Publications by Sophia Ananiadou

Papers by Sophia Ananiadou at NaCTeM, newest first. All publications

2026 | 2025 | 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994 | 1993 | 1992 | 1991 | 1990 | 1989 | 1988 | 1987 | 1986

530 publications

2026

zhang, H., Zhang, Z., Nie, E., Wang, M., Yu, Z., Su, Z., Wang, Y., Wang, Q., Yuan, S., Duan, X., Xue, Q., Yu, Z., Shang, C., Liang, X., Xiong, J. R., Shen, H., Tao, C., Liu, Z., Jin, S., Xi, Z., Zhang, D., Ananiadou, S., Gui, T., Xie, R., So, H. K., Schuetze, H., Huang, X., Zhang, Q. and Wong, N., Locate, Steer, and Improve: A Practical Survey of Actionable Mechanistic Interpretability in Large Language Models, in: Findings of the Association for Computational Linguistics:, pages 10317–10362, 2026 [Pure]

2025

Yu, Z., Belinkov, Y. and Ananiadou, S., Back Attention: Understanding and Enhancing Multi-Hop Reasoning in Large Language Models, in: Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing, pages 11257–11272, 2025 [DOI] [URL] [Pure]
Kabir, M., Abrar, A. and Ananiadou, S., Break the Checkbox: Challenging Closed-Style Evaluations of Cultural Alignment in LLMs, in: Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 24–51, 2025 [DOI] [URL]
Liu, Z., Thompson, P., Rong, J. and Ananiadou, S., ConspEmoLLM-v2: A robust and stable model to detect sentiment-transformed conspiracy theories, in: Proceedings of the 14th Conference on Prestigious Applications of Intelligent Systems (PAIS-2025), pages 5311–5318, 2025 [URL]
Xu, B., Liu, Z. and Ananiadou, S., Disentangled VAD Representations via a Variational Framework for Political Stance Detection, in: arXiv, 2025 [URL]
Zhang, E., Wang, J., Xiao, M., Liu, J., Kuang, Z., Dong, R., Dong, E., Ananiadou, S., Peng, M. and Xie, Q., DITING: A Multi-Agent Evaluation Framework for Benchmarking Web Novel Translation, in: arXiv, 2025 [DOI] [URL]
Yano, K., Luo, Z., Huang, J., Xie, Q., Asada, M., Yuan, C., Yang, K, Miwa, M., Ananiadou, S. and Tsujii, J., ELAINE-medLLM: Lightweight English Japanese Chinese Trilingual Large Language Model for Bio-medical Domain, in: Proceedings of the 31st International Conference on Computational Linguistics (COLING 2025), pages 4670–4688, 2025 [URL]
Luo, Z., Yuan, C., Xie, Q. and Ananiadou, S., EMPEC: A Comprehensive Benchmark for Evaluating Large Language Models Across Diverse Healthcare Professions, in: Findings of the Association for Computational Linguistics: ACL 2025, pages 9945–9958, 2025 [DOI] [URL]
Soufleri, E. and Ananiadou, S., Enhancing Stress Detection on Social Media Through Multi-Modal Fusion of Text and Synthesized Visuals, in: Proceedings of the 24th Workshop on Biomedical Language Processing (BioNLP), pages 34–43, 2025 [DOI] [URL]
Cai, Y., Wang, F., Wang, H., Wang, K., Yang, K, Ananiadou, S., Li, M. and Fan, M., Exploring Safety Alignment Evaluation of LLMs in Chinese Mental Health Dialogues via LLM-as-Judge, in: arXiv, 2025 [DOI] [URL]
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, in: arXiv, 2025 [URL]
Xie, Z., Orel, D., Thareja, R., Sahnan, D., Madmoun, H., Zhang, F., Banerjee, D., Georgiev, G., Peng, X., Qian, L., Huang, J., Su, J., Singh, A., Xing, R., Elbadry, R., Xu, C., Li, H., Koto, F., Koychev, I., Chakraborty, T., Wang, Y., Lahlou, S., Stoyanov, V., Ananiadou, S. and Nakov, P., FinChain: A Symbolic Benchmark for Verifiable Chain-of-Thought Financial Reasoning, in: arXiv, 2025 [DOI] [URL]
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 [URL]
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, pages 13921–13934, 2025 [DOI] [URL]
Liu, Z., Zhang, X., Yang, K, Xie, Q., Huang, J. and Ananiadou, S., FMDLlama: Financial Misinformation Detection Based on Large Language Models, in: Proceedings of the ACM on Web Conference 2025, pages 1153–1157, 2025 [DOI] [URL]
Kabir, M., Tahsin, T. and Ananiadou, S., From n-gram to Attention: How Model Architectures Learn and Propagate Bias in Language Modelin, in: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 18478–18498, 2025 [DOI] [URL]
Kuang, Z., Zhu, F., Jiang, M., Lai, Y., Wang, Zelin, Wang, Zhitong, Qiu, M., Huang, Jiajia, Peng, M., Xie, Q. and Ananiadou, S., From Scores to Skills: A Cognitive Diagnosis Framework for Evaluating Financial Large Language Models, in: arXiv, 2025 [DOI] [URL]
Yano, K., Miwa, M. and Ananiadou, S., IRIS: Rapid Curation Framework for Iterative Improvement of Noisy Named Entity Annotations, in: Proceedings of the International Conference on Applications of Natural Language to Information Systems, pages 58-69, 2025 [DOI] [URL]
Hua, Y., Liu, F., Yang, K, Li, Z., Na, H., Sheu, Y.-H., Zhou, P., Moran, L. V., Ananiadou, S., Clifton, D. A., Beam, A. and Torous, J., Large Language Models in Mental Health Care: A Scoping Review, in: Current Treatment Options in Psychiatry, 12(27), 2025 [DOI] [URL]
Yu, Z. and Ananiadou, S., Locate-then-Merge: Neuron-Level Parameter Fusion for Mitigating Catastrophic Forgetting in Multimodal LLMs, in: Findings of the Association for Computational Linguistics: EMNLP 2025, pages 7065–7078, 2025 [DOI] [URL] [Pure]
Liu, Z., Qian, L., Xie, Q., Huang, J., Yang, K and Ananiadou, S., MMAFFBen: A Multilingual and Multimodal Affective Analysis Benchmark for Evaluating LLMs and VLMs, in: arXiv, 2025 [URL]
Peng, X., Qian, L., Wang, Y., Xiang, R., He, Y., Ren, Y., Jiang, M., Zhao, J., He, H., Han, Y., Feng, Y., Jiang, Y., Cao, Y., Li, H., Yu, Y., Wang, X., Gao, P., Lin, S., Wang, K., Yang, S., Zhao, Y., Liu, Z., Lu, P., Huang, J., Wang, S., Papadopoulos, T., Giannouris, P., Soufleri, E., Chen, N., Xiong, G., Deng, Z., Zhao, Y., Lin, M., Qiu, M., Smith, K., Cohan, A., Liu, X. -Y., Lopez-Lira, A., Chen, X., Tsujii, J., Nie, J., Ananiadou, S. and Xie, Q., MultiFinBen: A Multilingual, Multimodal, and Difficulty-Aware Benchmark for Financial LLM Evaluation, in: arXiv, 2025 [URL]
Yang, K, Leng, Y., Zhang, X., Zhang, T., Thompson, P., Keavney, B., Tomaszewski, M. and Ananiadou, S., Natural Language Processing for Cardiology: A Narrative Review, in: arXiv, 2025 [DOI] [URL]
Xiao, C., Zhao, K., Wang, X., Wu, S., Goldsack, T., Ananiadou, S., Al Moubayed, N., Zhan, L., Cheung, W. K. and Lin, C., Overview of the BioLaySumm 2025 Shared Task on Lay Summarization of Biomedical Research Articles and Radiology Reports, in: Proceedings of the 24th Workshop on Biomedical Language Processing, pages 365–377, 2025 [DOI] [URL]
Song, Y., Liu, B., Gutiérrez-Basulto, V., Hu, Z., Xie, Q., Peng, M., Ananiadou, S. and Pan, J. Z., Plan Then Retrieve: Reinforcement Learning-Guided Complex Reasoning over Knowledge Graphs, in: arXiv, 2025 [DOI] [URL]
Peng, X., Papadopoulos, T., Soufleri, E., Giannouris, P., Xiang, R., Wang, Y., Qian, L., Huang, J., Xie, Q. and Ananiadou, S., Plutus: Benchmarking Large Language Models in Low-Resource Greek Finance, in: Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 30176–30202, 2025 [DOI] [URL]
Liu, Z., Yang, K, Xie, Q., de Kock, C., Ananiadou, S. and Hovy, E., RAEmoLLM: Retrieval Augmented LLMs for Cross-Domain Misinformation Detection Using In-Context Learning based on Emotional Information, in: Proceedings of ACL 2025, pages 16508–16523, 2025 [DOI] [URL]
Abrar, A., Tabassum Oeshy, N., Kabir, M. and Ananiadou, S., Religious Bias Landscape in Language and Text-to-Image Models: Analysis, Detection, and Debiasing Strategies, in: AI & SOCIETY, 2025 [DOI] [URL]
Xiao, M., Jiang, Z., Qian, L., Chen, Z., He, Y., Xu, Y., Jiang, Y., Li, D., Weng, R. -L., Peng, M., Huang, J., Ananiadou, S. and Xie, Q., Retrieval-augmented Large Language Models for Financial Time Series Forecasting, in: arXiv, 2025 [URL]
Liu, Z., Yang, K, Hovy, E. and Ananiadou, S., Rumor Detection by Multi-task Suffix Learning based on Time-series Dual Sentiments, in: arXiv, 2025 [URL]
Yang, K, Liu, Z., Xie, Q., Huang, J., Min, E. and Ananiadou, S., Selective Preference Optimization via Token-Level Reward Function Estimation, in: Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 7032–7056, 2025 [DOI] [URL]
Kabir, M., Ahmed, T., Rahman, M. M., Giannouris, P. and Ananiadou, S., Semantic Label Drift in Cross-Cultural Translation, in: arXiv, 2025 [DOI] [URL]
Vasilakes, J., Zerva, C. and Ananiadou, S., Subjective Logic Encodings, in: arXiv, 2025 [URL]
Zhang, X., Wei, Q., Zhu, Y., Zhang, L., Zhou, D. and Ananiadou, S., SynGraph: A Dynamic Graph-LLM Synthesis Framework for Sparse Streaming User Sentiment Modeling, in: Findings of the Association for Computational Linguistics: ACL 2025, pages 16338–16356, 2025 [DOI] [URL]
Zhang, X., Wei, Q., Zhu, Y., Wu, F. and Ananiadou, S., THCM-CAL: Temporal-Hierarchical Causal Modelling with Conformal Calibration for Clinical Risk Prediction, in: Findings of the Association for Computational Linguistics: EMNLP 2024, pages 916–928, 2025 [DOI] [URL]
Partalidou, E., Passali, T., Zerva, C., Tsoumakas, G. and Ananiadou, S., Towards Trustworthy Summarization of Cardiovascular Articles: A Factuality-and-Uncertainty-Aware Biomedical LLM Approach, in: Proceedings of the 2nd Workshop on Uncertainty-Aware NLP (UncertaiNLP 2025), pages 200–207, 2025 [DOI] [URL]
Yu, Z. and Ananiadou, S., Understanding and Mitigating Gender Bias in LLMs via Interpretable Neuron Editing, in: arXiv, 2025 [URL]
Qian, L., Peng, X., Wang, Y., Zhang, V. J., He, H., Smith, H., Han, Y., He, Y., Li, H., Cao, Y., Yu, Y., Lopez-Lira, A., Lu, P., Nie., J. -Y., Xiong, G., Huang, J. and Ananiadou, S., When Agents Trade: Live Multi-Market Trading Benchmark for LLM Agents, in: arXiv, 2025 [DOI] [URL]

2024

Liu, Z., Yang, K., Xie, Q., Zhang, T. and Ananiadou, S., EmoLLMs: A Series of Emotional Large Language Models and Annotation Tools for Comprehensive Affective Analysis, 2024 [DOI] [URL] [Pure]
Yang, K., Liu, Z., Xie, Q., Huang, J., Zhang, T. and Ananiadou, S., MetaAligner: Towards Generalizable Multi-Objective Alignment of Language Models, in: Thirty-Eighth Annual Conference on Neural Information Processing Systems, Vancouver, Canada, 10/12/24, 2024 [URL] [Pure]
Yang, K., Zhang, T., Kuang, Z., Xie, Q., Huang, J. and Ananiadou, S., MentaLLaMA: interpretable mental health analysis on social media with large language models, in: WWW '24:, pages 4489–4500, 2024 [DOI] [URL] [Pure]
Yuan, C., Xie, Q. and Ananiadou, S., Temporal relation extraction with contrastive prototypical sampling, in: Knowledge-Based Systems, 2024 [DOI] [Pure]
Luo, Z., Yuan, C., Xie, Q. and Ananiadou, S., Are Large Language Models True Healthcare Jacks-of-All-Trades? Benchmarking Across Health Professions Beyond Physician Exams, in: arXiv, 2024 [URL]
Dwivedi, Y. K., Hughes, L., Bhadeshia, H. K. D. H., Ananiadou, S., Cohn, A. G., Cole, J. M., Conduit, G. J., Desarkar, M. S. and Wang, X., Artificial intelligence (AI) futures: India-UK collaborations emerging from the 4th Royal Society Yusuf Hamied workshop, in: International Journal of Information Management(102725), 2024 [DOI] [URL]
Yuan, C., Xie, Q., Huang, J. and Ananiadou, S., Back to the Future: Towards Explainable Temporal Reasoning with Large Language Models, in: Proceedings of the ACM on Web Conference 2024 (WWW '24), pages 1963–1974, 2024 [URL]
Liu, Z., Liu, B, Thompson, P., Yang, K and Ananiadou, S., ConspEmoLLM: Conspiracy Theory Detection Using an Emotion-Based Large Language Model, in: Proceedings of the 13th International Conference on Prestigious Applications of Intelligent Systems (PAIS-2024), pages 4649–4656, 2024 [DOI] [URL]
Zhang, X., Xiang, R., Yuan, C., Feng, D., Han, W., Lopez-Lira, A., Liu, X. -Y., Ananiadou, S., Peng, M., Huang, J. and Xie, Q., Dólares or Dollars? Unraveling the Bilingual Prowess of Financial LLMs Between Spanish and English, in: Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD '24), pages 6236-6246, 2024 [DOI] [URL]
Liu, Z., Zhang, T., Yang, K., Thompson, P., Yu, Z. and Ananiadou, S., Emotion detection for misinformation: A review, in: Information Fusion, 2024 [DOI] [Pure]
Luo, Z., Xie, Q. and Ananiadou, S., Factual consistency evaluation of summarization in the Era of large language models, in: Expert Systems with Applications, 254(124456), 2024 [DOI] [URL]
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 [URL]
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 [URL]
Liu, Z., Zhang, X., Yang, K, Xie, Q., Huang, J. and Ananiadou, S., FMDLlama: Financial Misinformation Detection based on Large Language Models, in: arXiv, 2024 [URL]
Luo, Z., Liu, L., Ananiadou, S. and Xie, Q., Graph Contrastive Topic Model, in: Expert Systems with Applications, 255:Part C(124631), 2024 [DOI] [URL]
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 [URL]
Yu, Z. and Ananiadou, S., How do Large Language Models Learn In-Context?: Query and Key Matrices of In-Context Heads are Two Towers for Metric Learning, in: Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing, pages 3281–3292, 2024 [DOI] [URL] [Pure]
Yu, Z. and 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, pages 3293–3306, 2024 [DOI] [URL] [Pure]
Yano, K., Miwa, M. and Ananiadou, S., IRIS: Iterative Improvement of Distantly Supervised Named Entity Annotations, in: Research Square, 2024 [DOI] [URL]
Hua, Y., Liu, F., Yang, K, Li, Z., Sheu, Y., Zhou, P., Moran, L. V., Ananiadou, S. and Beam, A., Large Language Models in Mental Health Care: a Scoping Review, in: arXiv, 2024 [URL]
Bishop, J., Xie, Q. and Ananiadou, S., LongDocFACTScore: Evaluating the Factuality of Long Document Abstractive Summarisation, in: Proceedings of LREC-COLING 2024, pages 10777-10789, 2024 [URL]
Yu, Z. and Ananiadou, S., Neuron-Level Knowledge Attribution in Large Language Models, in: Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing, pages 3267–3280, 2024 [DOI] [URL] [Pure]
Hu, G., Qin, K., Yuan, C., Peng, M., Lopez-Lira, A., Wang, B., Ananiadou, S., Huang, J. and Xie, Q., No Language is an Island: Unifying Chinese and English in Financial Large Language Models, Instruction Data, and Benchmarks, in: arXiv, 2024 [URL]
Xie, Q., Li, D., Xiao, M., Jiang, Y., Xiang, R., Zhang, X., Chen, Z., He, Y., Han, W., Yang, Y., Chen, S., Zhang, Y., Shen, L., Kim, D., Liu, Z., Luo, Z., Yu, Y., Cao, Y., Deng, Z., Yao, Z., Li, H., Feng, D., Dai, Y., Somasundaram, V., Lu, P., Zhao, Y., Long, Y., Xiong, G., Smith, K., Yu, H., Lai, Y., Peng, M., Nie, J., Suchow, J., Liu, X. -Y., Wang, B., Lopez-Lira, A., Huang, J. and Ananiadou, S., Open-FinLLMs: Open Multimodal Large Language Models for Financial Applications, in: arXiv, 2024 [URL]
Goldsack, T., Luo, Z., Xie, Q., Scarton, C., Shardlow, M., Ananiadou, S. and Lin, C., Overview of the BioLaySumm 2023 Shared Task on Lay Summarization of Biomedical Research Articles, in: Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, pages 468-477, 2024 [DOI] [URL]
Yang, K, Liu, Z., Xie, Q., Huang, J., Min, E. and Ananiadou, S., Selective Preference Optimization via Token-Level Reward Function Estimation, in: arXiv, 2024 [URL]
Zhang, T., Yang, K, Ji, S., Liu, B, Xie, Q. and Ananiadou, S., SuicidEmoji: Derived Emoji Dataset and Tasks for Suicide-Related Social Content, in: Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR '24), pages 1136–1141, 2024 [URL]
Thompson, P., Ananiadou, S., Basinas, I., Brinchmann, B. C., Cramer, C., Galea, K. S., Ge, C., Georgiadis, P., Kirkeleit, J., Kuijpers, E., Nguyen, N. T. H., Nuñez, R., Schlünssen, V., Stokholm, Z. A., Taher, E. A., Tinnerberg, H., van Tongeren, M. and Xie, Q., Supporting the working life exposome: Annotating occupational exposure for enhanced literature search, in: PLoS ONE, 19:8(e0307844), 2024 [DOI] [URL]
Luo, Z., Xie, Q. and Ananiadou, S., The Lay Person’s Guide to Biomedicine: Orchestrating Large Language Models, in: arXiv, 2024 [URL]
Yu, Z. and Ananiadou, S., Understanding Multimodal LLMs: the Mechanistic Interpretability of Llava in Visual Question Answering, in: arXiv, 2024 [URL]

