A Comparative Evaluation Of Transformer Models For De-Identification Of Clinical Text Data

Objective: To comparatively evaluate several transformer model architectures at identifying protected health information (PHI) in the i2b2/UTHealth 2014 clinical text de-identification challenge corpus. Methods: The i2b2/UTHealth 2014 corpus contains N=1304 clinical notes obtained from N=296 patients. Using a transfer learning framework, we fine-tune several transformer model architectures on the corpus, including: BERT-base, BERT-large, ROBERTA-base, ROBERTA-large, ALBERT-base and ALBERT-xxlarge. During fine-tuning we vary the following model hyper-parameters: batch size, number training epochs, learning rate and weight decay. We fine tune models on a training data set, we evaluate and select optimally performing models on an independent validation dataset, and lastly assess generalization performance on a held-out test dataset. We assess model performance in terms of accuracy, precision (positive predictive value), recall (sensitivity) and F1 score (harmonic mean of precision and recall). We are interested in overall model performance (PHI identified vs. PHI not identified), as well as PHI-specific model performance. Results: We observe that the ROBERTA-large models perform best at identifying PHI in the i2b2/UTHealth 2014 corpus, achieving >99% overall accuracy and 96.7% recall/precision on the heldout test corpus. Performance was good across many PHI classes; however, accuracy/precision/recall decreased for identification of the following entity classes: professions, organizations, ages, and certain locations. Conclusions: Transformers are a promising model class/architecture for clinical text de-identification. With minimal hyper-parameter tuning transformers afford researchers/clinicians the opportunity to obtain (near) state-of-the-art performance.
Comment: 38 pages, 3 figures, 6 tables, arxiv pre-print