Jun'ichi Tsujii

Kenjiro Taura, Takuya Matsuzaki, Makoto Miwa, Yoshikazu Kamoshida, Daisaku Yokoyama, Nan Dun, Takeshi Shibata, Choi Sung Jun, Jun'ichi Tsujii: Design and implementation of GXP make - A workflow system based on make. Future Generation Comp. Syst. 29(2): 662-672 (2013)

Xu Sun, Yao-zhong Zhang, Takuya Matsuzaki, Yoshimasa Tsuruoka, Jun'ichi Tsujii: Probabilistic Chinese word segmentation with non-local information and stochastic training. Inf. Process. Manage. 49(3): 626-636 (2013)

Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Junichi Tsujii, Sophia Ananiadou: Event extraction across multiple levels of biological organization. Bioinformatics 28(18): 575-581 (2012)

Ngan L. T. Nguyen, Jin-Dong Kim, Makoto Miwa, Takuya Matsuzaki, Junichi Tsujii: Improving protein coreference resolution by simple semantic classification. BMC Bioinformatics 13: 304 (2012)

Jin-Dong Kim, Ngan Nguyen, Yue Wang, Jun'ichi Tsujii, Toshihisa Takagi, Akinori Yonezawa: The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011. BMC Bioinformatics 13(S-11): S1 (2012)

Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou: Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics 13(S-11): S2 (2012)

Yan Xu, Junichi Tsujii, Eric I.-Chao Chang: Named entity recognition of follow-up and time information in 20 000 radiology reports. JAMIA 19(5): 792-799 (2012)

Yan Xu, Kai Hong, Junichi Tsujii, Eric I.-Chao Chang: Feature engineering combined with machine learning and rule-based methods for structured information extraction from narrative clinical discharge summaries. JAMIA 19(5): 824-832 (2012)

Yan Xu, Jiahua Liu, Jiajun Wu, Yue Wang, Zhuowen Tu, Jian-Tao Sun, Junichi Tsujii, Eric I.-Chao Chang: A classification approach to coreference in discharge summaries: 2011 i2b2 challenge. JAMIA 19(5): 897-905 (2012)

Yao-zhong Zhang, Takuya Matsuzaki, Jun'ichi Tsujii: Structure-guided supertagger learning. Natural Language Engineering 18(2): 205-234 (2012)

Tingting Mu, John Yannis Goulermas, Jun'ichi Tsujii, Sophia Ananiadou: Proximity-Based Frameworks for Generating Embeddings from Multi-Output Data. IEEE Trans. Pattern Anal. Mach. Intell. 34(11): 2216-2232 (2012)

Daniel Andrade, Takuya Matsuzaki, Jun'ichi Tsujii: Statistical Extraction and Comparison of Pivot Words for Bilingual Lexicon Extension. ACM Trans. Asian Lang. Inf. Process. 11(2): 6 (2012)

Xianchao Wu, Takuya Matsuzaki, Jun'ichi Tsujii: Akamon: An Open Source Toolkit for Tree/Forest-Based Statistical Machine Translation. ACL (System Demonstrations) 2012: 127-132

Jun Hatori, Takuya Matsuzaki, Yusuke Miyao, Jun'ichi Tsujii: Incremental Joint Approach to Word Segmentation, POS Tagging, and Dependency Parsing in Chinese. ACL (1) 2012: 1045-1053

Pontus Stenetorp, Sampo Pyysalo, Goran Topic, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii: brat: a Web-based Tool for NLP-Assisted Text Annotation. EACL 2012: 102-107

Atsushi Hanamoto, Takuya Matsuzaki, Jun'ichi Tsujii: Coordination Structure Analysis using Dual Decomposition. EACL 2012: 430-438

Xinkai Wang, Paul Thompson, Jun'ichi Tsujii, Sophia Ananiadou: Biomedical Chinese-English CLIR Using an Extended CMeSH Resource to Expand Queries. LREC 2012: 1148-1155

Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun'ichi Tsujii: AGRA: analysis of gene ranking algorithms. Bioinformatics 27(8): 1185-1186 (2011)

Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun'ichi Tsujii, Sophia Ananiadou: Discovering and visualizing indirect associations between biomedical concepts. Bioinformatics [ISMB/ECCB] 27(13): 111-119 (2011)

Xinglong Wang, Iain McKendrick, Ian Barrett, Ian Dix, Tim French, Jun'ichi Tsujii, Sophia Ananiadou: Automatic extraction of angiogenesis bioprocess from text. Bioinformatics 27(19): 2730-2737 (2011)

Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12: 481 (2011)

Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, Jun'ichi Tsujii: Extracting Bio-molecular Events from literature - the BioNLP'09 Shared Task. Computational Intelligence 27(4): 513-540 (2011)

Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Toshihisa Takagi, Jun'ichi Tsujii: Bio-molecular Event Extraction with Markov Logic. Computational Intelligence 27(4): 558-582 (2011)

Yoshinobu Kano, Makoto Miwa, K. Bretonnel Cohen, Lawrence Hunter, Sophia Ananiadou, Jun'ichi Tsujii: U-Compare: A modular NLP workflow construction and evaluation system. IBM Journal of Research and Development 55(3): 11 (2011)

Xianchao Wu, Takuya Matsuzaki, Jun'ichi Tsujii: Effective Use of Function Words for Rule Generalization in Forest-Based Translation. ACL 2011: 22-31

Shun'ya Iwasawa, Hiroki Hanaoka, Takuya Matsuzaki, Yusuke Miyao, Jun'ichi Tsujii: A Collaborative Annotation between Human Annotators and a Statistical Parser. Linguistic Annotation Workshop 2011: 56-64