2023

Liu, B., Schlegel, V., Batista-Navarro, R. T. and Ananiadou, S., Argument mining as a multi-hop generative machine reading comprehension task, in: Findings of the Association for Computational Linguistics: EMNLP 2023, pages 10846–10858, 2023 [DOI] [URL] [Pure]
Liu, B., Schlegel, V., Thompson, P., Batista-Navarro, R. T. and Ananiadou, S., Global information-aware argument mining based on a top-down multi-turn QA model, in: Information Processing & Management, 2023 [DOI] [URL] [Pure]
Zhang, T., Yang, K., Alhuzali, H. and Ananiadou, S., PHQ-aware depressive symptoms identification with similarity contrastive learning on social media, in: Information Processing & Management, 2023 [DOI] [URL] [Pure]
Liu, B., Schlegel, V., Batista-Navarro, R. T. and Ananiadou, S., Entity Coreference and Co-occurrence Aware Argument Mining from Biomedical Literature, in: Proceedings of the 4th Workshop on Computational Approaches to Discourse (CODI 2023), pages 54–60, 2023 [DOI] [URL] [Pure]
Zhang, T., Yang, K. and Ananiadou, S., Sentiment-guided Transformer with Severity-aware Contrastive Learning for Depression Detection on Social Media, in: The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, pages 114–126, 2023 [DOI] [URL] [Pure]
Vasilakes, J., Georgiadis, P., Nguyen, N. T. H., Miwa, M. and Ananiadou, S., Contextualized medication event extraction with levitated markers, in: Journal of Biomedical Informatics, 2023 [DOI] [URL] [Pure]
Yang, K., Zhang, T. and Ananiadou, S., Disentangled Variational Autoencoder for Emotion Recognition in Conversations, in: IEEE Transactions on Affective Computing, 2023 [DOI] [URL] [Pure]
Zhang, T., Yang, K. and Ananiadou, S., Emotion fusion for mental illness detection from social media: A survey, in: Information Fusion, pages 231–246, 2023 [DOI] [URL] [Pure]
Yang, K., Zhang, T., Alhuzali, H. and Ananiadou, S., Cluster-Level Contrastive Learning for Emotion Recognition in Conversations, in: IEEE Transactions on Affective Computing, 2023 [DOI] [URL] [Pure]
Yang, K, Zhang, T. and Ananiadou, S., A Bipartite Graph is All We Need for Enhancing Emotional Reasoning with Commonsense Knowledge, in: Proceedings of CIKM 2023, pages 2917–2927, 2023 [URL]
Cao, J., van Veen, E. M., Peek, N., Renehan, A. G and Ananiadou, S., A Novel Automated Approach to Mutation-Cancer Relation Extraction by Incorporating Heterogeneous Knowledge, in: IEEE Journal of Biomedical and Health Informatics, 27:2(1096 - 1105), 2023 [DOI]
Xie, Q., Luo, Z. and Ananiadou, S., A Survey for Biomedical Text Summarization: From Pre-trained to Large Language Models, in: arXiv, 2023 [URL]
Goldsack, T., Luo, Z., Xie, Q., Scarton, C., Shardlow, M., Ananiadou, S. and Lin, C., BioLaySumm 2023 Shared Task: Lay Summarisation of Biomedical Research Articles, in: Proceedings of BioNLP 2023, pages 468–477, 2023 [URL]
Luo, Z., Xie, Q. and Ananiadou, S., ChatGPT as a Factual Inconsistency Evaluator for Text Summarization, in: arXiv, 2023 [DOI]
Luo, Z., Xie, Q. and Ananiadou, S., CitationSum: Citation-aware Graph Contrastive Learning for Scientific Paper Summarization, in: Proceedings of the ACM Web Conference, pages 1843–1852, 2023 [DOI] [URL]
Miwa, M. and Ananiadou, S., DISTANT: Distantly Supervised Entity Span Detection and Classification, in: Proceedings of BioNLP 2023, pages 171–177, 2023 [URL]
Ji, S., Zhang, T., Yang, K and Ananiadou, S., Domain-specific Continued Pretraining of Language Models for Capturing Long Context in Mental Health, in: arXiv, 2023 [URL]
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 [URL]
Xie, Q., Tiwari, P. and Ananiadou, S., Knowledge-enhanced Graph Topic Transformer for Explainable Biomedical Text Summarization, in: IEEE Journal of Biomedical and Health Informatics, 2023 [DOI] [URL]
Min, E. and Ananiadou, S., PESTO: A Post-User Fusion Network for Rumour Detection on Social Media, in: Proceedings of the 13th Workshop on Computational Approaches to Subjectivity, Sentiment, & Social Media Analysis, pages 1-10, 2023 [DOI] [URL]
Ji, S., Zhang, T., Yang, K and Ananiadou, S., Rethinking large language models in mental health applications, in: arXiv, 2023 [URL]
Nguyen, N. T. H., Miwa, M. and Ananiadou, S., Span-based Named Entity Recognition by Generating and Compressing Information, in: Proceedings of EACL 2023, pages 1984–1996, 2023 [URL]
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 [URL]
Yuan, C., Xie, Q. and Ananiadou, S., Zero-shot Temporal Relation Extraction with ChatGPT, in: Proceedings of BioNLP 2023, pages 92–102, 2023 [URL]

2022

Alhuzali, H., Zhang, T. and Ananiadou, S., Emotions and Topics Expressed on Twitter During the COVID-19 Pandemic in the United Kingdom: Comparative Geolocation and Text Mining Analysis, in: JOURNAL OF MEDICAL INTERNET RESEARCH, 2022 [DOI] [Pure]
Odbal, O., Zhang, G. and Ananiadou, S., Examining and mitigating gender bias in text emotion detection task, in: Neurocomputing, pages 422–434, 2022 [DOI] [URL] [Pure]
Min, E., Rong, Y., Xu, T., Bian, Y., Luo, D., Lin, K., Huang, J., Ananiadou, S. and Zhao, P., Neighbour Interaction based Click-Through Rate Prediction via Graph-masked Transformer, in: SIGIR '22: Proceedings of the 45th International ACM SIGIR Conference on Research and Development in Information Retrieval, 11/07/22, pages 353–362, 2022 [DOI] [URL] [Pure]
Xie, Q., Bishop, J., Tiwari, P. and Ananiadou, S., Pre-trained language models with domain knowledge for biomedical extractive summarization, in: Knowledge-Based Systems, 2022 [DOI] [URL] [Pure]
Espinosa, K. J., Georgiadis, P., Christopoulou, E., Ju, M., Makoto, M. and Ananiadou, S., Comparing Neural Models for Nested and Overlapping Biomedical Event Detection, in: BMC Bioinformatics, 2022 [DOI] [URL] [Pure]
Bishop, J., Xie, Q. and Ananiadou, S., GenCompareSum: a hybrid unsupervised summarization method using salience, in: Proceedings of the 21st Workshop on Biomedical Language Processing, pages 220, 2022 [URL] [Pure]
Husain, N., Tofique, S., Chaudhry, I. B., Kiran, T., Taylor, P., Williams, C., Memon, R., Aggarwal, S., Alvi, M. H., Ananiadou, S., Ansari, M. A., Aseem, S., Beck, A., Alam, S., Colucci, E., Davidson, K., Edwards, S., Emsley, R., Green, J., Gumber, A., Hawton, K., Jafri, F., Khaliq, A., Mason, T., Mcreath, A., Minhas, A., Naeem, F., Naqvi, H. A., Noureen, A., Panagioti, M., Patel, A., Poppleton, A., Shiri, T., Simic, M., Sultan, S., Nizami, A. T., Zadeh, Z., Zafar, S. N. and Chaudhry, N., Youth Culturally adapted Manual Assisted Problem Solving Training (YCMAP) in Pakistani adolescent with a history of self-harm: protocol for multicentre clinical and cost-effectiveness randomised controlled trial, in: BMJ Open, pages e056301, 2022 [DOI] [URL] [Pure]
Yang, K, Zhang, T. and Ananiadou, S., A Mental State Knowledge-Aware and Contrastive Network for Early Stress and Depression Detection on Social Media, in: Information Processing and Management, 59:4(102961), 2022 [DOI] [URL]
Schoene, A, Basinas, I., van Tongeren, M. and Ananiadou, S., A Narrative Literature Review of Natural Language Processing Applied to the Occupational Exposome, in: Int. J. Environ. Res. Public Health, 19:14(8544), 2022 [DOI] [URL]
Trieu, H-L., Miwa, M. and Ananiadou, S., BioVAE: a pre-trained latent variable language model for biomedical text mining, in: 38:3(872-874), 2022 [DOI] [URL]
Schoene, A, Bojanic, L., Nghiem, M-. Q., Hunt, I. M. and Ananiadou, S., Classifying suicide-related content and emotions on Twitter using Graph Convolutional Neural Networks, in: IEEE Transactions on Affective Computing(1-12), 2022 [DOI] [URL]
Min, E., Rong, Y, Xu, T., Bian, Y., Zhao, Y., Huang, J. and Ananiadou, S., Divide-and-Conquer: Post-User Interaction Network for Fake News Detection on Social Media, in: Proceedings of The Web Conference 2022, pages 1148–1158, 2022 [URL]
Saha, T and Ananiadou, S., Emotion-aware and Intent-controlled Empathetic Response Generation using Hierarchical Transformer Network, in: Proceedings of IJCNN at 2022 IEEE World Congress on Computational Intelligence, pages 1-8, 2022 [DOI] [URL]
Alhuzali, H., Zhang, T. and Ananiadou, S., Emotions and Topics Expressed on Twitter During the COVID-19 Pandemic in the United Kingdom: Comparative Geolocation and Text Mining Analysis, in: Journal of Medical Internet Research, 24:10(e40323), 2022 [DOI] [URL]
Xie, Q., Huang, J., Saha, T and Ananiadou, S., GRETEL: Graph Contrastive Topic Enhanced Language Model for Long Document Extractive Summarization, in: Proceedings of COLING, pages 6259–6269, 2022 [URL]
Liu, B, Schlegel, V., Batista-Navarro, R. and Ananiadou, S., Incorporating Zoning Information into Argument Mining from Biomedical Literature, in: Proceedings of LREC 2022, pages 6162-6169, 2022 [URL]
Inan, E., Thompson, P., Christopoulou, F., Yates, T. and Ananiadou, S., Knowledge Graph Enrichment of a Semantic Search System for Construction Safety, in: Intelligent Systems and Applications. IntelliSys 2022., Springer, Cham, pages 33-52, 2022 [DOI] [URL]
Vasilakes, J., Zerva, C., Miwa, M. and Ananiadou, S., Learning Disentangled Representations of Negation and Uncertainty., pages 8380–8397, 2022 [URL] [Pure]
Trieu, H-L., Miwa, M. and Ananiadou, S., Named Entity Recognition for Cancer Immunology Research Using Distant Supervision, in: Proceedings of BioNLP 2022, pages 171-177, 2022 [URL]
Zhang, T., Schoene, A and Ananiadou, S., Natural Language Processing Applied to Mental Illness Detection: A Narrative Review, in: n p j Digital Medicine, 5(46), 2022 [DOI] [URL]
Li, M. and Ananiadou, S., Neural Architectures for Aggregating Sequence Labels from Multiple Annotators, in: Neurocomputing, 2022 [DOI] [URL]
Luo, Z., Xie, Q. and Ananiadou, S., Readability Controllable Biomedical Document Summarization, in: Findings of the Association for Computational Linguistics: EMNLP 2022, pages 4667–4680, 2022 [URL]
Schoene, A and Ananiadou, S., RELATE: Generating a linguistically inspired Knowledge Graph for fine-grained emotion classification, in: Proceedings of LREC 2022, pages 6317-6327, 2022 [URL]
Nghiem, M-. Q., Baylis, P., Freitas, A. and Ananiadou, S., Text Classification and Prediction in the Legal Domain, pages 4717-4722, 2022 [URL]
Vásquez-Rodríguez, L., Nguyen, N., Shardlow, M. and Ananiadou, S., UoM&MMU at TSAR-2022 Shared Task: Prompt Learning for Lexical Simplification, 2022 [URL] [Pure]

