Publications by Jun'ichi Tsujii

Papers by Jun'ichi Tsujii at NaCTeM, newest first. All publications

2025 | 2021 | 2020 | 2019 | 2018 | 2017 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2002 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991

214 publications

2025

Yano, K., Luo, Z., Huang, J., Xie, Q., Asada, M., Yuan, C., Yang, K, Miwa, M., Ananiadou, S. and Tsujii, J., ELAINE-medLLM: Lightweight English Japanese Chinese Trilingual Large Language Model for Bio-medical Domain, in: Proceedings of the 31st International Conference on Computational Linguistics (COLING 2025), pages 4670–4688, 2025 [URL]
Peng, X., Qian, L., Wang, Y., Xiang, R., He, Y., Ren, Y., Jiang, M., Zhao, J., He, H., Han, Y., Feng, Y., Jiang, Y., Cao, Y., Li, H., Yu, Y., Wang, X., Gao, P., Lin, S., Wang, K., Yang, S., Zhao, Y., Liu, Z., Lu, P., Huang, J., Wang, S., Papadopoulos, T., Giannouris, P., Soufleri, E., Chen, N., Xiong, G., Deng, Z., Zhao, Y., Lin, M., Qiu, M., Smith, K., Cohan, A., Liu, X. -Y., Lopez-Lira, A., Chen, X., Tsujii, J., Nie, J., Ananiadou, S. and Xie, Q., MultiFinBen: A Multilingual, Multimodal, and Difficulty-Aware Benchmark for Financial LLM Evaluation, in: arXiv, 2025 [URL]

2021

Tsujii, J., Natural Language Processing and Computational Linguistics, in: Computational Linguistics, 47:4(707-727), 2021 [DOI] [URL]
Dengel, A., Etzioni, O., DeCario, N., Hoos, H., Li, F. -F., Tsujii, J. and Traverso, P., Next Big Challenges in Core AI Technology, in: Springer, pages 90-115, 2021 [DOI] [URL]

2020

El Boukkouri, H, Ferret, O., Lavergne, T., Noji, H., Zweigenbaum, P. and Tsujii, J., CharacterBERT: Reconciling ELMo and BERT for Word-Level Open-Vocabulary Representations From Characters, in: Proceedings of the 28th International Conference on Computational Linguistics (COLING 2020), pages 6903–6915, 2020 [URL]
Arase, Y. and Tsujii, J., Compositional Phrase Alignment and Beyond, in: Proceedings of EMNLP 2020, pages 1611–1623, 2020 [URL]

2019

Wang, Y., Fan, X., Chen, L., Chang, E. I., Ananiadou, S., Tsujii, J. and Xu, Y., Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries, in: BMC Bioinformatics, 2019 [DOI] [URL] [Pure]

2018

Tsujii, J., Ananiadou, S. and Wang, Y., Improve Chinese Clinical Named Entity Recognition Performance by Using the Graphical and Phonetic Feature, in: Proceedings of BIBM 2018 (IEEE), pages 1582–1586, 2018 [URL] [Pure]
Thompson, P., Daikou, S., Ueno, K., Batista-Navarro, R. T., Tsujii, J. and Ananiadou, S., Annotation and Detection of Drug Effects in Text for Pharmacovigilance, in: Journal of Cheminformatics, 2018 [DOI] [URL] [Pure]

2017

Sato, M., Brockmeier, A., Kontonatsios, G., Mu, T., Goulermas, J., Tsujii, J. and Ananiadou, S., Distributed Document and Phrase Co-embeddings for Descriptive Clustering, in: Proceedings of EACL 2017, pages 991–1001, 2017 [URL] [Pure]
Arase, Y. and Tsujii, J., Monolingual Phrase Alignment on Parse Forests, in: Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing, pages 1-11, 2017 [URL]
Thompson, P., Ananiadou, S. and Tsujii, J., The GENIA Corpus: Annotation Levels and Applications, in: Handbook of Linguistic Annotation, Springer, pages 1395-1432, 2017 [DOI] [URL]

2015

Pyysalo, S., Ohta, T., Rak, R., Rowley, A., Chun, H. W., Jung, S. J., Choi, S. P., Tsujii, J. and Ananiadou, S., Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013, in: BMC Bioinformatics, 2015 [DOI] [URL] [Pure]
Xu, Y., Chen, L., Wei, J., Ananiadou, S., Fan, Y., Qian, Y., Chang, E. I. and Tsujii, J., Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary, in: B M C Bioinformatics, 2015 [DOI] [URL] [Pure]

2014

Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S., Combining String and Context Similarity for Bilingual Term Alignment from Comparable Corpora, in: Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 1701–1712, 2014 [URL] [Pure]
Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S., Using a Random Forest Classifier to Compile Bilingual Dictionaries of Technical Terms from Comparable Corpora, in: Proceedings of the 14th Conference of the European Chapter of the Association for Computational Linguistics, volume 2: Short Papers, pages 111–116, 2014 [URL] [Pure]
Xu, Y., Hua, J., Ni, Z., Chen, Q., Fan, Y., Ananiadou, S., Chang, E. I. and Tsujii, J., Anatomical entity recognition with a hierarchical framework augmented by external resource, in: P L o S One, 2014 [DOI] [URL] [Pure]
Mu, T., Miwa, M., Tsujii, J. and Ananiadou, S., Discovering robust embeddings in (Dis)similarity space for high-dimensional linguistic features, in: Computational Intelligence, pages 285–315, 2014 [DOI] [URL] [Pure]
Stenetorp, P., Pyysalo, S., Ananiadou, S. and Tsujii, J., Generalising semantic category disambiguation with large lexical resources for fun and profit, in: Journal of Biomedical Semantics, 2014 [DOI] [URL] [Pure]

2013

Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S., Using Random Forest to recognise translation equivalents of biomedical terms across languages, in: Proceedings of the Sixth Workshop on Building and Using Comparable Corpora, pages 95–104, 2013 [URL] [PDF] [Pure]

2012

Pyysalo, S., Ohta, T., Miwa, M., Cho, H. C., Tsujii, J. and Ananiadou, S., Event extraction across multiple levels of biological organization, in: Bioinformatics, pages 575–581, 2012 [DOI] [URL] [Pure]
Stenetorp, P., Pyysalo, S., Topić, G., Ohta, T., Ananiadou, S. and Tsujii, J., brat: a Web-based Tool for NLP-Assisted Text Annotation, in: Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics, pages 102–107, 2012 [URL] [Pure]
Stenetorp, P., Pyysalo, S., Ohta, T., Ananiadou, S. and Tsujii, J., Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far, in: Proceedings of ExProM 2012, pages 47–56, 2012 [URL] [Pure]
Ohta, T., Pyysalo, S., Tsujii, J. and Ananiadou, S., Open-domain Anatomical Entity Mention Detection, in: Proceedings of the ACL Workshop on Detecting Stucture in Scholarly Discourse (DSSD), pages 27–36, 2012 [URL] [Pure]
Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J. and Ananiadou, S., Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011., in: BMC Bioinformatics, pages S2, 2012 [DOI] [URL] [Pure]
Mu, T., Goulermas, J. Y., Tsujii, J. and Ananiadou, S., Proximity-based frameworks for generating embeddings from multi-output data, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, pages 2216–2232, 2012 [DOI] [URL] [Pure]
Kim, J., Pyysalo, S., Nédellec, C., Ananiadou, S. and Tsujii, J., Selected articles from the BioNLP Shared Task 2011, in: host publication, 2012 [URL] [Pure]

