Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical-drug relation extraction?

Database (Oxford). 2022 Aug 25;2022:baac070. doi: 10.1093/database/baac070.

ABSTRACT

Collecting relations between chemicals and drugs is crucial in biomedical research. The pre-trained transformer model, e.g. Bidirectional Encoder Representations from Transformers (BERT), is shown to have limitations on biomedical texts; more specifically, the lack of annotated data makes relation extraction (RE) from biomedical texts very challenging. In this paper, we hypothesize that enriching a pre-trained transformer model with syntactic information may help improve its performance on chemical-drug RE tasks. For this purpose, we propose three syntax-enhanced models based on the domain-specific BioBERT model: Chunking-Enhanced-BioBERT and Constituency-Tree-BioBERT in which constituency information is integrated and a Multi-Task-Learning framework Multi-Task-Syntactic (MTS)-BioBERT in which syntactic information is injected implicitly by adding syntax-related tasks as training objectives. Besides, we test an existing model Late-Fusion which is enhanced by syntactic dependency information and build ensemble systems combining syntax-enhanced models and non-syntax-enhanced models. Experiments are conducted on the BioCreative VII DrugProt corpus, a manually annotated corpus for the development and evaluation of RE systems. Our results reveal that syntax-enhanced models in general degrade the performance of BioBERT in the scenario of biomedical RE but improve the performance when the subject-object distance of candidate semantic relation is long. We also explore the impact of quality of dependency parses. [Our code is available at: https://github.com/Maple177/syntax-enhanced-RE/tree/drugprot (for only MTS-BioBERT); https://github.com/Maple177/drugprot-relation-extraction (for the rest of experiments)] Database URL https://github.com/Maple177/drugprot-relation-extraction.

PMID:36006843 | PMC:PMC9408061 | DOI:10.1093/database/baac070