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BOOTStrep Project Related Publications



2009

  • Buyko, E., E. Fäßler, J. Wermter, U. Hahn. Event Extraction from Trimmed Dependency Graphs. In BioNLP Shared Task on Event Extraction at NAACL-HLT 2009, June 4-5, 2009, Boulder, Colorado, USA. (accepted)
  • Hahn, U., K. Tomanek, E. Buyko, J.J. Kim, D. Rebholz-Schuhmann. How Feasible and Robust is the Automatic Extraction of Gene Regulation Events? A Cross-Method Evaluation under Lab and Real-Life Conditions. In Workshop on BioNLP at NAACL-HLT 2009, June 4-5, 2009, Boulder, Colorado, USA. (accepted)
  • Jimeno-Yepes, Antonio; Rafael Berlanga-Llavore, Dietrich Rebholz-Schuhmann. Terminological cleansing for improved information retrieval based on ontological terms. In: Proceedings of Second ACM International Conference on Web Search and Data Mining WSDM 2009, Barcelona, Spain - February 9-12, 2009:6-14.
  • Jimeno-Yepes, Antonio; Rafael Berlanga-Llavore, Dietrich Rebholz-Schuhmann. Topic template queries to enhance document retrieval. Workshop on Contextual Information Access, Seeking and Retrieval Evaluation (in conjunction with the 31th European Conference on Information Retrieval), Toulouse, April 6th 2009.
  • Jimeno-Yepes, Antonio, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann. Exploitation of ontological resources for scientific literature analysis: searching genes and related diseases. Journal IEEE Engineering in Medicine and Biology Society (EMBC, accepted for publication).
  • Jimeno-Yepes, Antonio, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann. Ontology refinement for improved information retrieval. Journal of Information Processing and Management (accepted for publication)
  • Jimeno-Yepes, A., E. Jimenez-Ruiz, R. Berlanga, D. Rebholz-Schuhmann. Use of shared lexical resources for efficient ontological engineering. BMC Bioinformatics (accepted for publication)
  • Kano, Yoshinobu; William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, and Jun'ichi Tsujii (in press) U-Compare: share and compare text mining tools with UIMA. In: Bioinformatics.
  • Kano, Y. McCrohon L., Ananiadou, S. and Tsujii, J. (2009). Integrated NLP Evaluation System for Pluggable Evaluation Metrics with Extensive Interoperable Toolkit. NAACL (accepted)
  • Olsson, F., K. Tomanek. An Intrinsic Stopping Criterion for Committee-Based Active Learning. In CoNLL 2009, 4-5 June, Boulder, USA. (accepted)
  • Pezik, P.; A. Jimeno Yepes and D. Rebholz-Schuhmann. (2009). Using Biomedical Terminological Resources for Information Retrieval. In Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration. IGI Global Publishing. (In press)
  • Quochi, Valeria; Riccardo Del Gratta, Eva Sassolini, Roberto Bartolini, Monica Monachini, and Nicoletta Calzolari. (forthcoming) "A Standard Lexical-Terminological Resource for the Bio Domain". LNAI, Heidelberg: Springer.
  • Sasaki, Y. & Ananiadou, S. (in press) Clinical Text Classification under the Open and Closed Topic Assumptions. International Journal on Data Mining and Bioinformatics (IJDMB).
  • Sasaki, Yutaka; Paul Thompson, John McNaught and Sophia Ananiadou,Three BioNLP Tools Powered by a Biological Lexicon. In Proceedings of 12th Conference of the European Chapter of the Association for Computational Linguistics (EACL-09), Athens, March 2009.
  • Schulz, Stefan; Elena Beisswanger, László van den Hoek, Olivier Bodenreider, Erik M. van Mulligen (2009). Alignment of the UMLS Semantic Network with BioTop. Methodology and Assessment. In: Bioinformatics. (accepted for publication)
  • Schulz S.; Boeker M.; Stenzhorn H.; Niggemann J. Granularity issues in the alignment of upper ontologies. In: Methods Inf Med. 2009;48(2):184-9.
