Biomedical Relation Extraction Using Dependency Graph and Decoder-Enhanced Transformer Model

The identification of drug-drug and chemical-protein interactions is essential for understanding unpredictable changes in the pharmacological effects of drugs and mechanisms of diseases and developing therapeutic drugs. In this study, we extract drug-related interactions from the DDI (Drug-Drug Interaction) Extraction-2013 Shared Task dataset and the BioCreative ChemProt (Chemical-Protein) dataset using various transfer transformers. We propose BERT_GAT that uses a graph attention network (GAT) to take into account the local structure of sentences and embedding features of nodes under the self-attention scheme and investigate whether incorporating syntactic structure can help relation extraction. In addition, we suggest T5_{slim_dec}, which adapts the autoregressive generation task of the T5 (text-to-text transfer transformer) to the relation classification problem by removing the self-attention layer in the decoder block. Furthermore, we evaluated the potential of biomedical relation extraction of GPT-3 (Generative Pre-trained Transformer) using GPT-3 variant models. As a result, T5_{slim_dec}, which is a model with a tailored decoder designed for classification problems within the T5 architecture, demonstrated very promising performances for both tasks. We achieved an accuracy of 91.15% in the DDI dataset and an accuracy of 94.29% for the CPR (Chemical-Protein Relation) class group in ChemProt dataset. However, BERT_GAT did not show a significant performance improvement in the aspect of relation extraction. We demonstrated that transformer-based approaches focused only on relationships between words are implicitly eligible to understand language well without additional knowledge such as structural information.