Ananiadou, S. - NaCTeM Publications

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First name(s):	S.
Last name(s):	Ananiadou

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Ju., M., Miwa, M. and Ananiadou, S., A Neural Layered Model for Nested Named Entity Recognition, in: Proceedings of NAACL 2018, pages 1446-1459, 2018

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Ju., M., Nguyen, N. T. H., Miwa, M. and Ananiadou, S., An Ensemble of Neural Models for Nested Adverse Drug Events and Medication Extraction with Subwords (2019), in: Journal of the American Medical Informatics Association, 27:1(22-30)

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Ju., M., Short, A.D., Thompson, P., Bakerly, N. D., Gkoutos, G., Tsaprouni, L. and Ananiadou, S., Annotating and Detecting Phenotypic Information for Chronic Obstructive Pulmonary Disease (2019), in: JAMIA Open, 2:2(261-271)

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Kano, Y., Baumgartner Jr., W. A, McCrochon, L., Ananiadou, S., Cohen, K. B., Hunter, L. and Tsujii, J., U-Compare: share and compare text mining tools with UIMA (2009), in: Bioinfomatics, 25:15(1997--1998)

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Kano, Y., BjÃ¶rne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K. B., Verspoor, K., Roeder, C., Hunter, L., Kilicoglu, H., Bergler, S., Van Landeghem, S., Van Parys, T., Van de Peer, Y., Miwa, M., Ananiadou, S., Neves, M., Pascual-Montano, A., Ozgur, A., Radev, D. R., Riedel, S., SÃ¦tre, 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 (2011), in: BMC Bioinformatics, 12(481)

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Kano, Y., Dobson, P., Nakanishi, M., Tsujii, J. and Ananiadou, S., Text Mining Meets Workflow: Linking U-Compare with Taverna (2010), in: Bioinformatics, 26:19(2486-2487)

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Kano, Y., Dorado, R., McCrochon, L., Ananiadou, S. and Tsujii, J., U-Compare: An integrated language resource evaluation platform including a comprehensive UIMA resource library, in: Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC 2010), pages 428--434, 2010

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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

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Kano, Y., Miwa, M., Cohen, K. B., Hunter, L., Ananiadou, S. and Tsujii, J., U-Compare: a modular NLP workflow construction and evaluation system (2011), in: IBM Journal of Research and Development, 55:3(11:1 - 11:10)

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Kano, Y., Nguyen, N. T. H., SÃ¦tre, 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

Kano, Y., Nguyen, N. T. H., SÃ¦tre, 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

Kano, Y., Nguyen, N. T. H., SÃ¦tre, 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: Proceedings of the Pacific Symposium on Biocomputing 2008 (PSB 2008), pages 616--627, 2008

Kemper, B., Matsuzaki, T., Matsuoka, Y., Tsuruoka, Y., Kitano, H., Ananiadou, S. and Tsujii, J., PathText: A Text Mining Integrator for Biological Pathway Visualizations (2010), in: Bioinformatics, 26:12(i374-i381)

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

Selected articles from the BioNLP Shared Task 2011, 2012

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

Kocbek, S., SÃ¦tre, R., Stiglic, G., Kim, J.-D., 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

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Kocbek, S., SÃ¦tre, R., Stiglic, G., Kim, J.-D., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., AGRA: Analysis of Gene Ranking Algorithms (2011), in: Bioinformatics, 27:8(1185-1186)

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Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J. and Ananiadou, S., Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry (2011), in: PLoS ONE, 6:5(e20181)

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Kolluru, B., Nakjang, S., Hirt, R. P, Wipat, A. and Ananiadou, S., Automatic extraction of microorganisms and their habitats from free text using text mining workflows (2011), in: Journal of Integrative Bioinformatics, 8:2(184)

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Kolluru, B., Nakjang, S., Rupp, C. J., Hirt, R. P, Wipat, A. and Ananiadou, S., Automatic extraction of microorganisms and their habitats from free text using text-mining workflows, in: Proceedings of the International Symposium on Integrative Bioinformatics, 2011, 2011

Kontonatsios, G., Brockmeier, A. J., Przybyɫa, P., McNaught, J., Mu, T., Goulermas, J. Y and Ananiadou, S., A semi-supervised approach using label propagation to support citation screening (2017), in: Journal of Biomedical Informatics, 72(67-76)

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Kontonatsios, G., Korkontzelos, I. and Ananiadou, S., Developing Multilingual Text Mining Workflows in UIMA and U-Compare, in: Proceedings of the 17th International conference on Applications of Natural Language Processing to Information Systems, Groningen, Netherlands, pages 82 - 93, Springer, 2012

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Kontonatsios, G., Korkontzelos, I., Kolluru, B. and Ananiadou, S., Adding Text Mining Workflows as Web Services to the BioCatalogue, in: Proceedings of the 4th International Workshop on Semantic Web Aplications and Tools for the Life Sciences (SWAT4LS)., 2011

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Kontonatsios, G., Korkontzelos, I., Kolluru, B., Thompson, P. and Ananiadou, S., Deploying and Sharing U-Compare Workflows as Web Services (2013), in: Journal of Biomedical Semantics, 4(7)

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