  • Tomanek, K., U. Hahn. Semi-Supervised Active Learning for Sequence Labeling. In:ACL-IJCNLP 2009, 2.-7. August, Singapore. (accepted)
  • Tomanek, K., F. Olsson. A Web Survey on the Use of Active Learning to support Annotation of Text Data. In Workshop on Active Learning for Natural Language Processing at NAACL-HLT 2009, June 5, 2009, Boulder, Colorado, USA. (accepted)
  • Tomanek, K., F. Laws, U. Hahn, H. Schütze. On Proper Unit Selection in Active Learning: Co-Selection Effects for Named Entity Recognition. In Workshop on Active Learning for Natural Language Processing at NAACL-HLT 2009, June 5, 2009, Boulder, Colorado, USA. (accepted)
  • Trieschnigg, Dolf; Piotr Pezik, Vivian Lee, Franciska de Jong, Wessel Kraaij, Dietrich Rebholz-Schuhmann. MeSH Up: Effective MeSH Text Classification for Improved Document Retrieval. Bioinformatics Advance Access published April 17, 2009.
  • Tsuruoka, Yoshimasa; Jun'ichi Tsujii, and Sophia Ananiadou.Fast Full Parsing by Linear-Chain Conditional Random Fields, In Proceedings of EACL, pp. 790-798.
  • Tsuruoka,Yoshimasa; Tsujii, Jun'ichi and Sophia Ananiadou. 2009. Stochastic Gradient Descent Training for L1-regularized Log-linear Models with Cumulative Penalty, In Proceedings of ACL-IJCNLP. (to appear).
  • Venturi, Giuila; Simonetta Montemagni, Simone Marchi, Yutaka Sasaki, Paul Thompson, John McNaught, and Sophia Ananiadou, Bootstrapping a Verb Lexicon for Biomedical Information Extraction. In Proceedings of Computational Linguistics and Intelligent Text Processing (CICLing-2009), Mexico, March 2009.
  • Wermter, J.; K. Tomanek, U. Hahn (2009)."High-Performance Gene Name Normalization with GENO." In: Bioinformatics 2009, 25(6):815-821.

2008

2007

2006

Other Selected Relevant Publications (starting 2005) from the Institutions Involved in BOOTStrep


Friedrich-Schiller-Universität Jena
  • C. Fellbaum, U. Hahn & B. Smith: Towards New Information Resources for Public Health – From WordNet to Medical WordNet In: Journal of Biomedical Informatics, Vol. 39, 2006, No.3, pp.321-332.
  • U. Hahn, P. Daumke, S. Schulz & K. Markó: Cross-Language Mining for Acronyms and their Completions from the Web In: A. Hoffmann, H. Motoda & T. Scheffer (Eds.), Discovery Science DS 2005 – Proceedings of the 8th International Conference on Discovery Science. Singapore, 8-11 October 2005. Berlin etc.: Springer, 2005, pp.113-123 (Lecture Notes in Artificial Intelligence, 3735).
  • U. Hahn & J. Wermter: Levels of Natural Language Processing for Text Mining In: S. Ananiadou & J. McNaught (Eds.), Text Mining for Biology and Biomedicine. Boston, London: Artech House Books, 2006, pp.13-41.
  • U. Hahn, J. Wermter, R. Blasczyk & P. Horn: Automated Text Mining as an Alternative to Structured Digital Abstracts (Correspondence) In: Nature, Vol. 410, 2007 [in press]
  • U. Hahn, J. Wermter & J. Fluck: Noun Phrases and Named Entities in Biomedical Texts: Does Domain Change without Retraining Matter? In: RANLP 2005 – Proceedings of the 5th International Conference on Recent Advances in Natural Language Processing. Ed. by G. Angelova, K. Bontcheva, R. Mitkov, N. Nicolov & N. Nikolov. Borovets, Bulgaria, 21-23 September, 2005. Shoumen, 2005, pp.615-621.
