Key Coverage Matters: Semi-Structured Extraction of OCR Clinical Reports

Clinical reports are often fragmented across healthcare institutions because privacy regulations and data silos limit direct information sharing. When patients seek care at a different hospital, they often carry paper or scanned reports from prior visits. This hinders EHR integration and longitudinal review, and downstream applications that depend on more complete patient records, such as patient management, follow-up care, real-world studies, and clinical-trial matching. Although OCR can digitize such reports, reliable extraction remains challenging because clinical documents are heterogeneous, OCR text is noisy, and many healthcare settings require low-cost on-premise deployment. We formulate this problem as canonical key-conditioned extractive question answering over OCR-derived clinical reports. Because the key fields are neither fixed nor known in advance, the key space is open. We maintain a canonical key inventory through iterative key mining, normalization, clustering, and lightweight human verification, and introduce key coverage as a metric to quantify inventory completeness. Using a 0.2B BERT-based model, experiments on real-world reports from more than 20 hospitals show performance improves monotonically with key coverage. The model achieves F1 scores of 0.839 and 0.893 under exact match and boundary-tolerant matching, respectively, once the Top-90 canonical keys are covered. These results show that key coverage is a dominant factor for end-to-end performance. At Top-90 coverage, our model outperforms a fine-tuned Qwen3-0.6B baseline under exact match. Although our annotated corpus is Chinese, the method relies on the language-agnostic key-value organization of semi-structured clinical reports and can be adapted to other settings given an appropriate canonical key inventory and alias mapping.

MedStruct-S: A Benchmark for Key Discovery, Key-Conditioned QA and Semi-Structured Extraction from OCR Clinical Reports

Semi-structured information extraction (IE) from OCR-derived clinical reports is crucial for efficiently reconstructing patients' longitudinal medical histories. In practice, this scenario commonly involves three tasks: (i) field-header (key) discovery, (ii) key-conditioned question answering (QA), and (iii) end-to-end key-value pair extraction. However, existing evaluations often under-model two factors: heterogeneous and incompletely known key representations, and OCR-induced noise. This makes it difficult to assess model robustness in real-world settings. We present MedStruct-S, a benchmark specifically designed to evaluate these tasks under unknown keys and OCR noise. MedStruct-S contains 3,582 annotated real-world clinical report pages. Using MedStruct-S, we benchmark two representative paradigms: encoder-only sequence labeling with post-processing and decoder-only structured generation, covering four encoder-only and five decoder-only models spanning 0.11B to 103B parameters. Our results show that encoder-only models achieve the best performance for non-null-value key-conditioned QA despite being substantially smaller than decoder-only models. When comparing models of similar order of magnitude, encoder-only models still perform better overall. Without controlling for model scale, fine-tuned decoder-only models deliver the strongest overall results. These findings show that the benchmark provides a reliable and practical basis for selecting and comparing models across different semi-structured IE settings.