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Jonny Pearson

Publications and source records attributed to Jonny Pearson.

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Designing Ambiguity-Aware Clerical Review: A Stratified Sampling Framework for Record Linkage and Deduplication

Clerical review of candidate record pairs remains the de facto gold standard for evaluating record linkage, but it is resource-intensive and often designed informally. We propose a design-based framework that treats clerical review as finite-population sampling over fine-grained strata defined by match weight, comparison pattern, record-level ambiguity, and demographic group. Match-probability bands are constructed from model-based score deciles. Within bands, strata combine comparison patterns with an ambiguity factor derived from matchability and conditional candidate perplexity. A band-specific margin-of-error profile encodes substantive priorities, such as tighter precision in high-score bands, while a single scaling parameter enforces the overall clerical budget. We evaluate the framework using a labelled dataset deduplicated in Splink, comprising 50,000 records and approximately 478,000 candidate pairs. We compare a baseline design reviewing about 23% of pairs with a budget-constrained design reviewing about 7%. The baseline accurately estimates global and band-specific match rates, while sampled distributions of comparison patterns, gender, and ambiguity broadly track the population. Under the budget design, global error approximately doubles, with the largest band-level errors in middle-score bands where matches, non-matches, and ambiguous cases are intermixed. Accuracy in the highest-score bands and the band-wise ambiguity profile are largely preserved, although representativeness by comparison pattern and gender declines. The framework generalises to other clerical-review objectives and can incorporate gold-standard data as prior information for design and calibration. It makes explicit the negotiable trade-offs between workload, precision, representativeness, and coverage of linkage uncertainty.

stat.ME

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.

cs.CL