RankPref: Ranking sentences describing relations between biomedical entities with an application

BioNLP@HLT-NAACL 2012 - Workshop on Biomedical Natural Language Processing, Proceedings

Volumn , Issue , 2012, Pages 163-171

  Tudor, Catalina O ^a   Vijay Shanker, K ^a  

^a University of Delaware   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION (OF INFORMATION); COMPUTATIONAL LINGUISTICS; LEARNING ALGORITHMS; NATURAL LANGUAGE PROCESSING SYSTEMS;

BINARY CLASSIFICATION; CLASSIFICATION TASKS; COMPLEX SENTENCES; LEARN+; LEARNING PROCESS; MACHINE LEARNING APPROACHES; SIMPLE STRUCTURES;

LEARNING SYSTEMS;

EID: 84908078683     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (26)

1. Michele Banko, Michael J Cafarella, Stephen Soderland, Matt Broadhead, and Oren Etzioni. 2007. Open Information Extraction from the Web. In Proceedings of IJCAI.
2. John Carroll, Guido Minnen, Yvonne Canning, Siobhan Devlin, and John Tait. 1998. Practical simplification of English newspaper text to assist aphasic readers. Proceedings of the AAAI98 Workshop on Integrating AI and Assistive Technology, pages 7-10.
3. Ben Carterette, Paul N Bennett, David Maxwell Chickering, and Susan T Dumais. 2008. Here or there: Preference judgments for relevance. In Proceedings of the IR research, 30th European conference on Adv. in IR.
4. R Chandrasekar, Christine Doran, and B Srinivas. 1996. Motivations and methods for text simplification. In Proceedings of the 16th conference on Computational linguistics, volume 2, pages 1041-1044. Association for Computational Linguistics.
5. Wiliam W Cohen, Robert E Schapire, and Yoram Singer. 1999. Learning to order things. Journal of Artificial Intelligence Research, 10:243-270.
6. Siobhan Devlin and John Tait. 1998. The use of a psycholinguistic database in the simplification of text for aphasic readers. Linguistic Databases, pages 161- 173.
7. Yoav Freund, Raj Iyer, Robert E Schapire, and Yoram Singer. 2003. An efficient boosting algorithm for combining preferences. Journal of Machine Learning Research, 4:933-969.
8. Arek Gladki, Pawel Siedlecki, Szymon Kaczanowski, and Piotr Zielenkewicz. 2008. e-LiSe-an online tool for finding needles in the 'Medline haystack'. Bioinformatics, 24(8):1115-1117.
9. Andrew B Goldberg, David Andrzejewski, Jurgen Van Gael, Burr Settles, Xiaojin Zhu, and Mark Craven. 2008. Ranking biomedical passages for relevance and diversity. In Proceedings of TREC.
10. William Hersh, Aaron M Cohen, Phoebe Roberts, and Hari Krishna Rekapalli. 2006. TREC 2006 Genomics Track Overview.
11. Kalervo Jarvelin and Jaana Kekalainen. 2002. Cumulated gain-based evaluation of IR techniques. ACM Transactions on Information Systems, 20(4):422-446.
12. Feng Jin, Minlie Huang, Zhiyong Lu, and Xiaoyan Zhu. 2009. Towards automatic generation of gene summary. In Proceedings of the BioNLP 2009 Workshop, pages 97-105. Association for Computational Linguistics, June.
13. Siddhartha Jonnalagadda, Luis Tari, Jorg Hakenberg, Chitta Baral, and Graciela Gonzalez. 2009. Towards effective sentence simplification for automatic processing of biomedical text. In Proceedings of NAACL HLT 2009: Short Papers, pages 177-180.
14. Szymon Kaczanowski, Pawel Siedlecki, and Piotr Zielenkewicz. 2009. The high throughput sequence annotation service (HT-SAS) - the shortcut from sequence to true medline words. BMC Bioinformatics, 10:148-154, May.
15. Jung-Jae Kim, Piotr Pezik, and Dietrich Rebholz- Schuhmann. 2008. MedEvi: Retrieving textual evidence of relations between biomedical concepts from medline. Bioinformatics, 24(11):1410-1412.
16. Xu Ling, Jing Jiang, Xin He, Qiaozhu Mei, Chengxiang Zhai, and Bruce Schatz. 2007. Generating gene summaries from biomedical literature: A study of semi-structured summarization. Information Processing and Management, 43:1777-1791, March.
17. Yue Lu, Hui Fang, and Chengxiang Zhai. 2009. An empirical study of gene synonym query expansion in biomedical information retrieval. Information Retrieval, 12:51-68, February.
18. Aurélie Névéol, W John Wilbur, and Zhiyong Lu. 2011. Extraction of data deposition statements from the literature: a method for automatically tracking research results. Bioinformatics, 27(23):3306-3312.
19. Filip Radlinski and Thorsten Joachims. 2005. Query chains: Learning to rank from implicit feedback. In Proceedings of KDD'05.
20. Advaith Siddharthan. 2004. Syntactic Simplification and Text Cohesion. Ph.D. thesis, University of Cambridge.
21. Neil R Smalheiser, Wei Zhou, and Vetle I Torvik. 2008. Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results. Journal of Biomedical Discovery and Collaboration, 3(1):2-11.
22. Brian P Suomela and Miguel A Andrade. 2005. Ranking the whole MEDLINE database according to a large training set using text indexing. BMC Bioinformatics, 6(75), March.
23. Yoshimasa Tsuruoka, Yuka Tateishi, Jing-Dong Kim, Tomoko Ohta, John McNaught, Sophia Ananiadou, and Jun'ichi Tsujii. 2005. Developing a robust partof- speech tagger for biomedical text. In Advances in Informatics - 10th Panhellenic Conference on Informatics, LNCS 3746, pages 382-392.
24. Catalina O Tudor, Carl J Schmidt, and K Vijay-Shanker. 2010. eGIFT: Mining Gene Information from the Literature. BMC Bioinformatics, 11:418.
25. Jianji Yang, Aaron Cohen, and William Hersh. 2009. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets. BMC Bioinformatics, 10(Suppl 2):S5.
26. Lana Yeganova, Donald C Comeau, Won Kim, and W John Wilbur. 2011. Text Mining Techniques for Leveraging Positively Labeled Data. In Proceedings of ACL Workshop BioNLP, pages 155-163.