Prof Sophia Ananiadou

Chair in Computer Science

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Publications

  1. 2019
  2. E-pub ahead of print

    Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries

    Wang, Y., Fan, X., Chen, L., Chang, E. I., Ananiadou, S., Tsujii, J. & Xu, Y., 17 Aug 2019, In : BMC Bioinformatics. 20, 1

    Research output: Contribution to journalArticle

  3. Published

    Adverse Drug Events and Medication Relation Extraction in EHRs with Ensemble Deep Learning Methods

    Christopoulou, F., Tran, T., Sahu, S., Miwa, M. & Ananiadou, S., 7 Aug 2019, In : Journal of the American Medical Informatics Association.

    Research output: Contribution to journalArticle

  4. Published

    Improving classification of Adverse Drug Reactions through Using Sentiment Analysis and Transfer Learning

    Alhuzali, H. & Ananiadou, S., 1 Jul 2019, Improving classification of Adverse Drug Reactions through Using Sentiment Analysis and Transfer Learning. p. 339 347 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  5. Published

    A Text Mining Pipeline Using Active and Deep Learning for Curating Information in Computational Neuroscience

    Shardlow, M., Ju, M., Li, M., O'Reilly, C., Iavarone, E., McNaught, J. & Ananiadou, S., Jul 2019, In : Neuroinformatics. 17, 3, p. 391-406 16 p.

    Research output: Contribution to journalArticle

  6. Published

    Inter-sentence Relation Extraction with Document-level Graph Convolutional Neural Network

    Sahu, S., Christopoulou, E., Miwa, M. & Ananiadou, S., Jul 2019, Inter-sentence Relation Extraction with Document-level Graph Convolutional Neural Network. p. 4309-4316 7 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  7. Published

    An Ensemble of Neural Models for Nested Adverse Drug Events and Medication Extraction with Subwords

    Ju, M., Nguyen, N., Miwa, M. & Ananiadou, S., 14 Jun 2019, In : Journal of the American Medical Informatics Association.

    Research output: Contribution to journalArticle

  8. Published

    Modelling Instance-Level Annotator Reliability for Natural Language Labelling Tasks

    Li, M., Fahlström Myrman, A., Mu, T. & Ananiadou, S., Jun 2019, Modelling Instance-Level Annotator Reliability for Natural Language Labelling Tasks. p. 2873-2883 10 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  9. Published

    Annotating and Detecting Phenotypic Information for Chronic Obstructive Pulmonary Disease

    Ju, M., Short, A., Thompson, P., Diar Bakerly, N., Gkoutos, G., Tsaprouni, L. & Ananiadou, S., 26 Apr 2019, In : Journal of the American Medical Informatics Association.

    Research output: Contribution to journalArticle

  10. Published

    Hypothesis, analysis and synthesis, it's all Greek to me

    Iliopoulos, I., Ananiadou, S., Danchin, A., Ioannidis, J. P., Katsikis, P. D., Ouzounis, C. A. & Promponas, V. J., 2019, In : eLife. 8

    Research output: Contribution to journalArticle

  11. Published
  12. Published

    Machine learning algorithms for systematic review: Reducing workload in a preclinical review of animal studies and reducing human screening error

    Bannach-Brown, A., Przybyła, P., Thomas, J., Rice, A. S. C., Ananiadou, S., Liao, J. & Macleod, M. R., 2019, In : Systematic Reviews. 8, 1, 23.

    Research output: Contribution to journalReview article

  13. Published

    Quantifying Risk Factors in Medical Reports with a Context-Aware Linear Model

    Przybyla, P., Brockmeier, A. & Ananiadou, S., 2019, In : Journal of the American Medical Informatics Association.

