An Experimental Evaluation of Transformer-based Language Models in the Biomedical Domain

With the growing amount of text in health data, there have been rapid advances in large pre-trained models that can be applied to a wide variety of biomedical tasks with minimal task-specific modifications. Emphasizing the cost of these models, which renders technical replication challenging, this paper summarizes experiments conducted in replicating BioBERT and further pre-training and careful fine-tuning in the biomedical domain. We also investigate the effectiveness of domain-specific and domain-agnostic pre-trained models across downstream biomedical NLP tasks. Our finding confirms that pre-trained models can be impactful in some downstream NLP tasks (QA and NER) in the biomedical domain; however, this improvement may not justify the high cost of domain-specific pre-training.

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