Jun'ichi Tsujii: Computational Linguistics and Natural Language Processing. CICLing (1) 2011: 52-67

Daniel Andrade, Takuya Matsuzaki, Jun'ichi Tsujii: Effective Use of Dependency Structure for Bilingual Lexicon Creation. CICLing (2) 2011: 80-92

Jun Hatori, Akiko Murakami, Jun'ichi Tsujii: Multi-topical Discussion Summarization Using Structured Lexical Chains and Cue Words. CICLing (2) 2011: 313-327

Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun'ichi Tsujii: Poster: Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from PubMed publications. ICCABS 2011: 249

Tadayoshi Hara, Takuya Matsuzaki, Yusuke Miyao, Jun'ichi Tsujii: Exploring Difficulties in Parsing Imperatives and Questions. IJCNLP 2011: 749-757

Jun Hatori, Takuya Matsuzaki, Yusuke Miyao, Jun'ichi Tsujii: Incremental Joint POS Tagging and Dependency Parsing in Chinese. IJCNLP 2011: 1216-1224

Kun Yu, Yusuke Miyao, Takuya Matsuzaki, Xiangli Wang, Jun'ichi Tsujii: Analysis of the Difficulties in Chinese Deep Parsing. IWPT 2011: 48-57

Xinglong Wang, Jun'ichi Tsujii, Sophia Ananiadou: Disambiguating the species of biomedical named entities using natural language parsers. Bioinformatics 26(5): 661-667 (2010)

Naoaki Okazaki, Sophia Ananiadou, Jun'ichi Tsujii: Building a high-quality sense inventory for improved abbreviation disambiguation. Bioinformatics 26(9): 1246-1253 (2010)

Brian Kemper, Takuya Matsuzaki, Yukiko Matsuoka, Yoshimasa Tsuruoka, Hiroaki Kitano, Sophia Ananiadou, Jun'ichi Tsujii: PathText: a text mining integrator for biological pathway visualizations. Bioinformatics [ISMB] 26(12): 374-381 (2010)

Jari Björne, Filip Ginter, Sampo Pyysalo, Jun'ichi Tsujii, Tapio Salakoski: Complex event extraction at PubMed scale. Bioinformatics [ISMB] 26(12): 382-390 (2010)

Yoshinobu Kano, Paul Dobson, Mio Nakanishi, Jun'ichi Tsujii, Sophia Ananiadou: Text mining meets workflow: linking U-Compare with Taverna. Bioinformatics 26(19): 2486-2487 (2010)

Tomoko Ohta, Takuya Matsuzaki, Naoaki Okazaki, Makoto Miwa, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii: Medie and Info-pubmed: 2010 update. BMC Bioinformatics 11(S-5): P7 (2010)

Makoto Miwa, Rune Sætre, Jin-Dong Kim, Jun'ichi Tsujii: Event Extraction with Complex Event Classification Using Rich Features. J. Bioinformatics and Computational Biology 8(1): 131-146 (2010)

Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: Improving the Inter-Corpora Compatibility for protein Annotations. J. Bioinformatics and Computational Biology 8(5): 901-916 (2010)

Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim, Jun'ichi Tsujii: A Re-Evaluation of Biomedical Named Entity-Term Relations. J. Bioinformatics and Computational Biology 8(5): 917-928 (2010)

Xianchao Wu, Takuya Matsuzaki, Jun'ichi Tsujii: Improve syntax-based translation using deep syntactic structures. Machine Translation 24(2): 141-157 (2010)

Rune Sætre, Kazuhiro Yoshida, Makoto Miwa, Takuya Matsuzaki, Yoshinobu Kano, Jun'ichi Tsujii: Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System. IEEE/ACM Trans. Comput. Biology Bioinform. 7(3): 442-453 (2010)

Xianchao Wu, Takuya Matsuzaki, Jun'ichi Tsujii: Fine-Grained Tree-to-String Translation Rule Extraction. ACL 2010: 325-334

Daniel Andrade, Tetsuya Nasukawa, Jun'ichi Tsujii: Robust Measurement and Comparison of Context Similarity for Finding Translation Pairs. COLING 2010: 19-27

Makoto Miwa, Sampo Pyysalo, Tadayoshi Hara, Jun'ichi Tsujii: Evaluating Dependency Representations for Event Extraction. COLING 2010: 779-787

Makoto Miwa, Rune Sætre, Yusuke Miyao, Jun'ichi Tsujii: Entity-Focused Sentence Simplification for Relation Extraction. COLING 2010: 788-796

Tingting Mu, Xinglong Wang, Jun'ichi Tsujii, Sophia Ananiadou: Imbalanced Classification Using Dictionary-based Prototypes and Hierarchical Decision Rules for Entity Sense Disambiguation. COLING (Posters) 2010: 851-859

Naoaki Okazaki, Jun'ichi Tsujii: Simple and Efficient Algorithm for Approximate Dictionary Matching. COLING 2010: 851-859

Yao-zhong Zhang, Takuya Matsuzaki, Jun'ichi Tsujii: Forest-guided Supertagger Training. COLING 2010: 1281-1289

Kun Yu, Yusuke Miyao, Xiangli Wang, Takuya Matsuzaki, Jun'ichi Tsujii: Semi-automatically Developing Chinese HPSG Grammar from the Penn Chinese Treebank for Deep Parsing. COLING (Posters) 2010: 1417-1425

