Publication list - NaCTeM Publications

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Wang, K., Stevens, R., Alachram, H., Li, Y., Soldatova, L. N., King, R. D., Ananiadou, S., Schoene, A, Li, M., Christopoulou, F., Ambite, J. L., Matthew, J., Garg, S., Hermjakob, U., Marcu, D., Sheng, E., Beissbarth, T., Wingender, E., Galstyan, A., Gao, X., Chambers, B., Pan, W., Khomtchouk, B. B., Evans, J. A. and Rzhetsky, A., NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding (2021), in: npj systems biology and applications, 7(38)

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Wang, X. and Ananiadou, S., A Task-Oriented Extension of the Chinese MeSH Concepts Hierarchy, in: Proceedings of the Second Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM), LREC 2010, pages 23--30, 2010

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Wang, X. and Matthews, M., Distinguishing the species of biomedical named entities for term identification (2008), in: BMC Bioinformatics, 9:Suppl 11(S6)

Wang, X., McKendrick, I., Barrett, I., Dix, I., French, T., Tsujii, J. and Ananiadou, S., Automatic Extraction of Angiogenesis Bio-Process from Text (2011), in: Bioinformatics, 27:19(2730-2737)

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Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R., Nawaz, R. and Ananiadou, S., Detecting Experimental Techniques and Selecting Relevant Documents for Protein-Protein Interactions from Biomedical Literature (2011), in: BMC Bioinformatics, 12:Suppl 8(S11)

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Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R., Nawaz, R. and Ananiadou, S., NaCTeM Systems for BioCreative III PPI Tasks, in: Proceedings of the BioCreative III Workshop, pages 142-147, 2010

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Wang, X., Thompson, P. and Ananiadou, S., Biomedical Chinese-English CLIR Using an Extended CMeSH Resource to Expand Queries, in: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pages 1148-1155, 2012

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Wang, X., Tsujii, J. and Ananiadou, S., Disambiguating the Species of Biomedical Named Entities Using Natural Language Parsers (2010), in: Bioinformatics, 26:5(661--667)

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Wang, X., Tsujii, J. and Ananiadou, S., Classifying Relations for Biomedical Named Entity Disambiguation, in: Procedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP'09), pages 1513--1522, 2009

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Wang, Y., Ananiadou, S. and Tsujii, J., Improve Chinese Clinical Named Entity Recognition Performance by Using the Graphical and Phonetic Feature, in: Proceedings of the 2018 International Workshop on Biomedical and Health Informatics, 2018

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Wang, Y., Fan, X., Chen, L., Chang, E. I-C., Ananiadou, S., Tsujii, J. and Xu, Y., Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries (2019), in: BMC Bioinformatics, 20(430)

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Wang, Y., Feng, D., Dai, Y., Chen, Z., Huang, J., Ananiadou, S., Xie, Q. and Wang, H., HARMONIC: Harnessing LLMs for Tabular Data Synthesis and Privacy Protection, in: Proceedings of the Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS), 2024

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Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S., Ohta, T. and Tsujii, J., Improving the Inter-corpora Compatibility for Protein Annotations (2010), in: Journal of Bioinformatics and Computational Biology (JBCB), 8:5(901-916)

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Wang, Y., Kim, J.-D., SÃ¦tre, R., Pyysalo, S., Ohta, T. and Tsujii, J., Demystifying protein annotations: toward increasing the compatibility of different corpora, in: Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM 2009), pages 103--108, 2009

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

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Williams, J., Matragkas, N., Kolovos, D. S., Korkontzelos, I., Ananiadou, S. and Paige, R. F., Software Analytics for MDE Communities, in: Proceedings of the Open Source Software for Model Driven Engineering Workshop (OSS4MDEâ€™14), 2014

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Wu, X., Matsuzaki, T., Okazaki, N., Miyao, Y. and Tsujii, J., The UOT System: Improve String-to-Tree Translation Using Head-Driven Phrase Structure Grammar and Predicate-Argument Structures, in: Proceedings on the International Workshop on Spoken Language Translation (IWSLT), pages 99--106, 2009

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Wu, X., Matsuzaki, T. and Tsujii, J., Effective Use of Function Words for Rule Generalization in Forest-Based Translation, in: Proceedings of ACL-HLT 2011, pages 22-31, 2011

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Wu, X., Matsuzaki, T. and Tsujii, J., Improve Syntax-based Translation Using Deep Syntactic Structures (2010), in: Machine Translation (Special Issue : Pushing the frontiers of SMT)

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Wu, X., Matsuzaki, T. and Tsujii, J., Fine-grained Tree-to-String Translation Rule Extraction, in: Proceedings of The 48th Annual Meeting of the Association for Computational Linguistics (ACL 2010), pages 325--334, 2010

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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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Xie, Q., Bishop, J., Tiwari, P. and Ananiadou, S., Pre-trained language models with domain knowledge for biomedical extractive summarization (2022), in: Knowledge-Based Systems, 252(109460)

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Xie, Q., Han, W., Chen, Z., Xiang, R., Zhang, X., He, Y., Xiao, M., Li, D., Dai, Y., Feng, D., Xu, Y., Kang, H., Kuang, Z., Yuan, C., Yang, K, Luo, Z., Zhang, T., Liu, Z., Xiong, G., Deng, Z., Jiang, Y., Yao, Z., Li, H., Yu, Y., Lopez-Lira, A., Wang, B., Lai, Y., Wang, H., Peng, M., Ananiadou, S. and Huang, J., FinBen: An Holistic Financial Benchmark for Large Language Models, in: Proceedings of the Thirty-Eighth Annual Conference on Neural Information Processing Systems (NeurIPS), 2024

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Xie, Q., Huang, J., Du, P., Peng, M. and 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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Xie, Q., Huang, J., Li, D., Chen, Z., Xiang, R., Xiao, M., Yu, Y., Somasundaram, V., Yang, K, Yuan, C., Luo, Z., Liu, Z., He, Y., Jiang, Y., Li, H., Feng, D., Liu, X. -Y., Wang, B., Wang, H., Lai, Y., Suchow, J., Lopez-Lira, A., Peng, M. and Ananiadou, S., FinNLP-AgentScen-2024 Shared Task: Financial Challenges in Large Language Models - FinLLMs, in: Proceedings of the Eighth Financial Technology and Natural Language Processing and the 1st Agent AI for Scenario Planning, pages 119- 126, 2024

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