A Multilevel Analysis of PubMed-only BERT-based Biomedical Models

AbstractBiomedical NLP models play a big role in the automatic extraction of information from biomedical documents, such as COVID research papers. Three landmark models have led the way in this area: BioBERT, MSR BiomedBERT, and BioLinkBERT. However, their shallow evaluation –a single mean score– forbid us to better understand how the contributions proposed in each model advance the Biomedical NLP field. We show through a Multilevel Analysis how we can assess these contributions. Our analyses across 5000 fine-tuned models show that, actually, BiomedBERT’s true effect is bigger than BioLinkBERT’s effect, and the success of BioLinkBERT does not seem to be due to its contribution –the Link function– but due to an unknown factor.