title: Domain adaptation for semantic role labeling of clinical text.
abstract: OBJECTIVE
  Semantic role labeling (SRL), which extracts a shallow semantic relation representation from different surface textual forms of free text sentences, is important for understanding natural language. Few studies in SRL have been conducted in the medical domain, primarily due to lack of annotated clinical SRL corpora, which are time-consuming and costly to build. The goal of this study is to investigate domain adaptation techniques for clinical SRL leveraging resources built from newswire and biomedical literature to improve performance and save annotation costs.
  
  
  METHODS
  Multisource Integrated Platform for Answering Clinical Questions (MiPACQ), a manually annotated SRL clinical corpus, was used as the target domain dataset. PropBank and NomBank from newswire and BioProp from biomedical literature were used as source domain datasets. Three state-of-the-art domain adaptation algorithms were employed: instance pruning, transfer self-training, and feature augmentation. The SRL performance using different domain adaptation algorithms was evaluated by using 10-fold cross-validation on the MiPACQ corpus. Learning curves for the different methods were generated to assess the effect of sample size.
  
  
  CONCLUSIONS
  When all three source domain corpora were used, the feature augmentation algorithm achieved statistically significant higher F-measure (83.18%), compared to the baseline with MiPACQ dataset alone (F-measure, 81.53%), indicating that domain adaptation algorithms may improve SRL performance on clinical text. To achieve a comparable performance to the baseline method that used 90% of MiPACQ training samples, the feature augmentation algorithm required <50% of training samples in MiPACQ, demonstrating that annotation costs of clinical SRL can be reduced significantly by leveraging existing SRL resources from other domains.
authors.affiliation: University of Texas School of Biomedical Informatics at Houston, Houston, TX, USA.
authors.forename: Yaoyun
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: University of Texas School of Biomedical Informatics at Houston, Houston, TX, USA Department of Computer Science, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong, China.
authors.forename: Buzhou
authors.initials: B
authors.lastname: Tang
authors.affiliation: University of Texas School of Biomedical Informatics at Houston, Houston, TX, USA.
authors.forename: Min
authors.initials: M
authors.lastname: Jiang
authors.affiliation: University of Texas School of Biomedical Informatics at Houston, Houston, TX, USA.
authors.forename: Jingqi
authors.initials: J
authors.lastname: Wang
authors.affiliation: University of Texas School of Biomedical Informatics at Houston, Houston, TX, USA hua.xu@uth.tmc.edu.
authors.forename: Hua
authors.initials: H
authors.lastname: Xu
mesh_terms: D000465:Algorithms; D066264:Datasets as Topic; D009323:Natural Language Processing; D012660:Semantics
keywords: clinical natural language processing; domain adaptation; semantic role labeling; shallow semantic parsing; transfer learning