Publication list - NaCTeM Publications

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Thew, S., Sutcliffe, A., Procter, R., de Bruijn, O., McNaught, J., Venters, C.C. and Buchan, I., Requirements Engineering for E-science: Experiences in Epidemiology (2009), in: IEEE Software, 26:1(80-87)

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

Ji, S., Zhang, T., Yang, K and Ananiadou, S., Rethinking large language models in mental health applications, arXiv, 2023

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Tran, T. T., Le, P. and Ananiadou, S., Revisiting Unsupervised Relation Extraction, in: Proceedings of ACL 2020, pages 7498–7505, 2020

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Bahor, Z., Liao, J., Macleod, M. R., Bannach-Brown, A., McCann, S. K., Wever, K. E., Thomas, J., Ottavi, T., Howells, D. W., Rice, A., Ananiadou, S. and Sena, E., Risk of bias reporting in the recent animal focal cerebral ischaemia literature (2017), in: Clinical Science, 131:20(2525--2532)

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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

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Sousselier, L., Roncaglioni, A., Raitano, G., Petoumenou, M., Benfenati, E., Ananiadou, S., Nguyen, N. T. H., Do, Q. T., Paya, E., Olivier, E., Wakx, A., Michel, S., Dufat, H. and Rat, P., Role of in silico tools and text mining in the risk assessment of selected alkaloids (2018), in: Toxicology Letters, 295:Supplement 1(S159)

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Raitano, G., Benfenati, E., Ananiadou, S., Nguyen, N. T. H., Do, Q. T., Rat, P. and Sousselier, L., Role of in silico tools and text mining in the safety assessment of selected plant coumarins (2017), in: Toxicology Letters, 280:Supplement 1(S96)

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Venkatesan, A., Kim, J. -H., Talo, F., Ide-Smith, M., Gobeill, J., Carter, J., Batista-Navarro, R., Ananiadou, S., Ruch, P. and McEntyre, J. R., SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data [version 2; referees: 2 approved, 1 approved with reservations]. (2017), in: Wellcome Open Res, 1:25

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

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Selected articles from the BioNLP Shared Task 2011, 2012

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Yang, K, Liu, Z., Xie, Q., Huang, J., Min, E. and Ananiadou, S., Selective Preference Optimization via Token-Level Reward Function Estimation, arXiv, 2024

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Brockmeier, A. J., Mu, T., Ananiadou, S. and Goulermas, J. Y, Self-Tuned Descriptive Document Clustering using a Predictive Network (2018), in: Transactions on Knowledge and Data Engineering

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Thompson, P., Yates, T., Inan, E. and Ananiadou, S., Semantic Annotation for Improved Safety in Construction Work, in: Proceedings of LREC 2020, pages 1983‑1992, 2020

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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

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

Thompson, P., Carter, J., McNaught, J. and Ananiadou, S., Semantically Enhanced Search System for Historical Medical Archives, in: Proceedings of DigitalHeritage 2015, pages 387 - 390, 2015

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Korkontzelos, I., Zesch, T., Zanzotto, F. M. and Biemann, C., SemEval-2013 Task 5: Evaluating Phrasal Semantics., in: Proceedings of the 6th International Workshop on Semantic Evaluation (SemEval 2013), 2013

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Batista-Navarro, R., Carter, J. and Ananiadou, S., Semi-automatic curation of chronic obstructive pulmonary disease phenotypes using Argo, in: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain, pages 403-408, 2015

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MihÄƒilÄƒ, C. and Ananiadou, S., Semi-supervised learning of causal relations in biomedical scientific discourse (2014), in: BioMedical Engineering OnLine, 13:Suppl 2(S1)

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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

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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

Piao, S., Tsuruoka, Y. and Ananiadou, S., Sentiment Analysis with Knowledge Resource and NLP Tools (2009), in: The International Journal of Interdisciplinary Social Sciences, 4:5(17--28)

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Zhang, T., Yang, K and Ananiadou, S., Sentiment-guided Transformer with Severity-aware Contrastive Learning for Depression Detection on Social Media, in: Proceedings of BioNLP 2023, pages 114–126, 2023

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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

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