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Selected Publications

2009

• Ananiadou, S. (2009)
  Text Mining for Biomedicine. In Violaine Prince and Mathieu Roche (Eds.), Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration, IGI Global. In press
• Ananiadou, S., Weissenbacher, D., Rea, B., Pieri, E., Lin, Y., Vis, F., Procter, R. & Halfpenny P. (2009)
  Supporting Frame Analysis using Text Mining. In Proceedings of the 5th International Conference on e-Social Science. (to appear)
• Ananiadou, S., Okazaki, N., Procter, R., Rea, B., & Thomas, J. (2009)
  Supporting Systematic Reviews using Text Mining. In Social Science Computer Review, special issue.
• Kano, Y, Baumgartner Jr., W.A, McCrohon, L., Ananiadou, S., Cohen, K.B., Hunter, L. & Tsujii, J. (2009)
  U-Compare: share and compare text mining tools with UIMA. Bioinformatics.
• Kano, Y. McCrochon L., Ananiadou, S. & Tsujii, J. (2009)
  Integrated NLP Evaluation System for Pluggable Evaluation Metrics with Extensive Interoperable Toolkit. In Proceedings of NAACL HLT 2009 (to appear).
• Piao, S., Tsuruoka, Y. & Ananiadou, S. (2009)
  HYSEAS: A HYbrid SEntiment Analysis System. In Proceedings of the Fourth International Conference on Interdisciplinary Social Sciences. (to appear)
• Sasaki, Y., Thompson, P., McNaught, J. & Ananiadou, S. (2009)
  Three BioNLP Tools Powered by the BioLexicon. In Proceeedings of EACL 2009 Demonstration Session, pp 61-64
• Sierra, G.E., Cedeņo, A.B. & Ananiadou, S. (2009)
  An Improved Automatic Term Recognition method for Spanish. In Proceedings of tht 10th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing 2009). pp. 125 - 136
• Tsuruoka, Y., Tsujii, J., & Ananiadou, S. (2009).
  Stochastic Gradient Descent Training for L1-regularized Log-linear Models with Cumulative Penalty. ACL-IJCNLP 2009. (to appear)
• Tsuruoka, Y., Tsujii, J. & Ananiadou, S. (2009)
  Fast Full Parsing by Linear-Chain Conditional Random Fields. In Proceedings of the 12th Conference of European Chapter of the Association for Computational Linguistics (EACL-09), pp. 790-798
• Venturi, G., Montemagni, S., Marchi, S., Sasaki, Y., Thompson, P., McNaught, J. & Ananiadou, S. (2009)
  Bootstrapping a Verb Lexicon for Biomedical Information Extraction. In Proceedings of the 10th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing 2009), pp 137- 148.

2008

• Hirohata, K., Okazaki, N., Ananiadou, S. & Ishizuka, M. (2008)
  Identifying Sections in Scientific Abstracts using Conditional Random Fields. In Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP 2008).
• Kano, Y., Nguyen, N., Sætre, R., Yoshida, K., Miyao, Y., Tsuruoka, Y., Matsubayashi, Y., Ananiadou, S. & Tsujii, J. (2008)
  Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example. In Proceedings of the Pacific Symposium on Biocomputing 2008 (PSB 2008), pp. 616-627
• Kano, Y., Nguyen, N., Sætre, R, Fukamachi, K., Yoshida, K., Miyao, Y., Tsuruoka, Y., Ananiadou, S. & Tsujii, J. (2008)
  Sharable type system design for tool inter-operability and combinatorial comparison. In Proceedings of the First International Conference on Global Interoperability for Language Resources (ICGL). pp. 122-129
• Kano, Y., Nguyen, N., Sætre, R., Yoshida, K., Fukamachi, K., Miyao, K, Tsuruoka, Y., Ananiadou, S. & Tsujii, J (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 (IJCNLP 2008), pp. 859-864
• Kim, J.-D., Ohta, T. & Tsujii, J. (2008)
  Corpus annotation for mining biomedical events from literature. BMC Bioinformatics 9:10
• Kim, J.-D., Ohta, T., Oda, K. & Tsujii, J (2008)
  From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. In Brazma, A., Miyano, S. & Akutsu, T (Eds.), Proceedings of the 6th Asia Pacific Bioinformatics Conference. Series on Advances in Bioinformatics and Computational Biology 6, pp. 165-176
• Meziane, F., Athanasakis, N. & Ananiadou, S. (2008)
  Generating Natural Language specifications from UML class diagrams. Requirements Engineering 13(10), 1-18.
