MedDeID enables locally governed clinical-text de-identification from real or synthetic training data

Abstract:Clinical notes contain personally identifiable information (PII), restricting reuse for research and medical AI, especially when data cannot leave an institution. We developed MedDeID, an on-premises framework combining in-house annotation and synthetic-note generation with model training, inference, pseudonymisation and evaluation. On an independently annotated, adjudicated 300-note Dutch hospital benchmark, a hospital-trained compact transformer detected 98.9% of identifying text while redacting 0.24% of text outside annotated identifiers; a synthetic-only counterpart detected 96.1%. On 100 primary-care notes, the synthetic-trained model achieved higher recall than the hospital-trained model (90.3% versus 87.0%) and greater robustness to identifier-format perturbations. An English instantiation trained without real text detected 99.7% and 98.9% of annotated identifier characters on two external synthetic benchmarks. These results demonstrate transfer of the workflow to another language, but not clinical English performance. MedDeID provides a route to locally governed de-identification using real or synthetic training data.

Computation and Language (cs.CL); Machine Learning (cs.LG)

arXiv:2609.10049 [cs.CL]

(or arXiv:2609.10049v1 [cs.CL] for this version)

https://doi.org/10.48550/arXiv.2609.10049 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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