NDLI: Extracting Biomedical Event with Dual Decomposition Integrating Word Embeddings

Content Provider	ACM Digital Library
Author	Li, Lishuang Huang, Degen Qin, Meiyue Liu, Shanshan Wang, Yiwen
Copyright Year	2016
Description	Author Affiliation: College of Computer Science and Technology Dalian University of Technology(Huang, Degen; Wang, Yiwen; Qin, Meiyue; Liu, Shanshan; Li, Lishuang)
Abstract	AbstractExtracting biomedical event from literatures has attracted much attention recently. By now, most of the state-of-the-art systems have been based on pipelines which suffer from cascading errors, and the words encoded by one-hot are unable to represent the semantic information. Joint inference with dual decomposition and novel word embeddings are adopted to address the two problems, respectively, in this work. Word embeddings are learnt from large scale unlabeled texts and integrated as an unsupervised feature into other rich features based on dependency parse graphs to detect triggers and arguments. The proposed system consists of four components: trigger detector, argument detector, jointly inference with dual decomposition, and rule-based semantic post-processing, and outperforms the state-of-the-art systems. On the development set of BioNLP'09, the F-score is 59.77 percent on the primary task, which is 0.96 percent higher than the best system. On the test set of BioNLP'11, the F-score is 56.09 and 0.89 percent higher than the best published result that do not adopt additional techniques. On the test set of BioNLP'13, the F-score reaches 53.19 percent which is 2.22 percent higher than the best result.
Starting Page	669
Ending Page	677
Page Count	9
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2015.2476876
Volume Number	13
Issue Number	4
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2016-07-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Biomedical event extraction Dual decomposition Natural language processing Word embeddings
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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