2021

Alhuzali, H. and Ananiadou, S., Improving Textual Emotion Recognition Based on Intra- and Inter-Class Variation, in: IEEE Transactions on Affective Computing, pages 1–1, 2021 [DOI] [URL] [Pure]
Navarro, T., Parrish, R., Cotoi, C., Germini, F., Linkins, L., Iorio, A., Haynes, R. B., Ananiadou, S. and Lokker, C., A Deep Learning Approach to Refine the Identification of High-Quality Clinical Research Articles From the Biomedical Literature: Protocol for Algorithm Development and Validation, in: JMIR Research Protocols, 10:11(e29398), 2021 [DOI] [URL]
Zerva, C., Taylor, S., Soto, A., Nguyen, N. T. H. and Ananiadou, S., A term-based and citation network-based search system for COVID-19, in: JAMIA Open, 4:4(ooab104), 2021 [DOI] [URL]
Zhang, T., Schoene, A and Ananiadou, S., Automatic identification of suicide notes with a transformer-based deep learning model, in: Internet Interventions(100422), 2021 [DOI] [URL]
Christopoulou, F., Miwa, M. and Ananiadou, S., Distantly Supervised Relation Extraction with Sentence Reconstruction and Knowledge Base Priors, in: Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics - Human Language Technologies (NAACL-HLT), pages 11-26, 2021 [URL]
Cao, J., van Veen, E. M., Peek, N., Renehan, A. G and Ananiadou, S., EPICURE: Ensemble Pretrained Models for Extracting Cancer Mutations from Literature, in: Proceedings of IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS), pages 461-467, 2021 [DOI] [URL]
Cao, J. and Ananiadou, S., GenerativeRE: Incorporating a Novel Copy Mechanism and Pretrained Model for Joint Entity and Relation Extraction, in: Findings of EMNLP, pages 2119–2126, 2021 [DOI] [URL]
Inan, E., Thompson, P., Yates, T. and Ananiadou, S., HSEarch: semantic search system for workplace accident reports, in: Proceedings of the 43rd European Confererence on Information Retrieval (ECIR 2021), pages 514-519, 2021 [URL]
Vásquez-Rodríguez, L., Shardlow, M., Przybyla, P. and Ananiadou, S., Investigating Text Simplification Evaluation, in: Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021, 2021 [URL] [Pure]
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, in: npj systems biology and applications, 7(38), 2021 [DOI] [URL]
Tran, T. T., Le, P. and Ananiadou, S., One-shot to Weakly-Supervised Relation Classification using Language Models, in: Proceedings of the 3rd Conference on Automated Knowledge Base Construction, 2021 [URL]
Nghiem, M-. Q., Baylis, P. and Ananiadou, S., Paladin: an annotation tool based on active and proactive learning, in: Proceedings of the 16th conference of the European Chapter of the Association for Computational Linguistics (EACL 2021): System Demonstrations, pages 238–243, 2021 [URL]
Alhuzali, H., Zhang, T. and Ananiadou, S., Predicting Sign of Depression via Using Frozen Pre-trained Models and Random Forest Classifier, in: CLEF (Working Notes), 2021 [URL] [Pure]
Alhuzali, H. and Ananiadou, S., SpanEmo: Casting Multi-label Emotion Classification as Span-prediction, in: In Proceedings of the 16th conference of the European Chapter of the Association for Computational Linguistics (EACL-2021), 2021 [URL] [Pure]
Vásquez-Rodríguez, L., Shardlow, M., Przybyła, P. and Ananiadou, S., The Role of Text Simplification Operations in Evaluation, in: CEUR Workshop Proceedings, 2021 [URL] [Pure]

2020

Ananiadou, S., DeepEventMine: End-to-end Neural Nested Event Extraction from Biomedical Texts, in: Bioinformatics (Oxford, England), 2020 [DOI] [Pure]
Tran, T., Miwa, M. and Ananiadou, S., Syntactically-Informed Word Representations from Graph Neural Network, in: Neurocomputing, 2020 [DOI] [URL] [Pure]
Zerva, C., Nghiem, M., Nguyen, N. T. H. and Ananiadou, S., Cited text span identification for scientific summarisation using pre-trained encoders, in: Scientometrics, 2020 [DOI] [Pure]
Leroi, A. M., Lambert, B. C., Mauch, M., Papadopoulou, M., Ananiadou, S., Lindberg, S. I. I. and Lindenfors, P., On Revolutions, in: Palgrave Communications, pages 1–11, 2020 [DOI] [URL] [Pure]
Li, M., Takamura, H. and Ananiadou, S., A Neural Model for Aggregating Coreference Annotation in Crowdsourcing, in: Proceedings of the 28th International Conference on Computational Linguistics (COLING 2020), pages 5760-5773, 2020 [URL]
Christopoulou, F., Tran, T., Sahu, S., Miwa, M. and Ananiadou, S., Adverse Drug Events and Medication Relation Extraction in EHRs with Ensemble Deep Learning Methods, in: Journal of the American Medical Informatics Association, pages 39–46, 2020 [DOI] [Pure]
Ju, M., Nguyen, N., Miwa, M. and Ananiadou, S., An Ensemble of Neural Models for Nested Adverse Drug Events and Medication Extraction with Subwords, in: Journal of the American Medical Informatics Association, pages 22–30, 2020 [DOI] [Pure]
Tran, T. T., Le, P. and Ananiadou, S., Revisiting Unsupervised Relation Extraction, in: Proceedings of ACL 2020, pages 7498–7505, 2020 [URL]
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 [URL]
Lambert, B. C., Kontonatsios, G., Mauch, M., Kokkoris, T., Jockers, M., Ananiadou, S. and Leroi, A. M., The pace of modern culture, in: Nature Human Behaviour, 2020 [DOI] [URL]
Hamulyak, E. N., Brockmeier, A. J., Killas, J. D., Ananiadou, S., Middeldorp, S. and Leroi, A. M., Women’s health in The BMJ: a data science history, in: BMJ Open, 10(e039759), 2020 [DOI] [URL]

2019

Wang, Y., Fan, X., Chen, L., Chang, E. I., Ananiadou, S., Tsujii, J. and Xu, Y., Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries, in: BMC Bioinformatics, 2019 [DOI] [URL] [Pure]
Christopoulou, E., Miwa, M. and Ananiadou, S., Connecting the Dots: Document-level Neural Relation Extraction with Edge-oriented Graphs, in: Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP), pages 4925–4936, 2019 [DOI] [URL] [Pure]
Sahu, S., Christopoulou, E., Miwa, M. and Ananiadou, S., Inter-sentence Relation Extraction with Document-level Graph Convolutional Neural Network, in: Inter-sentence Relation Extraction with Document-level Graph Convolutional Neural Network, pages 4309–4316, 2019 [DOI] [URL] [Pure]
Li, M., Myrman, A. F., Mu, T. and Ananiadou, S., Modelling Instance-Level Annotator Reliability for Natural Language Labelling Tasks, in: Proceedings of NAACL-HLT 2019, pages 2873–2883, 2019 [URL] [Pure]
Przybyla, P., Brockmeier, A. and Ananiadou, S., Quantifying Risk Factors in Medical Reports with a Context-Aware Linear Model, in: Journal of the American Medical Informatics Association, pages 537–546, 2019 [DOI] [URL] [Pure]
Ju, M., Short, A., Thompson, P., Bakerly, N. D., Gkoutos, G., Tsaprouni, L. and Ananiadou, S., Annotating and Detecting Phenotypic Information for Chronic Obstructive Pulmonary Disease, in: Journal of the American Medical Informatics Association, 2019 [DOI] [URL] [Pure]
Iliopoulos, I., Ananiadou, S., Danchin, A., Ioannidis, J. P., Katsikis, P. D., Ouzounis, C. A. and Promponas, V. J., Hypothesis, analysis and synthesis, it's all Greek to me, in: eLife, 2019 [DOI] [URL] [Pure]
Bannach-Brown, A., Przybyła, P., Thomas, J., Rice, A. S. C., Ananiadou, S., Liao, J. and Macleod, M. R., Machine learning algorithms for systematic review: Reducing workload in a preclinical review of animal studies and reducing human screening error, in: Systematic Reviews, 2019 [DOI] [URL] [Pure]
Espinosa, K., Miwa, M. and Ananiadou, S., A Search-based Neural Model for Biomedical Nested and Overlapping Event Detection, in: Proceedings of EMNLP 2019, pages 3670-3677, 2019 [URL]
Nguyen, N. T. H., Gabud, R. and Ananiadou, S., COPIOUS: A gold standard corpus of named entities towards extracting species occurrence from biodiversity literature, in: Biodiversity Data Journal, 7(e29626), 2019 [DOI] [URL]
Trieu, H-L., Duong, K. N. A., Nguyen, N. T. H., Miwa, M., Takamura, H. and Ananiadou, S., Coreference Resolution in Full Text Articles with BERT and Syntax-based Mention Filtering, in: Proceedings of the 5th Workshop on BioNLP Open Shared Tasks, pages 196-205, 2019 [URL]
Alhuzali, H. and Ananiadou, S., Improving classification of Adverse Drug Reactions through Using Sentiment Analysis and Transfer Learning, pages 339, 2019 [URL] [Pure]
Brockmeier, A. J., Ju., M., Przybyɫa, P. and Ananiadou, S., Improving reference prioritisation with PICO recognition, in: BMC Medical Informatics and Decision Making, 19(256), 2019 [DOI] [URL]

2018

Tsujii, J., Ananiadou, S. and Wang, Y., Improve Chinese Clinical Named Entity Recognition Performance by Using the Graphical and Phonetic Feature, in: Proceedings of BIBM 2018 (IEEE), pages 1582–1586, 2018 [URL] [Pure]
Soto, A., Przybyla, P. and Ananiadou, S., Thalia: Semantic search engine for biomedical abstracts, in: Bioinformatics, 2018 [DOI] [URL] [Pure]
Przybyła, P., Brockmeier, A., Kontonatsios, G., Pogam, M. L., McNaught, J., von Elm, E., Nolan, K. and Ananiadou, S., Prioritising references for systematic reviews with RobotAnalyst: a user study, in: Research Synthesis Methods, pages 470–488, 2018 [DOI] [URL] [Pure]
Christopoulou, E., Miwa, M. and Ananiadou, S., A Walk-based Model on Entity Graphs for Relation Extraction., pages 81–88, 2018 [DOI] [URL] [Pure]
Thompson, P., Daikou, S., Ueno, K., Batista-Navarro, R. T., Tsujii, J. and Ananiadou, S., Annotation and Detection of Drug Effects in Text for Pharmacovigilance, in: Journal of Cheminformatics, 2018 [DOI] [URL] [Pure]
Yamada, T., Kamata, R., Ishinohachi, K., Shojima, N., Ananiadou, S., Nom, H., Yamauchi, T. and Kadowaki, T., Biosimilar vs originator insulins: Systematic review and meta-analysis, in: Diabetes, Obesity and Metabolism, pages 1787–1792, 2018 [DOI] [URL] [Pure]
Trieu, H., Nguyen, N., Miwa, M. and Ananiadou, S., Investigating Domain-Specific Information for Neural Coreference Resolution on Biomedical Texts, in: Proceedings of the BioNLP 2018 workshop, pages 183–188, 2018 [URL] [Pure]
Ju, M., Miwa, M. and Ananiadou, S., A Neural Layered Model for Nested Named Entity Recognition, in: Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers), pages 1446–1459, 2018 [DOI] [URL] [Pure]
Thompson, P. and Ananiadou, S., Extracting Gene-Disease Relations from Text to Support Biomarker Discovery, in: Digital Health 2017: Global Public Health, Personalised Medicine, and Emergency Medicine in the Age of Big Data, 2018 [DOI] [URL] [Pure]
Zerva, C. and Ananiadou, S., Paths for uncertainty: Exploring the intricacies of uncertainty identification for news, in: Proceedings of the NAACL Workshop on Computational Semantics Beyond Events and Roles (SemBEaR), pages 6–20, 2018 [URL] [Pure]
Shardlow, M., Nguyen, N., Owen, G., Turner, S., Leach, A., O'Donovan, C., McNaught, J. and Ananiadou, S., A New Corpus to Support Text Mining for the Curation of Metabolites in the ChEBI Database, in: Proceedings of the Eleventh International Conference on Language Resources and Evaluation, Miyazaki, Japan, 7/05/18, pages 280–285, 2018 [URL] [Pure]
Thompson, P. and Ananiadou, S., HYPHEN: A flexible, hybrid method to map phenotype concept mentions to terminological resources, in: Terminology, pages 91–121, 2018 [DOI] [URL] [Pure]
Soto, A., Zerva, C., Batista-Navarro, R. T. and Ananiadou, S., LitPathExplorer: A Confidence-based Visual Text Analytics Tool for Exploring Literature-Enriched Pathway Models, in: Bioinformatics, pages 1389–1397, 2018 [DOI] [Pure]
Shardlow, M., Ju., M., Li, M., O'Reilly, C., Iavarone, E., McNaught, J. and Ananiadou, S., A Text Mining Pipeline Using Active and Deep Learning for Curating Information in Computational Neuroscience, in: Neuroinformatics, 2018 [DOI] [URL]
Nghiem, M-. Q. and Ananiadou, S., APLenty: annotation tool for creating high-quality datasets using active and proactive learning, in: Proceedings of Empirical Methods in Natural Language Processing (System Demonstrations), 2018 [URL]
Sousselier, L., Roncaglioni, A., Raitano, G., Petoumenou, M., Benfenati, E., Ananiadou, S., Nguyen, N. T. H., Do, Q. T., Olivier, E., Wakx, A. and Rat, P., Are all flavonoids safe for use in Cosmetics?, in: Proceedings of the 30th IFSCC Congress, pages Poster S2-296, 2018
Shardlow, M., Batista-Navarro, R., Thompson, P., Nawaz, R., McNaught, J. and Ananiadou, S., Identification of Research Hypotheses and New Knowledge from Scientific Literature, in: BMC Medical Informatics and Decision Making, 18(46), 2018 [DOI] [URL]
Leroi, A. M., Lambert, B. C., Mauch, M., Papadopoulou, M., Ananiadou, S., Lindberg, S. I. I. and Lindenfors, P., On Revolutions, in: V-Dem Working Paper(63), 2018 [DOI] [URL]
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, in: Toxicology Letters, 295:Supplement 1(S159), 2018 [URL]
Brockmeier, A. J., Mu, T., Ananiadou, S. and Goulermas, J. Y, Self-Tuned Descriptive Document Clustering using a Predictive Network, in: Transactions on Knowledge and Data Engineering, 2018 [URL]

2017

Przybyła, P., Soto, A. and Ananiadou, S., Identifying Personalised Treatments and Clinical Trials for Precision Medicine using Semantic Search with Thalia, in: Proceedings of the Twenty-Fifth Text REtrieval Conference (TREC 2017), 2017 [URL] [Pure]
Raitano, G., Benfenati, E., Ananiadou, S., Fu, X., Do, Q. T., Rat, P. and Sousselier, L., Role of in silico tools and text mining in the safety assessment of selected plant coumarins, in: Toxicology Letters, pages S96, 2017 [DOI] [URL] [Pure]
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, in: Clinical Science, pages 2525–2532, 2017 [DOI] [URL] [Pure]
Kontonatsios, G., Brockmeier, A., Przybyla, P., McNaught, J., Mu, T., Goulermas, J. Y. and Ananiadou, S., A semi-supervised approach using label propagation to support citation screening, in: Journal of Biomedical Informatics, pages 67–76, 2017 [DOI] [URL] [Pure]
Li, M., Nguyen, N. and Ananiadou, S., Proactive Learning for Named Entity Recognition, in: Proceedings of BioNLP 2017, pages 117–125, 2017 [URL] [Pure]
Swainston, N., Batista-Navarro, R. T., Carbonell, P., Dobson, P., Dunstan, M., Jervis, A., Vinaixa, M., Williams, A., Ananiadou, S., Faulon, J., Mendes, P. P., Kell, D., Scrutton, N. and Breitling, R., biochem4j: integrated and extensible biochemical knowledge through graph databases, in: PLoS ONE, pages 1–14, 2017 [DOI] [URL] [Pure]
Brockmeier, A., Mu, T., Ananiadou, S. and Goulermas, J. Y., Quantifying the Informativeness of Similarity Measurements, in: Journal of Machine Learning Research, pages 16–296, 2017 [URL] [Pure]
Venkatesan, A., Kim, J., Talo, F., Ide-Smith, M., Gobeill, J., Carter, J., Batista-Navarro, R. T., Ananiadou, S., Ruch, P. and McEntyre, J., SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data, in: Wellcome Open Research, 2017 [DOI] [URL] [Pure]
Zerva, C., Batista-Navarro, R. T., Day, P. and Ananiadou, S., Using uncertainty to link and rank evidence from biomedical literature for model curation, in: Bioinformatics, 2017 [DOI] [URL] [Pure]
Mu, T., Goulermas, J. Y. and Ananiadou, S., Data Visualization with Structural Control of Global Cohort and Local Data Neighborhoods, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, pages 1323–1337, 2017 [DOI] [URL] [Pure]
Thompson, P., Nawaz, R., McNaught, J. and Ananiadou, S., Enriching News Events with Meta-knowledge Information, in: Language Resources and Evaluation, pages 409–438, 2017 [DOI] [URL] [Pure]
Nguyen, N., Soto, A., Kontonatsios, G., Batista-Navarro, R. T. and Ananiadou, S., Constructing a biodiversity terminological inventory, in: PLoS ONE, pages 1–23, 2017 [DOI] [URL] [Pure]
Ananiadou, S. and Thompson, P., Supporting Biological Pathway Curation Through Text Mining, in: Communications in Computer and Information Science, pages 59–73, 2017 [DOI] [URL] [Pure]
Batista-navarro, R., Zerva, C., Nguyen, N. T. H. and Ananiadou, S., A Text Mining-Based Framework for Constructing an RDF-Compliant Biodiversity Knowledge Repository, in: Communications in Computer and Information Science, pages 30–42, 2017 [DOI] [URL] [Pure]
Sato, M., Brockmeier, A., Kontonatsios, G., Mu, T., Goulermas, J., Tsujii, J. and Ananiadou, S., Distributed Document and Phrase Co-embeddings for Descriptive Clustering, in: Proceedings of EACL 2017, pages 991–1001, 2017 [URL] [Pure]
Thompson, P., Boylan, K., Freemont, A. and Ananiadou, S., Supporting biomarker discovery using text mining, in: Proceedings of Informatics for Health 2017, 2017 [URL]
Thompson, P., Ananiadou, S. and Tsujii, J., The GENIA Corpus: Annotation Levels and Applications, in: Handbook of Linguistic Annotation, Springer, pages 1395-1432, 2017 [DOI] [URL]