  • U. Hahn & A. Valencia (Eds.): SMBM 2005  Proceedings of the 1st International Symposium on Semantic Mining in Biomedicine. Hinxton, Cambridge, U.K., April 10-13, 2005. Online-Proceedings: http://CEUR-WS.org/Vol-148/
  • K. Markó, S. Schulz & U. Hahn: Unsupervised Multilingual Word Sense Disambiguation via an Interlingua In: AAAI‘05 / IAAI‘05 – Proceedings of the 20th National Conference on Artificial Intelligence & 17th Innovative Applications of Artificial Intelligence Conference. Pittsburgh, PA, July 9-13, 2005. Menlo Park/CA, Cambridge/MA: AAAI Press - MIT Press, 2005, pp.1075-1080.
  • K. Markó, S. Schulz, A. Medelyan & U. Hahn: Boostrapping Dictionaries for Cross-Language Information Retrieval In: SIGIR 2005 – Proceedings of the 28th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval. Ed. By G. Marchionini, A. Moffat, J. Tait, R. Baeta-Yates & N. Ziviani. Salvador, Brazil, August 15-19, 2005. New York/NY: ACM Press, 2005, pp.528-535.
  • K. Markó, S. Schulz & U. Hahn: Automatic Lexeme Acquisition for a Multilingual Medical Subword Thesaurus In: International Journal of Medical Informatics, Vol. 76, 2006, Nos.2-3 (Feb/Mar), pp.184-189.
  • M. Poprat & U. Hahn: Enough is enough! – Estimating Upper Bounds of the Size of Training Corpora for Unsupervised PP Attachment Disambiguation In: RANLP 2005 – Proceedings of the 5th International Conference on Recent Advances in Natural Language Processing. Ed. by G. Angelova, K. Bontcheva, R. Mitkov, N. Nicolov & N. Nikolov. Borovets, Bulgaria, 21-23 September, 2005. Shoumen, 2005, pp.405-411.
  • S. Schulz, P. Daumke, B. Smith & U. Hahn: How to Distinguish Parthood from Location in Bioontologies In: AMIA 2005 Symposium – Proceedings of the Annual Symposium of the American Medical Informatics Association. Biomedical and Health Informatics: From Foundations to Applications to Policy. Washington, D.C., USA, October 22-26, 2005. Philadelphia/PA: Hanley & Belfus, 2005, pp.669-673.
  • S. Schulz & U. Hahn: Part-Whole Representation and Reasoning in Formal Biomedical Ontologies In: Artificial Intelligence in Medicine, Vol. 34, 2005, No.3, pp.179-200.
  • S. Schulz, S. Hanser, U. Hahn & J. Rogers: The Semantics of Procedures and Diseases in SNOMED CT In: Methods of Information in Medicine, Vol. 45, 2006, No.4, pp.354-358.
  • S. Schulz & U. Hahn: Towards the Ontological Foundations of Symbolic Biological Theories In: Artificial Intelligence in Medicine, Vol. 39, 2007, No. 3, pp.237-250.
  • S. Schulz, K. Marko & U. Hahn: Spatial Location and its Relevance for Terminological Inferences in Bio-Ontologies In: BMC Bioinformatics, Vol. 8, 2007, No. 134
  • J. Wermter & U. Hahn: Finding New Terminology in Very Large Corpora In: K-CAP ‘05 – Proceedings of the 3rd International Conference on Knowledge Capture (BEST PAPER AWARD). Banff, Canada, October 2-5, 2005. New York/NY: ACM Press, 2005, pp.137-144.
  • J. Wermter & U. Hahn: Paradigmatic Modifiability Statistics for the Extraction of Complex Multi-Word Terms In: HLT/EMNLP 2005 – Proceedings of the Human Language Technology Conference and the Conference on Empirical Methods in Natural Language Processing. Vancouver, B.C., Canada, 6-8 October 2005. East Stroudsburg/PA : Association for Computational Linguistics (ACL), 2005, pp.843-850.
