@inproceedings{frei-etal-2026-infherno,
    title = "Infherno: End-to-end Agent-based {FHIR} Resource Synthesis from Free-form Clinical Notes",
    author = "Frei, Johann  and
      Feldhus, Nils  and
      Raithel, Lisa  and
      Roller, Roland  and
      Meyer, Alexander  and
      Kramer, Frank",
    editor = "Croce, Danilo  and
      Leidner, Jochen  and
      Moosavi, Nafise Sadat",
    booktitle = "Proceedings of the 19th Conference of the {E}uropean Chapter of the {A}ssociation for {C}omputational {L}inguistics (Volume 3: System Demonstrations)",
    month = mar,
    year = "2026",
    address = "Rabat, Marocco",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-eacl/2026.eacl-demo.13/",
    pages = "163--174",
    ISBN = "979-8-89176-382-1",
    abstract = "For clinical data integration and healthcare services, the HL7 FHIR standard has established itself as a desirable format for interoperability between complex health data. Previous attempts at automating the translation from free-form clinical notes into structured FHIR resources address narrowly defined tasks and rely on modular approaches or LLMs with instruction tuning and constrained decoding. As those solutions frequently suffer from limited generalizability and structural inconformity, we propose an end-to-end framework powered by LLM agents, code execution, and healthcare terminology database tools to address these issues. Our solution, called Infherno, is designed to adhere to the FHIR document schema and competes well with a human baseline in predicting FHIR resources from unstructured text. The implementation features a front end for custom and synthetic data and both local and proprietary models, supporting clinical data integration processes and interoperability across institutions. Gemini 2.5-Pro excels in our evaluation on synthetic and clinical datasets, yet ambiguity and feasibility of collecting ground-truth data remain open problems."
}