    Research output: Contribution to journalArticle

  14. 2018
  15. Published

    Improve Chinese Clinical Named Entity Recognition Performance by Using the Graphical and Phonetic Feature

    Tsujii, J., Ananiadou, S. & Wang, Y., 3 Dec 2018, Proceedings of BIBM 2018 (IEEE). p. 1582-1586 5 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  16. Published

    Prioritising references for systematic reviews with RobotAnalyst: a user study

    Przybyła, P., Brockmeier, A., Kontonatsios, G., Le Pogam, M-A., McNaught, J., von Elm, E., Nolan, K. & Ananiadou, S., 25 Sep 2018, In : Research Synthesis Methods. 9, 3, p. 470-488

    Research output: Contribution to journalArticle

  17. Published

    Investigating Domain-Specific Information for Neural Coreference Resolution on Biomedical Texts

    Trieu, H-L., Nguyen, N., Miwa, M. & Ananiadou, S., 19 Jul 2018, Proceedings of the BioNLP 2018 workshop . p. 183-188 6 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  18. Published

    Biosimilar vs originator insulins: Systematic review and meta-analysis

    Yamada, T., Kamata, R., Ishinohachi, K., Shojima, N., Ananiadou, S., Nom, H., Yamauchi, T. & Kadowaki, T., 1 Jul 2018, In : Diabetes, Obesity and Metabolism. 20, 7, p. 1787-1792

    Research output: Contribution to journalArticle

  19. Published

    Identification of research hypotheses and new knowledge from scientific literature

    Shardlow, M., Batista-Navarro, R. T., Thompson, P., McNaught, J. & Ananiadou, S., 25 Jun 2018, In : BMC Medical Informatics and Decision Making. 18, 13 p., 46.

    Research output: Contribution to journalArticle

  20. Published

    Paths for uncertainty: Exploring the intricacies of uncertainty identification for news

    Zerva, C. & Ananiadou, S., 5 Jun 2018, Proceedings of the NAACL Workshop on Computational Semantics Beyond Events and Roles (SemBEaR). p. 6-20 15 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  21. Published

    Extracting Gene-Disease Relations from Text to Support Biomarker Discovery

    Thompson, P. & Ananiadou, S., 2 Jun 2018, Digital Health 2017: Global Public Health, Personalised Medicine, and Emergency Medicine in the Age of Big Data. ACM Digital Library

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  22. Published

    A Neural Layered Model for Nested Named Entity Recognition

    Ju, M., Miwa, M. & Ananiadou, S., 1 Jun 2018, Proceedings of NAACL 2018. p. 1446-1459 11 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  23. Published

    A New Corpus to Support Text Mining for the Curation of Metabolites in the ChEBI Database

    Shardlow, M., Nguyen, N., Owen, G., Turner, S., Leach, A., O'Donovan, C., McNaught, J. & Ananiadou, S., May 2018, p. 280-285. 6 p.

    Research output: Contribution to conferencePaper

  24. Published

    LitPathExplorer: A Confidence-based Visual Text Analytics Tool for Exploring Literature-Enriched Pathway Models

    Soto, A., Zerva, C., Batista-Navarro, R. T. & Ananiadou, S., 15 Apr 2018, In : Bioinformatics. 34, 8, p. 1389-1397

    Research output: Contribution to journalArticle

  25. Published

    On Revolutions

    Leroi, A. M., Lambert, B. C., Mauch, M., Papadopoulou, M., Ananiadou, S., Lindberg, S. I. I. & Lindenfors, P., 15 Mar 2018, In : SSRN Working Paper Series. 63.

    Research output: Contribution to journalArticle

  26. Published

    Self-Tuned Descriptive Document Clustering using a Predictive Network

    Brockmeier, A., Mu, T., Ananiadou, S. & Goulermas, J. Y., 23 Feb 2018, In : IEEE Transactions on Knowledge and Data Engineering.