2011

Kano, Y., Björne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K. B., Verspoor, K., Roeder, C., Hunter, L. E., Kilicoglu, H., Bergler, S., Landeghem, S. V., Parys, T. V., de Peer, Y. V., Miwa, M., Ananiadou, S., Neves, M., Pascual-Montano, A., Özgür, A., Radev, D. R., Riedel, S., Sætre, R., Chun, H. W., Kim, J. D., Pyysalo, S., Ohta, T. and Tsujii, J., U-Compare bio-event meta-service: Compatible BioNLP event extraction services, in: BMC Bioinformatics, 2011 [DOI] [URL] [Pure]
Wang, X., McKendrick, I., Barrett, I., Dix, I., French, T., Tsujii, J. and Ananiadou, S., Automatic Extraction of Angiogenesis Bio-Process from Text, in: Bioinformatics, 2011 [DOI] [URL] [Pure]
Tsuruoka, Y., Miwa, M., Hamamoto, K., Tsujii, J. and Ananiadou, S., Discovering and visualizing indirect associations between biomedical concepts, in: Bioinformatics, pages 111–119, 2011 [DOI] [URL] [Pure]
Kano, Y., Miwa, M., Cohen, K. B., Hunter, L. E., Ananiadou, S. and Tsujii, J., U-Compare: A modular NLP workflow construction and evaluation system, in: IBM Journal of Research and Development, 2011 [DOI] [URL] [Pure]
Kocbek, S., Sætre, R., Stiglic, G., Kim, J. D., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., AGRA: Analysis of gene ranking algorithms, in: Bioinformatics, pages 1185–1186, 2011 [DOI] [URL] [Pure]
Iwasawa, S., Hanaoka, H., Matsuzaki, T., Miyao, Y. and Tsujii, J., A Collaborative Annotation between Human Annotators and a Statistical Parser, in: Proceedings of the 5th Linguistic Annotation Workshop, Association for Computational Linguistics, pages 56–64, 2011 [URL]
Stenetorp, P., Pyysalo, S., Ananiadou, S. and Tsujii, J., Almost Total Recall: Semantic Category Disambiguation Using Large Lexical Resources and Approximate String Matching, in: Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011), 2011 [Pure]
Kocbek, S., Saetre, R., Stiglic, G., Kim, J., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from Pubmed publications, in: Proceedings of the 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2011 [URL] [Pure]
Usami, Y., Cho, H. -C., Okazaki, N. and Tsujii, J., Automatic Acquisition of Huge Training Data for Bio-Medical Named Entity Recognition, in: Proceedings of the BioNLP 2011 Workshop, Association for Computational Linguistics, pages 65–73, 2011 [URL]
Riedel, S., SÃ¦tre, R., Chun, H.-W., Takagi, T. and Tsujii, J., Bio-Molecular Event Extraction with Markov Logic, in: Computational Intelligence, 27:4(558-582), 2011 [DOI] [URL]
Stenetorp, P., TopiÄ‡, G., Pyysalo, S., Ohta, T., Kim, J.-D. and Tsujii, J., BioNLP Shared Task 2011: Supporting Resources, in: Proceedings of the BioNLP Shared Task 2011 Workshop, Association for Computational Linguistics, pages 112–120, 2011 [URL]
Andrade, D., Matsuzaki, T. and Tsujii, J., Effective use of dependency structure for bilingual lexicon creation, in: Proceedings of the 12th international conference on Computational linguistics and intelligent text processing (CICLing'11) - Volume Part II, Tokyo, Japan, Springer-Verlag, pages 80–92, 2011 [URL]
Wu, X., Matsuzaki, T. and Tsujii, J., Effective Use of Function Words for Rule Generalization in Forest-Based Translation, in: Proceedings of ACL-HLT 2011, pages 22-31, 2011 [URL]
Kim, J.-D., Ohta, T., Pyysalo, S., Kano, Y. and Tsujii, J., Extracting Bio-Molecular Events From Literatureâ€”The BioNLPâ€™09 Shared Task, in: Computational Intelligence, 27:4(513-540), 2011 [DOI] [URL]
Ohta, T., Pyysalo, S. and Tsujii, J., From Pathways to Biomolecular Events: Opportunities and Challenges, in: Proceedings of the BioNLP 2011 Workshop, Association for Computational Linguistics, pages 105–113, 2011 [URL]
Andrade, D., Matsuzaki, T. and Tsujii, J., Learning the Optimal Use of Dependency-parsing Information for Finding Translations with Comparable Corpora, in: Proceedings of the 4th Workshop on Building and Using Comparable Corpora: Comparable Corpora and the Web, Association for Computational Linguistics, pages 10–18, 2011 [URL]
Nobata, C., Dobson, P. D., Iqbal, S. A., Mendes, P., Tsujii, J., Kell, D. B. and Ananiadou, S., Mining metabolites: Extracting the yeast metabolome from the literature, in: Metabolomics, pages 94–101, 2011 [DOI] [URL] [Pure]
Hatori, J., Murakami, A. and Tsujii, J., Multi-Topical Discussion Summarization using Structured Lexical Chains and Cue Words, in: Proceedings of CICLing 2011, Lecture Notes in Computer Science, Springer, pages 313-327, 2011 [DOI] [URL]
Ananiadou, S., Sullivan, D., Black, W., Levow, G. A., Gillespie, J. J., Mao, C., Pyysalo, S., Kolluru, B., Tsujii, J. and Sobral, B., Named entity recognition for bacterial type IV secretion systems, in: PLoS ONE, 2011 [DOI] [URL] [Pure]
Nguyen, N. T. H., Kim, J.-D. and Tsujii, J., Overview of BioNLP 2011 Protein Coreference Shared Task, in: Proceedings of the BioNLP Shared Task 2011 Workshop, Association for Computational Linguistics, pages 74–82, 2011 [URL]
Kim, J.-D., Pyysalo, S., Ohta, T., Bossy, R., Nguyen, N. T. H. and Tsujii, J., Overview of BioNLP Shared Task 2011, in: Proceedings of the BioNLP Shared Task 2011 Workshop, Association for Computational Linguistics, pages 1–6, 2011 [URL]
Pyysalo, S., Ohta, T. and Tsujii, J., Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task 2011, in: Proceedings of theBioNLP Shared Task 2011 Workshop, Association for Computational Linguistics, pages 83–88, 2011 [URL]
Ohta, T., Pyysalo, S. and Tsujii, J., Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011, in: Proceedings of the BioNLP Shared Task 2011 Workshop, Association for Computational Linguistics, pages 16–25, 2011 [URL]
Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J. and Ananiadou, S., Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011, in: host publication, 2011 [URL] [Pure]
Ohta, T., Pyysalo, S., Ananiadou, S. and Tsujii, J., Pathway Curation Support as an Information Extraction Task, in: host publication, 2011 [URL] [Pure]
Stenetorp, P., Pyysalo, S. and Tsujii, J., SimSem: Fast Approximate String Matching in Relation to Semantic Category Disambiguation, in: Proceedings of the BioNLP 2011 Workshop, Association for Computational Linguistics, pages 136-145, 2011 [URL]
Pyysalo, S., Ohta, T., Miwa, M. and Tsujii, J., Towards Exhaustive Event Extraction for Protein Modifications, in: Proceedings of the BioNLP 2011 Workshop, Association for Computational Linguistics, pages 114–123, 2011 [URL]
Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J. and Ananiadou, S., Using workflows to explore and optimise named entity recognition for chemistry, in: PLoS ONE, 2011 [DOI] [Pure]