Kenjiro Taura, Takuya Matsuzaki, Makoto Miwa, Yoshikazu Kamoshida, Daisaku Yokoyama, Nan Dun, Takeshi Shibata, Choi Sung Jun, Jun'ichi Tsujii: Design and Implementation of GXP Make - A Workflow System Based on Make. eScience 2010: 214-221

Hiroki Hanaoka, Hideki Mima, Jun'ichi Tsujii: A Japanese Particle Corpus Built by Example-Based Annotation. LREC 2010

Yoshinobu Kano, Ruben Dorado, Luke McCrohon, Sophia Ananiadou, Jun'ichi Tsujii: U-Compare: An Integrated Language Resource Evaluation Platform Including a Comprehensive UIMA Resource Library. LREC 2010

Yao-zhong Zhang, Takuya Matsuzaki, Jun'ichi Tsujii: A Simple Approach for HPSG Supertagging Using Dependency Information. HLT-NAACL 2010: 645-648

Yusuke Miyao, Alastair Butler, Kei Yoshimoto, Jun'ichi Tsujii: A Modular Architecture for the Wide-Coverage Translation of Natural Language Texts into Predicate Logic Formulas. PACLIC 2010: 481-488

Tomoko Ohta, Sampo Pyysalo, Makoto Miwa, Jun'ichi Tsujii: Event extraction for DNA methylation. Semantic Mining in Biomedicine 2010

Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: An Analysis of gene/protein associations at PubMed scale. Semantic Mining in Biomedicine 2010

Yusuke Miyao, Kenji Sagae, Rune Sætre, Takuya Matsuzaki, Jun'ichi Tsujii: Evaluating contributions of natural language parsers to protein-protein interaction extraction. Bioinformatics 25(3): 394-400 (2009)

Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, Jun'ichi Tsujii: U-Compare: share and compare text mining tools with UIMA. Bioinformatics 25(15): 1997-1998 (2009)

Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii: Investigating heterogeneous protein annotations toward cross-corpora utilization. BMC Bioinformatics 10: 403 (2009)

Timothy Baldwin, Takenobu Tokunaga, Jun'ichi Tsujii: Hozumi Tanaka. Computational Linguistics 35(4): 475-481 (2009)

Katsuya Masuda, Jun'ichi Tsujii: Tag-Annotated Text Search Using Extended Region Algebra. IEICE Transactions 92-D(12): 2369-2377 (2009)

Makoto Miwa, Rune Sætre, Yusuke Miyao, Jun'ichi Tsujii: Protein-protein interaction extraction by leveraging multiple kernels and parsers. I. J. Medical Informatics 78(12): 39-46 (2009)

Takashi Tsunakawa, Naoaki Okazaki, Xiao Liu, Jun'ichi Tsujii: A Chinese-Japanese Lexical Machine Translation through a Pivot Language. ACM Trans. Asian Lang. Inf. Process. 8(2) (2009)

Yuichiroh Matsubayashi, Naoaki Okazaki, Jun'ichi Tsujii: A Comparative Study on Generalization of Semantic Roles in FrameNet. ACL/IJCNLP 2009: 19-27

Han-Cheol Cho, Do-Gil Lee, Jung-Tae Lee, Pontus Stenetorp, Jun'ichi Tsujii, Hae-Chang Rim: A Novel Word Segmentation Approach for Written Languages with Word Boundary Markers. ACL/IJCNLP (Short Papers) 2009: 29-32

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: Stochastic Gradient Descent Training for L1-regularized Log-linear Models with Cumulative Penalty. ACL/IJCNLP 2009: 477-485

Xu Sun, Naoaki Okazaki, Jun'ichi Tsujii: Robust Approach to Abbreviating Terms: A Discriminative Latent Variable Model with Global Information. ACL/IJCNLP 2009: 905-913

Takeshi S. Kobayakawa, Tadashi Kumano, Hideki Tanaka, Naoaki Okazaki, Jin-Dong Kim, Jun'ichi Tsujii: Opinion classification with tree kernel SVM using linguistic modality analysis. CIKM 2009: 1791-1794

Xu Sun, Jun'ichi Tsujii: Sequential Labeling with Latent Variables: An Exact Inference Algorithm and its Efficient Approximation. EACL 2009: 772-780

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: Fast Full Parsing by Linear-Chain Conditional Random Fields. EACL 2009: 790-798

Makoto Miwa, Rune Sætre, Yusuke Miyao, Jun'ichi Tsujii: A Rich Feature Vector for Protein-Protein Interaction Extraction from Multiple Corpora. EMNLP 2009: 121-130

Tadayoshi Hara, Yusuke Miyao, Jun'ichi Tsujii: Descriptive and Empirical Approaches to Capturing Underlying Dependencies among Parsing Errors. EMNLP 2009: 1162-1171

Yusuke Miyao, Jun'ichi Tsujii: Supervised Learning of a Probabilistic Lexicon of Verb Semantic Classes. EMNLP 2009: 1328-1337

Xinglong Wang, Jun'ichi Tsujii, Sophia Ananiadou: Classifying Relations for Biomedical Named Entity Disambiguation. EMNLP 2009: 1513-1522

Xu Sun, Takuya Matsuzaki, Daisuke Okanohara, Jun'ichi Tsujii: Latent Variable Perceptron Algorithm for Structured Classification. IJCAI 2009: 1236-1242

Sumire Uematsu, Jun'ichi Tsujii: Evaluating Contribution of Deep Syntactic Information to Shallow Semantic Analysis. IWPT 2009: 85-88

