Papers

• Kim, Jin-Dong, Tomoko Ohta, Yoshimasa Tsuruoka, Yuka Tateisi and Nigel Collier. (2004). Introduction to the Bio-Entity Recognition Task at JNLPBA. In the Proceedings of the International Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA-04). pp. 70--75. [PDF]
• Tsujii, Jun-ichi. (2004). Thesaurus or logical ontology, which do we need for mining text? (keynote speech). In the Proc. of Language resources and evaluation conference (LREC 2004). Vol.III. 55-57 rue Brillat Savarin 75013 Paris France. pp. pp IX-XVI. ELRA. [PDF]
• Tateisi, Yuka and Jun'ichi Tsujii. (2004). Part-of-Speech Annotation of Biology Research Abstracts. In the Proceedings of 4th International Conference on Language Resource and Evaluation (LREC2004). IV. pp. 1267-1270. [PDF]
• Kim, Jin-Dong and Jun'ichi Tsujii. (2004). Word Folding: Taking the Snapshot of Words Instead of the Whole. In the Proceedings of the First International Joint Conference on Natural Language Processing. pp. 61--68. [PDF]
• Tateisi, Yuka, Ohta, Tomoko and Tsujii, Jun-ichi. (2004). Annotation of Predicate-argument Structure of Molecular Biology Text. In the IJCNLP-04 workshop on Beyond Shallow Analyses. [PDF]



• Kim, Jin-Dong, Tomoko Ohta, Yuka Teteisi and Jun'ichi Tsujii. (2003). GENIA corpus - a semantically annotated corpus for bio-textmining. Bioinformatics. 19(suppl. 1). pp. i180-i182. Oxford University Press. [Abstract and PDF Downloads from Oxford Journals Online]
• Masuda, Katsuya, Takashi Ninomiya, Yusuke Miyao, Tomoko Ohta and Jun'ichi Tsujii. (2003). A Robust Retrieval Engine for Proximal and Structural Search. In the Proceedings of HLT-NAACL 2003 Short papers. pp. 58--60. [PDF]
• Tsuruoka, Yoshimasa and Jun'ichi Tsujii. (2003). Probabilistic Term Variant Generator for Biomedical Terms. In the Proceedings of the 26th Annual International ACM SIGIR Conference. pp. 167-173. [PDF]
• Tsuruoka, Yoshimasa and Jun'ichi Tsujii. (2003). Boosting Precision and Recall of Dictionary-Based Protein Name Recognition. In the Proceedings of the ACL-03 Workshop on Natural Language Processing in Biomedicine. pp. 41-48. PDF]
• Yu, Zhonghua, Yoshimasa Tsuruoka and Jun'ichi Tsujii. (2003). Automatic Resolution of Ambiguous Abbreviations in Biomedical Texts using Support Vector Machines and One Sense Per Discourse Hypothesis. In the Proceedings of the SIGIR'03 Workshop on Text Analysis and Search for Bioinformatics. pp. 57-62. [PDF]
• Tsuruoka, Yoshimasa and Jun'ichi Tsujii. (2003). Training a Naive Bayes Classifier via the EM Algorithm with a Class Distribution Constraint. In the Proceedings of the Seventh Conference on Natural Language Learning (CoNLL) at HLT-NAACL 2003. pp. 127--134. [PDF]



• Mima, Hideki, Sohia Ananiadou, Goran Nenadic and Jun'ichi Tsujii. (2002). XML Tag Information Management System: A Workbench for Ontology-based Knowledge Acquisition and Integration. In the Proceedings of Human Language Technology Conference (HLT 2002).
• Mima, Hideki, Sophia Ananiadou, Goran Nenadic and Jun'ichi Tsujii. (2002). TIMS - A Workbench for Ontology-based Knowledge Acquisition and Integration. In the Proceedings of Natural Language Processing in Biomedical Applications (NLPBA 2002).
• Ohta, Tomoko, Yuka Tateisi, Hideki Mima and Jun'ichi Tsujii. (2002). GENIA Corpus: an Annotated Research Abstract Corpus in Molecular Biology Domain. In the Proceedings of he Human Language Technology Conference (HLT 2002). pp73--77. [PDF]
• Ohta, Tomoko, Yuka Tateisi, Jin-Dong Kim and Jun'ichi Tsujii. (2002). The GENIA Corpus: an Annotated Corpus in Molecular Biology Domain. In the Proceedings of the 10th International Conference on Intelligent Systems for Molecular Biology (ISMB 2002) poster session.
• Kazama, Jun'ichi, Takaki Makino, Yoshihiro Ohta and Jun'ichi Tsujii. (2002). Tuning Support Vector Machines for Biomedical Named Entity Recognition. In the Proceedings of the Natural Language Processing in the Biomedical Domain (ACL 2002). Philadelphia, PA, USA. To appear. [PS][PDF]
• Kim, Jin-Dong and Jun'ichi Tsujii. (2002). Copus-Based Approach to Biological Entity Recognition. In the Proceedings of the Second Meeting of the Special Interest Group on Text Data Mining of ISMB 2002.



