| --- |
| pretty_name: MedCase-Bench |
| size_categories: |
| - n<1K |
| tags: |
| - medical-literature |
| - case-reports |
| - clinical-atoms |
| configs: |
| - config_name: metadata |
| default: true |
| data_files: |
| - split: evaluation |
| path: metadata.json |
| --- |
| |
| # MedCase-Bench |
|
|
| [Project page](https://huggingface.co/spaces/PediaMedAI/MedCaseAgent) |
| · MedCase-150K |
| · [Agent code](https://github.com/PediaMedAI/MedCaseAgent) |
|
|
| MedCase-Bench contains **584 cases** for medical case-report generation, with |
| one clinical-atom JSON file per case and source bibliography. Clinical atoms |
| are patient-specific facts extracted from published case reports, covering |
| history, presentation, examinations, treatment and outcome. |
|
|
| Each atom file contains five lists of strings: |
|
|
| | Field | Contents | |
| | --- | --- | |
| | `history` | Patient background and relevant medical history. | |
| | `presentation` | Symptoms and findings at presentation. | |
| | `diagnostics` | Examinations, laboratory results and diagnostic observations. | |
| | `management` | Treatments, procedures and clinical decisions. | |
| | `outcome` | Clinical course, response and follow-up. | |
|
|
| ## Files |
|
|
| | File | Contents | |
| | --- | --- | |
| | `atoms/<PMCID>_atoms.json` | 584 clinical-atom files. | |
| | `metadata.json` | 584 corresponding source records, including article identifiers, publication dates, licenses and source download links. | |
|
|
| This package contains textual inputs and source metadata. Full articles and |
| medical images can be obtained through the source links in `metadata.json`. |
| Source publications retain the licenses recorded in their metadata. |
|
|
| ## Use |
|
|
| ```python |
| import json |
| from pathlib import Path |
| |
| files = sorted(Path("atoms").glob("*_atoms.json")) |
| assert len(files) == 584 |
| atoms = json.loads(files[0].read_text(encoding="utf-8")) |
| print(atoms["history"]) |
| ``` |
|
|
| After installing [MedCaseAgent](https://github.com/PediaMedAI/MedCaseAgent) and |
| configuring a compatible model API: |
|
|
| ```bash |
| medcase-agent validate atoms/<PMCID>_atoms.json |
| medcase-agent generate atoms/<PMCID>_atoms.json \ |
| --exclude-ids path/to/your-exclusions.json --output runs |
| ``` |
|
|
| For generation with images, prepare each case's source images following the |
| [preprocessing guide](https://github.com/PediaMedAI/MedCaseAgent/blob/main/docs/preprocessing.md). |
| For retrieval-based evaluation, prepare your own PMCID, PMID and DOI exclusion |
| list for the benchmark sources and any related publications. |
|
|
