Omid Rohanian, Mohammadmahdi Nouriborji, Samaneh Kouchaki, David A Clifton

Language models pre-trained on biomedical corpora, such as BioBERT, have recently shown promising results on downstream biomedical tasks. Many existing pre-trained models, on the other hand, are resource-intensive and computationally heavy owing to factors such as embedding size, hidden dimension, and number of layers. The natural language processing (NLP) community has developed numerous strategies to compress these models utilising techniques such as pruning, quantisation, and knowledge distillation, resulting in models that are considerably faster, smaller, and subsequently easier to use in practice. By the same token, in this paper we introduce six lightweight models, namely, BioDistilBERT, BioTinyBERT, BioMobileBERT, DistilBioBERT, TinyBioBERT, and CompactBioBERT which are obtained either by knowledge distillation from a biomedical teacher or continual learning on the Pubmed dataset. We evaluate all of our models on three biomedical tasks and compare them with BioBERT-v1.1 to create the best efficient lightweight models that perform on par with their larger counterparts. We trained six different models in total, with the largest model having 65 million in parameters and the smallest having 15 million; a far lower range of parameters compared with BioBERT's 110M. Based on our experiments on three different biomedical tasks, we found that models distilled from a biomedical teacher and models that have been additionally pre-trained on the PubMed dataset can retain up to 98.8% and 98.6% of the performance of the BioBERT-v1.1, respectively. Overall, our best model below 30M parameters is BioMobileBERT, while our best models over 30M parameters are DistilBioBERT and CompactBioBERT, which can keep up to 98.2% and 98.8% of the performance of the BioBERT-v1.1, respectively. Codes are available at: https://github.com/nlpie-research/Compact-Biomedical-Transformers. Trained models can be accessed at: https://huggingface.co/nlpie. Supplementary data are available at Bioinformatics online.