• Miyao, Y. & Tsujii, J. (2008)
  Feature Forest Models for Probabilistic HPSG Parsing. Computational Linguistics. 34(1), 35-80.
• Miyao, Y., Sætre, R., Sagae, K., Matsuzaki, T. & Tsujii, J. (2008)
  Task-Oriented Evaluation of Syntactic Parsers and Their Representations. In Proceedings of the 45th Meeting of the Association for Computational Linguistics (ACL'08:HLT),pp. 46-54
• Nguyen, N., Kim, J.-D. & Tsujii, J. (2008)
  Challenges in Pronoun Resolution System for Biomedical Text. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008)
• Nobata, C., Cotter, P., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y., Tsujii, J. & Ananiadou, S. (2008)
  Kleio: a knowledge-enriched information retrieval system for biology. In Proceedings of the 31st Annual International ACM SIGIR Conference, pp. 787-788. (Poster)
• Oda, K., Kim, J.-D., Ohta, T., Okanohara, D., Matsuzaki, T., Tateisi, Y. & Tsujii, J. (2008)
  New challenges for text mining: Mapping between text and manually curated pathways. BMC Bioinformatics 9(Suppl 3):S5
• Okazaki, N., Tsuruoka, Y., Ananiadou, S. & Tsujii, J. (2008)
  A Discriminative Candidate Generator for String Transformations. In Proceedings of the 2008 Conference on Empirical Methods in Natural Language Processing (EMNLP 2008)
• Okazaki, N., Ishizuka, M. & Tsujii, J. (2008)
  A Discriminative Approach to Japanese Abbreviation Extraction. In Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP 2008), pp. 889-894
• Piao, S., McNaught, J. & Ananiadou, S. (2008)
  Clustering Related Terms with Definitions. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008).
• Rebholz-Schuhmann, D., Pezik, P., Lee, V., Kim, J.-J., del Gratta, R., Sasaki, Y., McNaught, J., Montemagni, S., Monachini, M., Calzolari, N. & Ananiadou, S. (2008)
  BioLexicon: Towards a Reference Terminological Resource in the Biomedical Domain. In Proceedings of the of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB-2008) (Poster).
• Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., Kitano, H., Tsuruoka, Y., Ananiadou, S. & Tsujii, J. (2008)
  Connecting Text Mining and Pathways using the PathText Resource. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008).
• Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., Kitano, H., Tsuruoka, Y., Ananiadou, S. & Tsujii, J. (2008)
  PathText: Text Mining Tools Integrated with Biological Pathway. In the Genomes to Systems Conference 2008 Handbook, p. 65.
• Sasaki, Y., Tsuruoka, Y., McNaught, J. & Ananiadou, S. (2008)
  How to make the most of NE dictionaries in statistical NER. BMC Bioinformatics 9(Suppl 11):S5
• Sasaki, Y., Montemagni, S., Pezik, P., Rebholz-Schumann, D., McNaught, J. & Ananiadou, S. (2008)
  A Lexical Resource for the Biology Domain. In Proceedings of The Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pp. 109-116.
