Hierarchical Section Matching Prediction (HSMP) BERT for Fine-Grained Extraction of Structured Data from Hebrew Free-Text Radiology Reports in Crohn's Disease

Zvi Badash; Hadas Ben-Atya; Naama Gavrielov; Liam Hazan; Gili Focht; Ruth Cytter-Kuint; Talar Hagopian; Dan Turner; Moti Freiman

arXiv · 2509.04519

Hierarchical Section Matching Prediction (HSMP) BERT for Fine-Grained Extraction of Structured Data from Hebrew Free-Text Radiology Reports in Crohn's Disease

Zvi Badash·Hadas Ben-Atya·Naama Gavrielov·Liam Hazan·Gili Focht·Ruth Cytter-Kuint·Talar Hagopian·Dan Turner·Moti Freiman

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Abstract

Extracting structured clinical information from radiology reports is challenging, especially in low-resource languages. This is pronounced in Crohn's disease, with sparsely represented multi-organ findings. We developed Hierarchical Structured Matching Prediction BERT (HSMP-BERT), a prompt-based model for extraction from Hebrew radiology text. In an administrative database study, we analyzed 9,683 reports from Crohn's patients imaged 2010-2023 across Israeli providers. A subset of 512 reports was radiologist-annotated for findings across six gastrointestinal organs and 15 pathologies, yielding 90 structured labels per subject. Multilabel-stratified split (66% train+validation; 33% test), preserving label prevalence. Performance was evaluated with accuracy, F1, Cohen's $\kappa$, AUC, PPV, NPV, and recall. On 24 organ-finding combinations with $>$15 positives, HSMP-BERT achieved mean F1 0.83$\pm$0.08 and $\kappa$ 0.65$\pm$0.17, outperforming the SMP zero-shot baseline (F1 0.49$\pm$0.07, $\kappa$ 0.06$\pm$0.07) and standard fine-tuning (F1 0.30$\pm$0.27, $\kappa$ 0.27$\pm$0.34; paired t-test $p < 10^{-7}$). Hierarchical inference cuts runtime 5.1$\times$ vs. traditional inference. Applied to all reports, it revealed associations among ileal wall thickening, stenosis, and pre-stenotic dilatation, plus age- and sex-specific trends in inflammatory findings. HSMP-BERT offers a scalable solution for structured extraction in radiology, enabling population-level analysis of Crohn's disease and demonstrating AI's potential in low-resource settings.

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Zvi Badash, Hadas Ben-Atya, Naama Gavrielov, Liam Hazan, Gili Focht, Ruth Cytter-Kuint, Talar Hagopian, Dan Turner, Moti Freiman. 2025-09-03. Hierarchical Section Matching Prediction (HSMP) BERT for Fine-Grained Extraction of Structured Data from Hebrew Free-Text Radiology Reports in Crohn's Disease. https://arxiv.org/abs/2509.04519

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