NaCTeM

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., N. Okazaki, R. Procter, B. Rea, and J. Thomas (2009) Supporting Systematic Reviews using Text Mining. In Social Science Computer Review, special issue (accepted)
  • Tsuruoka, Y., J. Tsujii and S. Ananiadou (2009) Fast Full Parsing by Linear-Chain Conditional Random Fields. In European Chapter of the Association for Computational Linguistics (EACL), Athens, Greece (accepted)
  • Venturi, Giuila, Simonetta Montemagni, Simone Marchi, Yutaka Sasaki, Paul Thompson, John McNaught and Sophia Ananiadou (2009) Bootstrapping a Verb Lexicon for Biomedical Information Extraction. In Proceedings of Conference on Computational Linguistics and Intelligent Text Processing (CICLing 2009), Mexico, March 2009 (accepted)
  • Sierra, G.E., A. B. Cedeño and S. Ananiadou (2009) An Improved Automatic Term Recognition method for Spanish. In Proceedings of Conference on Computational Linguistics and Intelligent Text Processing (CICLing 2009), Mexico, March 2009 (accepted)
  • Wang, Xinkai, Scott Piao and Sophia Ananiadou (2009) Organization Name Extraction for Chinese Using C-Value and Window-Based Mutual Information. In International Journal of Computer Interaction & Information Technology. (accepted)

2008

  • Tsuruoka, Yoshimasa, Jun'ichi Tsujii and Sophia Ananiadou (2008) FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics, doi:10.1093.
  • Thew, S., A. Sutcliffe, R. Procter, O. de Bruijn, J. McNaught, C. Venters and I. Buchan (in press) Requirements engineering for e-Science: Experiences in epidemiology. IEEE Software. Special issue "Developing Scientific Software".
  • Tsuruoka, Yoshimasa, Jun'ichi Tsujii, and Sophia Ananiadou (2008) Accelerating the annotation of sparse named entities by dynamic sentence selection. BMC Bioinformatics.
  • Sasaki, Yutaka, Yoshimasa Tsuruoka, John McNaught, and Sophia Ananiadou. (2008) How to make the most of NE dictionaries in statistical NER. BMC Bioinformatics.
  • Tsuruoka, Yoshimasa, John McNaught, and Sophia Ananiadou. 2008. Normalizing biomedical terms by minimizing ambiguity and variability, BMC Bioinformatics 2008, 9(Suppl 3):S2.
  • Okazaki, Naoaki Yoshimasa Tsuruoka, Sophia Ananiadou and Jun'ichi Tsujii (2008) A Discriminative Candidate Generator for String Transformations, EMNLP 2008
  • Thew, S., A. Sutcliffe, O. de Bruijn, J. McNaught, R. Procter, C. Venters, and I. Buchan (2008). Experience in e-Science requirements engineering. Proc. 16th IEEE International Requirements Engineering Conference (RE08).
  • Sasaki, Yutaka, Simonetta Montemagni, John McNaught and Sophia Ananiadou (2008). A Lexical Resource for the Biology Domain. In Proceedings of The Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008).
  • Sasaki, Y., Thompson, P., McNaught, J. and S. Ananiadou (2008) Event Frame Extraction Based on a Gene Regulation Corpus, 22nd International Conference on Computational Linguistics, COLING'08
  • Splendiani, Andrea, Scott Piao, Yutaka Sasaki, Sophia Ananiadou, John McNaught, Anita Burgun (2008) Compositional Enrichment of Bio-Ontologies, the 11th Annual Bio-Ontologies Meeting of at the Intelligent Systems for Molecular Biology 2008 Conference (ISMB), 20th July 2008 in Toronto, Canada. (poster)
  • Rebholz-Schuhmann, Dietrich, Piotr Pezik, Vivian Lee, Jung-Jae Kim, Riccardo del Gratta, Yutaka Sasaki, Jock McNaught, Simonetta Montemagni, Monica Monachini, Nicoletta Calzolari, Sophia Ananiadou, BioLexicon: Towards a Reference Terminological Resource in the Biomedical Domain, In Proc of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB-2008) (Poster), Toronto, Canada, 2008.