2016

Przybyla, P., Shardlow, M., Aubin, S., Bossy, R., de Castilho, R. E., Piperidis, S., McNaught, J. and Ananiadou, S., Text Mining Resources for the Life Sciences, in: Database, 2016 [DOI] [URL] [Pure]
Kim, S., Doğan, R. I., Chatr-Aryamontri, A., Chang, C. S., Oughtred, R., Rust, J., Batista-Navarro, R., Carter, J., Ananiadou, S., Matos, S., Santos, A., Campos, D., Oliveira, J. L., Singh, O., Jonnagaddala, J., Dai, H. J., Su, E. C. Y., Chang, Y. C., Su, Y. C., Chu, C. H., Chen, C. C., Hsu, W. L., Peng, Y., Arighi, C., Wu, C. H., Vijay-Shanker, K., Aydın, F., Hüsünbeyi, Z. M., Özgür, A., Shin, S. Y., Kwon, D., Dolinski, K., Tyers, M., Wilbur, W. J. and Comeau, D. C., BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID, in: Database: the journal of biological databases and curation, 2016 [DOI] [Pure]
Alnazzawi, N., Thompson, P. and Ananiadou, S., Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain- Specific Terminological Resource, in: PLoS One., 2016 [DOI] [URL] [Pure]
Wang, Q., Abdul, S. S., Almeida, L., Ananiadou, S., Balderas-Martínez, Y. I., Batista-Navarro, R., Campos, D., Chilton, L., Chou, H. J., Contreras, G., Cooper, L., Dai, H. J., Ferrell, B., Fluck, J., Gama-Castro, S., George, N., Gkoutos, G., Irin, A. K., Jensen, L. J., Jimenez, S., Jue, T. R., Keseler, I., Madan, S., Matos, S., McQuilton, P., Milacic, M., Mort, M., Natarajan, J., Pafilis, E., Pereira, E., Rao, S., Rinaldi, F., Rothfels, K., Salgado, D., Silva, R. M., Singh, O., Stefancsik, R., Su, C. H., Subramani, S., Tadepally, H. D., Tsaprouni, L., Vasilevsky, N., Wang, X., Chatr-Aryamontri, A., Laulederkind, S. J. F., Matis-Mitchell, S., McEntyre, J., Orchard, S., Pundir, S., Rodriguez-Esteban, R., Auken, K. V., Lu, Z., Schaeffer, M., Wu, C. H., Hirschman, L. and Arighi, C. N., Overview of the interactive task in BioCreative V, in: Database, 2016 [DOI] [Pure]
Batista-Navarro, R., Hammock, J., Ulate, W. and Ananiadou, S., A text mining framework for accelerating the semantic curation of literature, in: Research and Advanced Technology for Digital Libraries :, pages 459–462, 2016 [DOI] [URL] [Pure]
Korkontzelos, I., Nikfarjamb, A., Shardlow, M., Sarkerb, A., Ananiadou, S. and Gonzalez, G. H., Analysis of the effect of sentiment analysis on extracting adverse drug reactions from tweets and forum posts, in: Journal of Biomedical Informatics, pages 148–158, 2016 [DOI] [URL] [Pure]
Batista-Navarro, R. T., Soto, A., Ulate, W. and Ananiadou, S., Text Mining Workflows for Indexing Archives with Automatically Extracted Semantic Metadata, in: Research and Advanced Technology for Digital Libraries - 20th International Conference on Theory and Practice of Digital Libraries, TPDL 2016, , 8/09/16, pages 471–473, 2016 [DOI] [URL] [Pure]
Hashimoto, K., Kontonatsios, G., Miwa, M. and Ananiadou, S., Topic Detection Using Paragraph Vectors to Support Active Learning in Systematic Reviews, in: Journal of Biomedical Informatics, pages 59–65, 2016 [DOI] [URL] [Pure]
Black, W., Rowley, A., Miwa, M., McNaught, J. and Ananiadou, S., Text Mining for Semantic Search in Europe PubMed Central Labs, in: Working with Text, pages 111–131, 2016 [URL] [Pure]
Rehm, G., Uszkoreit, H., Garabik, R., Grobelnik, M., García-Mateo, C., van Genabith, J., Hajič, J., Hernáez, I., Judge, J., Koeva, S., Krek, S., Krstev, C., Ananiadou, S., Lindén, K., Magnini, B., Mariani, J., McNaught, J., Melero, M., Monachini, M., Moreno, A., Odijk, J., Ogrodniczuk, M., Pęzik, P., Bel, N., Piperidis, S., Przepiórkowski, A., Rögnvaldsson, E., Rosner, M., Pedersen, B. S., Skadiņa, I., Smedt, K. D., Tadíc, M., Thompson, P., Tufiș, D., Bielevičiené, A., Váradi, T., Vasiļjevs, A., Vider, K., Zabarskaitė, J., Borin, L., Branco, A., Budin, G., Calzolari, N. and Daelemans, W., The strategic impact of META-NET on the regional, national and international level, in: Language Resources and Evaluation, pages 351–374, 2016 [DOI] [URL] [Pure]
Batista-Navarro, R. T., Carter, J. and Ananiadou, S., Argo: Enabling the development of bespoke workflows and services for disease annotation, in: Database: The Journal of Biological Databases and Curation, 2016 [DOI] [URL] [Pure]
Thompson, P., McNaught, J. and Ananiadou, S., Customised OCR correction for historical medical text, in: 2015 Digital Heritage, pages 35–41, 2016 [DOI] [URL] [Pure]
Thompson, P., Carter, J., McNaught, J. and Ananiadou, S., Semantically enhanced search system for historical medical archives, in: 2015 Digital Heritage, pages 387–390, 2016 [DOI] [URL] [Pure]
Thompson, P., Batista-Navarro, R. T., Kontonatsios, G., Carter, J., Toon, E., McNaught, J., Timmermann, C., Worboys, M. and Ananiadou, S., Text mining the history of medicine, in: P L o S One, 2016 [DOI] [URL] [Pure]
Batista-Navarro, R., Zerva, C. and Ananiadou, S., Construction of a biodiversity knowledge repository using a text mining-based framework, in: Proceedings of the 3rd Annual International Symposium on Information Management and Big Data (SIMBig 2016), pages 22-25, 2016 [URL]
Korkontzelos, I., Thomas, B., Miwa, M. and Ananiadou, S., Ensemble Classification of Grants using LDA-based features, in: Proceedings of LREC 2016(1288-1294), 2016 [URL]
Shardlow, M., Przybyla, P., Batista-Navarro, R. T., Carter, J., McNaught, J. and Ananiadou, S., Facilitating and promoting web annotation with Argo, in: Proceedings of I Annotate 2016, 2016 [Pure]
Korkontzelos, I., Thompson, P. and Ananiadou, S., Identifying content types of messages related to Open Source Software projects, in: Proceedings of LREC 2016, pages 1837-1844, 2016 [URL]
Espinosa, K. J., Batista-Navarro, R. T. and Ananiadou, S., Learning to recognise named entities in tweets by exploiting weakly labelled data, 2016 [URL] [Pure]
Przybyla, P., Nguyen, N., Shardlow, M., Kontonatsios, G. and Ananiadou, S., NaCTeM at SemEval-2016 Task 1: Inferring sentence-level semantic similarity from an ensemble of complementary lexical and sentence-level features, in: Proceedings of the 10th International Workshop on Semantic Evaluation, 2016 [URL] [Pure]
Haynes, C., Kay, N., Harrison, K., McLeod, C., Shaw, B., Leng, G., Kontonatsios, G. and Ananiadou, S., Using text mining to facilitate study identification in public health systematic reviews, in: Guidelines International Network (G-I-N) conference, 2016

2015

Mo, Y., Kontonatsios, G. and Ananiadou, S., Supporting Systematic Reviews Using LDA-based Document Representations, in: Systematic Reviews, 2015 [DOI] [URL] [Pure]
Korkontzelos, I., Piliouras, D., Dowsey, A. and Ananiadou, S., Boosting Drug Named Entity Recognition Using an Aggregate Classifier, in: Artificial Intelligence in Medicine, pages 145–153, 2015 [DOI] [URL] [Pure]
Miwa, M. and Ananiadou, S., Adaptable, High Recall, Event Extraction System with Minimal Configuration, in: B M C Bioinformatics, 2015 [DOI] [URL] [Pure]
Ananiadou, S., Event Extraction in pieces: tackling the partial event identification problem on unseen corpora, in: Biomedical Natural Language Processing, pages 31–41, 2015 [URL] [Pure]
Bollegala, D., Kontonatsios, G. and Ananiadou, S., A Cross-lingual Similarity Measure for Detecting Biomedical Term Translations, in: P L o S One, 2015 [DOI] [URL] [Pure]
Pyysalo, S., Ohta, T., Rak, R., Rowley, A., Chun, H. W., Jung, S. J., Choi, S. P., Tsujii, J. and Ananiadou, S., Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013, in: BMC Bioinformatics, 2015 [DOI] [URL] [Pure]
Alnazzawi, N., Thompson, P., Batista-Navarro, R. T. and Ananiadou, S., Using text mining techniques to extract phenotypic information from the PhenoCHF corpus, in: B M C Medical Informatics and Decision Making, 2015 [DOI] [URL] [Pure]
Ananiadou, S., Thompson, P., Nawaz, R., McNaught, J. and Kell, D., Event-based text mining for biology and functional genomics, in: Briefings in functional genomics, pages 213–30, 2015 [DOI] [URL] [Pure]
Batista-Navarro, R., Rak, R. and Ananiadou, S., Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics, in: Journal of Cheminformatics, 2015 [DOI] [URL] [Pure]
O'Mara-Eves, A., Thomas, J., McNaught, J., Miwa, M. and Ananiadou, S., Using text mining for study identification in systematic reviews: a systematic review of current approaches, in: Systematic Reviews, 2015 [DOI] [URL] [Pure]
Batista-Navarro, R. T. and Ananiadou, S., Adapting ChER for the recognition of chemical mentions in patents, in: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, pages 149–153, 2015 [URL] [Pure]
Batista-Navarro, R. T. and Ananiadou, S., Augmenting the Medical Subject Headings vocabulary with semantically rich variants to improve disease mention normalisation, in: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, pages 311–316, 2015 [URL] [Pure]
Xu, Y., Chen, L., Wei, J., Ananiadou, S., Fan, Y., Qian, Y., Chang, E. I. and Tsujii, J., Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary, in: B M C Bioinformatics, 2015 [DOI] [URL] [Pure]
Batista-Navarro, R. T., Nawaz, R., Zerva, C. and Ananiadou, S., Bridging text-mined biomolecular events to pathway models using approximate subgraph matching techniques, in: Proceedings of the 16th International Conference on Systems Biology, Singapore, 2015 [Pure]
Batista-Navarro, R. T., Carter, J. and Ananiadou, S., Development of bespoke machine learning and biocuration workflows in a BioC-supporting text mining workbench., in: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, pages 51–56, 2015 [URL] [Pure]
Rosner, M., Attard, A., Thompson, P., Gatt, A. and Ananiadou, S., Extending a Tool Resource Framework with U-Compare, in: Human Language Technology Challenges for Computer Science and Linguistics, pages 315–326, 2015 [Pure]
Mihaila, C., Batista-Navarro, R. T., Alnazzawi, N., Kontonatsios, G., Korkontzelos, I., Rak, R., Thompson, P. and Ananiadou, S., Mining the biomedical literature, in: Healthcare Data Analytics, pages 251–308, 2015 [URL] [Pure]
Almeida, B., Ananiadou, S., Bagnato, A., Barbero, A. B., Di Rocco, J., Di Ruscio, D., Kolovos, D. S., Korkontzelos, I., Hansen, S., Malo, P., Matragkas, N., Paige, R. F. and Vinju, J., OSSMETER: Automated Measurement and Analysis of Open Source Software, in: Proceedings of the Projects Showcase at the Software Technologies: Applications and Foundations 2015 (STAF 2015), 2015 [URL]
Batista-Navarro, R. T., 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, pages 406–408, 2015 [URL] [Pure]
Fu, X., Batista-Navarro, R. T., Rak, R. and Ananiadou, S., Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows, in: Journal of Biomedical Semantics, 2015 [DOI] [Pure]
Batista-Navarro, R. T., Ulate, W., Hammock, J., Kontonatsios, G., Rose-Sandler, T. and Ananiadou, S., Unlocking knowledge in biodiversity legacy literature through automatic semantic metadata extraction., in: Proceedings of the TDWG 2015 Annual Conference, 2015 [Pure]

