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Reference Data And Model Adapters

CaseCrawler can run fully offline, but it is designed to pull in stronger models and reference datasets when available.

Reference Catalog

casecrawler reference-datasets
casecrawler datasets capabilities

Registered reference sources include:

  • Synthea FHIR/NDJSON/CSV imports
  • Asclepius synthetic clinical notes
  • SynthClinicalNotes
  • augmented clinical notes
  • MedSynth dialogue-note pairs
  • BeTraC/Synth-DoPaCo doctor-patient transcript to SOAP rows
  • clinical-note-to-FHIR references
  • radiology report consistency references
  • SynthCheX-75K-v2 image/text references
  • synthetic chest X-ray pneumonia references
  • Technetium-I de-identification and ICD-coding references
  • bundled offline fixtures for smoke tests

Import Hugging Face Or Local References

casecrawler import-reference-dataset asclepius \
  --dataset-id ds-asclepius-ref \
  --limit 100

casecrawler import-reference-dataset \
  --repo-id org/custom-synthetic-notes \
  --dataset-id ds-custom-ref \
  --note-field clinical_note \
  --question-field prompt \
  --answer-field completion \
  --split eval \
  --limit 100

casecrawler import-reference-dataset local-validation-notes \
  --path ./validation/local-notes.jsonl \
  --dataset-id ds-local-ref \
  --note-field clinical_note \
  --question-field prompt \
  --answer-field completion \
  --limit 100

Local imports support JSONL, NDJSON, JSON arrays, and {"rows": [...]}.

Synthea

casecrawler import-synthea ./synthea/output/fhir --dataset-id ds-synthea-ref

casecrawler run-synthea \
  --synthea-executable ./synthea/run_synthea \
  --output-dir ./synthea/output/fhir \
  --dataset-id ds-synthea-ref \
  --population 100

Synthea imports accept FHIR JSON bundles, Bulk FHIR NDJSON resource directories, and Synthea CSV directories.

Imaging

casecrawler imaging-models

Imaging profiles include Prompt2MedImage, MediSyn, CheXGenBench Sana, chest X-ray Stable Diffusion and DreamBooth profiles, symptom X-ray LoRA, and gated RoentGen profiles. Each profile exposes model id, license, gated status, use policy, prompt contract, output contract, and validation requirements.

Supported backends:

  • placeholder: deterministic local PNG for offline tests
  • diffusers: local Hugging Face/diffusers image generation
  • external: command adapter returning an ImagingAsset

Clinical Text

casecrawler clinical-text-models

Clinical text adapters include deterministic templates, LLM provider routing, MedGemma, Meditron, and generic external command profiles. Noisy text variants can use standard, message, ocr, or heavy profiles.

Time Series

casecrawler timeseries-models

Time-series profiles include deterministic generation plus external-command profiles for TimeDiff, RawMed-style workflows, and MIRA-style generation or validation. External adapters return TimeSeriesChannel[].

Image Validators

Image/report validation includes deterministic lexical checks and optional BiomedCLIP or MedGemma image-text validators when the relevant extras and model access are available.