DeIDClinic: A Risk-Aware Pseudonymization Framework for Clinical Text De-identification and Re-identification Risk Assessment
For healthcare and other privacy-critical domains, this framework provides a risk-aware approach to de-identification, enabling compliant data sharing while assessing residual privacy risks.
DeIDClinic presents a pseudonymization framework that integrates domain-adapted transformers (BioBERT, ClinicalBERT) with a novel risk assessment module to de-identify clinical text and quantify re-identification risk, achieving macro F1 > 0.96 on the i2b2 2014 dataset.
The increasing availability of sensitive textual data has created an urgent need for robust de-identification methods that enable compliant data sharing while preserving downstream utility. This paper presents DeID-Clinic, a multi-layered framework for automated pseudonymization and re-identification risk assessment of clinical free-text data. Our approach integrates domain-adapted transformer models, including BioBERT and ClinicalBERT, into the MASK de-identification framework to improve the detection and masking of protected health information (PHI). Beyond entity recognition, we introduce a novel document-level risk assessment module that quantifies residual re-identification risk using a combination of k-anonymity, l-diversity, t-closeness, contextual similarity, and entity co-occurrence analysis. Experiments conducted on the i2b2 2014 de-identification dataset demonstrate strong performance, achieving macro-level F1 scores above 0.96 for several entity categories, while enabling quantitative prioritization of high-risk documents for further review. Our results highlight the effectiveness of combining neural de-identification with explicit risk modeling, supporting privacy-preserving data sharing in sensitive domains. Although evaluated on clinical text, the proposed framework is generalizable to other privacy-critical domains such as legal and administrative documents, where reliable pseudonymization and risk-aware anonymization are essential. Keywords{Automated De-Identification, Risk Assessment, Patient Privacy, Pseudonymization, Personal Health Information}