2014

Mu, T., Goulermas, J. Y., Korkontzelos, I. and Ananiadou, S., Descriptive Document Clustering via Discriminant Learning in a Co-Embedded Space of Multilevel Similarities, in: Journal of the Association for Information Science and Technology, pages 106–133, 2014 [DOI] [URL] [Pure]
Mihaila, C., Mihăilă, C. and Ananiadou, S., Semi-supervised learning of causal relations in biomedical scientific discourse, in: BioMedical Engineering OnLine, 2014 [DOI] [URL] [Pure]
Gou, Y., Graff, F., Rossiter, P., Talo, F., Vartak, V., Coleman, L., Hawkins, C., Kinsey, A., Mansoor, S., Morris, V., Rowbotham, R., Chapman, D., Kilian, O., MacIntyre, R., Patel, Y., Ananiadou, S., Black, W., McNaught, J., Rak, R., Rowley, A., Kafkas, S., Katuri, J., Kim, J., Marinos, N., McEntyre, J., Morrison, A. and Pi, X., Europe PMC: a full-text literature database for the life sciences and platform for innovation, in: Nucleic acids research, pages 1–7, 2014 [DOI] [Pure]
Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S., Combining String and Context Similarity for Bilingual Term Alignment from Comparable Corpora, in: Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 1701–1712, 2014 [URL] [Pure]
Rak, R., Batista-Navarro, R. T., Rowley, A., Carter, J. and Ananiadou, S., Text Mining-assisted Biocuration Workflows in Argo, in: Database, pages 1–14, 2014 [DOI] [URL] [Pure]
Fu, X. and Ananiadou, S., Improving the Extraction of Clinical Concepts from Clinical Records, in: Proceedings of the 4th Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing, 2014 [Pure]
Rak, R., Rowley, A., Carter, J., Batista-Navarro, R. T. and Ananiadou, S., Interoperability and Customisation of Annotation Schemata in Argo, in: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14), pages 3837–3842, 2014 [URL] [Pure]
Korkontzelos, I. and Ananiadou, S., Locating Requests among Open Source Software Communication Messages, in: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14), pages 1347–1354, 2014 [URL] [Pure]
Mihaila, C. and Ananiadou, S., The Meta-knowledge of Causality in Biomedical Scientific Discourse, in: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14), pages 1984–1991, 2014 [URL] [Pure]
Rehm, G., Uszkoreit, H., Ananiadou, S., Bel, N., Bielevičiené, A., Borin, L., Branco, A., Budin, G., Calzolari, N., Daelemans, W., Garabik, R., Grobelnik, M., García-Mateo, C., van Genabith, J., Hajič, J., Hernáez, I., Judge, J., Koeva, S., Krek, S., Krstev, C., Lindén, K., Magnini, B., Mariani, J., McNaught, J., Melero, M., Monachini, M., Moreno, A., Odijk, J., Ogrodniczuk, M., Pęzik, P., Piperidis, S., Przepiórkowski, A., Rögnvaldsson, E., Rosner, M., Pedersen, B. S., Skadiņa, I., Smedt, K. D., Tadíc, M., Thompson, P., Tufiș, D., Váradi, T., Vasiļjevs, A., Vider, K. and Zabarskaitė, J., The Strategic Impact of META-NET on the Regional, National and International Level, in: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14), pages 1517–1524, 2014 [URL] [Pure]
Alnazzawi, N., Thompson, P. and Ananiadou, S., Building a semantically annotated corpus for congestive heart and renal failure from clinical records and the literature, in: Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi), pages 69–74, 2014 [URL] [Pure]
Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S., Using a Random Forest Classifier to Compile Bilingual Dictionaries of Technical Terms from Comparable Corpora, in: Proceedings of the 14th Conference of the European Chapter of the Association for Computational Linguistics, volume 2: Short Papers, pages 111–116, 2014 [URL] [Pure]
Pyysalo, S. and Ananiadou, S., Anatomical Entity Mention Recognition at Literature Scale, in: Bioinformatics, pages 868–875, 2014 [DOI] [URL] [Pure]
Kontonatsios, G., Mihăilă, C., Korkontzelos, I., Thompson, P. and Ananiadou, S., A hybrid approach to compiling bilingual dictionaries of medical terms from parallel corpora, in: Statistical Language and Speech Processing, Second International Conference, SLSP 2014, pages 57–69, 2014 [DOI] [Pure]
Fu, X., Batista-Navarro, R. T., Rak, R. and Ananiadou, S., A Strategy for Annotating Clinical Records with Phenotypic Information relating to the Chronic Obstructive Pulmonary Disease, in: Proceedings of the Phenotype day at ISMB 2014, pages 1–8, 2014 [Pure]
Xu, Y., Hua, J., Ni, Z., Chen, Q., Fan, Y., Ananiadou, S., Chang, E. I. and Tsujii, J., Anatomical entity recognition with a hierarchical framework augmented by external resource, in: P L o S One, 2014 [DOI] [URL] [Pure]
Miwa, M., Thompson, P., Korkontzelos, I. and Ananiadou, S., Comparable Study of Event Extraction in Newswire and Biomedical Domains, in: Proceedings of Coling 2014, pages 2270–2279, 2014 [URL] [Pure]
Mu, T., Miwa, M., Tsujii, J. and Ananiadou, S., Discovering robust embeddings in (Dis)similarity space for high-dimensional linguistic features, in: Computational Intelligence, pages 285–315, 2014 [DOI] [URL] [Pure]
Batista-Navarro, R. T., Islam, A., Ulate, W., Hammock, J., Soto, A., Ananiadou, S. and Milios, E., Enriching the legacy literature with OCR corrections and text-mined semantic metadata., in: Proceedings of the TDWG 2014 Annual Conference, 2014 [URL] [Pure]
Stenetorp, P., Pyysalo, S., Ananiadou, S. and Tsujii, J., Generalising semantic category disambiguation with large lexical resources for fun and profit, in: Journal of Biomedical Semantics, 2014 [DOI] [URL] [Pure]
Rak, R., Batista-Navarro, R. T., Carter, J., Rowley, A. and Ananiadou, S., Processing Biological Literature with Customizable Web Services Supporting Interoperable Formats, in: Database, 2014 [DOI] [URL] [Pure]
Miwa, M., Thomas, J., O'Mara-Eves, A. and Ananiadou, S., Reducing systematic review workload through certainty-based screening, in: Journal of Biomedical Informatics, pages 242–253, 2014 [DOI] [URL] [Pure]
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 [URL]
Korkontzelos, I. and Ananiadou, S., Term Extraction, in: The Oxford handbook of computational linguistics, 2014 [DOI] [URL] [Pure]

2013

Mihǎilǎ, C. and Ananiadou, S., A hybrid approach to recognising discourse causality in the biomedical domain, in: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2013, pages 361–366, 2013 [DOI] [Pure]
Mihăilă, C., Ananiadou, S. and Mihǎilǎ, C., Recognising Discourse Causality Triggers in the Biomedical Domain, in: Journal of Bioinformatics and Computational Biology, 2013 [DOI] [Pure]
Batista-Navarro, R. T., Rak, R. and Ananiadou, S., Chemistry-specific Features and Heuristics for Developing a CRF-based Chemical Named Entity Recogniser, in: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, pages 55–59, 2013 [URL] [Pure]
Rak, R., Batista-Navarro, R. T., Rowley, A., Carter, J. and Ananiadou, S., Customisable Curation Workflows in Argo, in: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, pages 270–278, 2013 [Pure]
Batista-Navarro, R. T., Rak, R. and Ananiadou, S., NaCTeM CTD Web Services, in: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, pages 85–89, 2013 [Pure]
Rak, R., Batista-Navarro, R. T., Rowley, A., Miwa, M., Carter, J. and Ananiadou, S., NaCTeM’s BioC Modules and Resources for BioCreative IV, in: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, pages 61–67, 2013 [Pure]
Thomas, J., O'Mara-Eves, A., McNaught, J. and Ananiadou, S., The potential of text mining to reduce screening workload in systematic reviews: a retrospective evaluation, in: 21st Cochrane Colloquium, Quebec, 19/09/13, pages 5–5, 2013 [Pure]
Rak, R., Rowley, A., Carter, J. and Ananiadou, S., Development and Analysis of NLP Pipelines in Argo, in: Proceedings of the 51st Annual Meeting of the Association for Computational Linguistics: System Demonstrations, pages 115–120, 2013 [URL] [PDF] [Pure]
Mihaila, C., Kontonatsios, G., Thompson, P., Batista-Navarro, R. T., Mihaila, C., Korkontzelos, I. and Ananiadou, S., Extending an interoperable platform to facilitate the creation of multilingual and multimodal NLP applications, in: Proceedings of the System Demonstration Session at The 51st Annual Meeting of the Association for Computational Linguistics, pages 43–48, 2013 [URL] [PDF] [Pure]
Rak, R. and Ananiadou, S., Making UIMA Truly Interoperable with SPARQL, in: Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse, pages 88–97, 2013 [URL] [PDF] [Pure]
Miwa, M. and Ananiadou, S., NaCTeM EventMine for BioNLP 2013 CG and PC tasks, in: Proceedings of BioNLP Shared Task 2013 Workshop, pages 94–98, 2013 [URL] [Pure]
Pyysalo, S., Ohta, T. and Ananiadou, S., Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, pages 58–66, 2013 [URL] [Pure]
Ohta, T., Pyysalo, S., Rak, R., Rowley, A., Chun, H., Jung, S. -., Choi, S. -. and Ananiadou, S., Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013, in: Proceedings of the BioNLP Shared Task 2013 Workshop, pages 67–75, 2013 [URL] [Pure]
Mihaila, C., Kontonatsios, G., Batista-Navarro, R. T., 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, pages 79–88, 2013 [URL] [PDF] [Pure]
Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S., Using Random Forest to recognise translation equivalents of biomedical terms across languages, in: Proceedings of the Sixth Workshop on Building and Using Comparable Corpora, pages 95–104, 2013 [URL] [PDF] [Pure]
Mihăilă, C. and Ananiadou, S., What causes a causal relation? Detecting causal triggers in biomedical scientific discourse, in: 51st Annual Meeting of the Association for Computational Linguistics Proceedings of the Student Research Workshop, pages 38–45, 2013 [URL] [PDF] [Pure]
Miwa, M., Ohta, T., Rak, R., Rowley, A., Kell, D. B., Pyysalo, S. and Ananiadou, S., A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text., in: Bioinformatics (Oxford, England), pages i44–i52, 2013 [DOI] [URL] [Pure]
Miwa, M., Pyysalo, S., Ohta, T. and Ananiadou, S., Wide coverage biomedical event extraction using multiple partially overlapping corpora, in: BMC Bioinformatics, 2013 [DOI] [URL] [Pure]
Mihǎilǎ, C., Ohta, T., Pyysalo, S. and Ananiadou, S., BioCause: Annotating and analysing causality in the biomedical domain, in: BMC Bioinformatics, 2013 [DOI] [URL] [Pure]
Nawaz, R., Thompson, P. and Ananiadou, S., Negated BioEvents: Analysis and Identification, in: BMC Bioinformatics, 2013 [DOI] [URL] [Pure]
Restificar, A., Korkontzelos, I. and Ananiadou, S., A method for discovering and inferring appropriate eligibility criteria in clinical trial protocols without labeled data, in: BMC Medical Informatics and Decision Making, 2013 [DOI] [URL] [Pure]
Piliouras, D., Korkontzelos, I., Dowsey, A. and Ananiadou, S., Dealing with data sparsity in Drug Named Entity Recognition, in: Proceedings of IEEE International Conference on Healthcare Informatics, Philadelhia, PA, pages 14-21, 2013 [DOI]
Kontonatsios, G., Korkontzelos, I., Kolluru, B., Thompson, P. and Ananiadou, S., Deploying and Sharing U-Compare Workflows as Web Services, in: Journal of Biomedical Semantics, 4(7), 2013 [DOI] [URL]
Pyysalo, S., Ginter, F., Moen, H., Salakoski, T. and Ananiadou, S., Distributional Semantics Resources for Biomedical Text Processing, in: Proceedings of LBM 2013, pages 39–44, 2013 [URL] [Pure]
Ananiadou, S., Thompson, P. and Nawaz, R., Enhancing Search: Events and their Discourse Context, in: Computational Linguistics and Intelligent Text Processing, pages 318–334, 2013 [DOI] [URL] [Pure]
Batista-Navarro, R. T., Kontonatsios, G., Mihǎilǎ, C., Thompson, P., Rak, R., Nawaz, R., Korkontzelos, I. and Ananiadou, S., Facilitating the analysis of discourse phenomena in an interoperable NLP platform, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 559–571, 2013 [DOI] [URL] [Pure]
Landeghem, S. V., Björne, J., Wei, C. H., Hakala, K., Pyysalo, S., Ananiadou, S., Kao, H. -., Lu, Z., Salakoski, T., de Peer, Y. V. and Ginter, F., Large-scale event extraction from literature with multi-level gene normalization, in: PLoS ONE, 2013 [DOI] [URL] [Pure]
Ananiadou, S., Thompson, P. and Nawaz, R., Mining events from the literature for bioinformatics applications, in: ACM SIGWEB Newsletter, 2013 [URL] [Pure]
Thompson, P., Nawaz, R., Korkontzelos, I., Black, W., McNaught, J. and Ananiadou, S., News search using discourse analytics, in: Proceedings of the DigitalHeritage 2013 - Federating the 19th Int'l VSMM, 10th Eurographics GCH, and 2nd UNESCO Memory of the World Conferences, Plus Special Sessions fromCAA, Arqueologica 2.0 et al., pages 597–604, 2013 [DOI] [URL] [PDF] [Pure]
Nawaz, R., Thompson, P. and Ananiadou, S., Something old, something new: identifying knowledge source in bio-events, in: International Journal of Computational Linguistics and Applications, 4:1(129-144), 2013 [URL]
Batista-Navarro, R. T., Kontonatsios, G., Mihaila, C., Thompson, P., Nawaz, R., Korkontzelos, I. and Ananiadou, S., Supporting Discourse Phenomena in an Interoperable NLP Framework, in: host publication, 2013 [Pure]
Rutter, M., Ananiadou, S., Ohta, T. and Rutter, M. K., Text Mining Supporting Search for Knowledge Discovery in Diabetes, in: Current Cardiovascular Risk Reports, pages 1–8, 2013 [DOI] [URL] [Pure]
Nawaz, R., Thompson, P. and Ananiadou, S., Towards Event-based Discourse Analysis of Biomedical Text, in: International Journal of Computational Linguistics and Applications, pages 101–120, 2013 [URL] [Pure]

2012

Pyysalo, S., Ohta, T., Miwa, M., Cho, H. C., Tsujii, J. and Ananiadou, S., Event extraction across multiple levels of biological organization, in: Bioinformatics, pages 575–581, 2012 [DOI] [URL] [Pure]
Liakata, M., Thompson, P., de Waard, A., Nawaz, R., Maat, H. P. and Ananiadou, S., A Three-Way Perspective on Scientific Discourse Annotation for Knowledge Extraction, in: Proceedings of the ACL Workshop on Detecting Structure in Scholarly Discourse (DSSD), pages 37–46, 2012 [Pure]
Miwa, M., Thompson, P. and Ananiadou, S., Boosting automatic event extraction from the literature using domain adaptation and coreference resolution, in: Bioinformatics, pages 1759–1765, 2012 [DOI] [URL] [Pure]
Black, W. J., Procter, R., Gray, S. and Ananiadou, S., A data and analysis resource for an experiment in text mining a collection of micro-blogs on a political topic, in: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pages 2083–2088, 2012 [URL] [Pure]
Mihaila, C., Batista-Navarro, R. T. and Ananiadou, S., Analysing Entity Type Variation across Biomedical Subdomains, in: Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012), pages 1–7, 2012 [URL] [Pure]
Rak, R., Rowley, A. and Ananiadou, S., Collaborative Development and Evaluation of Text-processing Workflows in a UIMA-supported Web-based Workbench, in: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pages 2971–2976, 2012 [URL] [Pure]
Nawaz, R., Thompson, P. and Ananiadou, S., Meta-Knowledge Annotation at the Event Level: Comparison between Abstracts and Full Papers, in: Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012), pages 24–31, 2012 [URL] [Pure]
Stenetorp, P., Pyysalo, S., Topić, G., Ohta, T., Ananiadou, S. and Tsujii, J., brat: a Web-based Tool for NLP-Assisted Text Annotation, in: Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics, pages 102–107, 2012 [URL] [Pure]
Batista-Navarro, R. T. and Ananiadou, S., What's in a Name? Entity Type Variation across Two Biomedical Subdomains, in: Proceedings of the Student Research Workshop at the 13th Conference of the European Chapter of the Association for Computational Linguistics, pages 38–45, 2012 [URL] [Pure]
Liakata, M., Thompson, P., de Waard, A., Nawaz, R., Pander Maat, H. and Ananiadou, S., A three-way perspective on scientiï¬c discourse annotation for knowledge extraction, in: Proceedings of the ACL Workshop on Detecting Structure in Scholarly Discourse (DSSD), pages 37-46, 2012 [URL]
Rak, R., Rowley, A., Black, W. and Ananiadou, S., Argo: An integrative, interactive, text mining-based workbench supporting curation, in: Database, 2012 [DOI] [URL] [Pure]
Korkontzelos, I., Mu, T. and Ananiadou, S., ASCOT: A text mining-based web-service for efficient search and assisted creation of clinical trials, in: BMC Medical Informatics and Decision Making, 2012 [DOI] [URL] [Pure]
Korkontzelos, I. and Ananiadou, S., ASCOT: Assisting search and creation of clinical trials, in: IHI'12 - Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, pages 855–858, 2012 [DOI] [Pure]
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 [URL] [Pure]
Stenetorp, P., Pyysalo, S., Ohta, T., Ananiadou, S. and Tsujii, J., Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far, in: Proceedings of ExProM 2012, pages 47–56, 2012 [URL] [Pure]
Rak, R., Kolluru, B. and Ananiadou, S., Building trainable taggers in a web-based, UIMA-supported NLP workbench, in: Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics (ACL 2012), pages 121–126, 2012 [URL] [Pure]
Kontonasios, G., Korkontzelos, I., Ananiadou, S. and Kontonatsios, G., Developing multilingual text mining workflows in UIMA and U-compare, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 82–93, 2012 [DOI] [URL] [Pure]
Miwa, M., Thompson, P., McNaught, J., Kell, D. and Ananiadou, S., Extracting semantically enriched events from biomedical literature., in: BMC Bioinformatics, 2012 [DOI] [URL] [Pure]
Nawaz, R., Thompson, P. and Ananiadou, S., Identification of Manner in Bio-Events, in: Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012), pages 3505–3510, 2012 [URL] [Pure]
Pyysalo, S., Stenetorp, P., Ohta, T., Kim, J. and Ananiadou, S., New Resources and Perspectives for Biomedical Event Extraction, in: Proceedings of BioNLP 2012, pages 100–108, 2012 [URL] [Pure]
Ohta, T., Pyysalo, S., Tsujii, J. and Ananiadou, S., Open-domain Anatomical Entity Mention Detection, in: Proceedings of the ACL Workshop on Detecting Stucture in Scholarly Discourse (DSSD), pages 27–36, 2012 [URL] [Pure]
Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J. and Ananiadou, S., Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011., in: BMC Bioinformatics, pages S2, 2012 [DOI] [URL] [Pure]
Mu, T., Goulermas, J. Y., Tsujii, J. and Ananiadou, S., Proximity-based frameworks for generating embeddings from multi-output data, in: IEEE Transactions on Pattern Analysis and Machine Intelligence, pages 2216–2232, 2012 [DOI] [URL] [Pure]
Björne, J., Landeghem, S. V., Pyysalo, S., Ohta, T., Ginter, F., de Peer, Y. V., Ananiadou, S. and Salakoski, T., PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations, in: Proceedings of BioNLP 2012, pages 82–90, 2012 [URL] [Pure]
Kim, J., Pyysalo, S., Nédellec, C., Ananiadou, S. and Tsujii, J., Selected articles from the BioNLP Shared Task 2011, in: host publication, 2012 [URL] [Pure]
Ananiadou, S., McNaught, J. and Thompson, P., The English Language in the Digital Age, in: White Paper Series, 2012 [URL] [Pure]

