2024/10/22 by John Morris, Morris, John X., Thomas R. Campion +11 · 1 citation
Biochemistry, Genetics and Molecular Biology · Computer Science · #Biomedical Text Mining and Ontologies #Computation and Language (cs.CL) #FOS: Computer and information sciences #Machine Learning in Healthcare #Topic Modeling
paper · doi:10.48550/arxiv.2410.17035
openalex publication_date 2024/10/22 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Sharing protected health information (PHI) is critical for furthering biomedical research. Before data can be distributed, practitioners often perform deidentification to remove any PHI contained in the text. Contemporary deidentification methods are evaluated on highly saturated datasets (tools achieve near-perfect accuracy) which may not reflect the full variability or complexity of real-world clinical text and annotating them is resource intensive, which is a barrier to real-world applications. To address this gap, we developed an adversarial approach using a large language model (LLM) to re-identify the patient corresponding to a redacted clinical note and evaluated the performance with a novel De-Identification/Re-Identification (DIRI) method. Our method uses a large language model to reidentify the patient corresponding to a redacted clinical note. We demonstrate our method on medical data from Weill Cornell Medicine anonymized with three deidentification tools: rule-based Philter and two deep-learning-based models, BiLSTM-CRF and ClinicalBERT. Although ClinicalBERT was the most effective, masking all identified PII, our tool still reidentified 9% of clinical notes Our study highlights significant weaknesses in current deidentification technologies while providing a tool for iterative development and improvement.