• Sasaki, Y., Thompson, P., McNaught, J. & Ananiadou, S. (2008)
  Event Frame Extraction Based on a Gene Regulation Corpus. In Proceedings of thhe 22nd International Conference on Computational Linguistics (COLING'08), pp.761-768
• Sasaki, Y. Tsuruoka, Y. , McNaught, J. & Ananiadou, S. (2008)
  How to make the most of NE dictionaries in statistical NER. In Proceedings of BioNLP 2008: Current Trends in Biomedical Natural Language Processing, pp. 63-70
• Splendiani, A., Piao, S., Sasaki, Y., Ananiadou, S., McNaught, J. & Burgun, A. (2008)
  Compositional Enrichment of Bio-Ontologies. The 11th Annual Bio-Ontologies Meeting, at the Intelligent Systems for Molecular Biology 2008 Conference (ISMB-2008). (Poster)
• Thew, S., Sutcliffe, A., Procter, R., de Bruijn, O., McNaught, J., Venters, C. & Buchan, I. (2008)
  Requirements Engineering for e-Science: Experiences in Epidemiology. IEEE Software 26(1), 80-87
• Thew, S., Sutcliffe, A., de Bruijn, O., McNaught, J., Procter, R., Venters, C. & Buchan, I. (2008)
  Experience in e-Science requirements engineering. In Proceedings of the 16th IEEE International Requirements Engineering Conference (RE08),pp. 277-282
• Thompson, P., Cotter, P., McNaught, J., Ananiadou, S., Montemagni, S., Trabucco, A. & Venturi, G. (2008)
  Building a Bio-Event Annotated Corpus for the Acquisition of Semantic Frames from Biomedical Corpora. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008).
• Thompson, P., Venturi, G. McNaught, J., Montemagni, S. & Ananiadou, S. (2008)
  Categorising Modality in Biomedical Texts. In Proceedings of the LREC 2008 Workshop on Building and Evaluating Resources for Biomedical Text Mining.
• Tsunakawa, T., & Tsujii, J. (2008)
  Bilingual Synonym Identification with Spelling Variations. In Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP 2008), pp. 457-464
• Tsunakawa, T., Okazaki, N. & Tsujii, J. (2008)
  Building Bilingual Lexicons Using Lexical Translation Probabilities via Pivot Languages. In Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008).
• Tsuruoka, Y., Tsujii, J. & Ananiadou, S. (2008)
  FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics 24(21), 2559-2560
• Tsuruoka, Y., Tsujii, J. & Ananiadou, S. (2008)
  Accelerating the annotation of sparse named entities by dynamic sentence selection. BMC Bioinformatics 9(Suppl 11):S8
• Tsuruoka, Y., McNaught,J. & Ananiadou, S. (2008)
  Normalizing biomedical terms by minimizing ambiguity and variability. BMC Bioinformatics 9(Suppl 3):S2
• Tsuruoka, Y., Tsujii, J. & Ananiadou, S. (2008)
  Accelerating the annotation of sparse named entities by dynamic sentence selection. In Proceedings of BioNLP 2008: Current Trends in Biomedical Natural Language Processing, pp. 30-37
• Wang, X. & Matthews, M. (2008).
  Distinguishing the Species of Biomedical Named Entities for Term Identification. BMC Bioinformatics 2008, 9(Suppl 11):S6

2007

• Ananiadou, S. (2007)
  The National Centre for Text Mining: a Vision for the Future. Ariadne (53)
• Ananiadou, S., Procter, R., Rea, B., Sasaki, Y. & Thomas, J. (2007)
  Supporting Systematic Reviews using Text Mining. In Proceedings of the 3rd International Conference on e-Social Science
• Araki, N., Yoshida. K., Tsuruoka, Y. & Tsujii, J. (2007)
  Move Prediction in Go with the Maximum Entropy Method. In Proceedings of IEEE Symposium on Computational Intelligence and Games (CIG 2007), pp. 189-195
• Ananiadou, S., Cotter, P., Nobata, C., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y. & Tsujii, J. (2007)
  SemText: a semantically enriched information retrieval system for biology. In Proceedings of the 8th International Conference on Systems Biology (ICSB 2007) (Poster)
• Frantzi, K. & Ananiadou, S. (2007)
  C-value for Authorship Identification. In Proceedings of the 8th Conference on Forensic Linguistics, Language and Law, International Association of Forensic Linguistics.