2010

Ananiadou, S., Pyysalo, S., Tsujii, J. and Kell, D. B., Event extraction for systems biology by text mining the literature, in: Trends in Biotechnology, pages 381–390, 2010 [DOI] [Pure]
Kemper, B., Matsuzaki, T., Matsuoka, Y., Tsuruoka, Y., Kitano, H., Ananiadou, S. and Tsujii, J., PathText: A text mining integrator for biological pathway visualizations, in: Bioinformatics, pages 374–381, 2010 [DOI] [URL] [Pure]
Okazaki, N., Ananiadou, S. and Tsujii, J., Building a high-quality sense inventory for improved abbreviation disambiguation, in: Bioinformatics, pages 1246–1253, 2010 [DOI] [URL] [Pure]
Wang, X., Tsujii, J. and Ananiadou, S., Disambiguating the species of biomedical named entities using natural language parsers, in: Bioinformatics, pages 661–667, 2010 [DOI] [URL] [Pure]
Miwa, M., Pyysalo, S., Hara, T. and Tsujii, J., A Comparative Study of Syntactic Parsers for Event Extraction, in: Proceedings of BioNLP 2010, ACL., pages 37–45, 2010 [URL]
Hanaoka, H., Mima, H. and Tsujii, J., A Japanese Particle Corpus Built by Example-Based Annotation, in: Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010), pages 1876–1880, 2010 [URL]
Ohta, T., Pyysalo, S., Kim, J.-D. and Tsujii, J., A re-evaluation of biomedical named entity-term relations, in: Journal of Bioinformatics and Computational Biology (JBCB), 8:5(917--928), 2010 [DOI] [URL]
Zhang, Y., Matsuzaki, T. and Tsujii, J., A Simple Approach for HPSG Supertagging Using Dependency Information, in: Proceedings of NAACL-HLT 2010, 2010 [URL]
Pyysalo, S., Ohta, T. and Tsujii, J., An Analysis of Gene/Protein Associations at PubMed Scale, in: Proceedings of the fourth International Symposium for Semantic Mining in Biomedicine (SMBM 2010), 2010 [URL]
Yu, K., Miyao, Y., Matsuzaki, T., Wang, X., Zhang, Y., Uchimoto, K. and Tsujii, J., Comparison of Chinese Treebanks for Corpus-oriented HPSG Grammar Development, in: Journal of Natural Language Processing (Special Issue on Empirical Methods for Asian Language Processing), 2010
BjÃ¶rne, J., Ginter, F., Pyysalo, S., Tsujii, J. and Salakoski, T., Complex event extraction at PubMed scale, in: Bioinformatics, 26:12(i382-i390), 2010 [DOI] [URL]
Taura, K., Matsuzaki, T., Miwa, M., Kamoshida, Y., Yokoyama, D., Dun, N., Shibata, T., Jun, C. S. and Tsujii, J., Design and Implementation of GXP Make -- A Workflow System Based on Make, in: Proceedings of the 2010 IEEE Sixth International Conference on e-Science, IEEE Computer Society, pages 214–221, 2010 [DOI]
Miwa, M., Miyao, Y., SÃ¦tre, R. and Tsujii, J., Entity-Focused Sentence Simplification for Relation Extraction, in: Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010), pages 788-796, 2010 [URL]
Miwa, M., Pyysalo, S., Hara, T. and Tsujii, J., Evaluating Dependency Representation for Event Extraction, in: Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010), pages 779-787, 2010 [URL]
Ohta, T., Pyysalo, S., Miwa, M. and Tsujii, J., Event Extraction for DNA Methylation, in: Proceedings of the fourth International Symposium for Semantic Mining in Biomedicine (SMBM 2010), 2010 [URL]
Ohta, T., Pyysalo, S., Miwa, M., Kim, J.-D. and Tsujii, J., Event Extraction for Post-Translational Modifications, in: Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, Association for Computational Linguistics, pages 19–27, 2010 [URL]
Miwa, M., SÃ¦tre, R., Kim, J.-D. and Tsujii, J., Event Extraction with Complex Event Classification Using Rich Features, in: Journal of Bioinformatics and Computational Biology, 8:1(131--146), 2010 [URL]
SÃ¦tre, R., Yoshida, K., Miwa, M., Matsuzaki, T., Kano, Y. and Tsujii, J., Extracting Protein-Interactions from Text with the Unified AkaneRE Event Extraction System, in: Transactions on Computational Biology and Bioinformatics (TCBB), BioCreative II.5 Special Issue, 7:3(442-453), 2010 [DOI]
Wu, X., Matsuzaki, T. and Tsujii, J., Fine-grained Tree-to-String Translation Rule Extraction, in: Proceedings of The 48th Annual Meeting of the Association for Computational Linguistics (ACL 2010), pages 325–334, 2010 [URL]
Black, W., Rupp, C., Nobata, C., McNaught, J., Tsujii, J. and Ananiadou, S., High-Precision Semantic Search by Generating and Testing Questions., in: Proceedings of the UK e-Science All Hands Meeting, pages 3pp, 2010 [URL] [Pure]
Mu, T., Wang, X., Tsujii, J. and Ananiadou, S., Imbalanced classification using dictionary-based prototypes and hierarchical decision rules for entity sense disambiguation, in: Coling 2010 - 23rd International Conference on Computational Linguistics, Proceedings of the Conference, pages 851–859, 2010 [URL] [Pure]
Wu, X., Matsuzaki, T. and Tsujii, J., Improve Syntax-based Translation Using Deep Syntactic Structures, in: Machine Translation (Special Issue : Pushing the frontiers of SMT), 2010 [DOI] [URL]
Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S., Ohta, T. and Tsujii, J., Improving the Inter-corpora Compatibility for Protein Annotations, in: Journal of Bioinformatics and Computational Biology (JBCB), 8:5(901-916), 2010 [DOI]
Ohta, T., Matsuzaki, T., Okazaki, N., Miwa, M., SÃ¦tre, R., Pyysalo, S. and Tsujii, J., Medie and Info-pubmed: 2010 update, in: BMC Bioinformatics, 11:Suppl 5(P7), 2010 [DOI] [URL]
Matsuzaki, T., Miyao, Y. and Tsujii, J., Probabilistic Context-Free Grammars with Latent Annotations, in: Supertagging - Using Complex Lexical Descriptions in Natural Language Processing, MIT Press, pages 337–354, 2010
Kano, Y., Dobson, P., Nakanishi, M., Tsujii, J. and Ananiadou, S., Text Mining Meets Workflow: Linking U-Compare with Taverna, in: Bioinformatics, 26:19(2486-2487), 2010 [DOI] [URL]
Ananiadou, S., Pyysalo, S., Ohta, T., Cho, H. -., Sullivan, D., Mao, C., Sobral, B. and Tsujii, J., Towards Event Extraction from Full Texts on Infectious Diseases, in: host publication, pages 132–140, 2010 [URL] [Pure]
Ananiadou, S., Kano, Y., Dorado, R., McCrochon, L. and Tsujii, J., U-Compare: An integrated language resource evaluation platform including a comprehensive UIMA resource library., in: host publication, pages 428–434, 2010 [URL] [Pure]

