Publication list - NaCTeM Publications

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SÃ¦tre, R., Yoshida, K., Miwa, M., Matsuzaki, T., Kano, Y. and Tsujii, J., Extracting Protein-Interactions from Text with the Unified AkaneRE Event Extraction System (2010), in: Transactions on Computational Biology and Bioinformatics (TCBB), BioCreative II.5 Special Issue, 7:3(442-453)

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Sasaki, Y., Wang, X. and Ananiadou, S., Extracting Secondary Bio-Event Arguments with Extraction Constraints (2011), in: Computational Intelligence, 27:4(702-721)

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Miwa, M., Thompson, P., McNaught, J., Kell, D. B. and Ananiadou, S., Extracting semantically enriched events from biomedical literature (2012), in: BMC Bioinformatics, 13(108)

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Chun, H.-W., Tsuruoka, Y., Kim, J.-D., Shiba, R., Nagata, N., Hishiki, T. and Tsujii, J., Extraction of Gene-Disease Relations from MedLine using Domain Dictionaries and Machine Learning, in: Proceedings of the Pacific Symposium on Biocomputing (PSB) 11, pages 4-15, 2006

Ninomiya, T., Matsuzaki, T., Tsuruoka, Y., Miyao, Y. and Tsujii, J., Extremely Lexicalized Models for Accurate and Fast HPSG Parsing, in: Proceedings of EMNLP 2006, pages 155--163, 2006

Shardlow, M., Przybyɫa, P., Batista-Navarro, R., Carter, J., McNaught, J. and Ananiadou, S., Facilitating and promoting web annotation with Argo, in: Proceedings of I Annotate 2016, 2016

Batista-Navarro, R., Kontonatsios, G., MihÄƒilÄƒ, C., Thompson, P., Rak, R., Nawaz, R., Korkontzelos, I. and Ananiadou, S., Facilitating the Analysis of Discourse Phenomena in an Interoperable NLP Platform, in: Computational Linguistics and Intelligent Text Processing, pages 559-571, Springer Berlin Heidelberg, 2013

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Tsuruoka, Y., Tsujii, J. and Ananiadou, S., FACTA: a text search engine for finding associated biomedical concepts (2008), in: Bioinformatics, 24:21(2259-60)

Luo, Z., Xie, Q. and Ananiadou, S., Factual consistency evaluation of summarization in the Era of large language models (2024), in: Expert Systems with Applications, 254(124456)

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Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Fast Full Parsing by Linear-Chain Conditional Random Fields, in: Proceedings of the 12th Conference of European Chapter of the Association for Computational Linguistics (EACL-09), pages 790--798, 2009

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Miyao, Y. and Tsujii, J., Feature Forest Models for Probabilistic HPSG Parsing (2008), in: Computational Linguistics, 34:1(35â€“80)

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

Cao, Y., Li, H., Yu, Y., Reddy Javaji, S., He, Y., Huang, J., Zhu, Z., Xie, Q., Liu, X. -Y., Subbalakshmi, K., Qiu, M., Ananiadou, S. and Nie., J. -Y., FinAudio: A Benchmark for Audio Large Language Models in Financial Applications, arXiv, 2025

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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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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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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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Liu, Z., Wang, K., Bao, Z., Zhang, X., Dong, J., Yang, K, Kabir, M., Giannouris, P., Xing, R., Park, S., Kim, J., Li, D., Xie, Q. and Ananiadou, S., FinNLP-FNP-LLMFinLegal-2025 Shared Task: Financial Misinformation Detection Challenge Task, in: Proceedings of the Joint Workshop of the 9th Financial Technology and Natural Language Processing (FinNLP), the 6th Financial Narrative Processing (FNP), and the 1st Workshop on Large Language Models for Finance and Legal (LLMFinLegal), pages 271–276, 2025

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Xiong, G., Deng, Z., Wang, K., Cao, Y., Li, H., Yu, Y., Peng, X., Lin, M., Smith, K., Liu, X. -Y., Huang, J., Ananiadou, S. and Xie, Q., FLAG-Trader: Fusion LLM-Agent with Gradient-based Reinforcement Learning for Financial Trading, in: Findings of the Association for Computational Linguistics: ACL 2025, In Press

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Liu, Z., Zhang, X., Yang, K, Xie, Q., Huang, J. and Ananiadou, S., FMDLlama: Financial Misinformation Detection based on Large Language Models, arXiv, 2024

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Tam, W.L., Miyao, Y. and Tsujii, J., Framework independent summarized parser output and its documentation, in: Proceedings of grammar engineering across framework 2007 (GEAF07), pages 319--331, 2007

Kabir, M., Tahsin, T. and Ananiadou, S., From n-gram to Attention: How Model Architectures Learn and Propagate Bias in Language Modelin, arXiv, 2025

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Ohta, T., Pyysalo, S. and Tsujii, J., From Pathways to Biomolecular Events: Opportunities and Challenges, in: Proceedings of the BioNLP 2011 Workshop, pages 105--113, Association for Computational Linguistics, 2011

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SÃ¦tre, R., Miwa, M., Yoshida, K. and Tsujii, J., From Protein-Protein Interaction to Molecular Event Extraction, in: Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pages 103--106, 2009

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Kim, J.-D., Ohta, T., Oda, K. and Tsujii, J., From Text to Pathway: Corpus Annotation for Knowledge Acquisition from Biomedical Literature, in: Proceedings of the 6th Asia Pacific Bioinformatics Conference, pages 165-176, Imperial College Press, 2008

Cao, J., Peek, N., Renehan, A. G and Ananiadou, S., Gaussian Distributed Prototypical Network for Few-shot Genomic Variant Detection, in: Proceedings of BioNLP 2023, pages 26–36, 2023

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