Fast max-margin clustering for unsupervised word sense disambiguation in biomedical texts

Weisi Duan, Min Song, Alexander Yates

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)


Background: We aim to solve the problem of determining word senses for ambiguous biomedical terms with minimal human effort. Methods: We build a fully automated system for Word Sense Disambiguation by designing a system that does not require manually-constructed external resources or manually-labeled training examples except for a single ambiguous word. The system uses a novel and efficient graph-based algorithm to cluster words into groups that have the same meaning. Our algorithm follows the principle of finding a maximum margin between clusters, determining a split of the data that maximizes the minimum distance between pairs of data points belonging to two different clusters. Results: On a test set of 21 ambiguous keywords from PubMed abstracts, our system has an average accuracy of 78%, outperforming a state-of-the-art unsupervised system by 2% and a baseline technique by 23%. On a standard data set from the National Library of Medicine, our system outperforms the baseline by 6% and comes within 5% of the accuracy of a supervised system. Conclusion: Our system is a novel, state-of-the-art technique for efficiently finding word sense clusters, and does not require training data or human effort for each new word to be disambiguated.

Original languageEnglish
Article numberS4
JournalBMC bioinformatics
Issue numberSUPPL. 3
Publication statusPublished - 2009 Mar 19

Bibliographical note

Funding Information:
Partial support for this research was provided by the National Science Foundation under grant DUE-0434581 and by the New Jersey Institute of Technology and Temple University. This work was carried out in part at Temple University's Center for Information Science and Technology. We would like to thank the anonymous reviewers for their helpful comments on previous drafts.

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics


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