Fine-Tuning Bidirectional Encoder Representations From Transformers (BERT)–Based Models on Large-Scale Electronic Health Record Notes: An Empirical Study
Bibliographic record
Abstract
BACKGROUND: The bidirectional encoder representations from transformers (BERT) model has achieved great success in many natural language processing (NLP) tasks, such as named entity recognition and question answering. However, little prior work has explored this model to be used for an important task in the biomedical and clinical domains, namely entity normalization. OBJECTIVE: We aim to investigate the effectiveness of BERT-based models for biomedical or clinical entity normalization. In addition, our second objective is to investigate whether the domains of training data influence the performances of BERT-based models as well as the degree of influence. METHODS: Our data was comprised of 1.5 million unlabeled electronic health record (EHR) notes. We first fine-tuned BioBERT on this large collection of unlabeled EHR notes. This generated our BERT-based model trained using 1.5 million electronic health record notes (EhrBERT). We then further fine-tuned EhrBERT, BioBERT, and BERT on three annotated corpora for biomedical and clinical entity normalization: the Medication, Indication, and Adverse Drug Events (MADE) 1.0 corpus, the National Center for Biotechnology Information (NCBI) disease corpus, and the Chemical-Disease Relations (CDR) corpus. We compared our models with two state-of-the-art normalization systems, namely MetaMap and disease name normalization (DNorm). RESULTS: EhrBERT achieved 40.95% F1 in the MADE 1.0 corpus for mapping named entities to the Medical Dictionary for Regulatory Activities and the Systematized Nomenclature of Medicine-Clinical Terms (SNOMED-CT), which have about 380,000 terms. In this corpus, EhrBERT outperformed MetaMap by 2.36% in F1. For the NCBI disease corpus and CDR corpus, EhrBERT also outperformed DNorm by improving the F1 scores from 88.37% and 89.92% to 90.35% and 93.82%, respectively. Compared with BioBERT and BERT, EhrBERT outperformed them on the MADE 1.0 corpus and the CDR corpus. CONCLUSIONS: Our work shows that BERT-based models have achieved state-of-the-art performance for biomedical and clinical entity normalization. BERT-based models can be readily fine-tuned to normalize any kind of named entities.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.006 | 0.021 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.004 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".