Team Fusion@ SU@ BC8 SympTEMIST track: transformer-based approach for symptom recognition and linking

Abstract

This paper presents a transformer-based approach to solving the SympTEMIST named entity recognition (NER) and entity linking (EL) tasks. For NER, we fine-tune a RoBERTa-based (1) token-level classifier with BiLSTM and CRF layers on an augmented train set. Entity linking is performed by generating candidates using the cross-lingual SapBERT XLMR-Large (2), and calculating cosine similarity against a knowledge base. The choice of knowledge base proves to have the highest impact on model accuracy.

6 pages, 3 tables, Proceedings of the BioCreative VIII Challenge and Workshop: Curation and Evaluation in the era of Generative Models, American Medical Informatics Association 2023 Annual Symposium