  • J. Wermter & U. Hahn. You Can’t Beat Frequency (Unless You Use Linguistic Knowledge): A Qualitative Evaluation of Association Measures for Collocation and Term Extraction. In: COLING – ACL 2006. Proceedings of the Joint 21st International Conference on Computational Linguistics and 44th Annual Meeting of the Association for Computational Linguistics. Vol. 2. Sydney, Australia, July 17-21, 2006. East Stroudsburg/PA: Association for Computational Linguistics (ACL), 2006, pp.785-792.

Institute for Infocomm Research Singapore
  • Yang Xiao Feng, Su Jian, Tan Chew Lim, A Twin-Candidate Model for Learning Based Coreference Resolution, Computational Linguistics 34: 2, 2008
  • Man Lan, Chew Lim Tan, Jian Su, Yue Lu, Supervised and Traditional Term Weighting Methods for Automatic Text Categorization, accepted by IEEE Transactions on Pattern Analysis and Machine Intelligence;
  • Yang Xiaofeng and Su Jian, Coreference Resolution Using Semantic Relatedness Information from Automatically Discovered Patterns, Proceedings of the 45th Annual Meeting of the Association of Computational Linguistics, P528-535. Prague, Czech Republic, 2007
  • Xiaofeng Yang, Jian Su and Chew-Lim Tan. Kernel-based Pronoun Resolution with Structured Syntactic Knowledge. In Proceedings of the 21st International Conference on Computational Linguistics and the 44th Annual Meeting of the Association for Computational Linguistics (COLING-ACL 2006), Pages 41-48. Sydney, Australia.
  • Guo Dong Zhou, Jian Su and Min Zhang. Modeling Commonality among Related Classes in Relation Extraction. In Proceedings of the 21st International Conference on Computational Linguistics and the 44th Annual Meeting of the Association for Computational Linguistics (COLING-ACL 2006), Pages 121-128. Sydney, Australia.
  • Min Zhang, Jie Zhang, Jian Su, Guodong Zhou. A Composite Kernel to Extract Relations between Entities with Both Flat and Structured Features. In Proceedings of the 21st International Conference on Computational Linguistics and the 44th Annual Meeting of the Association for Computational Linguistics (COLING-ACL 2006), Pages 825-832. Sydney, Australia.
  • Jinxiu Chen, Dong Hong Ji, Chew-Lim Tan, Zheng Yu Niu. Relation Extraction Using Label Propagation Based Semi-Supervised Learning. In Proceedings of the joint conference of the International Committee on Computational Linguistics and the Association for Computational Linguistics (COLING/ACL-2006). P129-136. Sydney, Australia.
  • Jinxiu Chen, Dong Hong Ji, Chew-Lim Tan, Zheng Yu Niu. Unsupervised Relation Disambiguation with Order Identification Capabilities. In Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP 2006). P568-575. Sydney, Australia.
  • Min Zhang, Jie Zhang and Jian Su. Exploring Syntactic Features for Relation Extraction using a Convolution Tree Kernel. In Proceedings of the Human Language Technology conference - North American chapter of the Association for Computational Linguistics annual meeting (HLT-NAACL 2006). P288-295.New York, USA.
  • Xiao Feng Yang, Jian Su, Chew Lim Tan, A twin candidate-model for learning based Anaphora Resolution, Accepted by Computation Linguistics.
  • Yang Xiao Feng, Su Jian and Tan Chew Lim. Improving Pronoun Resolution Using Statistics-Based Semantic Compatibility Information. Proceedings of the 43rd Annual meeting of the Association for Computational Linguistics (ACL05), Ann Arbor, Michigan, US, pp.165-172.
  • Zhou Guo Dong, Su Jian, Zhang Jie and Zhang Min. Combining Various Knowledge in Relation Extraction. Proceedings of the 43rd Annual meeting of the Association for Computational Linguistics (ACL05), Ann Arbor, Michigan, US, pp.427-434.
  • Zhang Jie, Shen Dan, Zhou GuoDong, Su Jian and Tan Chew Lim. Enhancing HMM-based Biomedical Named Entity Recognition by Studying Special Phenomena. Journal of Biomedical Informatics, 37(6), 2004, ISSN: 1532-0464, pp.411-422.
