero-shot LLMs, single-stage fine-tuned Bio-ClinicalBERT, and a fine-tuned LLM (Gemma) from a prior study. Ablation studies assessed the contribution of each pipeline stage and the effect of message filtering. Robustness was evaluated across 5 repeated runs. Results: from 0.59 to 0.67 and Mobility from 0.64 to 0.67. Ablation studies confirmed that restricting LLMs to revision only yielded optimal accuracy and efficiency. Conclusions: The 4M-ER pipeline enables accurate and scalable extraction of 4M entities from clinical TMs by combining fine-tuned Bio-ClinicalBERT with LLM revision using only locally deployed open-source models. The structured 4M data produced by the pipeline can support 4M taxonomy and ontology construction, as demonstrated in the prior work, and provides a foundation for downstream applications including real-time clinical surveillance, compliance with emerging age-friendly quality measures, and predictive modeling in long-term care settings.

medRxiv
Institute for Medical Informatics and Biostatistics (CH), University of Missouri (US)
National Institutes of Health
Quality Education
Openalex Percentile: Top 26%
Electronic Health Records Systems
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