• Hahn, U., Buyko, E., Tomanek, K., Piao, S., McNaught, J., Tsuruoka, Y. & Ananiadou, S. (2007)
  An Annotation Type System for a Data-Driven NLP Pipeline. In Proceedings of the Linguistic Annotation Workshop (LAW), pp. 33-40.
• Hara, T., Miyao, Y. & Tsujii, J. (2007)
  Evaluating Impact of Re-training a Lexical Disambiguation Model on Domain Adaptation of an HPSG Parser. In Proceedings of the Tenth International Conference on Parsing Technologies (IWPT), pp. 11-22
• Lok, T.W., Miyao, Y. & Tsujii, J. (2007)
  Framework Independent Summarized Parser Output in XML and its Example-based Documentation. In Holloway King, T. & Bender, E. (Eds.), Proceedings of Grammar Engineering Across Frameworks Workshop (GEAF07), pp. 319-331
• Matsuzaki, T., Miyao, Y. & Tsujii, J. (2007)
  Efficient HPSG Parsing with Supertagging and CFG-filtering. In Proceedings of the Twentieth International Joint Conference on Artificial Intelligence (IJCAI-07), pp. 1671-1676.
• Miyao, Y., Sagae, K. & Tsujii, J. (2007)
  Towards Framework-Independent Evaluation of Deep Linguistic Parsers. In Holloway King, T. & Bender, E. (Eds.), Proceedings of Grammar Engineering Across Frameworks Workshop (GEAF07), pp. 238-258.
• Ninomiya, T., Matsuzaki, T., Miyao, Y., & Tsujii, J. (2007)
  A log-linear model with an n-gram reference distribution for accurate HPSG parsing. In Proceedings of the Tenth International Conference on Parsing Technologies (IWPT), pp. 60-68.
• Okanohara, D. & Tsujii, J. (2007)
  A discriminative language model with pseudo-negative samples. In Proceedings of the 45th Annual Meeting of the Association of Computational Linguistics (ACL 2007). pp. 73-80.
• Piao, S., Buyko, E., Tsuruoka, Y., Tomanek, K., Kim, J.-D., McNaught, J. Hahn, U., Su, J. & Ananiadou, S. (2007)
  BOOTStrep Annotation Scheme: Encoding Information for Text Mining. In Proceedings of the 4th Corpus Linguistics Conference (CL2007)
• Piao, S., Ananiadou, S. & McNaught, J. (2007)
  Integrating Annotation Tools into UIMA for Interoperability. In Proceedings of the UK e-Science AHM Conference 2007, pp. 575-582.
• Piao, S., Ananiadou, S., Tsuruoka, Y., Sasaki, Y. & McNaught, J. (2007)
  Mining Opinion Polarity Relations of Citations. In Proceedings of the 7th International Workshop on Computational Semantics, pp. 366-371
• Rea, B. & Ananiadou, S. (2007)
  Text Mining Services to Support E-Research. UK e-Science All Hands Meeting
• Sætre, R., Sagae, K. & Tsujii, J. (2007)
  Syntactic features for protein-protein interaction extraction. In Baker, C.J.O. and Su, J. (Eds.), Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007), pp. 6.1-6.14
• Sagae, K., Miyao, Y. & Tsujii, J.(2007)
  HPSG parsing with shallow dependency constraints. In Proceedings of the 45th Annual Meeting of the Association for Computational Linguistics (ACL 2007), pp. 624-631.
• Sagae, K. & Tsujii, J. (2007)
  Dependency parsing and domain adaptation with LR models and parser ensembles. In Proceedings of the CoNLL 2007 Shared Task in the Joint Conferences on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL'07 shared task), pp. 1044-1050
• Sasaki, Y., Rea, B. & Ananiadou, S. (2007)
  Multi-topic aspects in clinical text classification. In Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine, pp. 62-70
• Tsuruoka, Y., McNaught, J., Tsujii, J. & Ananiadou, S. (2007)
  Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. Bioinformatics 23(20), 2768-2774.