    Research output: Contribution to journalArticle

  27. Published

    Annotation and Detection of Drug Effects in Text for Pharmacovigilance

    Thompson, P., Daikou, S., Ueno, K., Batista-Navarro, R. T., Tsujii, J. & Ananiadou, S., 2018, In : Journal of Cheminformatics. 10

    Research output: Contribution to journalArticle

  28. Published

    HYPHEN: A flexible, hybrid method to map phenotype concept mentions to terminological resources

    Thompson, P. & Ananiadou, S., 2018, In : Terminology. 24, 1, p. 91-121

    Research output: Contribution to journalArticle

  29. Published

    Thalia: Semantic search engine for biomedical abstracts

    Soto, A., Przybyla, P. & Ananiadou, S., 2018, In : Bioinformatics.

    Research output: Contribution to journalArticle

  30. 2017
  31. Published

    Identifying Personalised Treatments and Clinical Trials for Precision Medicine using Semantic Search with Thalia

    Przybyła, P., Soto, A. & Ananiadou, S., Nov 2017, Proceedings of the Twenty-Fifth Text REtrieval Conference (TREC 2017).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  32. Published

    Risk of bias reporting in the recent animal focal cerebral ischaemia literature

    Bahor, Z., Liao, J., Macleod, M., Bannach-brown, A., Mccann, S., Wever, K., Thomas, J., Ottavi, T., Howells, D., Rice, A., Ananiadou, S. & Sena, E., 15 Oct 2017, In : Clinical Science. 131, 20, p. 2525-2532

    Research output: Contribution to journalArticle

  33. Published

    Proactive Learning for Named Entity Recognition

    Li, M., Nguyen, N. & Ananiadou, S., Aug 2017, Proceedings of BioNLP 2017. p. 117-125 9 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  34. Published

    Using uncertainty to link and rank evidence from biomedical literature for model curation

    Zerva, C., Batista-Navarro, R. T., Day, P. & Ananiadou, S., 24 Jul 2017, In : Bioinformatics.

    Research output: Contribution to journalArticle

  35. Published

    Quantifying the Informativeness of Similarity Measurements

    Brockmeier, A., Mu, T., Ananiadou, S. & Goulermas, J. Y., 7 Jul 2017, In : Journal of Machine Learning Research.

    Research output: Contribution to journalArticle

  36. Published

    Data Visualization with Structural Control of Global Cohort and Local Data Neighborhoods

    Mu, T., Goulermas, J. Y. & Ananiadou, S., 15 Jun 2017, In : IEEE Transactions on Pattern Analysis and Machine Intelligence. PP, 99

    Research output: Contribution to journalArticle

  37. Published

    Enriching News Events with Meta-knowledge Information

    Thompson, P., Nawaz, R., McNaught, J. & Ananiadou, S., Jun 2017, In : Language Resources and Evaluation. 51, 2, p. 409-438 30 p.

    Research output: Contribution to journalArticle

  38. Published

    Supporting Biological Pathway Curation Through Text Mining

    Ananiadou, S. & Thompson, P., 23 Apr 2017, In : Communications in Computer and Information Science. p. 59-73 15 p.

    Research output: Contribution to journalArticle

  39. Published

    Constructing a biodiversity terminological inventory

    Nguyen, N., Soto, A., Kontonatsios, G., Batista-Navarro, R. T. & Ananiadou, S., 17 Apr 2017, In : PLoS ONE. p. 1-23 23 p.

    Research output: Contribution to journalArticle

  40. Published

    A Text Mining-Based Framework for Constructing an RDF-Compliant Biodiversity Knowledge Repository

    Batista-navarro, R., Zerva, C., Nguyen, N. T. H. & Ananiadou, S., 8 Mar 2017, Communications in Computer and Information Science . p. 30-42 13 p. (Information Management and Big Data).

    Research output: Chapter in Book/Report/Conference proceedingChapter

  41. Accepted/In press

    5Ws: What Went Wrong With Word embeddings

    Espinosa, K. J., Batista-Navarro, R. T. & Ananiadou, S., 2017, (Accepted/In press).

