Publication list - NaCTeM Publications

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Okazaki, N. and Ananiadou, S., Building an Abbreviation Dictionary using a Term Recognition Approach (2006), in: Bioinformatics, 22:24(3089-3095)

Okazaki, N. and Ananiadou, S., Clustering Acronyms in Biomedical Text for Disambiguation, in: Proceedings of Fifth International conference on Language Resources and Evaluation (LREC 2006), pages 959-962, 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

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

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

NenadiÄ‡, G. and Ananiadou, S., Mining Semantically Related Terms from Biomedical Literature (2006), in: ACM Transactions on Asian Language Information Processing (TALIP), 5:1(22--43)

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

Mima, H., Ananiadou, S. and Matsushima, K., Terminology-Based Knowledge Mining for New Knowledge Discovery (2006), in: ACM Transactions on Asian Language Information Processing (TALIP), 5:1(74--88)

Kim, J.-D. and Tsujii, J., Corpora and their Annotation, in: Text Mining for Biology and Biomedicine, Artech House, 2006

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

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

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

Ananiadou, S., Kell, D. B. and Tsujii, J., Text mining and its potential applications in systems biology (2006), in: Trends in Biotechnology, 24:12(571 - 579)

Second International Symposium on Semantic Mining in Biomedicine (SMBM), 2006

[URL]

Kim, J.-D., Ananiadou, S. and Tsujii, J., Ontology based Semantic Annotation for Knowledge Extraction, in: 2nd International Digital Curation Conference, 2006

Ananiadou, S. and NenadiÄ‡, G., Automatic Terminology Management in Biomedicine, in: Text Mining for Biology and Biomedicine, pages 67--98, Artech House, Inc., 2006

Ananiadou, S. and McNaught, J., Introduction to Text Mining in Biology, in: Text Mining for Biology and Biomedicine, pages 1--12, Artech House, Inc., 2006

Text Mining for Biology And Biomedicine, Artech House, Inc., 2006

[URL]

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

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

Tsuruoka, Y., McNaught, J., Tsujii, J. and Ananiadou, S., Learning string similarity measures for gene/protein name dictionary look-up using logistic regression (2007), in: Bioinformatics, 23:20(2768-2774)

Sasaki, Y., Rea, B. and Ananiadou, S., Multi-topic Aspects in Clinical Text Classification, in: BIBM '07: Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine, pages 62--70, IEEE Computer Society, 2007

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

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

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), pages 6.1-6.14, CEUR Workshop Proceedings (CEUR-WS.org), 2008

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