• Yoshida, K., Tsuruoka, Y., Miyao, Y. & Tsujii, J. (2007)
  Ambiguous Part-of-Speech Tagging for Improving Accuracy and Domain Portability of Syntactic Parsers. In Proceedings of the Twentieth International Joint Conference on Artificial Intelligence (IJCAI-07), pp. 1783-1788.
• Yoshida, K. & Tsujii, J. (2007)
  Reranking for Biomedical Named-Entity Recognition. In Proceedings of BioNLP 2007: Biological, translational, and clinical language processing, pp. 209- 216.

2006

• Ananiadou, S. & McNaught, J. (2006)
  Text Mining for Biology and Biomedicine. Artech House Books.
• Ananiadou, S. & McNaught, J. (2006)
  Introduction to Text Mining in Biology . In Ananiadou, S. & McNaught, J. (Eds) Text Mining for Biology and Biomedicine, pp. 1-12, Artech House Books.
• Ananiadou, S. & Nenadic, G. (2006)
  Automatic Terminology Management in Biomedicine . In Ananiadou, S. & McNaught, J. (Eds) Text Mining for Biology and Biomedicine, pp. 67-98, Artech House Books.
• Kim, J.D, Ananiadou, S. and Tsujii, J. (2006)
  Ontology based Semantic Annotation for Knowledge Extraction, in 2nd International Digital Curation Conference, Glasgow
• Ananiadou, S. and Fluck, J. (eds.) (2006)
  Second International Symposium on Semantic Mining in Biomedicine (SMBM), BMC Bioinformatics 2006, 7 (Suppl 3) : S1  (forthcoming, November 2006)
• Ananiadou, S., Kell, D.B. and Tsujii, J. (2006)
  Text Mining and its Potential Applications in Systems Biology, in Trends in Biotechnology (TIBTECH) (accepted)
• Chun, Hong-woo, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, and Jun'ichi Tsujii. Extraction of Gene-Disease Relations from MedLine using Domain Dictionaries and Machine Learning. The Pacific Symposium on Biocomputing (PSB) Maui , Hawaii , USA , pp. 4-15, January 2006.
  [PDF]
• Chun, Hong-woo, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, and Jun'ichi Tsujii. Automatic Recognition of Topic-Classified Relations between Prostate Cancer and Genes from Medline Abstracts. In the Proceedings of the second international symposium on semantic mining in Biomedicine. Jena , Germany , pp. 5-12, April 2006.
  [PDF]
• Daisuke, OKanohara, Yusuke Miyao, Yoshimasa Tsuruoka and Jun¡Çichi Tsujii. Improving the Scalability of Semi-Markov Conditional Random Fields for Named Entity Recognition. In the Proceedings of ACL 2006. Sydney , Australia , July 2006.
  [PDF]
• Kim, Jin-Dong and Jun'ichi Tsujii. Corpora and their Annotation. In Sophia Ananiadou and John McNaught, (Eds.), Text Mining for Biology and Biomedicine. 46 Gillingham Street , London SW1V 1AH UK , Artech House, 2006.
  [An introduction at the publisher's homepage]
• Mima, H., Ananiadou, S. & Katsushima, M. (2006)
  Terminology-based Knowledge Mining for New Knowledge Discovery, in ACM Transactions on Asian language information processing (TALIP) Special Issue on Text Mining and Management in Biomedicine, Vol. 5, No. 1, March 2006, 74-88
• Miyao, Yusuke, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya and Jun'ichi Tsujii. Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. In the Proceedings of COLING-ACL 2006. Sydney , Australia , pp. 1017--1024, July 2006.
