title: A neural joint model for entity and relation extraction from biomedical text.
abstract: BACKGROUND
  Extracting biomedical entities and their relations from text has important applications on biomedical research. Previous work primarily utilized feature-based pipeline models to process this task. Many efforts need to be made on feature engineering when feature-based models are employed. Moreover, pipeline models may suffer error propagation and are not able to utilize the interactions between subtasks. Therefore, we propose a neural joint model to extract biomedical entities as well as their relations simultaneously, and it can alleviate the problems above.
  
  
  RESULTS
  Our model was evaluated on two tasks, i.e., the task of extracting adverse drug events between drug and disease entities, and the task of extracting resident relations between bacteria and location entities. Compared with the state-of-the-art systems in these tasks, our model improved the F1 scores of the first task by 5.1% in entity recognition and 8.0% in relation extraction, and that of the second task by 9.2% in relation extraction.
  
  
  CONCLUSIONS
  The proposed model achieves competitive performances with less work on feature engineering. We demonstrate that the model based on neural networks is effective for biomedical entity and relation extraction. In addition, parameter sharing is an alternative method for neural models to jointly process this task. Our work can facilitate the research on biomedical text mining.
authors.affiliation: School of Computer, Wuhan University, Bayi Road, Wuhan, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.affiliation: School of Computer Science and Technology, Heilongjiang University, Xuefu Road, Harbin, China.
authors.forename: Meishan
authors.initials: M
authors.lastname: Zhang
authors.affiliation: School of Computer Science and Technology, Heilongjiang University, Xuefu Road, Harbin, China.
authors.forename: Guohong
authors.initials: G
authors.lastname: Fu
authors.affiliation: School of Computer, Wuhan University, Bayi Road, Wuhan, China. dhji@whu.edu.cn.
authors.forename: Donghong
authors.identifier: http://orcid.org/0000-0002-9244-2476
authors.initials: D
authors.lastname: Ji
mesh_terms: D035843:Biomedical Research; D057225:Data Mining; D016208:Databases, Factual; D008962:Models, Theoretical; D009000:Monocytes / Q000166:cytology / Q000378:metabolism; D016571:Neural Networks, Computer
keywords: Biomedical text; Entity recognition; Joint model; Neural network; Relation extraction