Publication list - NaCTeM Publications

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Sasaki, Y., McNaught, J. and Ananiadou, S., The Value of an In-Domain Lexicon in Genomics QA, in: Proceedings of 3rd International Symposium on Languages in Biology and Medicine (LBM-2009), pages 47--55, 2009

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Sasaki, Y., McNaught, J. and Ananiadou, S., The value of an in-domain lexicon in genomics qa (2010), in: Journal of bioinformatics and computational biology, 8:1(147--161)

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Tsujii, J. and Ananiadou, S., Thesaurus or Logical Ontology, Which One Do We Need for Text Mining? (2005), in: Language Resources and Evaluation, 39:1(77-90)

Sasaki, Y., Thompson, P., McNaught, J. and Ananiadou, S., Three BioNLP Tools Powered by the BioLexicon, in: Proceeedings of EACL 2009 Demonstration Session, pages 61--64, 2009

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Hashimoto, K., Kontonatsios, G., Miwa, M. and Ananiadou, S., Topic Detection Using Paragraph Vectors to Support Active Learning in Systematic Reviews (2016), in: Journal of Biomedical Informatics, 62(59â€“65)

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MihÄƒilÄƒ, C., Kontonatsios, G., Batista-Navarro, R., Thompson, P., Korkontzelos, I. and Ananiadou, S., Towards a Better Understanding of Discourse: Integrating Multiple Discourse Annotation Perspectives Using UIMA, in: Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse, Association for Computational Linguistics, Sofia, Bulgaria, pages 79-88, 2013

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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

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

Pyysalo, S., Ohta, T., Cho, H. -C., Sullivan, D., Mao, C., Sobral, B., Tsujii, J. and Ananiadou, S., Towards Event Extraction from Full Texts on Infectious Diseases, in: Proceedings of BioNLP 2010, ACL., pages 132--140, 2010

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Nawaz, R., Thompson, P. and Ananiadou, S., Towards Event-based Discourse Analysis of Biomedical Text (2013), in: International Journal of Computational Linguistics and Applications, 4:2(101-120)

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Pyysalo, S., Ohta, T., Miwa, M. and Tsujii, J., Towards Exhaustive Event Extraction for Protein Modifications, in: Proceedings of the BioNLP 2011 Workshop, pages 114--123, Association for Computational Linguistics, 2011

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Miyao, Y., Sagae, K. and Tsujii, J., Towards Framework-Independent Evaluation of Deep Linguistic Parsers, in: Proceedings of Grammar Engineering across Frameworks (GEAF2007), pages 238--258, CSLI Publications, 2007

Ananiadou, S., Thompson, P., Kano, Y., McNaught, J., Attwood, T. K., Day, P. J. R., Keane, J., Jackson, D. and Pettifer, S., Towards Interoperability of European Language Resources (2011), in: Ariadne, 67

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Yang, K, Ji, S., Zhang, T., Xie, Q., Kuang, Z. and Ananiadou, S., Towards Interpretable Mental Health Analysis with Large Language Models, in: Proceedings of EMNLP 2023, pages 6056–6077, 2023

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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, pages 850--857, Association for Computational Linguistics, 2006

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., 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., 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., 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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Lyte, V., Jones, S., Ananiadou, S. and Kerr, L., UK Institutional Repository Search: Innovation and Discovery (2009), in: Ariadne, 61

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McEntyre, J. R., Ananiadou, S., Andrews, S., Black, W.J., Boulderstone, R., Buttery, P., Chaplin, D., Chevuru, S., Cobley, N., Coleman, L., Davey, P., Gupta, B., Haji-Gholam, L., Hawkins, C., Horne, A., Hubbard, S. J., Kim, J. -H., Lewin, I., Lyte, V., MacIntyre, R., Mansoor, S., Mason, L., McNaught, J., Newbold, E., Nobata, C., Ong, E., Pillai, S., Rebholz-Schuhmann, D., Rosie, H., Rowbotham, R., Rupp, C. J., Stoehr, P. and Vaughan, P., UKPMC: a full text article resource for the life sciences (2010), in: Nucleic Acids Research, 39:Suppl. 1(D58-D65)

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Yu, Z. and Ananiadou, S., Understanding and Mitigating Gender Bias in LLMs via Interpretable Neuron Editing, arXiv, 2025

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Yu, Z. and Ananiadou, S., Understanding Multimodal LLMs: the Mechanistic Interpretability of Llava in Visual Question Answering, arXiv, 2024

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Vasquez-Rodriguez, L., Nguyen, N. T. H., Shardlow, M. and Ananiadou, S., UoM&MMU at TSAR-2022 Shared Task: Prompt Learning for Lexical Simplification, in: Proceedings of the Workshop on Text Simplification, Accessibility, and Readability (TSAR-2022), pages 218-224, 2022

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