Improving protein coreference resolution by simple semantic classification


Current research has shown that major difficulties in event extraction for the biomedical domain are traceable to coreference. Therefore, coreference resolution is believed to be useful for improving event extraction.

To address coreference resolution in molecular biology literature, the Protein Coreference (COREF) task was arranged in the BioNLP Shared Task (BioNLP-ST, hereafter) 2011, as a supporting task. However, the shared task results indicated that transferring coreference resolution methods developed for other domains to the biological domain was not a straight-forward task, due to the domain differences in the coreference phenomena.

Results: We analyzed the contribution of domain-specific information, including the information that indicates the protein type, in a rule-based protein coreference resolution system.

In particular, the domain-specific information is encoded into semantic classification modules for which the output is used in different components of the coreference resolution. We compared our system with the top four systems in the BioNLP-ST 2011; surprisingly, we found that the minimal configuration had outperformed the best system in the BioNLP-ST 2011.

Analysis of the experimental results revealed that semantic classification, using proteininformation, has contributed to an increase in performance by 2.3% on the test data, and 4.0% on the development data, in F-score.

Conclusions: The use of domain-specific information in semantic classification is important for effective coreferenceresolution. Since it is difficult to transfer domain-specific information across different domains, we need tocontinue seek for methods to utilize such information in coreference resolution.

Author: Ngan L.T. NguyenJin-Dong KimMakoto MiwaTakuya MatsuzakiJunichi Tsujii
Credits/Source: BMC Bioinformatics 2012, 13:304



Published on: 2012-11-17



News Provider: 7thSpace Interactive

Copyright by the authors listed above - made available via BioMedCentral (Open Access). Please make sure to read our disclaimer prior to contacting 7thSpace Interactive. To contact our editors, visit our online helpdesk. If you wish submit your own press release, click here.

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