BioBERT Large Results

These are the results of using BioBERT v1.2 (+Pubmed 1M, Large). Improved results are in bold.

NER datasets (Precision/Recall/F1 score (%))

Dataset	BioBERT v1.1 (reported)	BioBERT v1.2
NCBI disease	88.22/91.25/89.71	xx.xx/xx.xx/xx.xx
BC5CDR disease	86.47/87.84/87.15	xx.xx/xx.xx/xx.xx
BC5CDR drug/chem.	93.68/93.26/93.47	xx.xx/xx.xx/xx.xx
BC4CHEMD	92.80/91.92/92.36	xx.xx/xx.xx/xx.xx
BC2GM	84.32/85.12/84.72	xx.xx/xx.xx/xx.xx
JNLPBA	72.24/83.56/77.49	xx.xx/xx.xx/xx.xx
LINNAEUS	90.77/85.83/88.24	xx.xx/xx.xx/xx.xx
Species-800	72.80/75.36/74.06	xx.xx/xx.xx/xx.xx

RE datasets (Precision/Recall/F1 score (%))

Dataset	BioBERT v1.1 (reported)	BioBERT v1.2
GAD	77.32/82.68/79.83	xx.xx/xx.xx/xx.xx
EU-ADR	77.86/83.55/79.74	xx.xx/xx.xx/xx.xx

QA datasets (SAcc/LAcc/MRR (%))

Dataset	BioBERT v1.1 (reported)	BioBERT v1.2
BioASQ 4b	27.95/44.10/34.72	34.76/50.88/41.34
BioASQ 5b	46.00/60.00/51.64	46.66/60.38/52.12
BioASQ 6b	42.86/57.77/48.43	40.76/61.18/49.05