Tadayoshi Hara, Yusuke Miyao, Jun'ichi Tsujii: Effective Analysis of Causes and Inter-dependencies of Parsing Errors. IWPT 2009: 180-191

Yao-zhong Zhang, Takuya Matsuzaki, Jun'ichi Tsujii: HPSG Supertagging: A Sequence Labeling View. IWPT 2009: 210-213

Xu Sun, Yao-zhong Zhang, Takuya Matsuzaki, Yoshimasa Tsuruoka, Jun'ichi Tsujii: A Discriminative Latent Variable Chinese Segmenter with Hybrid Word/Character Information. HLT-NAACL 2009: 56-64

Daisuke Okanohara, Jun'ichi Tsujii: Learning Combination Features with L1 Regularization. HLT-NAACL (Short Papers) 2009: 97-100

Kun Yu, Jun'ichi Tsujii: Extracting Bilingual Dictionary from Comparable Corpora with Dependency Heterogeneity. HLT-NAACL (Short Papers) 2009: 121-124

Xianchao Wu, Naoaki Okazaki, Jun'ichi Tsujii: Semi-Supervised Lexicon Mining from Parenthetical Expressions in Monolingual Web Pages. HLT-NAACL 2009: 424-432

Kenta Oouchida, Jin-Dong Kim, Toshihisa Takagi, Jun'ichi Tsujii: GuideLink: A Corpus Annotation System that Integrates the Management of Annotation Guidelines. PACLIC 2009: 771-778

Xiangli Wang, Shun'ya Iwasawa, Yusuke Miyao, Takuya Matsuzaki, Kun Yu, Jun'ichi Tsujii: Design of Chinese HPSG Framework for Data-Driven Parsing. PACLIC 2009: 835-842

Daisuke Okanohara, Jun'ichi Tsujii: Text Categorization with All Substring Features. SDM 2009: 838-846

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics 24(21): 2559-2560 (2008)

Dina Demner-Fushman, Sophia Ananiadou, K. Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber: Themes in biomedical natural language processing: BioNLP08. BMC Bioinformatics 9(S-11) (2008)

Jin-Dong Kim, Tomoko Ohta, Jun'ichi Tsujii: Corpus annotation for mining biomedical events from literature. BMC Bioinformatics 9 (2008)

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: Accelerating the annotation of sparse named entities by dynamic sentence selection. BMC Bioinformatics 9(S-11) (2008)

Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi, Jun'ichi Tsujii: New challenges for text mining: mapping between text and manually curated pathways. BMC Bioinformatics 9(S-3) (2008)

Yusuke Miyao, Jun'ichi Tsujii: Feature Forest Models for Probabilistic HPSG Parsing. Computational Linguistics 34(1): 35-80 (2008)

Yusuke Miyao, Rune Sætre, Kenji Sagae, Takuya Matsuzaki, Jun'ichi Tsujii: Task-oriented Evaluation of Syntactic Parsers and Their Representations. ACL 2008: 46-54

Jin-Dong Kim, Tomoko Ohta, Kanae Oda, Jun'ichi Tsujii: From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature. APBC 2008: 165-176

Katsuya Masuda, Jun'ichi Tsujii: Nested region algebra extended with variables for tag-annotated text search. CIKM 2008: 1349-1350

Jun Hatori, Yusuke Miyao, Jun'ichi Tsujii: Word Sense Disambiguation for All Words using Tree-Structured Conditional Random Fields. COLING (Posters) 2008: 43-46

Yusuke Miyao, Jun'ichi Tsujii: Exact Inference for Multi-label Classification using Sparse Graphical Models. COLING (Posters) 2008: 63-66

Takashi Tsunakawa, Naoaki Okazaki, Jun'ichi Tsujii: Building a Bilingual Lexicon Using Phrase-based Statistical Machine Translation via a Pivot Language. COLING (Posters) 2008: 127-130

Takuya Matsuzaki, Jun'ichi Tsujii: Comparative Parser Performance Analysis across Grammar Frameworks through Automatic Tree Conversion using Synchronous Grammars. COLING 2008: 545-552

Naoaki Okazaki, Sophia Ananiadou, Jun'ichi Tsujii: A Discriminative Alignment Model for Abbreviation Recognition. COLING 2008: 657-664

Kenji Sagae, Jun'ichi Tsujii: Shift-Reduce Dependency DAG Parsing. COLING 2008: 753-760

Xu Sun, Louis-Philippe Morency, Daisuke Okanohara, Yoshimasa Tsuruoka, Jun'ichi Tsujii: Modeling Latent-Dynamic in Shallow Parsing: A Latent Conditional Model with Imrpoved Inference. COLING 2008: 841-848

Jian Su, Xiaofeng Yang, Huaqing Hong, Yuka Tateisi, Jun'ichi Tsujii: Coreference Resolution in Biomedical Texts: a Machine Learning Approach. Ontologies and Text Mining for Life Sciences 2008

Naoaki Okazaki, Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii: A Discriminative Candidate Generator for String Transformations. EMNLP 2008: 447-456

Takashi Tsunakawa, Jun'ichi Tsujii: Bilingual Synonym Identification with Spelling Variations. IJCNLP 2008: 457-464

Yoshinobu Kano, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Keiichiro Fukamachi, Yusuke Miyao, Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii: Towards Data and Goal Oriented Analysis: Tool Inter-operability and Combinatorial Comparison. IJCNLP 2008: 859-864

Naoaki Okazaki, Mitsuru Ishizuka, Jun'ichi Tsujii: A Discriminative Approach to Japanese Abbreviation Extraction. IJCNLP 2008: 889-894

