Specialized transformers-based models (such as BioBERT and BioMegatron) are adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We investigate the encoding and representation of biological knowledge in these models, and its potential utility to support inference in cancer precision medicine—namely, the interpretation of the clinical significance of genomic alterations. We compare the performance of different transformer baselines; we use probing to determine the consistency of encodings for distinct entities; and we use clustering methods to compare and contrast the internal properties of the embeddings for genes, variants, drugs, and diseases. We show that these models do indeed encode biological knowledge, although some of this is lost in fine-tuning for specific tasks. Finally, we analyze how the models behave with regard to biases and imbalances in the dataset.

This content is only available as a PDF.

Author notes


Kilburn Building, Oxford Rd, Manchester M13 9PL, United Kingdom. E-mail: oskar.wysocki@manchester.ac.uk. Secondary affiliation: Department of Computer Science, The University of Manchester.

Other affiliations: Digital Experimental Cancer Medicine Team, Cancer Biomarker Centre, CRUK Manchester Institute, University of Manchester; Department of Computer Science, The University of Manchester.

Action Editor: Byron Wallace

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits you to copy and redistribute in any medium or format, for non-commercial use only, provided that the original work is not remixed, transformed, or built upon, and that appropriate credit to the original source is given. For a full description of the license, please visit https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode.