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Ohta, T., Kim, J.-D., Pyysalo, S., Wang, Y. und Tsujii, J., Incorporating GENETAG-style annotation to GENIA corpus, in: Proceedings of BioNLP 2009 Workshop, Seiten 106--107, 2009

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Liu, B, Schlegel, V., Batista-Navarro, R. und Ananiadou, S., Incorporating Zoning Information into Argument Mining from Biomedical Literature, in: Proceedings of LREC 2022, Seiten 6162-6169, 2022

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Xie, Q., Huang, J., Du, P., Peng, M. und Nie., J. -Y., Inductive Topic Variational Graph Auto-Encoder for Text Classification, in: Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, 2021

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Kano, Y., McCrochon, L., Ananiadou, S. und 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, Seiten 22--30, 2009

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Piao, S., Ananiadou, S. und McNaught, J., Integrating Annotation Tools into UIMA for Interoperability, in: Proceedings of the UK e-Science AHM Conference 2007, Seiten 575--582, 2007

Sahu, S. K., Christopoulou, F., Miwa, M. und Ananiadou, S., Inter-sentence Relation Extraction with Document-level Graph Convolutional Neural Network, in: Proceedings of ACL 2019, Seiten 4309-4316, 2019

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Rak, R., Rowley, A., Carter, J., Batista-Navarro, R. und Ananiadou, S., Interoperability and Customisation of Annotation Schemata in Argo, in: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14), Reykjavik, Iceland, Seiten 3837-3842, European Language Resources Association (ELRA), 2014

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Yu, Z. und Ananiadou, S., Interpreting Arithmetic Mechanism in Large Language Models through Comparative Neuron Analysis, in: Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing, Seiten 3293–3306, 2024

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

Kim, J.-D., Ohta, T., Tsuruoka, Y., Tateisi, Y. und Collier, N., Introduction to the Bio-Entity Recognition Task at JNLPBA, in: Proceedings of the International Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA-04), Seiten 70--75, 2004

Ananiadou, S., Friedman, C. und Tsujii, J., Introduction: named entity recognition in biomedicine (2004), in: Journal of Biomedical Informatics, 37:6(393--395)

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Trieu, H-L., Nguyen, N. T. H., Miwa, M. und Ananiadou, S., Investigating Domain-Specific Information for Neural Coreference Resolution on Biomedical Texts, in: Proceedings of the BioNLP 2018 workshop, Seiten 183-188, 2018

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Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S. und Tsujii, J., Investigating heterogeneous protein annotations toward cross-corpora utilization (2009), in: BMC Bioinformatics, 10(403)

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Vasquez-Rodriguez, L., Shardlow, M., Przybyɫa, P. und Ananiadou, S., Investigating Text Simplification Evaluation, in: Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021, Seiten 876-882, 2021

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Yano, K., Miwa, M. und Ananiadou, S., IRIS: Iterative Improvement of Distantly Supervised Named Entity Annotations, Research Square, 2024

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Tsuruoka, Y. und Tsujii, J., Iterative CKY Parsing for Probabilistic Context-Free Grammars, in: Natural Language Processing - IJCNLP 2004, Seiten 52-60, Springer-Verlag, 2005

Nobata, C., Cotter, P., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y., Tsujii, J. und Ananiadou, S., Kleio: a knowledge-enriched information retrieval system for biology, in: Proceedings of the 31st annual international ACM SIGIR conference on Research and development in information retrieval, Singapore, Singapore, Seiten 787--788, ACM, 2008

Inan, E., Thompson, P., Christopoulou, F., Yates, T. und Ananiadou, S., Knowledge Graph Enrichment of a Semantic Search System for Construction Safety, in: Intelligent Systems and Applications. IntelliSys 2022., Seiten 33-52, Springer, Cham, 2022

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Xie, Q., Tiwari, P. und Ananiadou, S., Knowledge-enhanced Graph Topic Transformer for Explainable Biomedical Text Summarization (2023), in: IEEE Journal of Biomedical and Health Informatics

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Hua, Y., Liu, F., Yang, K, Li, Z., Sheu, Y., Zhou, P., Moran, L. V., Ananiadou, S. und Beam, A., Large Language Models in Mental Health Care: a Scoping Review, arXiv, 2024

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Van Landeghem, S., BjÃ¶rne, J., Wei, C-. H, Hakala, K., Pyysalo, S., Ananiadou, S., Kao, H. -Y., Lu, Z., Salakoski, T., Van de Peer, Y. und Ginter, F., Large-scale event extraction from literature with multi-level gene normalization (2013), in: PLOS ONE, 8:4(e55814)

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Sun, X., Matsuzaki, T., Okanohara, D. und Tsujii, J., Latent Variable Perceptron Algorithm for Structured Classification, in: Proceedings of International Joint Conferences on Artificial Intelligence (IJCAI), Seiten 1236--1242, 2009

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Okanohara, D. und Tsujii, J., Learning Combination Features with L1 Regularization, in: Proceedings of NAACL-HLT, short papers, Seiten 97--100, 2009

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Vasilakes, J., Zerva, C., Miwa, M. und Ananiadou, S., Learning Disentangled Representations of Negation and Uncertainty, in: Proceedings of ACL 2022, Seiten 8380–8397, 2022

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

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