2009

Matsuoka, Y., Ghosh, S., Kikuchi, N., Sætre, R., Kemper, B., Okazaki, N., Ananiadou, S., Tsujii, J. and Kitano, H., Community Platform for Pathway Model Building, in: 10th International Conference on Systems Biology, pages 139–140, 2009 [URL] [Pure]
Kano, Y., Baumgartner, W. A., McCrohon, L., Ananiadou, S., Cohen, K. B., Hunter, L. and Tsujii, J., U-Compare: Share and compare text mining tools with UIMA, in: Bioinformatics, pages 1997–1998, 2009 [DOI] [URL] [Pure]
Tsunakawa, T., Okazaki, N., Liu, X. and Tsujii, J., A Chinese-Japanese Lexical Machine Translation through a Pivot Language, in: ACM Transactions on Asian Language Information Processing, 8:2(9:1--9:21), 2009 [URL]
Matsubayashi, Y., Okazaki, N. and Tsujii, J., A Comparative Study on Generalization of Semantic Roles in FrameNet., in: Proceedings of ACL-IJCNLP 2009, pages 19–27, 2009 [URL]
Sun, X., Zhang, Y., Matsuzaki, T., Tsuruoka, Y. and Tsujii, J., A Discriminative Latent Variable Chinese Segmenter with Hybrid Word/Character Information, in: Proceedings of NAACL-HLT'09, pages 56–64, 2009 [URL]
Cho, H. -C., Lee, D. -G., Lee, J. -T., Stenetorp, P., Tsujii, J. and Rim, H. -C., A Novel Word Segmentation Approach for Written Languages with Word Boundary Markers, in: Proceedings of ACL-IJCNLP Short Papers, pages 29–32, 2009 [URL]
Miwa, M., SÃ¦tre, R., Miyao, Y. and Tsujii, J., A Rich Feature Vector for Protein-Protein Interaction Extraction from Multiple Corpora, in: Proceedings of EMNLP 2009, pages 121–130, 2009 [URL]
Matsubayashi, Y., Okazaki, N. and Tsujii, J., Accurate and Robust Semantic Role Labeling using Multiple Generalization Criteria in PropBank, in: Proceedings of the 5th International Conference on Generative Approaches to the Lexicon, pages 97–104, 2009
SÃ¦tre, R., Kazuhiro, Y., Miwa, M., Matsuzaki, T., Kano, Y. and Tsujii, J., AkaneRE Relation Extraction: Protein Interaction and Normalization in the BioCreAtIvE II.5 Challenge, in: BioCreative II.5 Workshop 2009 special session | Digital Annotations, CNIO, pages 33, 2009 [URL]
Yu, K. and Tsujii, J., Bilingual Dictionary Extraction from Wikipedia, in: Proceedings of Machine Translation Summit XII, 2009 [URL]
Uematsu, S., Kim, J.-D. and Tsujii, J., Bridging the Gap between Domain-Oriented and Linguistically-Oriented Semantics, in: Proceedings of BioNLP 2009 Workshop, pages 162–170, 2009 [URL]
Wang, X., Tsujii, J. and Ananiadou, S., Classifying relations for biomedical named entity disambiguation, in: EMNLP 2009 - Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: A Meeting of SIGDAT, a Special Interest Group of ACL, Held in Conjunction with ACL-IJCNLP 2009, pages 1513–1522, 2009 [URL] [Pure]
Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S., Ohta, T. and Tsujii, J., Demystifying protein annotations: toward increasing the compatibility of different corpora, in: Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM 2009), pages 103–108, 2009 [URL]
Hara, T., Miyao, Y. and Tsujii, J., Effective Analysis of Causes and Inter-dependencies of Parsing Errors, in: Proceedings of the 11th International Conference on Parsing Technologies (IWPT-09)., pages 180–191, 2009 [URL]
Uematsu, S. and Tsujii, J., Evaluating Contribution of Deep Syntactic Information to Shallow Semantic Analysis, in: Proceedings of the 11th International Conference on Parsing Technologies (IWPTâ€™09), pages 85–88, 2009 [URL]
Miyao, Y., Sagae, K., SÃ¦tre, R., Matsuzaki, T. and Tsujii, J., Evaluating Contributions of Natural Language Parsers to Protein-Protein Interaction Extraction, in: Bioinformatics, 25:3(394-400), 2009 [URL]
Yu, K. and Tsujii, J., Extracting Bilingual Dictionary from Comparable Corpora with Dependency Heterogeneity, in: Proceedings of NAACL-HLT 2009, pages 121–124, 2009 [URL]
Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Fast full parsing by linear-chain conditional random fields, in: EACL 2009 - 12th Conference of the European Chapter of the Association for Computational Linguistics, Proceedings, pages 790–798, 2009 [URL] [Pure]
