{
  "abstract": "Objectives We evaluated an on-premises, open-source large language model (LLM)-based data extraction pipeline for automated data extraction from unstructured electronic health records (EHRs).Methods Automated script-based EHR data preprocessing extracted 50 medical texts in German, which were entered into the LLM pipeline. 4-bit and 8-bit quantizations of 14 mid-sized LLMs (30B–90B parameters) were evaluated in 6 information extraction, 11 binary classification and 5 multilevel classification tasks comprising all variables of the European System for Cardiac Operative Risk Evaluation 2 (EuroSCORE 2) model for 1100 predictions each. LLM response consistency was assessed over three same-prompt iterations.Results In overall accuracy, Qwen3-30b-a3b-q8 presented the highest value (0.954) and 13 LLMs had values over 0.90. In information extraction accuracy, 12 LLMs exhibited a value of 1.0 and all 14 LLMs had values over 0.96. In binary classification accuracy, Llama3.2-vision-90b-q4 exhibited the highest value (0.972), 5 LLMs had values of at least 0.95 and all 14 LLMs showed values over 0.93. In multilevel classification accuracy, Qwen3-30b-a3b-q8 exhibited the highest value (0.940), four LLMs had values over 0.90 and all LLMs presented values over 0.80. Nine LLMs exhibited perfect response consistency and the remaining five LLMs had a Krippendorff’s alpha value of 0.999.Discussion Multiple LLMs exhibited high accuracy in information extraction, binary classification, multilevel classification and response consistency and seem able to reliably automate data extraction from EHRs.Conclusion This pilot study demonstrates the feasibility of on-premises, privacy-preserving, LLM-based automated EHR data extraction pipelines. Larger-scope studies are warranted to validate their potential in healthcare.",
  "authors": [
    {
      "affiliations": [
        "Department of Cardiac Surgery, University Hospital Zurich, Zurich, Switzerland",
        "Department of Cardiac Surgery, Municipal Hospital Zurich, Zurich, Switzerland"
      ],
      "name": "Vasileios Ntinopoulos"
    },
    {
      "affiliations": [
        "Department of Cardiac Surgery, University Hospital Zurich, Zurich, Switzerland",
        "Department of Cardiac Surgery, Municipal Hospital Zurich, Zurich, Switzerland",
        "Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland"
      ],
      "name": "Hector Rodriguez Cetina Biefer"
    },
    {
      "affiliations": [
        "Department of Cardiac Surgery, University Hospital Zurich, Zurich, Switzerland",
        "Department of Cardiac Surgery, Municipal Hospital Zurich, Zurich, Switzerland"
      ],
      "name": "Laura Rings"
    },
    {
      "affiliations": [
        "Department of Cardiac Surgery, University Hospital Zurich, Zurich, Switzerland"
      ],
      "name": "Rodney Alexander Rosalia"
    },
    {
      "affiliations": [
        "Department of Cardiac Surgery, University Hospital Zurich, Zurich, Switzerland",
        "Department of Cardiac Surgery, Municipal Hospital Zurich, Zurich, Switzerland",
        "Center for Translational and Experimental Cardiology (CTEC), Department of Cardiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland"
      ],
      "name": "Omer Dzemali"
    }
  ],
  "title": "Open-source large language model-based on-premises pipeline for automated data extraction from unstructured electronic health records: a pilot study",
  "uid": "6d491429-6e5a-5511-b92c-59e01b8e1e2a"
}