Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets
This work addresses the need for standardized evaluation in biomedical NLP, though it is incremental as it adapts existing methods to a new domain.
The authors introduced the Biomedical Language Understanding Evaluation (BLUE) benchmark to assess pre-trained language models in biomedicine, finding that a BERT model pre-trained on PubMed abstracts and MIMIC-III clinical notes achieved the best results across ten datasets.
Inspired by the success of the General Language Understanding Evaluation benchmark, we introduce the Biomedical Language Understanding Evaluation (BLUE) benchmark to facilitate research in the development of pre-training language representations in the biomedicine domain. The benchmark consists of five tasks with ten datasets that cover both biomedical and clinical texts with different dataset sizes and difficulties. We also evaluate several baselines based on BERT and ELMo and find that the BERT model pre-trained on PubMed abstracts and MIMIC-III clinical notes achieves the best results. We make the datasets, pre-trained models, and codes publicly available at https://github.com/ncbi-nlp/BLUE_Benchmark.