SÃ¦tre, R., Miwa, M., Yoshida, K. and Tsujii, J., From Protein-Protein Interaction to Molecular Event Extraction, in: Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pages 103–106, 2009 [URL]
Tekiner, F., Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Highly scalable text mining - Parallel tagging application, in: ICSCCW 2009 - 5th International Conference on Soft Computing, Computing with Words and Perceptions in System Analysis, Decision and Control, 2009 [DOI] [URL] [Pure]
Zhang, Y., Matsuzaki, T. and Tsujii, J., HPSG Supertagging: A Sequence Labeling View, in: Proceedings of 11th International Conference on Parsing Technology (IWPT'09), pages 210–213, 2009 [URL]
Ohta, T., Kim, J.-D., Pyysalo, S., Wang, Y. and Tsujii, J., Incorporating GENETAG-style annotation to GENIA corpus, in: Proceedings of BioNLP 2009 Workshop, pages 106–107, 2009 [URL]
Kano, Y., McCrochon, L., Ananiadou, S. and Tsujii, J., Integrated NLP Evaluation System for Pluggable Evaluation Metrics with Extensive Interoperable Toolkit, in: Proceedings of the NAACL HLT Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing, pages 22–30, 2009 [URL] [Pure]
Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S. and Tsujii, J., Investigating heterogeneous protein annotations toward cross-corpora utilization, in: BMC Bioinformatics, 10(403), 2009 [URL]
Sun, X., Matsuzaki, T., Okanohara, D. and Tsujii, J., Latent Variable Perceptron Algorithm for Structured Classification, in: Proceedings of International Joint Conferences on Artificial Intelligence (IJCAI), pages 1236–1242, 2009 [URL]
Okanohara, D. and Tsujii, J., Learning Combination Features with L1 Regularization, in: Proceedings of NAACL-HLT, short papers, pages 97–100, 2009 [URL]
Hatori, J., Miyao, Y. and Tsujii, J., On Contribution of Sense Dependencies to Word Sense Disambiguation, in: Information and Media Technologies, 4:4(1129--1155), 2009
Kim, J.-D., Ohta, T., Pyysalo, S., Kano, Y. and Tsujii, J., Overview of BioNLP'09 Shared Task on Event Extraction, in: Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pages 1–9, 2009 [URL]
Miwa, M., SÃ¦tre, R., Miyao, Y. and Tsujii, J., Protein-Protein Interaction Extraction by Leveraging Multiple Kernels and Parsers, in: International Journal of Medical Informatics, 78:12(e39--e46), 2009 [DOI]
Sun, X., Okazaki, N. and Tsujii, J., Robust Approach to Abbreviating Terms: A Discriminative Latent Variable Model with Global Information, in: Proceedings of ACL-IJCNLP 2009, pages 905–913, 2009 [URL]
Nobata, C., Sasaki, Y., Okazaki, N., Rupp, C. J., Tsujii, J. and Ananiadou, S., Semantic Search on Digital Document Repositories based on Text Mining Results, in: International Conferences on Digital Libraries and the Semantic Web 2009 (ICSD2009), pages 34–48, 2009 [PDF] [Pure]
Wu, X., Okazaki, N. and Tsujii, J., Semi-Supervised Lexicon Mining from Parenthetical Expressions in Monolingual Web Pages, in: Proceedings of HLT-NAACL 2009, pages 424–432, 2009 [URL]
Sun, X. and Tsujii, J., Sequential Labeling with Latent Variables: An Exact Inference Algorithm and An Efficient Approximation, in: Proceedings of EACL 2009, pages 772-780, 2009 [URL]
Pyysalo, S., Ohta, T., Kim, J.-D. and Tsujii, J., Static Relations: a Piece in the Biomedical Information Extraction Puzzle, in: Proceedings of BioNLP 2009 Workshop, pages 1–9, 2009 [URL]
Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Stochastic Gradient Descent Training for L1-regularized Log-linear Models with Cumulative Penalty, in: ACL-IJCNLP 2009, pages 477–485, 2009 [URL]
Miyao, Y. and Tsujii, J., Supervised Learning of a Probabilistic Lexicon of Verb Semantic Classes, in: Proceedings of EMNLP 2009, pages 1328–1337, 2009 [URL]
Okanohara, D. and Tsujii, J., Text Categorization with All Substring Features, in: SIAM International Conference on Data Mining (SDM), 2009 [PDF]
Wu, X., Matsuzaki, T., Okazaki, N., Miyao, Y. and Tsujii, J., The UOT System: Improve String-to-Tree Translation Using Head-Driven Phrase Structure Grammar and Predicate-Argument Structures, in: Proceedings on the International Workshop on Spoken Language Translation (IWSLT), pages 99–106, 2009 [URL]

