通过通用域资源增强生物医学命名实体识别
Yu Yin1, Hyunjae Kim2, Xiao Xiao1
1Department of Computer Science, University of Liverpool, Liverpool L69 3DR, United Kingdom.
Journal of biomedical informatics
|October 5, 2024
概括
通过使用通用域数据集,GERBERA增强了生物医学命名实体识别 (BioNER) 模型. 这种具有成本效益的转移学习方法提高了BioNER的性能,尤其是在有限的生物医学数据的情况下.
科学领域:
- 计算生物学是一种计算生物学.
- 自然语言处理自然语言处理.
- 机器学习 机器学习
背景情况:
- 生物医学命名实体识别 (BioNER) 模型培训需要广泛,昂贵的人类注释.
- 现有的BioNER多任务学习方法可能无法持续提高性能,并且可以在数据集中引入标签模糊性.
研究的目的:
- 为BioNER模型开发一种新的培训方法,减少对昂贵的人类注释的依赖.
- 通过利用来自一般域数据集的转移学习来提高BioNER模型性能.
主要方法:
- 提出了GERBERA,一种利用通用域名实体识别 (NER) 数据集进行培训的方法.
- 采用多任务学习来训练预训练的生物医学语言模型,使用BioNER和通用域数据集.
- 精心调整模型,特别针对目标BioNER数据集.
主要成果:
- 在GERBERA模型中,在5个数据集和8个实体类型中,经过额外的BioNER数据集训练的基线模型的表现优于基线模型.
- 在八个实体中,与最佳基线相比,实现了0.9%的平均绩效改善.
- 在数据有限的BioNER数据集上显著提高了性能,在JNLPBA-RNA上F1得分提高了4.7%.
结论:
- 引入了一种具有成本效益的培训方法,将BioNER模型与通用NER数据集增强.
- 显著提高了BioNER模型的性能,为缺乏生物医学数据的场景提供了有价值的解决方案.
- 公开提供数据,代码和模型,以促进进一步研究.
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