Table 2.

The overall performances of the FT-BERT and the FC-BERT methods on the n2c2 dataset. The Cased and Uncased models are original Google models; BioBERT corresponds to a model trained from PMC and PubMed data; and MIMIC BERT is trained on MIMIC III. P, R, and F represent precision, recall and F1 score, respectively. The boldface represents the best performance for each metric.

Dataset	Baseline			FT-BERT				FC-BERT
		CNN-RNN	JOINT	Cased	Uncased	Bio	MIMIC	Cased	Uncased	MIMIC
n2c2	P	0.9673	0.9715	0.9811	0.9803	0.9798	0.9838	0.9632	0.9653	0.9662
	R	0.8878	0.9079	0.899	0.9021	0.9018	0.9015	0.8524	0.8952	0.8769
	F	0.9258	0.9386	0.9383	0.9396	0.9392	0.9409	0.9044	0.9289	0.9194