2011

Batista-Navarro, R. T. and Ananiadou, S., Adapting the Cluster Ranking Supervised Model to Resolve Coreferences in the Drug Literature, in: Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011), pages 71–77, 2011 [Pure]
Kontonasios, G., Korkontzelos, I., Kolluru, B. K. and Ananiadou, S., Adding text mining workflows as web services to the BioCatalogue, in: SWAT4LS 2011, pages 50–57, 2011 [DOI] [URL] [Pure]
Kano, Y., Björne, J., Ginter, F., Salakoski, T., Buyko, E., Hahn, U., Cohen, K. B., Verspoor, K., Roeder, C., Hunter, L. E., Kilicoglu, H., Bergler, S., Landeghem, S. V., Parys, T. V., de Peer, Y. V., Miwa, M., Ananiadou, S., Neves, M., Pascual-Montano, A., Özgür, A., Radev, D. R., Riedel, S., Sætre, 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, in: BMC Bioinformatics, 2011 [DOI] [URL] [Pure]
Sasaki, Y., Wang, X. and Ananiadou, S., Extracting secondary bio-event arguments with extraction constraints, in: Computational Intelligence, pages 702–721, 2011 [DOI] [URL] [Pure]
Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C. J., Batista-Navarro, R. T. B., Nawaz, R. and Ananiadou, S., Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature, in: BMC Bioinformatics, 2011 [DOI] [URL] [Pure]
Thompson, P., Nawaz, R., McNaught, J. and Ananiadou, S., Enriching a biomedical event corpus with meta-knowledge annotation, in: BMC Bioinformatics, 2011 [DOI] [URL] [Pure]
Thompson, P., McNaught, J., Montemagni, S., Calzolari, N., del Gratta, R., Lee, V., Marchi, S., Monachini, M., Pezik, P., Quochi, V., Rupp, C., Sasaki, Y., Venturi, G., Rebholz-Schuhmann, D. and Ananiadou, S., The BioLexicon: A large-scale terminological resource for biomedical text mining, in: BMC Bioinformatics, 2011 [DOI] [URL] [Pure]
Wang, X., McKendrick, I., Barrett, I., Dix, I., French, T., Tsujii, J. and Ananiadou, S., Automatic Extraction of Angiogenesis Bio-Process from Text, in: Bioinformatics, 2011 [DOI] [URL] [Pure]
Tsuruoka, Y., Miwa, M., Hamamoto, K., Tsujii, J. and Ananiadou, S., Discovering and visualizing indirect associations between biomedical concepts, in: Bioinformatics, pages 111–119, 2011 [DOI] [URL] [Pure]
Kano, Y., Miwa, M., Cohen, K. B., Hunter, L. E., Ananiadou, S. and Tsujii, J., U-Compare: A modular NLP workflow construction and evaluation system, in: IBM Journal of Research and Development, 2011 [DOI] [URL] [Pure]
Kocbek, S., Sætre, R., Stiglic, G., Kim, J. D., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., AGRA: Analysis of gene ranking algorithms, in: Bioinformatics, pages 1185–1186, 2011 [DOI] [URL] [Pure]
Thomas, J., McNaught, J. and Ananiadou, S., Applications of text mining within systematic reviews, in: Research Synthesis Methods, pages 1–14, 2011 [DOI] [URL] [Pure]
Ananiadou, S. and Batista-Navarro, R. T., Discovering Potential Drugs by Extracting Biological Activities of Natural Products, in: Workshop on Mining the Pharmacogenomics Literature, Pacific Symopsium on Biocomputing 2011, 2011 [URL] [Pure]
McEntyre, J. R., Ananiadou, S., Andrews, S., Black, W. J., Boulderstone, R., Buttery, P., Chaplin, D., Chevuru, S., Cobley, N., Coleman, L. A., 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, in: Nucleic acids research., pages D58–D65, 2011 [DOI] [Pure]
Stenetorp, P., Pyysalo, S., Ananiadou, S. and Tsujii, J., Almost Total Recall: Semantic Category Disambiguation Using Large Lexical Resources and Approximate String Matching, in: Proceedings of the Fourth International Symposium on Languages in Biology and Medicine (LBM 2011), 2011 [Pure]
Soldatova, L. N., Kolluru, B., King, R. D., Qi, D. and Ananiadou, S., An ontology-based disambiguation of terms, in: Proceedings of the Workshop on Mining the Pharmacogenomics Literature, Pacific Symopsium on Biocomputing, 2011 [URL] [Pure]
Kocbek, S., Saetre, R., Stiglic, G., Kim, J., Pernek, I., Tsuruoka, Y., Kokol, P., Ananiadou, S. and Tsujii, J., Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from Pubmed publications, in: Proceedings of the 1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2011 [URL] [Pure]
Pyysalo, S., Ohta, T. and Ananiadou, S., Anatomical Entity Recognition with Open Biomedical Ontologies, in: host publication, 2011 [URL] [Pure]
Kolluru, B., Nakjang, S., Hirt, R. P., Wipat, A. and Ananiadou, S., Automatic extraction of microorganisms and their habitats from free text using text mining workflows., in: Journal of integrative bioinformatics, pages 184, 2011 [URL] [Pure]
Kolluru, B., Nakjang, S., Rupp, C. J., Hirt, R. P, Wipat, A. and Ananiadou, S., Automatic extraction of microorganisms and their habitats from free text using text-mining workflows, in: Proceedings of the International Symposium on Integrative Bioinformatics, 2011, 2011
Zervanou, K., Korkontzelos, I., van den Bosch, A. and Ananiadou, S., Enrichment and Structuring of Archival Description Metadata, in: Proceedings of the 5th ACL Workshop on Language Technology for Cultural Heritage, Social Sciences, and Humanities, pages 44-53, 2011 [URL]
Rosner, M., Attard, A., Thompson, P., Gatt, A. and Ananiadou, S., Extending a Tool Resource Framework with U-Compare, in: Proceedings of the 5th Language & Technology Conference (LTC'2011), 2011
Rosner, M., Attard, A., Thompson, P., Gatt, A. and Ananiadou, S., Extending a Tool Resource Framework with U-Compare, in: Proceedings of the 5th Language & Technology Conference (LTC'2011), 2011 [URL] [Pure]
Nobata, C., Dobson, P. D., Iqbal, S. A., Mendes, P., Tsujii, J., Kell, D. B. and Ananiadou, S., Mining metabolites: Extracting the yeast metabolome from the literature, in: Metabolomics, pages 94–101, 2011 [DOI] [URL] [Pure]
Ananiadou, S., Sullivan, D., Black, W., Levow, G. A., Gillespie, J. J., Mao, C., Pyysalo, S., Kolluru, B., Tsujii, J. and Sobral, B., Named entity recognition for bacterial type IV secretion systems, in: PLoS ONE, 2011 [DOI] [URL] [Pure]
Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., Sobral, B., Tsujii, J. and Ananiadou, S., Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011, in: host publication, 2011 [URL] [Pure]
Ohta, T., Pyysalo, S., Ananiadou, S. and Tsujii, J., Pathway Curation Support as an Information Extraction Task, in: host publication, 2011 [URL] [Pure]
Thompson, P., Kano, Y., McNaught, J., Pettifer, S., Attwood, T., Keane, J. and Ananiadou, S., Promoting Interoperability of Resources in META-SHARE, in: IJCNLP 2011 Proceedings of the Workshop on Language Resources,Technology and Services in the Sharing Paradigm, pages 50–58, 2011 [URL] [Pure]
Korkontzelos, I., Mu, T., Restificar, A. and Ananiadou, S., Text mining for efficient search and assisted creation of clinical trials, in: International Conference on Information and Knowledge Management, Proceedings, pages 43–50, 2011 [DOI] [URL] [Pure]
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, in: Ariadne, 2011 [URL] [Pure]
Kolluru, B., Hawizy, L., Murray-Rust, P., Tsujii, J. and Ananiadou, S., Using workflows to explore and optimise named entity recognition for chemistry, in: PLoS ONE, 2011 [DOI] [Pure]

2010

Ananiadou, S., Thompson, P., Thomas, J., Mu, T., Oliver, S., Rickinson, M., Sasaki, Y., Weissenbacher, D. and McNaught, J., Supporting the education evidence portal via text mining, in: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, pages 3829–3844, 2010 [DOI] [URL] [Pure]
Ananiadou, S., Pyysalo, S., Tsujii, J. and Kell, D. B., Event extraction for systems biology by text mining the literature, in: Trends in Biotechnology, pages 381–390, 2010 [DOI] [Pure]
Kemper, B., Matsuzaki, T., Matsuoka, Y., Tsuruoka, Y., Kitano, H., Ananiadou, S. and Tsujii, J., PathText: A text mining integrator for biological pathway visualizations, in: Bioinformatics, pages 374–381, 2010 [DOI] [URL] [Pure]
Ananiadou, S., McNaught, J., Thomas, J. and Oliver, S., Evaluating a text mining based educational search portal, in: Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010), pages 3344–3350, 2010 [URL] [Pure]
Okazaki, N., Ananiadou, S. and Tsujii, J., Building a high-quality sense inventory for improved abbreviation disambiguation, in: Bioinformatics, pages 1246–1253, 2010 [DOI] [URL] [Pure]
Sasaki, Y., McNaught, J. and Ananiadou, S., The value of an in-domain lexicon in genomics QA, in: Journal of Bioinformatics and Computational Biology, pages 147–161, 2010 [DOI] [Pure]
Wang, X., Tsujii, J. and Ananiadou, S., Disambiguating the species of biomedical named entities using natural language parsers, in: Bioinformatics, pages 661–667, 2010 [DOI] [URL] [Pure]
Rupp, C., Thompson, P., Black, W., McNaught, J. and Ananiadou, S., A Specialised Verb Lexicon as the Basis of Fact Extraction in the Biomedical Domain, in: Proceedings of interdisciplinary workshop on verbs: the identification and representation of verb features (Verb 2010), pages 6pp, 2010 [URL] [Pure]
Ananiadou, S. and Wang, X., A task oriented extension of the Chinese MeSH Concepts Hierarchy, in: host publication, pages 23–30, 2010 [URL] [Pure]
Ananiadou, S., Nawaz, R. and Thompson, P., Evaluating a meta-knowledge annotation scheme for bio-events, in: host publication, pages 69–77, 2010 [URL] [Pure]
Ananiadou, S., Nawaz, R. and Thompson, P., Event Interpretation: A Step towards Event-Centred Text Minin, in: host publication, pages 103–107, 2010 [PDF] [Pure]
Black, W., Rupp, C., Nobata, C., McNaught, J., Tsujii, J. and Ananiadou, S., High-Precision Semantic Search by Generating and Testing Questions., in: Proceedings of the UK e-Science All Hands Meeting, pages 3pp, 2010 [URL] [Pure]
Mu, T., Wang, X., Tsujii, J. and Ananiadou, S., Imbalanced classification using dictionary-based prototypes and hierarchical decision rules for entity sense disambiguation, in: Coling 2010 - 23rd International Conference on Computational Linguistics, Proceedings of the Conference, pages 851–859, 2010 [URL] [Pure]
Ananiadou, S., Thompson, P. and Nawaz, R., Improving search through Event-based Biomedical Text Mining, in: 1st Automated Motif Discovery in Cultural Heritage and Scientific Communication Texts (AMICUS) workshop, Vienna, 1/01/24, 2010 [PDF] [Pure]
Nawaz, R., Thompson, P., McNaught, J. and Ananiadou, S., Meta-knowledge annotation of bio-events, in: Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC2010), pages 2498–2505, 2010 [URL] [Pure]
Wang, X., Rak, R., Restificar, A., Nobata, C., Rupp, C., Batista-Navarro, R. T., Nawaz, R. and Ananiadou, S., NaCTeM Systems for BioCreative III PPI Tasks, in: Proceedings of the BioCreative III Workshop, pages 142–147, 2010 [URL] [Pure]
Mu, T. and Ananiadou, S., Proximity-based graph embeddings for multi-label classification, in: KDIR 2010 - Proceedings of the International Conference on Knowledge Discovery and Information Retrieval, pages 74–84, 2010 [URL] [Pure]
Kano, Y., Dobson, P., Nakanishi, M., Tsujii, J. and Ananiadou, S., Text Mining Meets Workflow: Linking U-Compare with Taverna, in: Bioinformatics, 26:19(2486-2487), 2010 [DOI] [URL]
Ananiadou, S., Pyysalo, S., Ohta, T., Cho, H. -., Sullivan, D., Mao, C., Sobral, B. and Tsujii, J., Towards Event Extraction from Full Texts on Infectious Diseases, in: host publication, pages 132–140, 2010 [URL] [Pure]
Ananiadou, S., Kano, Y., Dorado, R., McCrochon, L. and Tsujii, J., U-Compare: An integrated language resource evaluation platform including a comprehensive UIMA resource library., in: host publication, pages 428–434, 2010 [URL] [Pure]

2009

Ananiadou, S., Rea, B., Okazaki, N., Procter, R. and Thomas, J., Supporting systematic reviews using text mining, in: Social Science Computer Review, pages 509–523, 2009 [DOI] [URL] [Pure]
Thompson, P., Iqbal, S. A., McNaught, J. and Ananiadou, S., Construction of an annotated corpus to support biomedical information extraction, in: BMC Bioinformatics, 2009 [DOI] [URL] [Pure]
Matsuoka, Y., Ghosh, S., Kikuchi, N., Sætre, R., Kemper, B., Okazaki, N., Ananiadou, S., Tsujii, J. and Kitano, H., Community Platform for Pathway Model Building, in: 10th International Conference on Systems Biology, pages 139–140, 2009 [URL] [Pure]
Kano, Y., Baumgartner, W. A., McCrohon, L., Ananiadou, S., Cohen, K. B., Hunter, L. and Tsujii, J., U-Compare: Share and compare text mining tools with UIMA, in: Bioinformatics, pages 1997–1998, 2009 [DOI] [URL] [Pure]
Barrón-Cedeño, A., Sierra, G., Drouin, P. and Ananiadou, S., An improved automatic term recognition method for spanish, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 125–136, 2009 [DOI] [URL] [Pure]
Rea, B., Weissenbacher, D., Sasaki, Y., Thomas, J. and Ananiadou, S., ASSIST: Education Evidence Portal, in: Proceedings of the UK e-Science All Hands Meeting 2009, 2009 [Pure]
Sasaki, Y., Thompson, P., McNaught, J. and Ananiadou, S., Biological event recognition with textual induction, in: Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM-2009), pages 91–96, 2009 [URL] [Pure]
Venturi, G., Montemagni, S., Marchi, S., Sasaki, Y., Thompson, P., McNaught, J. and Ananiadou, S., Bootstrapping a verb lexicon for biomedical information extraction, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 137–148, 2009 [DOI] [URL] [Pure]
Wang, X., Tsujii, J. and Ananiadou, S., Classifying relations for biomedical named entity disambiguation, in: EMNLP 2009 - Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: A Meeting of SIGDAT, a Special Interest Group of ACL, Held in Conjunction with ACL-IJCNLP 2009, pages 1513–1522, 2009 [URL] [Pure]
Sasaki, Y., Rea, B. and Ananiadou, S., Clinical text classification under the open and closed topic assumptions, in: International Journal of Data Mining and Bioinformatics, pages 299–313, 2009 [DOI] [URL] [Pure]
Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Fast full parsing by linear-chain conditional random fields, in: EACL 2009 - 12th Conference of the European Chapter of the Association for Computational Linguistics, Proceedings, pages 790–798, 2009 [URL] [Pure]
Tekiner, F., Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Highly scalable text mining - Parallel tagging application, in: ICSCCW 2009 - 5th International Conference on Soft Computing, Computing with Words and Perceptions in System Analysis, Decision and Control, 2009 [DOI] [URL] [Pure]
Piao, S., Rea, B., McNaught, J. and Ananiadou, S., Improving full text search with text mining tools, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 301–302, 2009 [DOI] [PDF] [Pure]
Kano, Y., McCrochon, L., Ananiadou, S. and 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, pages 22–30, 2009 [URL] [Pure]
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 [PDF] [Pure]
Piao, S., Tsuruoka, Y. and Ananiadou, S., Sentiment analysis with knowledge resource and NLP tools, in: International Journal of Interdisciplinary Social Sciences, pages 17–28, 2009 [URL] [Pure]
Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Stochastic Gradient Descent Training for L1-regularized Log-linear Models with Cumulative Penalty, in: ACL-IJCNLP 2009, pages 477–485, 2009 [URL]
Ananiadou, S., Weissenbacher, D., Rea, B., Pieri, E., Lin, Y., Vis, F., Procter, R. and Halfpenny, P., Supporting Frame Analysis using Text Mining, in: Proceedings of the 5th International Conference on e-Social Science, 2009 [URL]
Ananiadou, S., Text mining for biomedicine, in: Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration, pages 1–9, 2009 [DOI] [URL] [Pure]
Ananiadou, S., Sasaki, Y. and McNaught, J., The Value of an In-Domain Lexicon in Genomics QA, in: host publication, pages 47–55, 2009 [URL] [Pure]
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 [URL]
Sasaki, Y., Thompson, P., McNaught, J. and Ananiadou, S., Three BioNLP Tools Powered by the BioLexicon, in: Proceeedings of EACL 2009, pages 61–64, 2009 [URL] [Pure]
Lyte, V., Jones, S., Ananiadou, S. and Kerr, L., UK Institutional Repository Search: Innovation and Discovery, in: Ariadne, 2009 [URL] [Pure]

