End-to-End Pseudonymization of Fine-Tuned Clinical BERT Models

Abstract

Abstract Many state-of-the-art results in natural language processing (NLP) rely on large pre-trained language models (PLMs). These models consist of large amounts of parameters that are tuned using vast amounts of training data. These factors cause the models to memorize parts of their training data, making them vulnerable to various privacy attacks. This is cause for concern, especially when these models are applied in the clinical domain, where data are very sensitive. One privacy-preserving technique that aims to mitigate these problems is training data pseudonymization. This technique automatically identifies and replaces sensitive entities with realistic but non-sensitive surrogates. Pseudonymization has yielded promising results in previous studies. However, no previous study has applied pseudonymization to both the pre-training data of PLMs and the fine-tuning data used to solve clinical NLP tasks. This study evaluates the predictive performance effects of end-to-end pseudonymization of clinical BERT models on five clinical NLP tasks compared to pre-training and fine-tuning on unaltered sensitive data. A large number of statistical tests are performed, revealing minimal harm to performance when using pseudonymized fine-tuning data. The results also find no deterioration from end-to-end pseudonymization of pre-training and fine-tuning data. These results demonstrate that pseudonymizing training data to reduce privacy risks can be done without harming data utility for training PLMs.

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