Publicly Available Clinical BERT Embeddings
Table 2: Accuracy (MedNLI) and Exact F1 score (i2b2) across various clinical NLP tasks.
['Model', 'MedNLI', 'i2b2 2006', 'i2b2 2010', 'i2b2 2012', 'i2b2 2014']
Clinical NLP Tasks On three of the five tasks (MedNLI, i2b2 2010, and i2b2 2012), clinically fine-tuned BioBERT shows improvements over BioBERT or general BERT. However, on our two de-ID tasks, i2b2 2006 and i2b2 2014, clinical BERT offers no improvements over Bio- or general BERT. This is actually not surprising, and is instead, we argue, a direct consequence of the nature of de-ID challenges.