A Transformer-Based Pipeline for German Clinical Document De-Identification

Abstract

OBJECTIVE: Commercially available large language models such as Chat Generative Pre-Trained Transformer (ChatGPT) cannot be applied to real patient data for data protection reasons. At the same time, de-identification of clinical unstructured data is a tedious and time-consuming task when done manually. Since transformer models can efficiently process and analyze large amounts of text data, our study aims to explore the impact of a large training dataset on the performance of this task. METHODS: We utilized a substantial dataset of 10,240 German hospital documents from 1,130 patients, created as part of the investigating hospital's routine documentation, as training data. Our approach involved fine-tuning and training an ensemble of two transformer-based language models simultaneously to identify sensitive data within our documents. Annotation Guidelines with specific annotation categories and types were created for annotator training. RESULTS: Performance evaluation on a test dataset of 100 manually annotated documents revealed that our fine-tuned German ELECTRA (gELECTRA) model achieved an F1 macro average score of 0.95, surpassing human annotators who scored 0.93. CONCLUSION: We trained and evaluated transformer models to detect sensitive information in German real-world pathology reports and progress notes. By defining an annotation scheme tailored to the documents of the investigating hospital and creating annotation guidelines for staff training, a further experimental study was conducted to compare the models with humans. These results showed that the best-performing model achieved better overall results than two experienced annotators who manually labeled 100 clinical documents.

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