Multilingual BERT language model for medical tasks: Evaluation on domain-specific adaptation and cross-linguality

In multilingual healthcare applications, the availability of domain-specific natural language processing(NLP) tools is limited, especially for low-resource languages. Although multilingual bidirectional encoder representations from transformers (BERT) offers a promising motivation to mitigate the language gap, the medical NLP tasks in low-resource languages are still underexplored. Therefore, this study investigates how further pre-training on domain-specific corpora affects model performance on medical tasks, focusing on three languages: Dutch, Romanian and Spanish. In terms of further pre-training, we conducted four experiments to create medical domain models. Then, these models were fine-tuned on three downstream tasks: Automated patient screening in Dutch clinical notes, named entity recognition in Romanian and Spanish clinical notes. Results show that domain adaptation significantly enhanced task performance. Furthermore, further differentiation of domains, e.g. clinical and general biomedical domains, resulted in diverse performances. The clinical domain-adapted model outperformed the more general biomedical domain-adapted model. Moreover, we observed evidence of cross-lingual transferability. Moreover, we also conducted further investigations to explore potential reasons contributing to these performance differences. These findings highlight the feasibility of domain adaptation and cross-lingual ability in medical NLP. Within the low-resource language settings, these findings can provide meaningful guidance for developing multilingual medical NLP systems to mitigate the lack of training data and thereby improve the model performance.

Biomedical Entity Linking for Dutch: Fine-tuning a Self-alignment BERT Model on an Automatically Generated Wikipedia Corpus

Biomedical entity linking, a main component in automatic information extraction from health-related texts, plays a pivotal role in connecting textual entities (such as diseases, drugs and body parts mentioned by patients) to their corresponding concepts in a structured biomedical knowledge base. The task remains challenging despite recent developments in natural language processing. This paper presents the first evaluated biomedical entity linking model for the Dutch language. We use MedRoBERTa.nl as base model and perform second-phase pretraining through self-alignment on a Dutch biomedical ontology extracted from the UMLS and Dutch SNOMED. We derive a corpus from Wikipedia of ontology-linked Dutch biomedical entities in context and fine-tune our model on this dataset. We evaluate our model on the Dutch portion of the Mantra GSC-corpus and achieve 54.7% classification accuracy and 69.8% 1-distance accuracy. We then perform a case study on a collection of unlabeled, patient-support forum data and show that our model is hampered by the limited quality of the preceding entity recognition step. Manual evaluation of small sample indicates that of the correctly extracted entities, around 65% is linked to the correct concept in the ontology. Our results indicate that biomedical entity linking in a language other than English remains challenging, but our Dutch model can be used to for high-level analysis of patient-generated text.