MedicalBERT: enhancing biomedical natural language processing using pretrained BERT-based model

TL;DR

MedicalBERT is a domain-specific pretrained BERT model tailored for biomedical NLP tasks, significantly outperforming existing models like BioBERT and SciBERT across various benchmarks by leveraging large biomedical datasets and specialized vocabulary.

Contribution

This paper introduces MedicalBERT, a pretrained BERT model optimized for biomedical NLP, demonstrating superior performance on multiple biomedical text understanding tasks.

Findings

MedicalBERT outperforms BioBERT, SciBERT, and ClinicalBERT on most benchmarks.

MedicalBERT achieves an average improvement of 5.67% over general BERT across evaluated tasks.

Fine-tuning MedicalBERT enhances its effectiveness in diverse biomedical NLP applications.

Abstract

Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits domain-specific terminology, poses challenges that models likeWord2Vec and bidirectional long short-term memory (Bi-LSTM) can't fullyaddress. GPT and T5, despite capturing context, fall short in tasks needingbidirectional understanding, unlike BERT. Addressing this, we proposedMedicalBERT, a pretrained BERT model trained on a large biomedicaldataset and equipped with domain-specific vocabulary that enhances thecomprehension of biomedical terminology. MedicalBERT model is furtheroptimized and fine-tuned to address diverse tasks, including named entityrecognition, relation extraction, question answering, sentence similarity, anddocument classification. Performance metrics such as the F1-score,accuracy, and Pearson correlation are employed to showcase the efficiencyof our model in comparison to other BERT-based models such as BioBERT,SciBERT, and ClinicalBERT. MedicalBERT outperforms these models onmost of the benchmarks, and surpasses the general-purpose BERT model by5.67% on average across all the tasks evaluated respectively. This work alsounderscores the potential of leveraging pretrained BERT models for medicalNLP tasks, demonstrating the effectiveness of transfer learning techniques incapturing domain-specific information. (PDF) MedicalBERT: enhancing biomedical natural language processing using pretrained BERT-based model. Available from: https://www.researchgate.net/publication/392489050_MedicalBERT_enhancing_biomedical_natural_language_processing_using_pretrained_BERT-based_model [accessed Jul 06 2025].