Kernel-based learning for biomedical relation extraction

Jiexun Li, Zhu Zhang, Xin Li, Hsinchun Chen

Research output: Contribution to journalArticlepeer-review

56 Scopus citations


Relation extraction is the process of scanning text for relationships between named entities. Recently, significant studies have focused on automatically extracting relations from biomedical corpora. Most existing biomedical relation extractors require manual creation of biomedical lexicons or parsing templates based on domain knowledge. In this study, we propose to use kernel-based learning methods to automatically extract biomedical relations from literature text. We develop a framework of kernel-based learning for biomedical relation extraction. In particular, we modified the standard tree kernel function by incorporating a trace kernel to capture richer contextual information. In our experiments on a biomedical corpus, we compare different kernel functions for biomedical relation detection and classification. The experimental results show that a tree kernel outperforms word and sequence kernels for relation detection, our trace-tree kernel outperforms the standard tree kernel, and a composite kernel outperforms individual kernels for relation extraction.

Original languageEnglish (US)
Pages (from-to)756-769
Number of pages14
JournalJournal of the American Society for Information Science and Technology
Issue number5
StatePublished - Mar 2008

ASJC Scopus subject areas

  • Software
  • Information Systems
  • Human-Computer Interaction
  • Computer Networks and Communications
  • Artificial Intelligence


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