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MedCase-Structured: A Text-to-FHIR Dataset for Benchmarking Diagnostic Reasoning in Clinically Realistic EHR Settings

Valentina Bui Muti, Eugénie Dulout, Ziquan Fu · May 28, 2026 · Citations: 0

Automatic Metrics Expert Verification Medicine
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How to use this page

Moderate trust

Use this for comparison and orientation, not as your only source.

Best use

Secondary protocol comparison source

What to verify

Validate the evaluation procedure and quality controls in the full paper before operational use.

Evidence quality

Moderate

Derived from extracted protocol signals and abstract evidence.

Abstract

Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited. Existing benchmarks often rely on static datasets or unstructured inputs that do not reflect the interoperable data formats used in clinical systems. We introduce a reusable pipeline for generating terminology-grounded HL7 FHIR R4 bundles from unstructured text, enabling controllable evaluation of clinical decision support systems over structured inputs. The pipeline combines staged LLM generation with terminology-grounded validation and repair to eliminate hallucinated codes and enforce structural and semantic consistency. Applying this approach to MedCaseReasoning, we construct MedCase-Structured, a synthetic dataset of 1,732 FHIR bundles derived from clinician-authored diagnostic cases, producing complete, valid bundles for 97.1% of attempted cases. Evaluation on MedCase-Structured reveals consistently lower diagnostic accuracy for LLMs on structured FHIR inputs than with plain text, highlighting the importance of deployment-aligned benchmarking.

Should You Rely On This Paper?

This paper has useful evaluation signal, but protocol completeness is partial; pair it with related papers before deciding implementation strategy.

Best use

Secondary protocol comparison source

Use if you need

A secondary eval reference to pair with stronger protocol papers.

Main weakness

No major weakness surfaced.

Trust level

Moderate

Usefulness score

65/100 • Medium

Useful as a secondary reference; validate protocol details against neighboring papers.

Human Feedback Signal

Detected

Evaluation Signal

Detected

Usefulness for eval research

Moderate-confidence candidate

Extraction confidence 70%

If you are doing eval pipeline work, start here:

Human Eval Hub LLM-as-Judge Hub Pairwise Preference Hub Tool-Use Eval Hub

What We Could Verify

These are the protocol signals we could actually recover from the available paper metadata. Use them to decide whether this paper is worth deeper reading.

Human Feedback Types

strong

Expert Verification

Directly usable for protocol triage.

"Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited."

Evaluation Modes

strong

Automatic Metrics

Includes extracted eval setup.

"Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited."

Quality Controls

missing

Not reported

No explicit QC controls found.

"Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited."

Benchmarks / Datasets

missing

Not extracted

No benchmark anchors detected.

"Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited."

Reported Metrics

strong

Accuracy

Useful for evaluation criteria comparison.

"Evaluation on MedCase-Structured reveals consistently lower diagnostic accuracy for LLMs on structured FHIR inputs than with plain text, highlighting the importance of deployment-aligned benchmarking."

Rater Population

strong

Domain Experts

Helpful for staffing comparability.

"Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited."

Human Feedback Details

  • Uses human feedback: Yes
  • Feedback types: Expert Verification
  • Rater population: Domain Experts
  • Expertise required: Medicine

Evaluation Details

  • Evaluation modes: Automatic Metrics
  • Agentic eval: None
  • Quality controls: Not reported
  • Evidence quality: Moderate
  • Use this page as: Secondary protocol comparison source

Protocol And Measurement Signals

Benchmarks / Datasets

No benchmark or dataset names were extracted from the available abstract.

Reported Metrics

accuracy

Research Brief

Metadata summary

Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited.

Based on abstract + metadata only. Check the source paper before making high-confidence protocol decisions.

Key Takeaways

  • Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited.
  • Existing benchmarks often rely on static datasets or unstructured inputs that do not reflect the interoperable data formats used in clinical systems.
  • We introduce a reusable pipeline for generating terminology-grounded HL7 FHIR R4 bundles from unstructured text, enabling controllable evaluation of clinical decision support systems over structured inputs.

Researcher Actions

  • Compare this paper against nearby papers in the same arXiv category before using it for protocol decisions.
  • Validate inferred eval signals (Automatic metrics) against the full paper.
  • Use related-paper links to find stronger protocol-specific references.

Caveats

  • Generated from abstract + metadata only; no PDF parsing.
  • Signals below are heuristic and may miss details reported outside the abstract.

Recommended Queries

Accuracy

Research Summary

Contribution Summary

  • Large language models (LLMs) show promise for clinical reasoning and decision support, but evaluation in structured, electronic health record-congruent settings remains limited.
  • We introduce a reusable pipeline for generating terminology-grounded HL7 FHIR R4 bundles from unstructured text, enabling controllable evaluation of clinical decision support systems over structured inputs.
  • Evaluation on MedCase-Structured reveals consistently lower diagnostic accuracy for LLMs on structured FHIR inputs than with plain text, highlighting the importance of deployment-aligned benchmarking.

Why It Matters For Eval

  • We introduce a reusable pipeline for generating terminology-grounded HL7 FHIR R4 bundles from unstructured text, enabling controllable evaluation of clinical decision support systems over structured inputs.
  • Evaluation on MedCase-Structured reveals consistently lower diagnostic accuracy for LLMs on structured FHIR inputs than with plain text, highlighting the importance of deployment-aligned benchmarking.

Researcher Checklist

  • Pass: Human feedback protocol is explicit

    Detected: Expert Verification

  • Pass: Evaluation mode is explicit

    Detected: Automatic Metrics

  • Gap: Quality control reporting appears

    No calibration/adjudication/IAA control explicitly detected.

  • Gap: Benchmark or dataset anchors are present

    No benchmark/dataset anchor extracted from abstract.

  • Pass: Metric reporting is present

    Detected: accuracy

Related Papers

Papers are ranked by protocol overlap, extraction signal alignment, and semantic proximity.