  • Sasaki, Y. Tsuruoka, Y. , McNaught, J. and S. Ananiadou (2008) How to make the most of NE dictionaries in statistical NER, BioNLP, ACL'08
  • Tsuruoka, Y., Tsujii, J. and S. Ananiadou (2008) Accelerating the annotation of sparse named entities by dynamic sentence selection, BioNLP, ACL'08
  • Nobata, C., Cotter, P., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y., Tsujii, J. and S. Ananiadou (2008) Kleio: a knowledge-enriched information retrieval system for biology, SIGIR 2008 (poster)
  • Piao, Scott, John McNaught and Ananiadou Sophia (2008). Clustering related terms with definitions. In the Proceedings of The Sixth International Conference on Language Resources and Evaluation (LREC 2008), Marrakech, Morocco.
  • Thompson, Paul, Philip Cotter, John McNaught, Sophia Ananiadou, Simonetta Montemagni, Andrea Trabucco and Giulia Venturi (2008). Building a bio-event annotated corpus for the acquisition of semantic frames from biomedical corpora. In the Proceedings of The Sixth International Conference on Language Resources and Evaluation (LREC 2008), Marrakech, Morocco.
  • Thompson, Paul, Giuila Venturi, John McNaught, Simonetta Montemagni and Sophia Ananiadou (2008). Categorising Modality in Biomedical Texts. In the Proceedings of the LREC 2008 workshop "Building and Evaluating resources for biomedical text mining", Marrakech, Morocco.
  • Sætre, Rune, B. Kemper, K. Oda, N. Okazaki, Y. Matsuoka, N. Kikuchi, H. Kitano, Y. Tsuruoka, S. Ananiadou and J. Tsujii (2008). Connecting Text Mining and Pathways using the PathText Resource. In the Proceedings of the 2008 Language Resources and Evaluation Conference (LREC 2008). Marrakech, Morocco.
  • Miyao, Yusuke and Jun'ichi Tsujii (2008). Feature Forest Models for Probabilistic HPSG Parsing. Computational Linguistics. 34(1). pp. 35–80, MIT Press, 2008.
    [MIT Press]
  • Sætre, Rune, B. Kemper, K. Oda, N. Okazaki, Y. Matsuoka, N. Kikuchi, H. Kitano, Y. Tsuruoka, S. Ananiadou and J. Tsujii (2008). PathText: Text Mining Tools Integrated with Biological Pathway. In the Genomes to Systems 2008. Manchester, UK, The Consortium for Post-Genome Science, March 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.
  • Kano, Yoshinobu, Ngan Nguyen, Rune Sætre, Keiichiro Fukamachi, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Sophia Ananiadou and Jun'ichi Tsujii (2008). Sharable type system design for tool inter-operability and combinatorial comparison. In the Proceedings of the First International Conference on Global Interoperability for Language Resources (ICGL). Hong Kong, January 2008.
  • Kano, Yoshinobu, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Keiichiro Fukamachi, Yusuke Miyao, Yoshimasa Tsur uoka, 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
  • 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
  • Kim, Jin-Dong, Tomoko Ohta and Jun'ichi Tsujii (2008) Corpus annotation for mining biomedical events from lterature. BMC Bioinformatics. 9(1). pp. 10, BioMed Central.
  • Oda, Kanae, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi and Jun'ichi Tsujii (2008) New challenges for text mining: Mapping between text and manually curated pathways. In Christopher JO Baker and Su Jian (Eds.), BMC Bioinformatics. BioMed Central.
  • Sætre, Rune, Kenji Sagae and Jun'ichi Tsujii (2008) Syntactic features for protein-protein interaction extraction. In the Christopher J.O. Baker and Su Jian (Eds.), Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007). ISSN 1613-0073319. Singapore, pp. 6.1-6.14, CEUR Workshop Proceedings (CEUR-WS.org), January.