2008

Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Accelerating the annotation of sparse named entities by dynamic sentence selection, in: BMC Bioinformatics, 2008 [DOI] [PDF] [Pure]
Tsuruoka, Y., Tsujii, J. and Ananiadou, S., FACTA: A text search engine for finding associated biomedical concepts, in: Bioinformatics, pages 2559–2560, 2008 [DOI] [PDF] [Pure]
Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., Kitano, H., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., Connecting Text Mining and Pathways using the PathText Resource, in: Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008), pages 1736–1740, 2008 [PDF] [Pure]
Kano, Y., Nguyen, N., Sætre, R., Fukamachi, K., Yoshida, K., Miyao, Y., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., 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), pages 122–129, 2008 [Pure]
Kano, Y., Nguyen, N., Sætre, R., Yoshida, K., Fukamachi, K., Miyao, Y., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., 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), pages 859–864, 2008 [PDF] [Pure]
Okazaki, N., Ishizuka, M. and Tsujii, J., A Discriminative Approach to Japanese Abbreviation Extraction, in: Proceedings of the Third International Joint Conference on Natural Language Processing (2008), pages 889-894, 2008 [PDF]
Okazaki, N., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., A discriminative candidate generator for string transformations, in: EMNLP 2008 - 2008 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference: A Meeting of SIGDAT, a Special Interest Group of the ACL, pages 447–456, 2008 [PDF] [Pure]
Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Accelerating the Annotation of Sparse Named Entities by Dynamic Sentence Selection, in: Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP 2008), Association for Computational Linguistics, pages 30–37, 2008 [PDF]
Tsunakawa, T. and Tsujii, J., Bilingual Synonym Identification with Spelling Variations, in: Proceedings of the 3rd international Joint Conference on Natural Language Processing, pages 457–464, 2008 [PDF]
Tsunakawa, T., Okazaki, N. and Tsujii, J., Building Bilingual Lexicons Using Lexical Translation Probabilities via Pivot Languages, in: Proceedings of the 6th International Conference on Language Resources and Evaluation, pages 1664–1667, 2008 [PDF]
Nguyen, N. T. H., Kim, J.-D. and Tsujii, J., Challenges in Pronoun Resolution System for Biomedical Text, in: Proceedings of the 6th International Conference on Language Resources and Evaluation (LREC 2008), pages 2408–2412, 2008 [PDF]
Kim, J.-D., Ohta, T. and Tsujii, J., Corpus annotation for mining biomedical events from literature, in: BMC Bioinformatics, 9:1(10), 2008 [PDF]
Miyao, Y. and Tsujii, J., Feature Forest Models for Probabilistic HPSG Parsing, in: Computational Linguistics, 34:1(35â€“80), 2008 [PDF]
Kano, Y., Nguyen, N., SÆtre, R., Yoshida, K., Miyao, Y., Tsuruoka, Y., Matsubayashi, Y., Ananiadou, S. and Tsujii, J., Filling the gaps between tools and users: A tool comparator, using protein-protein interaction as an example, in: Pacific Symposium on Biocomputing 2008, PSB 2008, pages 616–627, 2008 [PDF] [Pure]
Kim, J.-D., Ohta, T., Oda, K. and Tsujii, J., From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature, in: Proceedings of the 6th Asia Pacific Bioinformatics Conference, Imperial College Press, pages 165-176, 2008 [PDF]
Nobata, C., Cotter, P., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Kleio: a knowledge-enriched information retrieval system for biology, in: Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval, Singapore, Singapore, ACM, pages 787–788, 2008 [PDF]
Oda, K., Kim, J.-D., Ohta, T., Okanohara, D., Matsuzaki, T., Tateisi, Y. and Tsujii, J., New challenges for text mining: Mapping between text and manually curated pathways, in: BMC Bioinformatics, 9:Suppl 3(S5), 2008 [PDF]
Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., Kitano, H., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., PathText: Text Mining Tools Integrated with Biological Pathway, in: host publication, 2008 [Pure]
SÃ¦tre, R., Sagae, K. and Tsujii, J., Syntactic features for protein-protein interaction extraction, in: Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007), CEUR Workshop Proceedings (CEUR-WS.org), pages 6.1-6.14, 2008 [PDF]
Miyao, Y., SÃ¦tre, R., Sagae, K., Matsuzaki, T. and Tsujii, J., Task-Oriented Evaluation of Syntactic Parsers and Their Representations, in: Proceedings of ACL-08:HLT, pages 46-54, 2008 [PDF]
Pyysalo, S., SÃ¦tre, R., Tsujii, J. and Salakoski, T., Why Biomedical Relation Extraction Results are Incomparable and What to do about it, in: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pages 149–152, 2008 [URL]

2007

Tsuruoka, Y., McNaught, J., Tsujii, J. and Ananiadou, S., Learning string similarity measures for gene/protein name dictionary look-up using logistic regression, in: Bioinformatics, pages 2768–2774, 2007 [DOI] [PDF] [Pure]
Ananiadou, S., Cotter, P., Nobata, C., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y. and Tsujii, J., SemText: A semantically enriched information retrieval system for biology, in: Proceedings of the 8th International Conference on Systems Biology (ICSB 2007), 2007 [PDF] [Pure]
Okanohara, D. and Tsujii, J., A discriminative language model with pseudo-negative samples, in: Proceedings of the 45th Annual Meeting of the Association of Computational Linguistics (ACL 2007), Association for Computational Linguistics, pages 73–80, 2007 [PDF]
Ninomiya, T., Matsuzaki, T., Miyao, Y. and Tsujii, J., 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), Prague, Czech Republic, pages 60–68, 2007 [PDF]
Yoshida, K., Tsuruoka, Y., Miyao, Y. and Tsujii, J., 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), pages 1783-1788, 2007 [PDF]
Sagae, K. and Tsujii, J., 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), pages 1044-1050, 2007 [PDF]
Matsuzaki, T., Miyao, Y. and Tsujii, J., Efficient HPSG Parsing with Supertagging and CFG-filtering, in: Proceedings of the Twentieth International Joint Conference on Artificial Intelligence (IJCAI-07), pages 1671-1676, 2007 [PDF]
Hara, T., Miyao, Y. and Tsujii, J., 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 2007), pages 11–22, 2007 [PDF]
Tam, W.L., Miyao, Y. and Tsujii, J., Framework independent summarized parser output and its documentation, in: Proceedings of grammar engineering across framework 2007 (GEAF07), pages 319–331, 2007
Sagae, K., Miyao, Y. and Tsujii, J., HPSG parsing with shallow dependency constraints, in: Proceedings of the 44th Meeting of the Association for Computational Linguistics, pages 624–631, 2007 [PDF]
Araki, N., Yoshida, K., Tsuruoka, Y. and Tsujii, J., Move Prediction in Go with the Maximum Entropy Method, in: 2007 IEEE Symposium on Computational Intelligence and Games, pages 189-195, 2007 [PDF]
Yoshida, K. and Tsujii, J., Reranking for Biomedical Named-Entity Recognition, in: Proceedings of BioNLP 2007: Biological, translational, and clinical language processing, pages 209–216, 2007 [PDF]
Miyao, Y., Sagae, K. and Tsujii, J., Towards Framework-Independent Evaluation of Deep Linguistic Parsers, in: Proceedings of Grammar Engineering across Frameworks (GEAF2007), CSLI Publications, pages 238–258, 2007 [PDF]