2008

Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Accelerating the annotation of sparse named entities by dynamic sentence selection, in: BMC Bioinformatics, 2008 [DOI] [PDF] [Pure]
Tsuruoka, Y., Tsujii, J. and Ananiadou, S., FACTA: A text search engine for finding associated biomedical concepts, in: Bioinformatics, pages 2559–2560, 2008 [DOI] [PDF] [Pure]
Sasaki, Y., Tsuruoka, Y., McNaught, J. and Ananiadou, S., How to make the most of NE dictionaries in statistical NER, in: BMC Bioinformatics, 2008 [DOI] [PDF] [Pure]
Thompson, P., Cotter, P., McNaught, J., Ananiadou, S., Montemagni, S., Trabucco, A. and Venturi, G., Building a Bio-Event Annotated Corpus for the Acquisition of Semantic Frames from Biomedical Corpora, in: Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008), pages 2159–2166, 2008 [PDF] [Pure]
Thompson, P., Venturi, G., McNaught, J., Montemagni, S. and Ananiadou, S., Categorising Modality in Biomedical Texts, in: Proceedings of the LREC 2008 Workshop on Building and Evaluating Resources for Biomedical Text Mining., pages 27–34, 2008 [PDF] [Pure]
Piao, S., McNaught, J. and Ananiadou, S., Clustering Related Terms with Definitions, in: Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008), pages 2013–2019, 2008 [PDF] [Pure]
Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., Kitano, H., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., Connecting Text Mining and Pathways using the PathText Resource, in: Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008), pages 1736–1740, 2008 [PDF] [Pure]
Tsuruoka, Y., McNaught, J. and Ananiadou, S., Normalizing biomedical terms by minimizing ambiguity and variability, in: BMC Bioinformatics, 2008 [DOI] [PDF] [Pure]
Meziane, F., Athanasakis, N. and Ananiadou, S., Generating Natural Language specifications from UML class diagrams, in: Requirements Engineering, pages 1–18, 2008 [DOI] [PDF] [Pure]
Kano, Y., Nguyen, N., Sætre, R., Fukamachi, K., Yoshida, K., Miyao, Y., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., Sharable type system design for tool inter-operability and combinatorial comparison, in: Proceedings of the First International Conference on Global Interoperability for Language Resources (ICGL), pages 122–129, 2008 [Pure]
Kano, Y., Nguyen, N., Sætre, 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 [PDF] [Pure]
Okazaki, N., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., A discriminative candidate generator for string transformations, in: EMNLP 2008 - 2008 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference: A Meeting of SIGDAT, a Special Interest Group of the ACL, pages 447–456, 2008 [PDF] [Pure]
Tsuruoka, Y., Tsujii, J. and Ananiadou, S., Accelerating the Annotation of Sparse Named Entities by Dynamic Sentence Selection, in: Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP 2008), Association for Computational Linguistics, pages 30–37, 2008 [PDF]
Sasaki, Y., Montemagni, S., Pezik, P., Rebholz-Schuhmann, D., McNaught, J. and Ananiadou, S., BioLexicon: A Lexical Resource for the Biology Domain, in: Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, Turku Centre for Computer Science (TUCS), pages 109–116, 2008 [PDF]
Rebholz-Schuhmann, D., Pezik, P., Lee, V., Kim, J., del Gratta, R., Sasaki, Y., McNaught, J., Montemagni, S., Monachini, M., Calzolari, N. and Ananiadou, S., BioLexicon: Towards a Reference Terminological Resource in the Biomedical Domain, in: Proceedings of the of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB-2008), 2008 [PDF] [Pure]
Splendiani, A., Piao, S., Sasaki, Y., Ananiadou, S., McNaught, J. and Burgun, A., Compositional Enrichment of Bio-Ontologies, in: Proceedings of 11th Annual Bio-Ontologies Meeting, at the Intelligent Systems for Molecular Biology 2008 Conference (ISMB-2008), 2008 [Pure]
Sasaki, Y., Thompson, P., Cotter, P., McNaught, J. and Ananiadou, S., Event frame extraction based on a gene regulation corpus, in: Coling 2008 - 22nd International Conference on Computational Linguistics, Proceedings of the Conference, pages 761–768, 2008 [PDF] [Pure]
Kano, Y., Nguyen, N., SÆtre, 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: Pacific Symposium on Biocomputing 2008, PSB 2008, pages 616–627, 2008 [PDF] [Pure]
Sasaki, Y., Tsuruoka, Y., McNaught, J. and Ananiadou, S., How to Make the Most of NE Dictionaries in Statistical NER, in: Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing (BioNLP 2008), Association for Computational Linguistics, pages 63–70, 2008 [PDF]
Hirohata, K., Okazaki, N., Ananiadou, S. and Ishizuka, M., Identifying Sections in Scientific Abstracts using Conditional Random Fields, in: Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP 2008), pages 381–388, 2008 [PDF] [Pure]
Nobata, C., Cotter, P., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y., Tsujii, J. and 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, ACM, pages 787–788, 2008 [PDF]
Sætre, R., Kemper, B., Oda, K., Okazaki, N., Matsuoka, Y., Kikuchi, N., Kitano, H., Tsuruoka, Y., Ananiadou, S. and Tsujii, J., PathText: Text Mining Tools Integrated with Biological Pathway, in: host publication, 2008 [Pure]

2007

Tsuruoka, Y., McNaught, J., Tsujii, J. and Ananiadou, S., Learning string similarity measures for gene/protein name dictionary look-up using logistic regression, in: Bioinformatics, pages 2768–2774, 2007 [DOI] [PDF] [Pure]
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 [PDF] [Pure]
Hahn, U., Buyko, E., Tomanek, K., Piao, S., McNaught, J., Tsuruoka, Y. and Ananiadou, S., An annotation type system for a data-driven NLP pipeline, in: ACL 2007: The LAW - Proceedings of The Linguistic Annotation Workshop, pages 33–40, 2007 [PDF] [Pure]
Piao, S., Buyko, E., Tsuruoka, Y., Tomanek, K., Kim, J., McNaught, J., Hahn, U., Su, J. and Ananiadou, S., BOOTStrep Annotation Scheme: Encoding Information for Text Mining, in: Proceedings of the 4th Corpus Linguistics Conference (CL2007), 2007 [PDF] [Pure]
Frantzi, K. and Ananiadou, S., C-value for Authorship Identification, in: Proceedings of the 8th Conference on Forensic Linguistics, Language and Law, 2007 [Pure]
Piao, S., Ananiadou, S. and McNaught, J., Integrating Annotation Tools into UIMA for Interoperability, in: Proceedings of the UK e-Science AHM Conference 2007, pages 575–582, 2007 [PDF] [Pure]
Piao, S., Ananiadou, S., Tsuruoka, Y., Sasaki, Y. and McNaught, J., Mining Opinion Polarity Relations of Citations, in: Proceedings of the 7th International Workshop on Computational Semantics, pages 366–371, 2007 [PDF] [Pure]
Sasaki, Y., Rea, B. and Ananiadou, S., Multi-topic aspects in clinical text classification, in: Proceedings - 2007 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2007, pages 62–67, 2007 [DOI] [PDF] [Pure]
Ananiadou, S., Procter, R., Rea, B., Sasaki, Y. and Thomas, J., Supporting Systematic Reviews using Text Mining, in: Proceedings of the 3rd International Conference on e-Social Science, 2007 [PDF] [Pure]
Rea, B. and Ananiadou, S., Text Mining Services to Support E-Research, in: UK e-Science All Hands Meeting, 2007 [PDF] [Pure]
Ananiadou, S., The National Centre for Text Mining: a Vision for the Future, in: Ariadne, 2007 [URL] [Pure]

2006

Okazaki, N. and Ananiadou, S., Building an abbreviation dictionary using a term recognition approach, in: Bioinformatics, pages 3089–3095, 2006 [DOI] [PDF] [Pure]
Ananiadou, S., Kell, D. B. and Tsujii, J. i., Text mining and its potential applications in systems biology, in: Trends in Biotechnology, pages 571–579, 2006 [DOI] [PDF] [Pure]
Ananiadou, S. and Nenadic, G., Automatic Terminology Management in Biomedicine, in: Text Mining for Biology and Biomedicine, pages 67–98, 2006 [Pure]
Okazaki, N. and Ananiadou, S., Clustering Acronyms in Biomedical Text for Disambiguation, in: Proceedings of Fifth International conference on Language Resources and Evaluation (LREC 2006), pages 959–962, 2006 [PDF] [Pure]
Ananiadou, S. and McNaught, J., Introduction to Text Mining for Biology and Biomedicine, in: Text Mining for Biology and Biomedicine, pages 1–12, 2006 [Pure]
Ananiadou, S. and McNaught, J., Introduction to Text Mining in Biology, in: Text Mining for Biology and Biomedicine, pages 1–12, 2006 [Pure]
Nenadić, G. and Ananiadou, S., Mining semantically related terms from biomedical literature, in: ACM Transactions on Asian Language Information Processing, pages 22–43, 2006 [DOI] [PDF] [Pure]
Kim, J., Ananiadou, S. and Tsujii, J., Ontology based Semantic Annotation for Knowledge Extraction, in: 2nd International Digital Curation Conference, 2006 [PDF] [Pure]
Ananiadou, S. and Fluck, J., Proceedings of the Second International Symposium on Semantic Mining in Biomedicine (SMBM), in: host publication, 2006 [Pure]
Mima, H., Ananiadou, S. and Matsushima, K., Terminology-based knowledge mining for new knowledge discovery, in: ACM Transactions on Asian Language Information Processing, pages 74–88, 2006 [DOI] [PDF] [Pure]

2005

Spasic, I., Ananiadou, S., McNaught, J. and Kumar, A., Text mining and ontologies in biomedicine: Making sense of raw text, in: Briefings in Bioinformatics, pages 239–251, 2005 [DOI] [PDF] [Pure]
Tsujii, J. and Ananiadou, S., Thesaurus or logical ontology, which one do we need for text mining?, in: Language Resources and Evaluation, pages 77–90, 2005 [DOI] [PDF] [Pure]
Ananiadou, S., Chruszcz, J., Keane, J., McNaught, J. and Watry, P., The National Centre for Text Mining: Aims and Objectives, in: Ariadne, 2005 [URL] [Pure]
Spasić, I. and Ananiadou, S., A flexible measure of contextual similarity for biomedical terms, in: Proceedings of the Pacific Symposium on Biocomputing 2005, PSB 2005, pages 197–208, 2005 [PDF] [Pure]
Tsuruoka, Y., Ananiadou, S. and Tsujii, J., A Machine Learning Approach To Acronym Generation, in: Proceedings of the Workshop On Linking Biological Literature Ontologies And Databases, pages 25–31, 2005 [PDF] [Pure]
Tsuruoka, Y., Tateishi, Y., Kim, J. D., Ohta, T., McNaught, J., Ananiadou, S. and Tsujii, J., Developing a robust part-of-speech tagger for biomedical text, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 382–392, 2005 [DOI] [PDF] [Pure]
SpasiÄ‡, I., Ananiadou, S. and Tsujii, J., MaSTerClass: a case-based reasoning system for the classification of biomedical terms, in: Bioinformatics, 21:11(2748--2758), 2005 [PDF]
NenadiÄ‡, G., SpasiÄ‡, I. and Ananiadou, S., Mining Biomedical Abstracts: Whatâ€™s in a Term?, in: Natural Language Processing â€“ IJCNLP 2004, Springer-Verlag, 2005 [PDF]

2004

Ananiadou, S., Friedman, C. and Tsujii, J., Introduction: Named entity recognition in biomedicine, in: Journal of Biomedical Informatics, pages 393–395, 2004 [DOI] [URL] [Pure]
Spasić, I. and Ananiadou, S., Using automatically learnt verb selectional preferences for classification of biomedical terms, in: Journal of Biomedical Informatics, pages 483–497, 2004 [DOI] [PDF] [Pure]
Nenadić, G., Spasić, I. and Ananiadou, S., Automatic Discovery of Term Similarities Using Pattern Mining, in: COMPUTERM '02: COLING-02 on COMPUTERM 2002: second international workshop on computational terminology, pages 55–80, 2004 [DOI] [PDF] [Pure]
Nenadic, G., Ananiadou, S. and McNaught, J., Enhancing automatic term recognition through recognition of variation, in: Proceedings of COLING 2004, pages 604–610, 2004 [PDF] [Pure]
Spasić, I., Nenadić, G. and Ananiadou, S., Learning to classify biomedical terms through literature mining and genetic algorithms, in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), pages 345–351, 2004 [PDF] [Pure]

2003

Manios, K., Nenadic, G., Spasic, I. and Ananiadou, S., An Integrated Term-Based Corpus Query System, in: EACL 2003, 10th Conference of the European Chapter of the Association for Computational Linguistics, April 12-17, 2003, Agro Hotel, Budapest, Hungary, pages 243–250, 2003 [Pure]
Nenadic, G., Spasic, I. and Ananiadou, S., Morpho-Syntactic Clues for Terminological Processing in Serbian, in: Proc. EACL Workshop on Morphological Processing of Slavic Languages, pages 79–86, 2003 [Pure]
Nenadic, G., Spasic, I. and Ananiadou, S., Reducing Lexical Ambiguity in Serbo-Croatian by Using Genetic Algorithms, in: Investigations into Formal Slavic Linguistics, pages 287–298, 2003 [Pure]
Nenadic, G., Spasic, I. and Ananiadou, S., Terminology-driven mining of biomedical literature, in: Proceedings of the 2003 ACM Symposium on Applied Computing (SAC), March 9-12, 2003, Melbourne, FL, USA, pages 83–87, 2003 [Pure]
Spasic, I., Nenadic, G. and Ananiadou, S., Using Domain-Specific Verbs for Term Classification, in: Proc. ACL Workshop on NLP in Biomedicine, pages 17–24, 2003 [Pure]

