Named-entity recognition with BERT for anonymization of medical records

Sharing data is an important part of the progress of science in many fields. In the largely deep learning dominated field of natural language processing, textual resources are in high demand. In certain domains, such as that of medical records, the sharing of data is limited by ethical and legal restrictions and therefore requires anonymization. The process of manual anonymization is tedious and expensive, thus automated anonymization is of great value. Since medical records consist of unstructured text, pieces of sensitive information have to be identified in order to be masked for anonymization. Named-entity recognition (NER) is the subtask of information extraction named entities, such as person names or locations, are identified and categorized. Recently, models that leverage unsupervised training on large quantities of unlabeled training data have performed impressively on the NER task, which shows promise in their usage for the problem of anonymization. In this study, a small set of medical records was annotated with named-entity tags. Because of the lack of any training data, a BERT model already fine-tuned for NER was then evaluated on the evaluation set. The aim was to find out how well the model would perform on NER on medical records, and to explore the possibility of using the model to anonymize medical records. The most positive result was that the model was able to identify all person names in the dataset. The average accuracy for identifying all entity types was however relatively low. It is discussed that the success of identifying person names shows promise in the model’s application for anonymization. However, because the overall accuracy is significantly worse than that of models fine-tuned on domain-specific data, it is suggested that there might be better methods for anonymization in the absence of relevant training data