  • Miyao, Yusuke, Rune Saetre, Kenji Sagae, Takuya Matsuzaki and Jun'ichi Tsujii(2008) Task-Oriented Evaluation of Syntactic Parsers and Their Representations. In the Proceedings of ACL-08:HLT.
  • Tsunakawa, Takashi and Jun'ichi Tsujii (2008). Bilingual Synonym Identification with Spelling Variations In the Proceedings of the 3rd international Joint Conference on Natural Language Processing. Hyderabad, India, January.
  • Okazaki, Naoaki, Mitsuru Ishizuka and Jun'ichi Tsujii (2008). A Discriminative Approach to Japanese Abbreviation Extraction. In the Proceedings of the 3rd international Joint Conference on Natural Language Processing. Hyderabad, India, January
  • Tsunakawa, Takashi, Naoaki Okazaki and Jun'ichi Tsujii (2008). Building Bilingual Lexicons Using Lexical Translation Probabilities via Pivot Languages. In the Proceedings of the 5th International Conference on Language Resources and Evaluation.
  • Kim, Jin-Dong, Ohta, Tomoko, Oda, Kanae and Tsujii, Jun'ichi (2008). From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. In the Proceedings of the 6th Asia Pacific Bioinformatics Conference (APBC).
  • Ngan, Nguyen, Jin-Dong Kim and Jun'ichi Tsujii. Challenges in Pronoun Resolution System for Biomedical Text (2008). In the Proceedings of the 6th edition of the Language Resources and Evaluation. Marrakech (Morocco).

2007

  • S. Ananiadou (2007). The National Centre for Text Mining: a Vision for the Future, in Ariadne (53) , paper on line
  • Ananiadou, S., R. Procter, B. Rea, Y. Sasaki, and J. Thomas (2007) Supporting Systematic Reviews using Text Mining, in 3rd International Conference on e-Social Science, Ann Arbor.
  • Sasaki, Y., B. Rea and S.Ananiadou (2007) Multi-topic aspects in clinical text classification, in IEEE BIBM 2007.
  • Yoshimasa Tsuruoka, John McNaught, Jun'ichi Tsujii, and Sophia Ananiadou (2007) Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. Bioinformatics, Bioinformatics Advance Access published on August 12, 2007.
  • Scott Piao, Ekaterina Buyko, Yoshimasa Tsuruoka , Katrin Tomanek, Jin-Dong Kim, John McNaught, Udo  Hahn, Jian Su and Sophia Ananiadou (2007). BOOTStrep Annotation Scheme – Encoding  Information for Text Mining. Corpus Linguistics Conference, Birmingham. [PDF]
  • Scott Piao, Sophia Ananiadou and John McNaught (2007). Integrating Annotation Tools into UIMA for Interoperability. In Proceedings of the UK e-Science AHM Conference 2007, Nottingham, UK, pp. 575-582. [PDF]
  • Udo Hahn, Ekaterina Buyko, Katrin Tomanek , Scott Piao, John McNaught, Yoshimasa Tsuruoka and Sophia Ananiadou (2007). An Annotation Type System for a Data-Driven NLP Pipeline. Accepted. The Linguistic Annotation Workshop (LAW), ACL, Prague, Czech Republic.
  • Scott S. Piao, Sophia Ananiadou, Yoshimasa Tsuruoka, Yutaka Sasaki and John McNaught (2007) Mining Opinion Polarity Relations of Citations, in 7th International Workshop on Computational Semantics, Tilburg, 10-12 January [pdf]
  • Frantzi, K. and Ananiadou, S. (2007) C-value for Authorship Identification, in 8th Conference on Forensic Linguistics, Language and Law, International Association of Forensic Linguistics, Seattle.
