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

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.

Towards Multimodal Representation Learning in Paediatric Kidney Disease

Paediatric kidney disease varies widely in its presentation and progression, which calls for continuous monitoring of renal function. Using electronic health records collected between 2019 and 2025 at Great Ormond Street Hospital, a leading UK paediatric hospital, we explored a temporal modelling approach that integrates longitudinal laboratory sequences with demographic information. A recurrent neural model trained on these data was used to predict whether a child would record an abnormal serum creatinine value within the following thirty days. Framed as a pilot study, this work provides an initial demonstration that simple temporal representations can capture useful patterns in routine paediatric data and lays the groundwork for future multimodal extensions using additional clinical signals and more detailed renal outcomes.