2006

Ohta, T., Miyao, Y., Ninomiya, T., Tsuruoka, Y., Yakushiji, A., Masuda, K., Takeuchi, J., Yoshida, K., Hara, T., Kim, J.-D., Tateisi, Y. and Tsujii, J., An Intelligent Search Engine and GUI-based Efficient MEDLINE Search Tool Based on Deep Syntactic Parsing, in: Proceedings of the COLING/ACL 2006 Interactive Presentation Sessions, pages 17-20, 2006 [PDF]
Yakushiji, A., Miyao, Y., Ohta, T., Tateisi, Y. and Tsujii, J., Automatic Construction of Predicate-argument Structure Patterns for Biomedical Information Extraction, in: Proceedings of the 2006 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 284–292, 2006 [PDF]
Chun, H.-W., Tsuruoka, Y., Kim, J.-D., Shiba, R., Nagata, N., Hishiki, T. and Tsujii, J., Automatic Recognition of Topic-Classified Relations between Prostate Cancer and Genes from Medline Abstracts, in: Proceedings of the Second International Symposium on Semantic Mining in Biomedicine, pages 5-12, 2006 [PDF]
Kim, J.-D. and Tsujii, J., Corpora and their Annotation, in: Text Mining for Biology and Biomedicine, Artech House, 2006
Chun, H.-W., Tsuruoka, Y., Kim, J.-D., Shiba, R., Nagata, N., Hishiki, T. and Tsujii, J., Extraction of Gene-Disease Relations from MedLine using Domain Dictionaries and Machine Learning, in: Proceedings of the Pacific Symposium on Biocomputing (PSB) 11, pages 4-15, 2006 [PDF]
Ninomiya, T., Matsuzaki, T., Tsuruoka, Y., Miyao, Y. and Tsujii, J., Extremely Lexicalized Models for Accurate and Fast HPSG Parsing, in: Proceedings of EMNLP 2006, pages 155–163, 2006 [PDF]
Okanohara, D., Miyao, Y., Tsuruoka, Y. and Tsujii, J., Improving the Scalability of Semi-Markov Conditional Random Fields for Named Entity Recognition, in: Proceedings of ACL 2006, 2006 [PDF]
Ohta, T., Tateisi, Y., Kim, J.-D., Yakushiji, A. and Tsujii, J., Linguistic and Biological Annotations of Biological Interaction Events, in: Proceedings of The Fifth International Conference on Language Resources and Evaluation (LREC 2006), pages 1402–1405, 2006 [PDF]
Kim, J., Ananiadou, S. and Tsujii, J., Ontology based Semantic Annotation for Knowledge Extraction, in: 2nd International Digital Curation Conference, 2006 [PDF] [Pure]
Miyao, Y., Ohta, T., Masuda, K., Tsuruoka, Y., Yoshida, K., Ninomiya, T. and Tsujii, J., Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases, in: Proceedings of COLING-ACL 2006, pages 1017–1024, 2006 [PDF]
Unno, Y., Ninomiya, T., Miyao, Y. and Tsujii, J., Trimming CFG Parse Trees for Sentence Compression Using Machine Learning Approaches, in: Proceedings of the COLING/ACL 2006 Main Conference Poster Sessions, Association for Computational Linguistics, pages 850–857, 2006 [PDF]

2005

Tsujii, J. and Ananiadou, S., Thesaurus or logical ontology, which one do we need for text mining?, in: Language Resources and Evaluation, pages 77–90, 2005 [DOI] [PDF] [Pure]
Tsuruoka, Y., Ananiadou, S. and Tsujii, J., A Machine Learning Approach To Acronym Generation, in: Proceedings of the Workshop On Linking Biological Literature Ontologies And Databases, pages 25–31, 2005 [PDF] [Pure]
Ninomiya, T., Miyao, Y. and Tsujii, J., A Persistent Feature-Object Database for Intelligent Text Archive Systems, in: Natural Language Processing - IJCNLP 2004, Springer-Verlag, pages 197–205, 2005 [PDF]
Hara, T., Miyao, Y. and Tsujii, J., Adapting a probabilistic disambiguation model of an HPSG parser to a new domain, in: Natural Language Processing â€“ IJCNLP 2005, Springer-Verlag, pages 199–210, 2005 [PDF]
Okanohara, D. and Tsujii, J., Assigning Polarity Scores to Reviews Using Machine Learning Techniques, in: Natural Language Processing - IJCNLP 2005, Springer-Verlag, 2005 [PDF]
Tsuruoka, Y. and Tsujii, J., Bidirectional inference with the easiest-first strategy for tagging sequence data, in: HLT '05: Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing, Vancouver, British Columbia, Canada, Association for Computational Linguistics, pages 467–474, 2005 [PDF]
Yakushiji, A., Miyao, Y., Tateisi, Y. and Tsujii, J., Biomedical Information Extraction with Predicate-Argument Structure Patterns, in: Proceedings of the First International Symposium on Semantic Mining in Biomedicine (SMBM), pages 60–69, 2005 [PDF]
Tsuruoka, Y. and Tsujii, J., Chunk Parsing Revisited, in: Proceedings of the 9th International Workshop on Parsing Technologies (IWPT 2005), pages 133–140, 2005 [PDF]
Tsuruoka, Y., Tateishi, Y., Kim, J. D., Ohta, T., McNaught, J., Ananiadou, S. and Tsujii, J., Developing a robust part-of-speech tagger for biomedical text, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 382–392, 2005 [DOI] [PDF] [Pure]
Ninomiya, T., Tsuruoka, Y., Miyao, Y. and Tsujii, J., Efficacy of Beam Thresholding, Unification Filtering and Hybrid Parsing in Probabilistic HPSG Parsing, in: Proceedings of IWPT 2005, pages 103–114, 2005 [PDF]
Tsuruoka, Y. and Tsujii, J., Iterative CKY Parsing for Probabilistic Context-Free Grammars, in: Natural Language Processing - IJCNLP 2004, Springer-Verlag, pages 52-60, 2005 [PDF]
SpasiÄ‡, I., Ananiadou, S. and Tsujii, J., MaSTerClass: a case-based reasoning system for the classification of biomedical terms, in: Bioinformatics, 21:11(2748--2758), 2005 [PDF]
Kazama, J. and Tsujii, J., Maximum Entropy Models with Inequality Constraints: A case study on text categorization, in: Machine Learning, 60:1-3(169-194), 2005 [URL]
Matsuzaki, T., Miyao, Y. and Tsujii, J., Probabilistic CFG with Latent Annotations, in: Proceedings of ACL 2005, pages 75–82, 2005 [PDF]
Miyao, Y. and Tsujii, J., Probabilistic disambiguation models for wide-coverage HPSG parsing, in: Proceedings of ACL 2005, pages 83–90, 2005 [PDF]

2004

Ananiadou, S., Friedman, C. and Tsujii, J., Introduction: Named entity recognition in biomedicine, in: Journal of Biomedical Informatics, pages 393–395, 2004 [DOI] [URL] [Pure]
Nakanishi, H., Miyao, Y. and Tsujii, J., An Empirical Investigation of the Effect of Lexical Rules on Parsing with a Treebank Grammar, in: Proceedings of The Third Workshop on Treebanks and Lingustic Theories (TLT 2004), pages 103–114, 2004
Chun, H.-W., Ohta, T., Kim, J.-D. and Tsujii, J., Building Patterns for Biomedical Event Extraction, in: Proceedings of the 15th International conference on Genome Informatics (GIW), pages 163–164, 2004 [PDF]
Miyao, Y. and Tsujii, J., Deep Linguistic Analysis for the Accurate Identification of Predicate-Argument Relations, in: Proceedings of COLING 2004, pages 1392-1397, 2004 [PDF]
Tsuruoka, Y. and Tsujii, J., Improving the Performance of Dictionary-based Approaches in Protein Name Recognition, in: Journal of Biomedical Informatics, 37:6(461-470), 2004 [PDF]
Tateisi, Y. and Tsujii, J., Part-of-Speech Annotation of Biology Research Abstracts, in: Proceedings of 4th International Conference on Language Resources and Evaluation (LREC 2004), pages 1267-1270, 2004 [PDF]
Tsuruoka, Y., Miyao, Y. and Tsujii, J., Towards efficient probabilistic HPSG parsing: integrating semantic and syntactic preference to guide the parsing, in: Proceedings of IJCNLP-04 Workshop: Beyond shallow analyses - Formalisms and statistical modeling for deep analyses, 2004 [PDF]

