Coreference based event-argument relation extraction on biomedical text

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.

[1]  Jari Björne,et al.  Extracting Complex Biological Events with Rich Graph-Based Feature Sets , 2009, BioNLP@HLT-NAACL.

[2]  Masaaki Nagata,et al.  A Japanese Predicate Argument Structure Analysis using Decision Lists , 2008, EMNLP.

[3]  Udo Hahn,et al.  Event Extraction from Trimmed Dependency Graphs , 2009, BioNLP@HLT-NAACL.

[4]  Jian Su,et al.  Improving Noun Phrase Coreference Resolution by Matching Strings , 2004, IJCNLP.

[5]  Jun'ichi Tsujii,et al.  A Markov Logic Approach to Bio-Molecular Event Extraction , 2009, BioNLP@HLT-NAACL.

[6]  Jun'ichi Tsujii,et al.  Corpus annotation for mining biomedical events from literature , 2008, BMC Bioinformatics.

[7]  Scott Weinstein,et al.  Centering: A Framework for Modeling the Local Coherence of Discourse , 1995, CL.

[8]  Nathanael Chambers,et al.  Unsupervised Learning of Narrative Schemas and their Participants , 2009, ACL.

[9]  Matthew Richardson,et al.  Markov logic networks , 2006, Machine Learning.

[10]  Hoifung Poon,et al.  Joint Inference for Knowledge Extraction from Biomedical Literature , 2010, NAACL.

[11]  Jian Su,et al.  Coreference Resolution in Biomedical Texts: a Machine Learning Approach , 2008, Ontologies and Text Mining for Life Sciences.

[12]  Sampo Pyysalo,et al.  Overview of BioNLP’09 Shared Task on Event Extraction , 2009, BioNLP@HLT-NAACL.

[13]  Sebastian Riedel.  Improving the Accuracy and Efficiency of MAP Inference for Markov Logic , 2008, UAI.

[14]  Hwee Tou Ng,et al.  A Machine Learning Approach to Coreference Resolution of Noun Phrases , 2001, CL.

[15]  Eugene Charniak,et al.  Self-Training for Biomedical Parsing , 2008, ACL.