A Semi-Automated Annotation Workflow for Paediatric Histopathology Reports Using Small Language Models

• URL: http://arxiv.org/abs/2604.04168v2
• Date: Tue, 07 Apr 2026 07:29:28 GMT
• Title: A Semi-Automated Annotation Workflow for Paediatric Histopathology Reports Using Small Language Models
• Abstract summary: We develop a resource-efficient semi-automated annotation workflow using small language models (SLMs) to extract structured information from unstructured EPR data.<n>As a proof-of-concept, we apply the workflow to paediatric renal biopsy reports, a domain chosen for its constrained diagnostic scope and well-defined underlying biology.<n>We develop the workflow iteratively with clinical oversight across three meetings, manually annotating 400 reports from a dataset of 2,111 at Great Ormond Street Hospital as a gold standard, while developing an automated information extraction approach using SLMs.
• Score: 0.0
• License: http://creativecommons.org/licenses/by/4.0/
• Abstract: Electronic Patient Record (EPR) systems contain valuable clinical information, but much of it is trapped in unstructured text, limiting its use for research and decision-making. Large language models can extract such information but require substantial computational resources to run locally, and sending sensitive clinical data to cloud-based services, even when deidentified, raises significant patient privacy concerns. In this study, we develop a resource-efficient semi-automated annotation workflow using small language models (SLMs) to extract structured information from unstructured EPR data, focusing on paediatric histopathology reports. As a proof-of-concept, we apply the workflow to paediatric renal biopsy reports, a domain chosen for its constrained diagnostic scope and well-defined underlying biology. We develop the workflow iteratively with clinical oversight across three meetings, manually annotating 400 reports from a dataset of 2,111 at Great Ormond Street Hospital as a gold standard, while developing an automated information extraction approach using SLMs. We frame extraction as a Question-Answering task grounded by clinician-guided entity guidelines and few-shot examples, evaluating five instruction-tuned SLMs with a disagreement modelling framework to prioritise reports for clinical review. Gemma 2 2B achieves the highest accuracy at 84.3%, outperforming off-the-shelf models including spaCy (74.3%), BioBERT-SQuAD (62.3%), RoBERTa-SQuAD (59.7%), and GLiNER (60.2%). Entity guidelines improved performance by 7-19% over the zero-shot baseline, and few-shot examples by 6-38%, though their benefits do not compound when combined. These results demonstrate that SLMs can extract structured information from specialised clinical domains on CPU-only infrastructure with minimal clinician involvement. Our code is available at https://github.com/gosh-dre/nlp_renal_biopsy.

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