  • Meziane, F., Athanasakis, N. and S. Ananiadou (2007). Generating Natural Language specifications from UML class diagrams, Requirements Engineering, doi: 10.1007/s00766-007-0054-0, paper on line.
  • Tsuruoka, Y., McNaught, J. and S. Ananiadou(2007). Normalizing biomedical terms by minimizing ambiguity and variability, LBM2007 and BMC Bioinformatics.
  • 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, Ca.
  • Sasaki, Y., B. Rea and S.Ananiadou (2007) Multi-topic aspects in clinical text classification, in IEEE BIBM 2007.
  • Rea, B., Ananiadou, S. (2007). Text Mining Services to Support E-Research. UK e-Science All Hands Meeting, Nottingham, UK.
  • Nobuo, Araki Kazuhiro Yoshid Yoshimasa Tsuruoka and Jun'ichi Tsujii. Move Prediction in Go with the Maximum Entropy Method. In the IEEE Symposium Series on Computational Intelligence. April 2007.
    [PDF][PPT]
  • Tam, Wai Lok, Yusuke Miyao and Jun'ichi Tsujii (2007). Framework independent summarized parser output and its documentation. In the Proceeding of grammar engineering across framework 2007. Stanford, CSLI, 2007.
  • Miyao, Yusuke, Kenji Sagae and Jun'ichi Tsujii (2007). Towards Framework-Independent Evaluation of Deep Linguistic Parsers. In Tracy Holloway King and Emily Bender (Eds.), Proceedings of Grammar Engineering across Frameworks 2007. pp. 238-258, CSLI Publications, 2007. [CSLI Publications]
  • Ninomiya, Takashi, Takuya Matsuzaki, Yusuke Miyao and Jun'ichi Tsujii (2007). A log-linear model with an n-gram reference distribution for accurate HPSG parsing. In the Proceedings of IWPT 2007. June 2007. Prague, Czech Republic. [PDF]
  • Hara, Tadayoshi, Yusuke Miyao and Jun'ichi Tsujii (2007). Evaluating Impact of Re-training a Lexical Disambiguation Model on Domain Adaptation of an HPSG Parser. In the Proceedings of IWPT 2007. June 2007. Prague, Czech Republic. [PDF][PPT]
  • Sagae, Kenji, Yusuke Miyao and Jun'ichi Tsujii (2007). HPSG parsing with shallow dependency constraints. In the Proceedings of the 44th Meeting of the Association for Computational Linguistics. June 2007. Prague, Czech Republic. [PDF]
  • Okanohara, Daisuke and Jun'ichi Tsujii (2007). A discriminative language model with pseudo-negative samples. In the Proceedings of the 45th Annual Meeting of the Association of Computational Linguistics. pp. 73--80, Association for Computational Linguistics, June 2007. Prague, Czech Republic. [PDF]
  • Sagae, Kenji and Jun'ichi Tsujii. Dependency parsing and domain adaptation with LR models and parser ensembles. In the 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). 2007. Prague, Czech Republic. [PDF]
  • Yoshida, Kazuhiro, Yoshimasa Tsuruoka, Yusuke Miyao and Jun'ichi Tsujii (2007). Ambiguous Part-of-Speech Tagging for Improving Accuracy and Domain Portability of Syntactic Parsers. In the Proceedings of the Twentieth International Joint Conference on Artificial Intelligence. January 2007. [PDF]
  • Matsuzaki, Takuya, Yusuke Miyao and Jun'ichi Tsujii (2007). Efficient HPSG Parsing with Supertagging and CFG-filtering. In the Proceedings of the Twentieth International Joint Conference on Artificial Intelligence. January 2007. [gzipped PS][PS][PDF][slide]
  • Yoshida, Kazuhiro and Jun'ichi Tsujii (2007). Reranking for Biomedical Named-Entity Recognition. In the Proceedings of the Workshop on BioNLP 2007. June 2007. Prague, Czech Republic. [PDF]

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]