We are not ready yet: limitations of state-of-the-art disease named entity recognizers

Abstract

Abstract Background Intense research has been done in the area of biomedical natural language processing. Since the breakthrough of transfer learning-based methods, BERT models are used in a variety of biomedical and clinical applications. For the available data sets, these models show excellent results - partly exceeding the inter-annotator agreements. However, biomedical named entity recognition applied on COVID-19 preprints shows a performance drop compared to the results on test data. The question arises how well trained models are able to predict on completely new data, i.e. to generalize. Results Based on the example of disease named entity recognition, we investigate the robustness of different machine learning-based methods - thereof transfer learning - and show that current state-of-the-art methods work well for a given training and the corresponding test set but experience a significant lack of generalization when applying to new data. Conclusions We argue that there is a need for larger annotated data sets for training and testing. Therefore, we foresee the curation of further data sets and, moreover, the investigation of continual learning processes for machine learning-based models.