Ngan Nguyen, Jin-Dong Kim, Jun'ichi Tsujii: Challenges in Pronoun Resolution System for Biomedical Text. LREC 2008

Rune Sætre, Brian Kemper, Kanae Oda, Naoaki Okazaki, Yukiko Matsuoka, Norihiro Kikuchi, Hiroaki Kitano, Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii: Connecting Text Mining and Pathways using the PathText Resource. LREC 2008

Yuka Tateisi, Yusuke Miyao, Kenji Sagae, Jun'ichi Tsujii: GENIA-GR: a Grammatical Relation Corpus for Parser Evaluation in the Biomedical Domain. LREC 2008

Takashi Tsunakawa, Naoaki Okazaki, Jun'ichi Tsujii: Building Bilingual Lexicons using Lexical Translation Probabilities via Pivot Languages. LREC 2008

Yoshinobu Kano, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiroh Matsubayashi, Sophia Ananiadou, Jun'ichi Tsujii: Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example. Pacific Symposium on Biocomputing 2008: 616-627

Chikashi Nobata, Philip Cotter, Naoaki Okazaki, Brian Rea, Yutaka Sasaki, Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: Kleio: a knowledge-enriched information retrieval system for biology. SIGIR 2008: 787-788

Yoshimasa Tsuruoka, John McNaught, Jun'ichi Tsujii, Sophia Ananiadou: Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. Bioinformatics 23(20): 2768-2774 (2007)

Daisuke Okanohara, Jun'ichi Tsujii: A discriminative language model with pseudo-negative samples. ACL 2007

Kenji Sagae, Yusuke Miyao, Jun'ichi Tsujii: HPSG Parsing with Shallow Dependency Constraints. ACL 2007

Junichi Tsujii: Combining statistical models with symbolic grammar in parsing. ASRU 2007: 377-378

Nobuo Araki, Kazuhiro Yoshida, Yoshimasa Tsuruoka, Jun'ichi Tsujii: Move Prediction in Go with the Maximum Entropy Method. CIG 2007: 189-195

Kenji Sagae, Jun'ichi Tsujii: Dependency Parsing and Domain Adaptation with LR Models and Parser Ensembles. EMNLP-CoNLL 2007: 1044-1050

Takuya Matsuzaki, Yusuke Miyao, Jun'ichi Tsujii: Efficient HPSG Parsing with Supertagging and CFG-Filtering. IJCAI 2007: 1671-1676

Kazuhiro Yoshida, Yoshimasa Tsuruoka, Yusuke Miyao, Jun'ichi Tsujii: Ambiguous Part-of-Speech Tagging for Improving Accuracy and Domain Portability of Syntactic Parsers. IJCAI 2007: 1783-1788

Rune Sætre, Kenji Sagae, Jun'ichi Tsujii: Syntactic Features for Protein-Protein Interaction Extraction. LBM (Short Papers) 2007

Hong-Woo Chun, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, Jun'ichi Tsujii: Automatic recognition of topic-classified relations between prostate cancer and genes using MEDLINE abstracts. BMC Bioinformatics 7(S-3) (2006)

Yusuke Miyao, Tomoko Ohta, Katsuya Masuda, Yoshimasa Tsuruoka, Kazuhiro Yoshida, Takashi Ninomiya, Jun'ichi Tsujii: Semantic Retrieval for the Accurate Identification of Relational Concepts in Massive Textbases. ACL 2006

Tomoko Ohta, Yusuke Miyao, Takashi Ninomiya, Yoshimasa Tsuruoka, Akane Yakushiji, Katsuya Masuda, Jumpei Takeuchi, Kazuhiro Yoshida, Tadayoshi Hara, Jin-Dong Kim, Yuka Tateisi, Jun'ichi Tsujii: An Intelligent Search Engine and GUI-based Efficient MEDLINE Search Tool Based on Deep Syntactic Parsing. ACL 2006

Daisuke Okanohara, Yusuke Miyao, Yoshimasa Tsuruoka, Jun'ichi Tsujii: Improving the Scalability of Semi-Markov Conditional Random Fields for Named Entity Recognition. ACL 2006

Manabu Sato, Daisuke Bekki, Yusuke Miyao, Jun'ichi Tsujii: Translating HPSG-Style Outputs of a Robust Parser into Typed Dynamic Logic. ACL 2006

Yuya Unno, Takashi Ninomiya, Yusuke Miyao, Jun'ichi Tsujii: Trimming CFG Parse Trees for Sentence Compression Using Machine Learning Approaches. ACL 2006

Takashi Ninomiya, Takuya Matsuzaki, Yoshimasa Tsuruoka, Yusuke Miyao, Jun'ichi Tsujii: Extremely Lexicalized Models for Accurate and Fast HPSG Parsing. EMNLP 2006: 155-163

Akane Yakushiji, Yusuke Miyao, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii: Automatic Construction of Predicate-argument Structure Patterns for Biomedical Information Extraction. EMNLP 2006: 284-292

Hong-Woo Chun, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki, Jun'ichi Tsujii: Extraction of Gene-Disease Relations from Medline Using Domain Dictionaries and Machine Learning. Pacific Symposium on Biocomputing 2006: 4-15

Irena Spasic, Sophia Ananiadou, Jun'ichi Tsujii: MaSTerClass: a case-based reasoning system for the classification of biomedical terms. Bioinformatics 21(11): 2748-2758 (2005)

