title: A comparison of conditional random fields and structured support vector machines for chemical entity recognition in biomedical literature.
abstract: BACKGROUND
  Chemical compounds and drugs (together called chemical entities) embedded in scientific articles are crucial for many information extraction tasks in the biomedical domain. However, only a very limited number of chemical entity recognition systems are publically available, probably due to the lack of large manually annotated corpora. To accelerate the development of chemical entity recognition systems, the Spanish National Cancer Research Center (CNIO) and The University of Navarra organized a challenge on Chemical and Drug Named Entity Recognition (CHEMDNER). The CHEMDNER challenge contains two individual subtasks: 1) Chemical Entity Mention recognition (CEM); and 2) Chemical Document Indexing (CDI). Our study proposes machine learning-based systems for the CEM task.
  
  
  METHODS
  The 2013 CHEMDNER challenge organizers provided a manually annotated 10,000 UTF8-encoded PubMed abstracts according to a predefined annotation guideline: a training set of 3,500 abstracts, a development set of 3,500 abstracts and a test set of 3,000 abstracts. We developed machine learning-based systems, based on conditional random fields (CRF) and structured support vector machines (SSVM) respectively, for the CEM task for this data set. The effects of three types of word representation (WR) features, generated by Brown clustering, random indexing and skip-gram, on both two machine learning-based systems were also investigated. The performance of our system was evaluated on the test set using scripts provided by the CHEMDNER challenge organizers. Primary evaluation measures were micro Precision, Recall, and F-measure.
  
  
  RESULTS
  Our best system was among the top ranked systems with an official micro F-measure of 85.05%. Fixing a bug caused by inconsistent features marginally improved the performance (micro F-measure of 85.20%) of the system.
  
  
  CONCLUSIONS
  The SSVM-based CEM systems outperformed the CRF-based CEM systems when using the same features. Each type of the WR feature was beneficial to the CEM task. Both the CRF-based and SSVM-based systems using the all three types of WR features showed better performance than the systems using only one type of the WR feature.
authors: Department of Computer Science, Harbin Institute of Technology Shenzhen Guraduate, Shenzhen, Guangdong, China ; School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA.
authors: Buzhou
authors: B
authors: Tang
authors: Department of Pharmacy, the First Affiliated Hospital, Harbin Medical University Harbin, Heilongjiang, China.
authors: Yudong
authors: Y
authors: Feng
authors: Department of Computer Science, Harbin Institute of Technology Shenzhen Guraduate, Shenzhen, Guangdong, China.
authors: Xiaolong
authors: X
authors: Wang
authors: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA.
authors: Yonghui
authors: Y
authors: Wu
authors: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA.
authors: Yaoyun
authors: Y
authors: Zhang
authors: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA.
authors: Min
authors: M
authors: Jiang
authors: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA.
authors: Jingqi
authors: J
authors: Wang
authors: School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, USA.
authors: Hua
authors: H
authors: Xu