OncoNoteBERT: A Foundation Representation Model for Natural Language Processing of Real-World Outpatient Oncology Notes

Wuraola Oyewusi, Eliana Vasquez Osorio, Goran Nenadic, Gareth Price

Real-world outpatient oncology notes contain specialised terminology, tumour staging expressions, treatment names, toxicity descriptions, and institution-specific de-identification markers that may not be represented efficiently by general biomedical or adjacent clinical language models. We developed and evaluated oncology-specific BERT-style encoders using a governed UK outpatient oncology corpus comprising 290,026 notes from 21,564 patients treated for lung and head-and-neck cancer. We compared RadBERT and PathologyBERT with two local strategies: OncoNote-RadBERT, produced by continued masked language model pretraining, and OncoNoteBERT, trained from scratch with an oncology WordPiece tokenizer. Models were evaluated using masked language modelling loss and perplexity on the validation set, tokenizer fragmentation metrics, clinical term tokenisation, masked-token probes, and exploratory representation analysis. Both external encoders fit the oncology corpus poorly in zero-shot evaluation (perplexity 113.04 for RadBERT; 2035.03 for PathologyBERT), while continued pretraining produced the strongest fit (2.10 for OncoNote-RadBERT). OncoNoteBERT achieved perplexity 2.83 but…