  • Zhou Guo Dong and Su Jian. Machine Learning-based Named Entity Recognition via Effective Integration of Various Evidences. Natural Language Engineering 11(1) 2005, Cambridge Press, ISSN 1469-8110, pp.189-206.
  • Zhou Guo Dong, Shen Dan, Zhang Jie, Su Jian, Tan Soon Heng and Tan Chew Lim. Recognition of Protein and Gene Name Recognition from Text using an Ensemble of Classifiers and Effective Abbreviation Resolution. BMC Bioinformatics, 6(supp 1):S7, 24 May 2005, ISSN 1471-2105. [SCI Expanded]
  • Zhang Min, Su Jian, Wang Dan Mei and Zhou Guo Dong. Discovering Relations from a Large Raw Corpus Using Tree Similarity-based Clustering. In Proceedings of the 2nd International Joint Conference on Natural Language Processing (IJCNLP-05). Jeju Island, Korea.
  • Yang Xiao Feng, Su Jian and Tan Chew Lim. A Twin-Candidate Model of Coreference Resolution with Non-Anaphor Identification Capability. In Proceedings of the 2nd International Joint Conference on Natural Language Processing (IJCNLP-05). Jeju Island, Korea.

University of Manchester / National Centre for Text Mining
  • Kano, Yoshinobu, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Keiichiro Fukamachi, Yusuke Miyao, Yoshimasa Tsuruoka, Sophia Ananiadou and Jun'ichi Tsujii (2008) Towards Data And Goal Oriented Analysis: Tool Inter-Operability And Combinatorial Comparison. In Proceedings of the 3rd International Joint Conference on Natural Language Processing. Hyderabad, India, January 2008
  • Kano, Y., Nguyen, N., Saetre, R., Yoshida, K., Miyao, Y., Tsuruoka, Y., Matsubayashi, Y., Ananiadou, S. and Tsujii, J. (2008) Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example, in PSB 2008, Hawaii.
  • Hirohata, Kenji, Naoaki Okazaki, Sophia Ananiadou and Mitsuru Ishizuka (2008) Identifying Sections in Scientific Abstracts using Conditional Random Fields. In Proceedings of 3rd International Joint Conference on Natural Language Processing. Hyderabad, India, January 2008
  • Tsuruoka, Y., McNaught, J. and S. Ananiadou (2007) Normalizing biomedical terms by minimizing ambiguity and variability, BMC Bioinformatics accepted.
  • Ananiadou, S., Cotter, P., Nobata, C., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y. and Tsujii, J. (2007) SemText: a semantically enriched information retrieval system for biology, in 8th ICSB, Long Beach
  • Ananiadou, S., Kell, D.B. and Tsujii, J. (2006) Text Mining and its Potential Applications in Systems Biology, in Trends in Biotechnology (TIBTECH)
  • Spasic, S., Ananiadou, S., McNaught, J. & Kumar, A. (2005) Text Mining and Ontologies in Biomedicine: Making Sense of Raw Text. Briefings in Bioinformatics 6(3), September 2005.
  • Tsuruoka, Y., Tateishi, Y., Kim, J-D, Ohta, T. McNaught, J., Ananiadou, S. and Tsujii J. (2005) Developing a Robust Part-of-Speech Tagger for Biomedical Text, LNCS, Springer, pp. 382-392
  • Tsujii, J. & Ananiadou, S. (2005) Thesaurus or logical ontology, which one do we need for text mining? In Language Resources and Evaluation, Springer Science and Business Media B.V., vol. 39, no 1, 77-90.
  • Tsuruoka, Y., Ananiadou, S. & Tsujii, J. (2005) A Machine Learning Approach to Acronym Generation, BioLink 2005.
  • Irena Spasic, Sophia Ananiadou and Junichi Tsujii. (2005) MaSTerClass: a case-based reasoning system for the classification of biomedical terms, in Bioinformatics 21(11), pp. 2748-2758.
