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基于共指消解的生物医学文本事件-论元关系提取

Coreference based event-argument relation extraction on biomedical text.

作者信息

Yoshikawa Katsumasa, Riedel Sebastian, Hirao Tsutomu, Asahara Masayuki, Matsumoto Yuji

机构信息

Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan.

出版信息

J Biomed Semantics. 2011 Oct 6;2 Suppl 5(Suppl 5):S6. doi: 10.1186/2041-1480-2-S5-S6.

DOI:10.1186/2041-1480-2-S5-S6
PMID:22166257
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC3239306/
Abstract

This paper presents a new approach to exploit coreference information for extracting event-argument (E-A) relations from biomedical documents. This approach has two advantages: (1) it can extract a large number of valuable E-A relations based on the concept of salience in discourse; (2) it enables us to identify E-A relations over sentence boundaries (cross-links) using transitivity of coreference relations. We propose two coreference-based models: a pipeline based on Support Vector Machine (SVM) classifiers, and a joint Markov Logic Network (MLN). We show the effectiveness of these models on a biomedical event corpus. Both models outperform the systems that do not use coreference information. When the two proposed models are compared to each other, joint MLN outperforms pipeline SVM with gold coreference information.

摘要

本文提出了一种利用指代消解信息从生物医学文档中提取事件-论元(E-A)关系的新方法。该方法具有两个优点:(1)基于语篇显著性概念,它能够提取大量有价值的E-A关系;(2)利用指代关系的传递性,它使我们能够识别跨句子边界的E-A关系(交叉链接)。我们提出了两种基于指代消解的模型:一种基于支持向量机(SVM)分类器的流水线模型,以及一种联合马尔可夫逻辑网络(MLN)。我们在一个生物医学事件语料库上展示了这些模型的有效性。这两种模型均优于未使用指代消解信息的系统。当将这两种提出的模型相互比较时,联合MLN在使用金标准指代消解信息的情况下优于流水线SVM。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/179f/3239306/0203b94e1f7c/2041-1480-2-S5-S6-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/179f/3239306/388e21c8f9b4/2041-1480-2-S5-S6-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/179f/3239306/59e19bcce6df/2041-1480-2-S5-S6-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/179f/3239306/0203b94e1f7c/2041-1480-2-S5-S6-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/179f/3239306/388e21c8f9b4/2041-1480-2-S5-S6-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/179f/3239306/59e19bcce6df/2041-1480-2-S5-S6-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/179f/3239306/0203b94e1f7c/2041-1480-2-S5-S6-3.jpg

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本文引用的文献

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Corpus annotation for mining biomedical events from literature.用于从文献中挖掘生物医学事件的语料库标注。
BMC Bioinformatics. 2008 Jan 8;9:10. doi: 10.1186/1471-2105-9-10.
用于增强从生物医学文献中提取关系的类别指代消解。
BMC Bioinformatics. 2016 Apr 14;17:163. doi: 10.1186/s12859-016-1009-6.
4
Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text.生物共指消解评分系统(Bio-SCoRes):一种用于生物医学文本共指消解的混合架构
PLoS One. 2016 Mar 2;11(3):e0148538. doi: 10.1371/journal.pone.0148538. eCollection 2016.
5
An Overview of Biomolecular Event Extraction from Scientific Documents.科学文献中生物分子事件提取概述
Comput Math Methods Med. 2015;2015:571381. doi: 10.1155/2015/571381. Epub 2015 Oct 26.
6
Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis.EVEX资源在事件抽取与网络构建中的应用:共享任务参赛作品及结果分析
BMC Bioinformatics. 2015;16 Suppl 16(Suppl 16):S3. doi: 10.1186/1471-2105-16-S16-S3. Epub 2015 Oct 30.
7
The contribution of co-reference resolution to supervised relation detection between bacteria and biotopes entities.共指消解对细菌与生物栖息地实体之间监督关系检测的贡献。
BMC Bioinformatics. 2015;16 Suppl 10(Suppl 10):S6. doi: 10.1186/1471-2105-16-S10-S6. Epub 2015 Jul 13.
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J Biomed Inform. 2015 Feb;53:136-46. doi: 10.1016/j.jbi.2014.10.005. Epub 2014 Oct 17.
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PLoS Comput Biol. 2014 Jun 12;10(6):e1003666. doi: 10.1371/journal.pcbi.1003666. eCollection 2014 Jun.
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