2002

Spasic, I., Nenadic, G. and Ananiadou, S., A Genetic Algorithm Approach to Unsupervised Learning of Context Features, in: Proc. 5th National Colloquium for Computational Linguistics in the UK (CLUK), pages 12–19, 2002 [Pure]
Mima, H., Ananiadou, S., Nenadic, G. and Tsujii, J., A Methodology for Terminology-based Knowledge Acquisition and Integration, in: 19th International Conference on Computational Linguistics, COLING 2002, Howard International House and Academia Sinica, Taipei, Taiwan, August 24 - September 1, 2002, pages 667–673, 2002 [Pure]
Mima, H., Ananiadou, S., Nenadic, G. and Tsujii, J., An Integrated System for Ontology-based Knowledge Structuring and Discovery, in: Proc. SOFG 2002 (Standards and Ontologies for Functional Genomics), 2002 [Pure]
Nenadic, G., Spasic, I. and Ananiadou, S., Automatic Acronym Acquisition and Term Variation Management within Domain-Specific Texts, in: Proceedings of the Third International Conference on Language Resources and Evaluation, LREC 2002, May 29-31, 2002, Las Palmas, Canary Islands, Spain, pages 2155–2162, 2002 [Pure]
Nenadic, G., Spasic, I. and Ananiadou, S., Automatic discovery of term similarities using pattern mining, in: Proc. 2nd International Workshop on Computational Terminology, pages 1–7, 2002 [Pure]
Nenadic, G., Spasic, I. and Ananiadou, S., Reducing lexical ambiguity in Serbo-Croatian by using genetic algorithms, in: Proc. 4th Eur. Conf. on Formal Description of Slavic Languages (FDSL- 4), 2002 [Pure]
Spasic, I., Nenadic, G., Manios, K. and Ananiadou, S., Supervised Learning of Term Similarities, in: Intelligent Data Engineering and Automated Learning - IDEAL 2002, pages 429–434, 2002 [DOI] [Pure]
Ananiadou, S., Nenadic, G., Schuhmann, D. and Spasic, I., Term based literature mining from biomedical texts, in: Proc.Intelligent Systems for Molecular Biology (ISMB), 2002 [Pure]
Nenadic, G., Mima, H., Spasic, I., Ananiadou, S., Tsujii, J. and Spasić, I., Terminology-driven literature mining and knowledge acquisition in biomedicine, in: I. J. Medical Informatics, pages 33–48, 2002 [DOI] [Pure]
Spasic, I., Nenadic, G. and Ananiadou, S., Tuning Context Features with Genetic Algorithms, in: Proceedings of the Third International Conference on Language Resources and Evaluation, LREC 2002, May 29-31, 2002, Las Palmas, Canary Islands, Spain, pages 2048–2054, 2002 [Pure]
Mima, H., Ananiadou, S., Nenadic, G. and Tsujii, J., XML tag information management system: A workbench for ontology-based knowledge acquisition and integration, in: Proc. Human Language Technology Conference (HLT 2002), pages 286–292, 2002 [Pure]

2001

Ananiadou, S., Nenadic, G. and Mima, H., A terminology management workbench for Molecular Biology., in: Proc. 19th ESF/Twente Workshop on Language Technology: Information Extraction in Molecular Biology, pages 7–12, 2001 [Pure]
Maynard, D. and Ananiadou, S., Term extraction using a similarity-based approach, in: Recent Advances in Computational Terminology, pages 261–279, 2001 [Pure]
Mima, H., Ananiadou, S. and Nenadic, G., The ATRACT Workbench: Automatic Term Recognition and Clustering for Terms, in: Text, Speech and Dialogue, 4th International Conference, TSD 2001, Zelezna Ruda, Czech Republic, September 11-13, 2001, Proceedings, pages 126–133, 2001 [DOI] [Pure]

2000

Mima, H. and Ananiadou, S., An application and evaluation of the C/NC-value approach for the automatic term recognition of multi-word units in Japanese, in: Terminology, pages 175–194, 2000 [Pure]
Frantzi, K. T., Ananiadou, S. and Mima, H., Automatic recognition of multi-word terms: the C-value/NC-value method, in: International Journal on Digital Libraries, pages 115–130, 2000 [DOI] [Pure]
Maynard, D. and Ananiadou, S., Creating and Using Domain-specific Ontologies for Terminological Applications, in: Proceedings of the Second International Conference on Language Resources and Evaluation, LREC 2000, 31 May - June 2, 2000, Athens, Greece, pages 869–873, 2000 [Pure]
Ananiadou, S., Albert, S. and Schuhmann, D., Evaluation of automatic term recognition of nuclear receptors from Medline, in: Genome Informatics, pages 450–451, 2000 [Pure]
Maynard, D. and Ananiadou, S., Identifying Terms by their Family and Friends, in: COLING 2000, 18th International Conference on Computational Linguistics, Proceedings of the Conference, 2 Volumes, July 31 - August 4, 2000, Universität des Saarlandes, Saarbrücken, Germany, pages 530–536, 2000 [Pure]
Maynard, D. and Ananiadou, S., Terminological acquaintance: The importance of contextual information in terminology, in: Proc. Int. Workshop on Computational Terminology for Medical and Biological Applications, pages 19–28, 2000 [Pure]
Maynard, D. and Ananiadou, S., TRUCKS: A model for automatic multi-word term recognition, in: Journal of Natural Language Processing, pages 101–125, 2000 [Pure]

1999

Maynard, D. and Ananiadou, S., A linguistic approach to terminological context clustering, in: Proc. Natural Language Pacific Rim Symposium (NLPRS ???99), pages 346–351, 1999 [Pure]
Mima, H., Ananiadou, S. and Tsujii, J., A Web-based integrated knowledge mining aid system using term-oriented Natural Language Processing, in: Proc. Natural Language Pacific Rim Symposium (NLPRS ???99), pages 13–18, 1999 [Pure]
Frantzi, K., Ananiadou, S. and Tsujii, J., Automatic classification of technical terms using the NC-value method for term recognition, in: Proc. Int. Conf. on Computational Lexicography (COMPLEX ???99), pages 57–66, 1999 [Pure]
Frantzi, K. T., Ananiadou, S. and Tsujii, J., Classifying Technical Terms, in: Electronic Publishing '99, Redefining the Information Chain - New Ways and Voices: 3rd ICCC/IFIP conference held at the University of Karlskrona/Ronneby - ELPUB 1999, Karlskrona, Sweden, May 10-12, 1999. Proceedings, 1999 [Pure]
Frantzi, K. and Ananiadou, S., Clustering terms using the C-value method for automatic term recognition, in: Proc. 5th Int. Congress on Terminology and Knowledge Engineering (TKE 99), pages 356–366, 1999 [Pure]
Maynard, D. and Ananiadou, S., Identifying contextual information for multi-word term extraction, in: Proc. 5th Int. Congress on Terminology and Knowledge Engineering (TKE 99), pages 212–221, 1999 [Pure]
Maynard, D. and Ananiadou, S., Incorporating linguistic information for multi-word term extraction, in: Proc. 2nd Computational Linguistics, UK Research Colloquium (CLUK2), 1999 [Pure]

1998

Marshall, P., Bandar, Z. and Ananiadou, S., A connectionist approach to term recognition, in: Proc. 12th Int. Conf. on Artificial Intelligence and Expert Systems Applications, 1998 [Pure]
Maynard, D. and Ananiadou, S., Acquiring contextual information for term disambiguation, in: Proc. Int. Workshop on Computational Terminology (COMPUTERM ???98), pages 86–90, 1998 [Pure]
Ananiadou, S., Machine translation trends in Europe and in Japan, in: Proc. Translating and the Computer 20, 1998 [Pure]
Maynard, D. and Ananiadou, S., Term sense disambiguation using a domain-specific thesaurus, in: Proc. 1st Computational Linguistics, UK Research Colloquium (CLUK1), 1998 [Pure]
Mima, H., Frantzi, K., S, [. and Ananiadou, S., The C-value / Example-based approach to the automatic recognition of multi-word terms for cross-language terminology, in: Proc. Int. Joint Workshop on Cross-Language Issues in AI, pages 10–21, 1998 [Pure]
Frantzi, K. T., Ananiadou, S. and Tsujii, J., The C-value/NC-value Method of Automatic Recognition for Multi-Word Terms, in: Research and Advanced Technology for Digital Libraries, Second European Conference, ECDL '98, Heraklion, Crete, Greece, September 21-23, 1998, Proceedings, pages 585–604, 1998 [DOI] [Pure]

1997

Frantzi, K. and Ananiadou, S., A natural language approach to information retrieval, in: Proc. 3rd DELOS Workshop on Cross-Language Information Retrieval, 1997 [Pure]
Radford, I., Ananiadou, S. and Tsujii, J., Adding structural constraints to lexically based context matching techniques, in: Proc. Int. Joint Conf. on Artificial Intelligence (IJCAI-97), 1997 [Pure]
Frantzi, K. and Ananiadou, S., Context information for the extraction of terms, in: Proc. 18th Ann. Mtng. of the Department of Linguistics. Aristotle University of Thessaloniki., 1997 [Pure]
J, [., Tsujii, [., S, [. and Ananiadou, S., Information retrieval and natural language processing, in: Proc. Information Retrieval with Asian Languages (IRAL-97), 1997 [Pure]
S, [., Ananiadou, S. and Tsujii, J., Term disambiguation by adding structural constraints to lexically-based context matching techniques, in: Proc. Natural Language Processing Pacific Rim Symposium (NLPRS ???97), 1997 [Pure]
Frantzi, K., Ananiadou, S. and Tsujii, J., Term identification using contextual cues, in: Proc. 2nd Workshop on Multilinguality in the Software Industry: the AI Contribution (MULSAIC???97), 1997 [Pure]
S, [. and Ananiadou, S., Term recognition for information retrieval and information extraction, in: Proc. Int. Workshop on NLP and Information Retrieval., 1997 [Pure]
Arranz, M. V., Radford, I., Ananiadou, S. and Tsujii, J., Towards a sublanguage-based semantic clustering algorithm, in: Recent Advances in Natural Language Processing, pages 125–136, 1997 [Pure]

1996

Frantzi, K. and Ananiadou, S., A hybrid approach to automatic term recognition, in: Proc. Int. Conf. on Natural Language Processing and Industrial Applications, pages 93–98, 1996 [Pure]
Ananiadou, S., Radford, I. and Tsujii, J., Dynamic hypertext navigation using a conceptual graph representation, in: Proc. 4th Int. Conf. on Conceptual Structures, 1996 [Pure]
Frantzi, K., Ananiadou, S. and Tsujii, J., Extracting nested collocations, in: Proc. Second Ann. Mtng. Association for Natural Language Processing, pages 202–212, 1996 [Pure]
Frantzi, K., Ananiadou, S. and Tsujii, J., Extracting terminological expressions, in: Information Processing Society of Japan, pages 83–88, 1996 [Pure]
Ananiadou, S., Towards a linguistic treatment of compounds in a machine translation environment, in: Journal of Natural Language Processing, pages 45–66, 1996 [Pure]

1995

Ananiadou, S., Automatic recognition of medical terminology (Immunology), in: Proc. MedInfo ???95, pages 3–8, 1995 [Pure]
Radford, I., Arranz, V. M., Ananiadou, S. and Tsujii, J., Dynamic Context Matching for Knowledge Acquisition from Small Corpora, in: Analisi Statistica dei Dati Testuali, Vol. 1, pages 321–328, 1995 [Pure]
Frantzi, K. and Ananiadou, S., Statistical approaches for collocation extraction and term recognition., in: Proc. 16th Ann. Mtng. of the Department of Linguistics, pages 681–693, 1995 [Pure]
Frantzi, K. and Ananiadou, S., Statistical measures for terminological extraction, in: Analisi Statistica dei Dati Testuali, Vol. 1, pages 292–304, 1995 [Pure]
Ananiadou, S. and McNaught, J., Terms are not alone: Aids for term choice and choice terms, in: Aslib Proceedings, pages 47–60, 1995 [DOI] [Pure]
Arranz, M. V., Radford, I., Ananiadou, S., J, [. and Tsujii, [., Tools for sublanguage-based semantic knowledge acquisition from corpora, in: Procesamiento del Lenguaje Natural, pages 182–194, 1995 [Pure]
Frantzi, K. and Ananiadou, S., Towards automatic term recognition, in: Proc. 7th Int. Conf. on Artificial Intelligence and Expert Systems Applications (EXPERSYS-95), 1995 [Pure]

1994

Ananiadou, S., A computational linguistic approach to automatic term recognition, in: Knowledge Organization and Quality Management, Vol. 4, pages 134–141, 1994 [Pure]
Ananiadou, S., A Methodology For Automatic Term Recognition, in: 15th International Conference on Computational Linguistics, COLING 1994, Kyoto, Japan, August 5-9, 1994, pages 1034–1038, 1994 [Pure]
Tsujii, J. and Ananiadou, S., Knowledge-based processing in machine translation, in: Knowledge Building and Knowledge Sharing, pages 68–81, 1994 [Pure]
Ananiadou, S., Systematic knowledge elicitation from natural language texts, in: Proc. 6th Int. Conf. on Expert Systems Applications & Artificial Intelligence (EXPERSYS-94), pages 467–472, 1994 [Pure]

1993

Ananiadou, S., A sublanguage approach to automatic term recognition, in: Proc. Natural Language Processing Pacific Rim Symposium, pages 159–164, 1993 [Pure]
Tsujii, J. and Ananiadou, S., Epsilon [e]: Tool kit for knowledge acquisition based on a hierarchy of pseudotexts, in: Proc. Natural Language Processing Pacific Rim Symposium, pages 93–100, 1993 [Pure]
Tsujii, J. and Ananiadou, S., Knowledge-based processing in machine translation, in: Proc. Int. Conf. on Building and Sharing of Very Large-Scale Knowledge Bases, 1993 [Pure]
Tsujii, J. and Ananiadou, S., LBMT, KBMT, SBMT and EBMT: An attempt at integration, in: Proc. Int. Workshop on Speech Translation, 1993 [Pure]

1992

P, [., Olivier, [., Ananiadou, S. and Tsujii, J., A visualisation architecture based on the systematicity of language, in: Proc. Pacific Rim International Conference on AI (PRICAI), 1992 [Pure]
Sekine, S., Carroll, J. J., Ananiadou, S. and Tsujii, J., Automatic Learning for Semantic Collocation, in: Proc. Third Conf. on Applied Natural Language Processing, pages 104–110, 1992 [Pure]
Sekine, S., Ananiadou, S., Carroll, J. J. and Tsujii, J., Linguistic Knowledge Generator, in: 14th International Conference on Computational Linguistics, COLING 1992, Nantes, France, August 23-28, 1992, pages 560–566, 1992 [Pure]
Olivier, P., Ananiadou, S., Maeda, T. and Tsujii, J., Visualisation: mediating the interchange of information from the verbal to the visual domain, in: Mensch und Maschine - Informationelle Schnittstellen der Kommunikation: Proceedings des 3. Internationalen Symposiums für Informationswissenschaft, ISI 1992, Saarbrücken, Germany, November 5-7, 1992., pages 324–337, 1992 [Pure]

1991

Ananiadou, S. and Antona, M., Multilingual linguistic aspects of machine translation, in: Proc. 12th Ann. Mtng. of the Department of Linguistics: Studies in Greek Linguistics, pages 291–305, 1991 [Pure]
Ananiadou, S., Ralli, A. and Villalva, A., The treatment of derivational morphology in a multilingual transfer-based machine translation system: EUROTRA, in: Language Research, pages 627–638, 1991 [Pure]
Tsujii, J., Ananiadou, S., Carroll, J. J. and Phillips, J. D., Towards interaction during transfer, in: Proc. RCOLING III, pages 141–157, 1991 [Pure]

1990

Ananiadou, S., Sublanguage studies as the basis for computer support for multilingual communication, in: Proc. Terminology and Planning (Termplan-90), 1990 [Pure]
Ananiadou, S., The treatment of derivational morphology in a multilingual transfer-based machine translation system: EUROTRA, in: Proc. Seoul Int. Conf. on Natural Language Processing (SICONLP/90), pages 351–359, 1990 [Pure]
Ananiadou, S., The use of sublanguages in machine translation, in: Proc. UK Speech and Language Technology Club Workshop on Machine Translation, 1990 [Pure]
Ananiadou, S. and Mcnaught, J., Treatment of compounds in a transfer-based MT system, in: Proc. 3rd Int. Conf. on Theoretical and Methodological Issues in Machine Translation, pages 57–63, 1990 [Pure]

1989

Ananiadou, S., Machine translation: Unfulfilled promise?, in: Medium, pages 24–44, 1989 [Pure]

1988

Ananiadou, S., The Impact of Knowledge Engineering on the Training of Terminologists, in: TKE-87: Terminology and Knowledge Engineering, Supplement, pages 118–120, 1988 [Pure]

1987

Ananiadou, S., A brief survey of some current operational systems, in: Machine Translation Today, pages 171–191, 1987 [Pure]

1986

Ananiadou, S., Present and future contributions of the Eurotra project to languages for special purposes, in: Beads or Bracelet: How do we approach LSP?, pages 357–365, 1986 [Pure]