MedCaseAgent: From Multimodal Clinical Evidence to Rare Disease Case Reports
Organizations: PediaMed AI · University of Chinese Academy of Sciences · University of Illinois Urbana-Champaign · Carnegie Mellon University ·
Abstract
Although Large Language Models (LLMs) have demonstrated potential in clinical documentation, generating the rigorous, evidence-based reasoning required for unprecedented, atypical, and rare disease case reports remains a significant challenge. We present MedCaseAgent, an end-to-end agentic reasoning paradigm that bridges this gap by synthesizing publication-quality reports from unstructured clinical notes. MedCaseAgent leverages a hierarchical structure, integrating patient-level data mining with iterative, tool-integrated reasoning. By dynamically querying medical literature and knowledge bases, the agent maintains high clinical fidelity and assesses case novelty. The framework is inherently modular, supporting various backbone LLMs in a plug-and-play fashion. To facilitate this research, we release MedCase-150K, a large-scale multimodal clinical case-report corpus, and MedCase-Bench, a robust temporally held-out evaluation suite. We also introduce an open-source model post-trained from Qwen3.5-9B and optimized specifically for this task. Under both LLM-judged and rule-based evaluation, MedCaseAgent outperforms existing general-purpose and specialized medical LLMs and agents. Blinded expert reviews and ablations further support the system's clinical relevance and evidence grounding.
Figures & tables
| Method | Centered LLM | COVID-19 | Small-Cell Lung Cancer | Erdheim-Chester Disease | Rare Genetic Disorder | Ultra-Rare Disease | Average |
| Human Publication | - | 82.96 | 76.84 | 73.75 | 73.28 | 71.07 | 75.58 |
| Qwen3.5-9B ( Yang et al., 2025 ) | - | 62.46 | 55.84 | 54.35 | 53.44 | 53.79 | 55.98 |
| Qwen3.5-397B-A17B | - | 78.28 | 74.64 | 66.21 | 66.15 | 64.11 | 69.88 |
| Gemma-4-31B | - | 72.34 | 69.26 | 64.25 | 63.03 | 62.45 | 66.27 |
| Claude Opus 4.6 | - | 82.05 | 75.18 | 74.62 | 73.58 | 67.75 | 74.64 |
| GPT-5.4 | - | 84.41 | 79.41 | 74.34 | 70.65 | 73.36 | 76.43 |
| Method | Exact DOI | Novel Rec. | Fig. Seq. | Auth. Indist. | P0 Recall | P1 Recall |
| Qwen3.5-9B | 22.00 | 38.12 | 54.75 | 31.95 | 62.63 | 31.54 |
| Qwen3.5-397B-A17B | 36.27 | 57.39 | 66.93 | 45.53 | 66.70 | 35.32 |
| Gemma-4-31B | 31.11 | 52.88 | 63.36 | 38.92 | 65.87 | 34.87 |
| Claude Opus 4.6 | 43.22 | 66.75 | 73.45 | 53.79 | 68.60 | 35.62 |
| GPT-5.4 | 46.90 | 69.01 | 75.92 | 50.89 | 69.15 | 36.13 |
| Gemini 3.1 Pro | 44.50 | 68.01 | 76.56 | 52.76 | 68.83 | 35.59 |
| Report | Quality | Timeline | Omission control |
| Raw records | 7.4 | 7.5 | 7.8 |
| Atoms | 7.6 | 7.6 | 7.6 |
| Clinician | 7.5 | 7.8 | 7.9 |
Appendix figures & tables16 assets
Supplementary material from the paper’s appendix.
Appendix
| Review stage | Reviewed ( ) | Excluded (%) | Retained (%) | Pre-adjudication agreement |
| Clinical-atom fidelity | 632 | 30 (4.75%) | 602 (95.25%) | 94% |
| Rarity/novelty label | 602 | 18 (2.99%) | 584 (97.01%) | 87% |
| Raw documentation | Corresponding report-derived atom | Information compressed |
| Dated entries separately record fever, marrow findings, impaired consciousness, visual loss, and later motor milestones. | Visual dysfunction persisting for over four months after EBV-associated encephalitis. | The central presentation is retained, while earlier events, care transitions, and temporal context are compressed. |
| Visual findings occur in narrative text and photographed reports. Several BAEP, P-VEP, and OCT screenshots contain demographic details inconsistent with the index patient. | P-VEP showed bilateral NPN waveforms with prolonged latencies; fundoscopy showed no obvious structural abnormality. | Summarized findings are retained, while provenance and possible wrong-patient contamination may be lost. |
| A summary specifies occipital rTMS at 90–100% motor threshold and 5–6 Hz. The contemporaneous plan records 20% intensity, a 25% threshold, 5 Hz, and 750 stimuli. | Occipital rTMS at 90–100% resting motor threshold, 5–6 Hz, and 20 minutes per day. | A single-version atom may obscure conflicting treatment parameters across sources. |
| Left/right optic-radiation streamline counts are 20/496, 314/21, and 483/10 across scans. The final diffusion scan changes from 3 T to 7 T. | Left optic-radiation fiber count increased, whereas the right decreased. | A direction-only atom may omit acquisition differences between scans. |
| Evaluation dimension | Agreement | Reported correlation / exact agreement | Weighted | ICC |
| Factuality | 23/30 | 0.74 | 0.74 | |
| Clinical coherence | 24/30 | 0.76 | 0.77 | |
| Omission | 26/30 | 0.69 | 0.69 | |
| Hallucination | 30/30 | 1.00 | N/A | N/A |
| Citation accuracy | 24/30 | 0.73 | 0.74 |
| Method | Identified as Generated (%) | Identified as Human (%) | Preference vs. Ground Truth (%) |
| Qwen3.5-9B | 86.53 | 13.47 | 24.84 |
| Gemma-4-31B | 82.31 | 17.69 | 30.58 |
| Claude Opus 4.6 | 72.18 | 27.82 | 45.28 |
| GPT-5.4 | 70.24 | 29.76 | 53.70 |
| Gemini 3.1 Pro | 71.07 | 28.93 | 50.48 |
| MedCaseAgent-Base | 79.67 | 20.33 | 36.29 |
| System | Qwen | Gemini | Claude | GPT | Average |
| Human Publication | 76.74 | 78.35 | 74.85 | 72.13 | 75.52 |
| GPT-5.4 | 77.65 | 78.32 | 75.84 | 74.78 | 76.65 |
| Gemini 3.1 Pro | 76.14 | 78.83 | 74.96 | 72.75 | 75.67 |
| Claude Opus 4.6 | 75.60 | 77.02 | 75.10 | 70.84 | 74.64 |
| MedCaseAgent-Base | 66.24 | 67.70 | 64.36 | 62.42 | 65.18 |
| MedCaseAgent-Max | 84.10 | 85.48 | 82.34 | 80.76 | 83.17 |
Medical Report Generation
Medical report generation turns medical images, clinical records, or conversations into structured, clinically useful reports.
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