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

TL;DR

MedStruct-S is a benchmark designed to evaluate key discovery, key-conditioned question answering, and semi-structured extraction from OCR clinical reports, addressing real-world challenges like unknown keys and OCR noise.

Contribution

It introduces a new benchmark with real-world data and evaluates multiple models, revealing insights into their performance under challenging conditions.

Findings

Encoder-only models perform best for key-conditioned QA despite smaller size.

Fine-tuned decoder-only models achieve the strongest overall results.

The benchmark enables reliable comparison of models in semi-structured IE tasks.

Abstract

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.