  [PDF]
• Nenadic, G. & Ananiadou, S. (2006)
  Mining Term Associations from Biomedical Literature to Support Knowledge Discovery, in ACM Transactions on Asian language information processing (TALIP) Special Issue on Text Mining and Management in Biomedicine, Vol. 5, No. 1, March 2006, 1-22 [pdf]
• Ninomiya, Takashi, Takuya Matsuzaki, Yoshimasa Tsuruoka, Yusuke Miyao and Jun'ichi Tsujii. Extremely Lexicalized Models for Accurate and Fast HPSG Parsing. In the Proc. of EMNLP 2006. Sydney , Australia , pp. 155--163, July 2006.
  [PDF]
• Ohta, Tomoko, Yuka Tateisi, Jin-Dong Kim, Akane Yakushiji and Jun-ichi Tsujii. Linguistic and Biological Annotations of Biological Interaction Events. In the Proceedings of The Fifth International Conference on Language Resource and Evaluation (LREC 2006). Genoa , Italy , pp. 1405--1408, May 2006.
• Ohta, Tomoko, Yusuke Miyao, Takashi Ninomiya, Yoshimasa Tsuruoka, Akane Yakushiji, Katsuya Masuda, Jumpei Takeuchi, Kazuhiro Yoshida, Tadayoshi Hara, Jin-Dong Kim, Yuka Tateisi and Jun'ichi Tsujii. An Intelligent Search Engine and GUI-based Efficient MEDLINE Search Tool Based on Deep Syntactic Parsing. In the Proceedings of the COLING/ACL 2006 Interactive Presentation Sessions. Sydney , Australia , pp. 17--20, July 2006.
  [PDF]
• Okazaki, N. and Ananiadou, S. (2006)
  Clustering acronyms in biomedical text for disambiguation, in Proceedings of LREC.
• Okazaki, N. and Ananiadou, S. (2006)
  Building an Abbreviation Dictionary using a Term Recognition Approach, in Bioinformatics, (accepted)
• Rebholz-Schuhmann, D., Kirsch, H., Nenadic, G.: .: IeXML: towards an annotation framework for biomedical semantic types enabling interoperability of text processing modules, Proceedings of Joint BioLINK and Bio-Ontologies SIG Meeting, ISMB 2006, Fortaleza, Brazil
• Unno, Yuya, Takashi Ninomiya, Yusuke Miyao and Jun'ichi Tsujii. Trimming CFG Parse Trees for Sentence Compression Using Machine Learning Approaches. In the Proceedings of the COLING/ACL 2006 Main Conference Poster Sessions. Sydney , Australia , pp. 850--857, Association for Computational Linguistics, July 2006.
  [PDF][poster]
• Yakushiji, Akane, Miyao, Yusuke, Ohta, Tomokoand Tateisi, Yuka and Tsujii, Jun'ichi. Automatic Construction of Predicate-argument Structure Patterns for Biomedical Information Extraction. In the Proceedings of the 2006 Conference on Empirical Methods in Natural Language Processing. Sydney , Australia , pp. 284--292, July 2006.
  [PDF]

2005

• Ananiadou, S., Chruszcz, J., Keane, J., McNaught, J. & Watry, P. (2005) The National Centre for Text Mining: Aims and Objectives. In Ariadne, Issue 42, January 2005. [url]
• Chun, Hong-Woo, Young-Sook Hwang, Hae-Chang Rim. Unsupervised Event Extraction from Biomedical Literature using Co-occurrence Information and Basic Patterns. In the Lecture Notes in Artificial Intelligence. pp. 777-786, Springer, 2005. [PDF]
• Hara, Tadayoshi, Yusuke Miyao and Jun'ichi Tsujii. Adapting a probabilistic disambiguation model of an HPSG parser to a new domain. In Robert Dale, Kam-Fai Wong, Jian Su and Oi Yee Kwong (Eds.), Natural Language Processing – IJCNLP 2005. Lecture Notes in Artificial Intelligence3651. Jeju Island , Korea , pp. 199--210, Springer-Verlag, October 2005. ISSN 0302-9743. [PS][PDF]