2002

Mima, H., Ananiadou, S., Nenadic, G. and Tsujii, J., A Methodology for Terminology-based Knowledge Acquisition and Integration, in: 19th International Conference on Computational Linguistics, COLING 2002, Howard International House and Academia Sinica, Taipei, Taiwan, August 24 - September 1, 2002, pages 667–673, 2002 [Pure]
Mima, H., Ananiadou, S., Nenadic, G. and Tsujii, J., An Integrated System for Ontology-based Knowledge Structuring and Discovery, in: Proc. SOFG 2002 (Standards and Ontologies for Functional Genomics), 2002 [Pure]
Nenadic, G., Mima, H., Spasic, I., Ananiadou, S., Tsujii, J. and Spasić, I., Terminology-driven literature mining and knowledge acquisition in biomedicine, in: I. J. Medical Informatics, pages 33–48, 2002 [DOI] [Pure]
Mima, H., Ananiadou, S., Nenadic, G. and Tsujii, J., XML tag information management system: A workbench for ontology-based knowledge acquisition and integration, in: Proc. Human Language Technology Conference (HLT 2002), pages 286–292, 2002 [Pure]

1999

Mima, H., Ananiadou, S. and Tsujii, J., A Web-based integrated knowledge mining aid system using term-oriented Natural Language Processing, in: Proc. Natural Language Pacific Rim Symposium (NLPRS ???99), pages 13–18, 1999 [Pure]
Frantzi, K., Ananiadou, S. and Tsujii, J., Automatic classification of technical terms using the NC-value method for term recognition, in: Proc. Int. Conf. on Computational Lexicography (COMPLEX ???99), pages 57–66, 1999 [Pure]
Frantzi, K. T., Ananiadou, S. and Tsujii, J., Classifying Technical Terms, in: Electronic Publishing '99, Redefining the Information Chain - New Ways and Voices: 3rd ICCC/IFIP conference held at the University of Karlskrona/Ronneby - ELPUB 1999, Karlskrona, Sweden, May 10-12, 1999. Proceedings, 1999 [Pure]

1998

Frantzi, K. T., Ananiadou, S. and Tsujii, J., The C-value/NC-value Method of Automatic Recognition for Multi-Word Terms, in: Research and Advanced Technology for Digital Libraries, Second European Conference, ECDL '98, Heraklion, Crete, Greece, September 21-23, 1998, Proceedings, pages 585–604, 1998 [DOI] [Pure]

1997

Radford, I., Ananiadou, S. and Tsujii, J., Adding structural constraints to lexically based context matching techniques, in: Proc. Int. Joint Conf. on Artificial Intelligence (IJCAI-97), 1997 [Pure]
S, [., Ananiadou, S. and Tsujii, J., Term disambiguation by adding structural constraints to lexically-based context matching techniques, in: Proc. Natural Language Processing Pacific Rim Symposium (NLPRS ???97), 1997 [Pure]
Frantzi, K., Ananiadou, S. and Tsujii, J., Term identification using contextual cues, in: Proc. 2nd Workshop on Multilinguality in the Software Industry: the AI Contribution (MULSAIC???97), 1997 [Pure]
Arranz, M. V., Radford, I., Ananiadou, S. and Tsujii, J., Towards a sublanguage-based semantic clustering algorithm, in: Recent Advances in Natural Language Processing, pages 125–136, 1997 [Pure]

1996

Ananiadou, S., Radford, I. and Tsujii, J., Dynamic hypertext navigation using a conceptual graph representation, in: Proc. 4th Int. Conf. on Conceptual Structures, 1996 [Pure]
Frantzi, K., Ananiadou, S. and Tsujii, J., Extracting nested collocations, in: Proc. Second Ann. Mtng. Association for Natural Language Processing, pages 202–212, 1996 [Pure]
Frantzi, K., Ananiadou, S. and Tsujii, J., Extracting terminological expressions, in: Information Processing Society of Japan, pages 83–88, 1996 [Pure]

1995

Radford, I., Arranz, V. M., Ananiadou, S. and Tsujii, J., Dynamic Context Matching for Knowledge Acquisition from Small Corpora, in: Analisi Statistica dei Dati Testuali, Vol. 1, pages 321–328, 1995 [Pure]
Ananiadou, S. R. and Tsujii, J., Sublanguage knowledge acquisition for hypertext optimisation, in: Proc. Natural Language Processing Pacific Rim Symposium, pages 455–460, 1995 [Pure]

1994

Tsujii, J. and Ananiadou, S., Knowledge-based processing in machine translation, in: Knowledge Building and Knowledge Sharing, pages 68–81, 1994 [Pure]

1993

Tsujii, J. and Ananiadou, S., Epsilon [e]: Tool kit for knowledge acquisition based on a hierarchy of pseudotexts, in: Proc. Natural Language Processing Pacific Rim Symposium, pages 93–100, 1993 [Pure]
Tsujii, J. and Ananiadou, S., Knowledge-based processing in machine translation, in: Proc. Int. Conf. on Building and Sharing of Very Large-Scale Knowledge Bases, 1993 [Pure]
Tsujii, J. and Ananiadou, S., LBMT, KBMT, SBMT and EBMT: An attempt at integration, in: Proc. Int. Workshop on Speech Translation, 1993 [Pure]

1992

P, [., Olivier, [., Ananiadou, S. and Tsujii, J., A visualisation architecture based on the systematicity of language, in: Proc. Pacific Rim International Conference on AI (PRICAI), 1992 [Pure]
Sekine, S., Carroll, J. J., Ananiadou, S. and Tsujii, J., Automatic Learning for Semantic Collocation, in: Proc. Third Conf. on Applied Natural Language Processing, pages 104–110, 1992 [Pure]
Sekine, S., Ananiadou, S., Carroll, J. J. and Tsujii, J., Linguistic Knowledge Generator, in: 14th International Conference on Computational Linguistics, COLING 1992, Nantes, France, August 23-28, 1992, pages 560–566, 1992 [Pure]
Olivier, P., Ananiadou, S., Maeda, T. and Tsujii, J., Visualisation: mediating the interchange of information from the verbal to the visual domain, in: Mensch und Maschine - Informationelle Schnittstellen der Kommunikation: Proceedings des 3. Internationalen Symposiums für Informationswissenschaft, ISI 1992, Saarbrücken, Germany, November 5-7, 1992., pages 324–337, 1992 [Pure]

1991

Tsujii, J., Ananiadou, S., Carroll, J. J. and Phillips, J. D., Towards interaction during transfer, in: Proc. RCOLING III, pages 141–157, 1991 [Pure]