Wei Chih-Hsuan, Leaman Robert, Lu Zhiyong
8600 Rockville Pike, National Center for Biotechnology Information (NCBI), Bethesda, Maryland, USA, 20894.
ACM BCB. 2014;2014:138-146. doi: 10.1145/2649387.2649420.
Many text-mining studies have focused on the issue of named entity recognition and normalization, especially in the field of biomedical natural language processing. However, entity recognition is a complicated and difficult task in biomedical text. One particular challenge is to identify and resolve composite named entities, where a single span refers to more than one concept(e.g., BRCA1/2). Most bioconcept recognition and normalization studies have either ignored this issue, used simple ad-hoc rules, or only handled coordination ellipsis, which is only one of the many types of composite mentions studied in this work. No systematic methods for simplifying composite mentions have been previously reported, making a robust approach greatly needed. To this end, we propose a hybrid approach by integrating a machine learning model with a pattern identification strategy to identify the antecedent and conjuncts regions of a concept mention, and then reassemble the composite mention using those identified regions. Our method, which we have named SimConcept, is the first method to systematically handle most types of composite mentions. Our method achieves high performance in identifying and resolving composite mentions for three fundamental biological entities: genes (89.29% in F-measure), diseases (85.52% in F-measure) and chemicals (84.04% in F-measure). Furthermore, our results show that, using our SimConcept method can subsequently help improve the performance of gene and disease concept recognition and normalization.
许多文本挖掘研究都聚焦于命名实体识别与规范化问题,尤其是在生物医学自然语言处理领域。然而,在生物医学文本中,实体识别是一项复杂且困难的任务。一个特殊的挑战是识别和解析复合命名实体,即一个单一的跨度指代多个概念(例如,BRCA1/2)。大多数生物概念识别与规范化研究要么忽略了这个问题,使用简单的临时规则,要么只处理了并列省略,而并列省略只是本研究中所探讨的多种复合提及类型之一。此前尚未有简化复合提及的系统方法被报道,因此迫切需要一种强大的方法。为此,我们提出了一种混合方法,将机器学习模型与模式识别策略相结合,以识别概念提及的先行词和连接词区域,然后使用这些识别出的区域重新组合复合提及。我们的方法名为SimConcept,是第一种系统处理大多数类型复合提及的方法。我们的方法在识别和解析三种基本生物实体的复合提及方面取得了高性能:基因(F值为89.29%)、疾病(F值为85.52%)和化学物质(F值为84.04%)。此外,我们的结果表明,使用我们的SimConcept方法随后可以帮助提高基因和疾病概念识别与规范化的性能。