• Kazama, Jun'ichi and Jun'ichi Tsujii. Maximum Entropy Models with Inequality Constraints: A case study on text categorization. Machine Learning Journal special issue on Learning in Speech and Language Technologies. 60(1-3). pp. 169-194, Springer SBM, September 2005. [Machine Learning]
• Matsuzaki, Takuya, Yusuke Miyao and Jun'ichi Tsujii. Probabilistic CFG with Latent Annotations. In the Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics. Michigan , USA , pp. 75-82, June 2005. [PDF]
• Miyao, Yusuke and Jun'ichi Tsujii. Probabilistic disambiguation models for wide-coverage HPSG parsing. In the Proceedings of ACL 2005. Ann Arbor , Michigan , pp. 83-90, June 2005. [PDF]
• Ninomiya, Takashi, Yoshimasa Tsuruoka, Yusuke Miyao and Jun'ichi Tsujii. Efficacy of Beam Thresholding, Unification Filtering and Hybrid Parsing in Probabilistic HPSG Parsing. In the Proc. of IWPT 2005. Vancouver , BC , Canada , pp. 103--114, October 2005. [PS][PDF]
• Ninomiya, Takashi, Yusuke Miyao and Jun'ichi Tsujii. A Persistent Feature-Object Database for Intelligent Text Archive Systems. In Keh-Yih Su, Jun'ichi Tsujii, Jong-Hyeok Lee and Oi Yee Kwong (Eds.), Natural Language Processing - IJCNLP 2004. LNAI3248. Hainan Island , China , pp. 197--205, Springer-Verlag, 2005. ISSN 0302-9743. [PS][PDF]
• 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 [pdf]
• Okanohara, Daisuke and Jun'ichi Tsujii. Assigning Polarity Scores to Reviews Using Machine Learning Techniques. In Robert Dale, Kam-Fai Wong, Jian Su and Oi Yee Kwong (Eds.), Natural Language Processing - IJCNLP 2005. LNCS3651. Jeju Island , Korea , Springer-Verlag, October 2005. [PDF]
• Rice, S., Nenadic, G., Stapley, B.: Mining protein function from text using term-based support vector machines, BMC Bioinformatics 2005, 6(Suppl 1):S22, "Critical assessment of text mining methods in molecular biology" (full text)
• 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. [pdf]
• Spasic, Irena, 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. [pdf]
• 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 .[pdf]
• 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 [pdf]
• 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. [pdf]
• Tsuruoka, Y., Ananiadou, S. & Tsujii, J. (2005) A Machine Learning Approach to Acronym Generation, BioLink 2005. [pdf]
• 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 [pdf]
• 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. [pdf]
• Tsuruoka, Y., Ananiadou, S. & Tsujii, J. (2005) A Machine Learning Approach to Acronym Generation, BioLink 2005. [pdf]
• Tsuruoka, Yoshimasa, Yuka Tateishi, Jin-Dong Kim, Tomoko Ohta, John McNaught, Sophia Ananiadou and Jun'ichi Tsujii. Developing a Robust Part-of-Speech Tagger for Biomedical Text. In the Advances in Informatics - 10th Panhellenic Conference on Informatics. LNCS 3746. Volos , Greece , pp. 382--392, November 2005. ISSN 0302-9743. [PDF]
• Tsuruoka, Yoshimasa and Jun'ichi Tsujii. Iterative CKY Parsing for Probabilistic Context-Free Grammars. In Keh-Yih Su, Jun'ichi Tsujii, Jong-Hyeok Lee and Oi Yee Kwong (Eds.), Natural Language Processing - IJCNLP 2004. LNAI 3248. Hainan Island , China , pp. 52-60, Springer-Verlag, 2005. ISSN 0302-9743. [PDF]
• Tsuruoka, Yoshimasa and Jun'ichi Tsujii. Bidirectional Inference with the Easiest-First Strategy for Tagging Sequence Data. In the Proceedings of HLT/EMNLP 2005. Vancouver , BC , Canada , pp. 467-474, October 2005. [PDF]