Jun'ichi Tsujii, Sophia Ananiadou: Thesaurus or Logical Ontology, Which One Do We Need for Text Mining? Language Resources and Evaluation 39(1): 77-90 (2005)

Jun'ichi Kazama, Jun'ichi Tsujii: Maximum Entropy Models with Inequality Constraints: A Case Study on Text Categorization. Machine Learning 60(1-3): 159-194 (2005)

Takuya Matsuzaki, Yusuke Miyao, Jun'ichi Tsujii: Probabilistic CFG with Latent Annotations. ACL 2005

Yusuke Miyao, Jun'ichi Tsujii: Probabilistic Disambiguation Models for Wide-Coverage HPSG Parsing. ACL 2005

Tadayoshi Hara, Yusuke Miyao, Jun'ichi Tsujii: Adapting a Probabilistic Disambiguation Model of an HPSG Parser to a New Domain. IJCNLP 2005: 199-210

Daisuke Okanohara, Jun'ichi Tsujii: Assigning Polarity Scores to Reviews Using Machine Learning Techniques. IJCNLP 2005: 314-325

Yoshimasa Tsuruoka, Jun'ichi Tsujii: Bidirectional Inference with the Easiest-First Strategy for Tagging Sequence Data. HLT/EMNLP 2005

Yoshimasa Tsuruoka, Yuka Tateishi, Jin-Dong Kim, Tomoko Ohta, John McNaught, Sophia Ananiadou, Jun'ichi Tsujii: Developing a Robust Part-of-Speech Tagger for Biomedical Text. Panhellenic Conference on Informatics 2005: 382-392

Keh-Yih Su, Jun'ichi Tsujii, Jong-Hyeok Lee, Oi Yee Kwong (Eds.): Natural Language Processing - IJCNLP 2004, First International Joint Conference, Hainan Island, China, March 22-24, 2004, Revised Selected Papers. Lecture Notes in Computer Science 3248, Springer 2005, isbn 3-540-24475-1

Sophia Ananiadou, Carol Friedman, Jun'ichi Tsujii: Introduction: named entity recognition in biomedicine. Journal of Biomedical Informatics 37(6): 393-395 (2004)

Yoshimasa Tsuruoka, Jun'ichi Tsujii: Improving the performance of dictionary-based approaches in protein name recognition. Journal of Biomedical Informatics 37(6): 461-470 (2004)

Yusuke Miyao, Jun'ichi Tsujii: Deep Linguistic Analysis for the Accurate Identification of Predicate-Argument Relations. COLING 2004

Yoshimasa Tsuruoka, Jun'ichi Tsujii: Iterative CKY Parsing for Probabilistic Context-Free Grammars. IJCNLP 2004: 52-60

Takashi Ninomiya, Jun'ichi Tsujii, Yusuke Miyao: A Persistent Feature-Object Database for Intelligent Text Archive Systems. IJCNLP 2004: 197-205

Jin-Dong Kim, Jun'ichi Tsujii: Word Folding: Taking the Snapshot of Words Instead of the Whole. IJCNLP 2004: 406-415

Yusuke Miyao, Takashi Ninomiya, Jun'ichi Tsujii: Corpus-Oriented Grammar Development for Acquiring a Head-Driven Phrase Structure Grammar from the Penn Treebank. IJCNLP 2004: 684-693

Yuka Tateisi, Jun'ichi Tsujii: Part-of-Speech Annotation of Biology Research Abstracts. LREC 2004

Junichi Tsujii: Thesaurus or Logical Ontology, Which do we Need for Mining Text? LREC 2004

Akane Yakushiji, Yuka Tateisi, Yusuke Miyao, Naoki Yoshinaga, Jun'ichi Tsujii: A Debug Tool for Practical Grammar Development. ACL (Companion) 2003: 173-176

Naoki Yoshinaga, Kentaro Torisawa, Jun'ichi Tsujii: Comparison between CFG Filtering Techniques for LTAG and HPSG. ACL (Companion) 2003: 185-188

Jin-Dong Kim, Hae-Chang Rim, Jun'ichi Tsujii: Self-Organizing Markov Models and Their Application to Part-of-Speech Tagging. ACL 2003: 296-302

Yusuke Miyao, Takashi Ninomiya, Jun'ichi Tsujii: Lexicalized Grammar Acquisition. EACL 2003: 127-130

Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii: GENIA corpus - a semantically annotated corpus for bio-textmining. ISMB (Supplement of Bioinformatics) 2003: 180-182

Katsuya Masuda, Takashi Ninomiya, Yusuke Miyao, Tomoko Ohta, Jun'ichi Tsujii: A Robust Retrieval Engine for Proximal and Structural Search. HLT-NAACL 2003

Yoshimasa Tsuruoka, Jun'ichi Tsujii: Probabilistic term variant generator for biomedical terms. SIGIR 2003: 167-173

Lynette Hirschman, Jong C. Park, Jun'ichi Tsujii, Limsoon Wong, Cathy H. Wu: Accomplishments and challenges in literature data mining for biology. Bioinformatics 18(12): 1553-1561 (2002)

Goran Nenadic, Hideki Mima, Irena Spasic, Sophia Ananiadou, Jun'ichi Tsujii: Terminology-driven literature mining and knowledge acquisition in biomedicine. I. J. Medical Informatics 67(1-3): 33-48 (2002)

Kam-Fai Wong, Jun'ichi Tsujii: Prologue. ACM Trans. Asian Lang. Inf. Process. 1(1): 1-2 (2002)