• Mima, Hideki, Sophia Ananiadou and Goran Nenadic. (2001). Improving Knowledge Acquisition Through Automatic Term Recognition. In the Proceedings of Panhellenic Conference on Human Computer Interaction (PC-HCI 2001). Patras, Greece. pp. 177-182.
• Ohta, Tomoko, Yuka Tateisi, Jin-Dong Kim, Hideki Mima and Jun'ichi Tsujii. (2001). Ontology Based Corpus Annotation and Tools. In the Proceedings of the 12th Genome Informatics 2001. pp. 469--470. [PDF]
• Kim, Jin-Dong, Tomoko Ohta, Yuka Tateisi, Hideki Mima and Jun'ichi Tsujii. (2001). XML-Based Linguistic Annotation of Corpus. In the Proceedings of the first NLP and XML Workshop held at NLPRS 2001. pp. 47--53.
• Ohta, Tomoko, Yuka Tateisi, Jin-Dong Kim, Sang-Zoo Lee and Jun'ichi Tsujii. (2001). GENIA corpus: A Semantically Annotated Corpus in Molecular Biology Domain. In the Proceedings of the ninth International Conference on Intelligent Systems for Molecular Biology (ISMB 2001) poster session. pp. 68.
• Ohta, Tomoko, Yuka Tateisi and Jun'ichi Tsujii. (2001). Tools for Ontology-based Corpus Annotation. In the Proceedings of the sixth Pacific Symposium on Biocomputing (PSB 2001). Hawaii, U.S.A.. pp. 112. [PPT]
• Yakushiji, Akane, Yuka Tateisi, Yusuke Miyao and Jun'ichi Tsujii. (2001). Event extraction from biomedical papers using a full parser. In the Proceedings of the sixth Pacific Symposium on Biocomputing (PSB 2001). Hawaii, U.S.A.. pp. 408-419. [PDF]
• Mima, Hideki, Sophia Ananiadou and Goran Nenadic. (2001). The ATRACT Workbench: An Automatic Term Recognition and Clustering of Terms. In the Text Speech and Dialogue (TSD 2001), Lecture Notes in Artificial Intelligence. 2166. pp. 126--133. Springer Verlag.



• Yuka Tateisi, Ohta, Tomoko, Nigel Collier, Chikashi Nobata and Jun'ichi Tsujii. (2000). Building an Annotated Corpus from Biology Research Papers. In the Proceedings COLING 2000 Workshop on Semantic Annotation and Intelligent Content. Luxembourg. pp. 28-34. [PDF]
• Nobata, Chikashi, Nigel Collier and Jun'ichi Tsujii. (2000). Comparison between Tagged Corpora for the Named Entity Task. In the Proceedings of ACL 2000 Workshop on Comparing Corpora. Hong Kong, China. pp. 20-27. [PDF]
• Collier, Nigel, Chikashi Nobata and Jun'ichi Tsujii. (2000). Comparison between Tagged Corpora for the Named Entity Task. In the Proceedings of the 18th International Conference on Computational Linguistics (COLING 2000). Saarbrucken, German. pp. 201-207. [PDF]
• Ohta, Tomoko, Yuka Tateisi, Takako Takai and Jun'ichi Tsujii. (1999). A Semantically Annotated Corpus from MEDLINE Abstracts. In the Proceedings of Genome Informatics. Tokyo, Japan. Universal Academy Press Inc..



• Imai, Hisao, Nigel Collier and Jun'ichi Tsujii. (1999). A Combined Query Expansion Approach for Information Retrieval. In the Proceedings of Genome Informatics. Tokyo, Japan. Universal Academy Press Inc.. [gzipped PS]
• Ibushi, Katsutoshi, Nigel Collier and Jun'ichi Tsujii. (1999). Classification of MEDLINE abstracts. In the Proceedings of Genome Informatics. Tokyo, Japan. Universal Academy Press Inc..
• Tateisi, Yuka, Tomoko Ohta, Takako Takai and Jun'ichi Tsujii. (1999). An Ontology for Biological Reaction Events. In the Proceedings of Genome Informatics. Tokyo, Japan. Universal Academy Press Inc.. [PDF]
• Collier, Nigel, Hyun Seok Park, Norihiro Ogata, Yuka Tateisi, Chikashi Nobata, Takeshi Sekimizu, Hisao Imai and Jun'ichi Tsujii. (1999). The GENIA project: corpus-based knowledge acquisition and information extraction from genome research papers. In the Proceedings of the European Association for Computational Linguistics (EACL 1999). [gzipped PS]
• Nobata, Chikashi, Nigel Collier and Jun'ichi Tsujii. (1999). Automatic Term Identification and Classification in Biology Texts. In the Proceedings of the fifth Natural Language Processing Pacific Rim Symposium (NLPRS). Beijin, China. pp. 369--374. [gzipped PS]
• Collier, Nigel, Hyun Seok Park and Jun'ichi Tsujii. (1999). Progress on Human-Computer Interaction in the GENIA Project on the Internet. In the Proceedings of the fifth Natural Language Processing Pacific Rim Symposium (NLPRS). Beijin, China. pp. 443--446. [gzipped PS]
• Hishiki, Teruyoshi, Nigel Collier, Chikashi Nobata, , Tomoko Ohta, Norihiro Ogata, Takeshi Sekimizu, Roland Steiner, Hyun Seok Park and Jun'ichi Tsujii. (1998). Developing NLP tools for genome informatics: An information extraction perspective. In the Proceedings of Genome Informatics. Tokyo, Japan. Universal Academy Press Inc..
• Sekimizu, Takeshi, Hyun Seok Park and Jun'ichi Tsujii. (1998). Identifying the interaction between genes and gene products based on frequently seen verbs in MEDLINE abstracts. In the Proceedings of Genome Informatics. Tokyo, Japan. pp. 62--71. Universal Academy Press Inc..

The pages were last updated on the 7th January 2003 by Yuka Tateisi.

Department of Information Science, Faculty of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113, Japan.