Ontology Attention Layer for Medical Named Entity Recognition

Abstract

Named entity recognition (NER) is particularly challenging for medical texts due to the high domain specificity, abundance of technical terms, and sparsity of data in this field. In this work, we propose a novel attention layer, called the “ontology attention layer”, that enhances the NER performance of a language model for clinical text by utilizing an ontology consisting of conceptual classes related to the target entity set. The proposed layer computes the relevance between each input token and the classes in the ontology and then fuses the encoded token vectors and the class vectors to enhance the token vectors by explicit superior knowledge. In our experiments, we apply the proposed layer to various language models for an NER task based on a Chinese clinical dataset to evaluate the performance of the layer. We also investigate the influence of the granularity of the classes utilized in the ontology attention layer. The experimental results show that the proposed ontology attention layer improved F1 scores by 0.4% to 0.5%. The results suggest that the proposed method is an effective approach to improving the NER performance of existing language models for clinical datasets.