Jun'ichi Kazama, Takaki Makino, Yoshihiro Ohta, Jun'ichi Tsujii: Tuning support vector machines for biomedical named entity recognition. ACL Workshop on Natural Language Processing in the Biomedical Domain 2002: 1-8

Hideki Mima, Sophia Ananiadou, Goran Nenadic, Jun'ichi Tsujii: A Methodology for Terminology-based Knowledge Acquisition and Integration. COLING 2002

Takashi Ninomiya, Yusuke Miyao, Jun'ichi Tsujii: Lenient Default Unification for Robust Processing within Unification Based Grammar Formalisms. COLING 2002

Takashi Ninomiya, Takaki Makino, Jun'ichi Tsujii: An Indexing Scheme for Typed Feature Structures. COLING 2002

Lynette Hirschman, Jong C. Park, Jun'ichi Tsujii, Cathy H. Wu, Limsoon Wong: Literature Data Mining for Biology - Session Introduction. Pacific Symposium on Biocomputing 2002: 323-325

Toru Hisamitsu, Jun'ichi Tsujii: Measuring Term Representativeness. SCIE 2002: 45-76

Jun'ichi Tsujii: Are NLP technologies really ready for application? (Panel). NLPRS 2001: 37-38

Jun'ichi Kazama, Yusuke Miyao, Jun'ichi Tsujii: A Maximum Entropy Tagger with Unsupervised Hidden Markov Models. NLPRS 2001: 333-340

Jun'ichi Tsujii: LiLFeS/GENIA Project --- NLP Tools and A Biology Domain Corpus ---. NLPRS 2001: 765-766

Jun'ichi Tsujii, Limsoon Wong: Natural Language Processing for Biology - Session Introduction. Pacific Symposium on Biocomputing 2001: 372-373

Akane Yakushiji, Yuka Tateisi, Yusuke Miyao, Jun'ichi Tsujii: Event Extraction from Biomedical Papers Using a Full Parser. Pacific Symposium on Biocomputing 2001: 408-419

Stephan Oepen, Dan Flickinger, Hans Uszkoreit, Jun'ichi Tsujii: Introduction to this Special Issue. Natural Language Engineering 6(1): 1-14 (2000)

Yusuke Miyao, Takaki Makino, Kentaro Torisawa, Jun'ichi Tsujii: The LiLFeS Abstract Machine and its evaluation with the LinGO grammar. Natural Language Engineering 6(1): 47-61 (2000)

Kentaro Torisawa, Kenji Nishida, Yusuke Miyao, Jun'ichi Tsujii: An HPSG parser with CFG filtering. Natural Language Engineering 6(1): 63-80 (2000)

Sang-Zoo Lee, Jun'ichi Tsujii, Hae-Chang Rim: Part-of-Speech Tagging Based on Hidden Markov Model Assuming Joint Independence. ACL 2000

Sang-Zoo Lee, Jun'ichi Tsujii, Hae-Chang Rim: Hidden Markov Model-Based Korean Part-of-Speech Tagging Considering High Agglutinativity, Word-Spacing, and Lexical Correlativity. ACL 2000

Chikashi Nobata, Satoshi Sekine, Jun'ichi Tsujii: Difficulty Indices for the Named Entity Task in Japanese. ACL 2000

Jun'ichi Tsujii: Invited Talk: Generic NLP Technologies: Language, Knowledge and Information Extraction. ACL 2000

Nigel Collier, Chikashi Nobata, Jun'ichi Tsujii: Extracting the Names of Genes and Gene Products with a Hidden Markov Model. COLING 2000: 201-207

Toru Hisamitsu, Yoshiki Niwa, Jun'ichi Tsujii: A Method of Measuring Term Representativeness - Baseline Method Using Co-occurrence Distribution. COLING 2000: 320-326

Hiroshi Kanayama, Kentaro Torisawa, Yutaka Mitsuishi, Jun'ichi Tsujii: A Hybrid Japanese Parser with Hand-crafted Grammar and Statistics. COLING 2000: 411-417

Sang-Zoo Lee, Jun'ichi Tsujii, Hae-Chang Rim: Lexicalized Hidden Markov Models for Part-of-Speech Tagging. COLING 2000: 481-487

Nigel Collier, Hyun Seok Park, Norihiro Ogata, Yuka Tateishi, Chikashi Nobata, Tomoko Ohta, Tateshi Sekimizu, Hisao Imai, Katsutoshi Ibushi, Jun'ichi Tsujii: The GENIA project: corpus-based knowledge acquisition and information extraction from genome research papers. EACL 1999: 271-272

Katerina T. Frantzi, Sophia Ananiadou, Jun'ichi Tsujii: Classifying Technical Terms. ELPUB 1999

Takaki Makino, Minoru Yoshida, Kentaro Torisawa, Jun'ichi Tsujii: LiLFes - Towards a Practical HPSG Parser. COLING-ACL 1998: 807-811

Yutaka Mitsuishi, Kentaro Torisawa, Jun'ichi Tsujii: HPSG-Style Underspecified Japanese Grammar with Wide Coverage. COLING-ACL 1998: 876-880

Takashi Ninomiya, Kentaro Torisawa, Jun'ichi Tsujii: An Efficient Parallel Substrate tor Typed Feature Structures on Shared Memory Parallel Machines. COLING-ACL 1998: 968-974

Katerina T. Frantzi, Sophia Ananiadou, Jun'ichi Tsujii: The C-value/NC-value Method of Automatic Recognition for Multi-Word Terms. ECDL 1998: 585-604