• Tsuruoka, Yoshimasa and Jun'ichi Tsujii. Chunk Parsing Revisited. In the Proceedings of the 9th International Workshop on Parsing Technologies (IWPT 2005). Vancouver , BC , Canada , pp. 133-140, October 2005. [PDF]
• Yakushiji, Akane, Yusuke Miyao, Yuka Tateisi and Jun'ichi Tsujii. Biomedical Information Extraction with Predicate-Argument Structure Patterns. In the the Proceedings of the First International Symposium on Semantic Mining in Biomedicine. Hinxton, Cambridgeshire , UK , pp. 60--69, 2005. [PDF]

2004

• Ananiadou, S., Friedman, C. & Tsujii, J (2004) Introduction to Named Entity Recognition in Biomedicine, editorial, Special Issue, Journal of Biomedical Informatics, vol. 37 (6), 393-395
• Chun, Hong-Woo, Tomoko Ohta, Jin-Dong Kim and Jun'ichi Tsujii. Building Patterns for Biomedical Event Extraction. The 15th International conference on Genome Informatics (GIW)(163--164). December 2004. [PDF]
• Kim, Jin-Dong, Tomoko Ohta, Yoshimasa Tsuruoka, Yuka Tateisi and Nigel Collier. 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, 2004. [PDF]
• Krauthammer, M., Nenadic, G.: Term Identification in the Biomedical Literature, Journal of Biomedical Informatics (Special Issue on Named Entity Recognition in Biomedicine), Vol. 37(6):512-526, 2004 (pre-print)
• Miyao, Yusuke and Jun'ichi Tsujii. Deep Linguistic Analysis for the Accurate Identification of Predicate-Argument Relations. In the Proceedings of COLING 2004. Geneva , Switzerland , pp. 1392-1397, 2004. [PDF]
• Nakanishi, Hiroko, Yusuke Miyao and Jun'ichi Tsujii. An Empirical Investigation of the Effect of Lexical Rules on Parsing with a Treebank Grammar. In the Proceedings of the third TLT2004. Tubingen , Germany , pp. 103--114, 2004. [PDF]
• Nenadic, G., Ananiadou, S. & McNaught, J. (2004) Enhancing Automatic Term Recognition through Term Variation, in Proceedings of 20 th Int. Conference on Computational Linguistics, Coling 2004, Geneva, Switzerland. [pdf]
• Spasic, I. & Ananiadou, S. (2004) Using Automatically Learnt Verb Selectional Preferences for Classification of Biomedical Terms, in Journal of Biomedical Informatics, vol.37, (6), 483-497. [pdf]
• Nenadic, G., Spasic, I. , Ananiadou, S. (2004) Automatic Discovery of Term Similarities Using Pattern Mining, in International Journal ofTerminology.10:1, 55-80 [pdf]
• Spasic, I. , Nenadic, G. & Ananiadou, S. (2004) Learning to Classify Biomedical Terms through Literature Mining and Genetic Algorithms. In Zheng Rong Yang, Richard Everson & Hujun Yin (Eds.) Intelligent Data Engineering and Automated Learning – IDEAL 2004, LNCS 3177: 345-351: Springer-Verlag. [pdf]
• Tateisi, Yuka and Jun'ichi Tsujii. Part-of-Speech Annotation of Biology Research Abstracts. In the Proceedings of 4th International Conference on Language Resource and Evaluation (LREC2004). IV. Lisbon , Portugal , pp. 1267-1270, May 2004. [PDF]
• Tsuruoka, Yoshimasa and Jun'ichi Tsujii. Improving the Performance of Dictionary-based Approaches in Protein Name Recognition. Journal of Biomedical Informatics. 37(6). pp. 461-470, Elsevier, 2004. [link]
• Tsuruoka, Yoshimasa, Yusuke Miyao and Jun'ichi Tsujii. Towards efficient probabilistic HPSG parsing: integrating semantic and syntactic preference to guide the parsing. In the Proceedings of IJCNLP-04 Workshop: Beyond shallow analyses - Formalisms and statistical modeling for deep analyses. Hainan Island , China , 2004. [PDF]