  • Nenadic, G., Spasic, I. & Ananiadou, S. (2005) Mining Biomedical Abstracts: What’s in a Term? In Keh-Yih Su, Jun’ichi Tsujii, Jong-Hyeok Lee, et al (Eds.) Natural Language Processing – IJCNLP 2004 First International Joint Conference , Lecture Notes in Computer Science vol. 3248
  • Spasic, I. & Ananiadou, S. (2005) A Flexible Measure of Contextual Similarity for Biomedical Terms, in Proceedings of Pacific Symposium on Biocomputing (PSB, 2005), Hawaii , USA .
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pdfpdf I2R_2008_YongWai_Keong_IJCNLP.pdf manage 135.7 K 16 Mar 2009 - 10:45 MareileKnees I2R_2008_YongWai Keong_IJCNNLP
pdfpdf +FSU_2008_Beisswanger_smbm.pdf manage 62.7 K 13 Mar 2009 - 14:09 MareileKnees FSU_2008_Beisswanger_smbm
pdfpdf UoM_2007_Tsuruoka_Bioinformatics.pdf manage 151.8 K 25 Mar 2009 - 16:36 MareileKnees UoM?_2007_Tsuruoka_Bioinformatics
pdfpdf UKLFR_2006_Schulz_AMIA.pdf manage 173.7 K 25 Mar 2009 - 09:42 MareileKnees UKLFR_2006_Schulz_AMIA
pdfpdf FSU_2007_Hahn_BIO-Link.pdf manage 128.3 K 16 Apr 2009 - 15:29 MareileKnees FSU_2007_Hahn_BIO-Link
pdfpdf I2R_2007_Yang_ACL.pdf manage 177.1 K 16 Mar 2009 - 10:26 MareileKnees I2R_2007_Yang_ACL
pdfpdf UoM_2008_Tsuruoka_BMC_BioInformatics.pdf manage 406.7 K 23 Mar 2009 - 14:13 MareileKnees UoM?_2008_Tsuruoka_BMC_BioInformatics
pdfpdf CNR_2007_Toral_RANLP.pdf manage 123.8 K 13 Mar 2009 - 14:54 MareileKnees CNR_2007_Toral_RANLP
pdfpdf UoM_2008_Piao_LREC.pdf manage 239.8 K 23 Mar 2009 - 11:16 MareileKnees UoM?_2008_Piao_LREC
pdfpdf UoM_2008_Thompson_LREC_event.pdf manage 156.8 K 16 Mar 2009 - 11:41 MareileKnees UoM?_2008_Thompson_LREC_event
pdfpdf FSU_2008_Tomanek_LREC.pdf manage 106.6 K 19 Mar 2009 - 15:04 MareileKnees FSU_2008_Tomanek_LREC
pdfpdf UKLFR_2006_Schulz_FOIS.pdf manage 93.7 K 25 Mar 2009 - 10:05 MareileKnees UKLFR_2006_Schulz_FOIS
pdfpdf UoM_2008_Tsuruoka_BMC_BioInformatics_acc.pdf manage 406.7 K 25 Mar 2009 - 15:20 MareileKnees UoM?_2008_Tsuruoka_BMC_BioInformatics_acc
pdfpdf FSU_2007_Tomanek_MedInfo.pdf manage 61.4 K 27 Mar 2009 - 11:40 MareileKnees FSU_2007_Tomanek_MedInfo
pdfpdf FSU_2007_Hahn_ACL.pdf manage 72.9 K 23 Mar 2009 - 13:21 MareileKnees FSU_2007_Hahn_ACL
pdfpdf FSU_2007_Tomanek_ACL.pdf manage 108.1 K 19 Mar 2009 - 15:15 MareileKnees FSU_2007_Tomanek_ACL
pdfpdf UKLFR_2008_Schulz_Bioinformatics.pdf manage 267.3 K 25 Mar 2009 - 10:32 MareileKnees UKLFR_2008_Schulz_Bioinformatics
pdfpdf FSU_2008_Buyko_Coling.pdf manage 81.7 K 23 Mar 2009 - 13:25 MareileKnees FSU_2008_Buyko_Coling
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