Kentaro Torisawa, Jun'ichi Tsujii: Computing Phrasal-signs in HPSG prior to Parsing. COLING 1996: 949-955

Satoshi Sekine, Jun'ichi Tsujii: Automatic acquisition of semantic collocation from corpora. Machine Translation 10(3): 219-258 (1995)

Patrick Olivier, Jun'ichi Tsujii: Quantitative Perceptual Representation of Prepositional Semantics. Artif. Intell. Rev. 8(2-3): 147-158 (1994)

Patrick Olivier, Toshiyuki Maeda, Jun'ichi Tsujii: Automatic Depiction of Spatial Descriptions. AAAI 1994: 1405-1410

Patrick Olivier, Jun'ichi Tsujii: A Computational View of the Cognitive Semantics of Spatial Prepostions. ACL 1994: 303-309

Masaki Kiyono, Jun'ichi Tsujii: Combination of Symbolic and Statistical Approaches for Grammatical Knowledge Acquisition. ANLP 1994: 72-77

Fumiyo Fukumoto, Jun'ichi Tsujii: Automatic Recognition of Verbal Polysemy. COLING 1994: 762-768

Masaki Kiyono, Jun'ichi Tsujii: Hypothesis Selection in Grammar Acquisition. COLING 1994: 837-841

Jun-ichi Fukumoto, Jun'ichi Tsujii: Breaking Down Rhetorical Relations for the purpose of Analysing Discourse Structures. COLING 1994: 1177-1183

Masaki Kiyono, Jun'ichi Tsujii: Linguistic Knowledge Acquisition from Parsing Failures. EACL 1993: 222-231

Satoshi Sekine, Jeremy J. Carroll, Sophia Ananiadou, Jun'ichi Tsujii: Automatic Learning for Semantic Collocation. ANLP 1992: 104-110

Satoshi Sekine, Sophia Ananiadou, Jeremy J. Carroll, Jun'ichi Tsujii: Linguistic Knowledge Generator. COLING 1992: 560-566

Satoshi Kinoshita, John Phillips, Jun'ichi Tsujii: Interaction between Structural Changes in Machine Translation. COLING 1992: 679-685

Jun'ichi Tsujii, Kimikazu Fujita: Lexical Transfer based on bilingual signs: Towards interaction during transfer. EACL 1991: 275-280

Harold L. Somers, Jun'ichi Tsujii, Danny Jones: Machine Translation without a source text. COLING 1990: 271-276

Jun-ichi Nakamura, Jun'ichi Tsujii, Makoto Nagao: GRADE: A software environment for machine translation. Machine Translation 3(1): 69-82 (1988)

Jun'ichi Tsujii: Reasons why I do not care grammar formalism. COLING 1988: 452

Jun'ichi Tsujii, Yukiyoshi Muto, Yuuji Ikeda, Makoto Nagao: How to get preferred readings in natural language analysis. COLING 1988: 683-687

Jun'ichi Tsujii, Makoto Nagao: Dialogue translation vs. text translation. COLING 1988: 688-693

Makoto Nagao, Jun'ichi Tsujii: The Transfer Phase of the Mu Machine Translation System. COLING 1986: 97-103

Jun-ichi Nakamura, Jun'ichi Tsujii, Makoto Nagao: Solutions for Problems of MT Parser. Methods used in Mu-Machine Translation Project. COLING 1986: 133-135

Jun'ichi Tsujii: Future Directions of Machine Translation. COLING 1986: 655-668

Makoto Nagao, Jun'ichi Tsujii, Jun-ichi Nakamura: The Japanese Government Project for Machine Translation. Computational Linguistics 11(2-3): 91-110 (1985)

Jun'ichi Tsujii, Jun-ichi Nakamura, Makoto Nagao: Analysis Grammar of Japanese in the Mu-Project: A Procedural Approach to Analysis Grammar. COLING 1984: 267-274

Jun-ichi Nakamura, Jun'ichi Tsujii, Makoto Nagao: Grammar Writing System (GRADE) of Mu-Machine Translation Project and its Characteristics. COLING 1984: 338-343

Makoto Nagao, Toyoaki Nishida, Jun'ichi Tsujii: Dealing With Incompleteness Of Linguistic Knowledge In Language Translation - Transfer And Generation Stage Of MU Machine Translation Project. COLING 1984: 420-427

Makoto Nagao, Jun'ichi Tsujii, Koji Yada, Toshihiro Kakimoto: An English Japanese Machine Translation System Of The Titles Of Scientific And Engineering Papers. COLING 1982: 245-252

Jun'ichi Tsujii: The Transfer Phase In an English-Japanese Translation System. COLING 1982: 383-390

Makoto Nagao, Jun'ichi Tsujii, Kei Mitamura, Hideki Hirakawa, Masako Kume: A Machine Translation System From Japanese Into English - Another Perspective Of MT Systems. COLING 1980: 414-423

Makoto Nagao, Jun'ichi Tsujii, Yoshihiro Ueda, M. Takiyama: An Attempt To Computerized Dictionary Data Bases. COLING 1980: 534-542

Makoto Nagao, Jun'ichi Tsujii: S-Net: A Foundation for Knowledge Representation Languages. IJCAI 1979: 617-624

Makoto Nagao, Jun'ichi Tsujii, Katsuto Nakajima, Kei Mitamura, Hachidai Ito: LISP Machine NK3 and Measurement of Its Performance. IJCAI 1979: 625-627

Makoto Nagao, Jun'ichi Tsujii: Mechanism of Deduction in a Question-Answering System with Natural Language Inputd. IJCAI 1973: 285-290