    Research output: Contribution to conferencePaper

  42. Published

    A semi-supervised approach using label propagation to support citation screening

    Kontonatsios, G., Brockmeier, A., Przybyla, P., McNaught, J., Mu, T., Goulermas, J. Y. & Ananiadou, S., 2017, In : Journal of Biomedical Informatics.

    Research output: Contribution to journalArticle

  43. Published

    biochem4j: integrated and extensible biochemical knowledge through graph databases

    Swainston, N., Batista-Navarro, R. T., Carbonell, P., Dobson, P., Dunstan, M., Jervis, A., Vinaixa, M., Williams, A., Ananiadou, S., Faulon, J-L., Pedrosa Mendes, P., Kell, D., Scrutton, N. & Breitling, R., 2017, In : PLoS ONE. 12, 7, e0179130.

    Research output: Contribution to journalArticle

  44. Published

    Distributed document and phrase co-embeddings for descriptive clustering

    Tsujii, J., Sato, M., Brockmeier, A., Kontonatsios, G., Mu, T. & Ananiadou, S., 2017, Proceedings of EACL 2017. p. 991-1001 11 p.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  45. Published

    Role of in silico tools and text mining in the safety assessment of selected plant coumarins

    Raitano, G., Benfenati, E., Ananiadou, S., Fu, X., Do, Q. T., Rat, P. & Sousselier, L., 2017, In : Toxicology Letters. 280, p. S96

    Research output: Contribution to journalArticle

  46. 2016
  47. Published

    Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain- Specific Terminological Resource

    Alnazzawi, N., Thompson, P. & Ananiadou, S., 19 Sep 2016, In : PLoS One.. 11, 9, e0162287.

    Research output: Contribution to journalArticle

  48. Published

    Overview of the interactive task in BioCreative V

    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. & 36 others, 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., Van Auken, K., Lu, Z., Schaeffer, M., Wu, C. H., Hirschman, L. & Arighi, C. N., 1 Sep 2016, In : Database. 2016, baw119.

    Research output: Contribution to journalArticle

  49. Published

    A text mining framework for accelerating the semantic curation of literature

    Batista-Navarro, R., Hammock, J., Ulate, W. & Ananiadou, S., 10 Aug 2016, Research and Advanced Technology for Digital Libraries : 20th International Conference on Theory and Practice of Digital Libraries, TPDL 2016 Hannover, Germany, September 5-9, 2016 proceedings. Springer Nature, p. 459-462 4 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9819).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  50. Published

    Text Mining Workflows for Indexing Archives with Automatically Extracted Semantic Metadata

    Batista-Navarro, R. T., Soto, A., Ulate, W. & Ananiadou, S., 10 Aug 2016, p. 471-473.

    Research output: Contribution to conferenceOther

  51. Published

    Analysis of the effect of sentiment analysis on extracting adverse drug reactions from tweets and forum posts

    Korkontzelos, I., Azadeh Nikfarjamb, Shardlow, M., Sarkerb, A., Ananiadou, S. & Graciela H. Gonzalez, Aug 2016, In : Journal of Biomedical Informatics. 62, p. 148–158

    Research output: Contribution to journalArticle

  52. Published

    Topic Detection Using Paragraph Vectors to Support Active Learning in Systematic Reviews

    Hashimoto, K., Kontonatsios, G., Miwa, M. & Ananiadou, S., Aug 2016, In : Journal of Biomedical Informatics. 62, p. 59–65

    Research output: Contribution to journalArticle

  53. Published

    Text Mining for Semantic Search in Europe PubMed Central Labs

    Black, W., Rowley, A., Miwa, M., McNaught, J. & Ananiadou, S., 12 Jul 2016, Working with Text: Tools, Techniques and Approaches for Text Mining. Tonkin, E. & Tourte, G. (eds.). Cambridge: Chandos, p. 111-131 (Chandos Information Professional Series).

    Research output: Chapter in Book/Report/Conference proceedingChapter

  54. Published

    The strategic impact of META-NET on the regional, national and international level

    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. & 24 others, Odijk, J., Ogrodniczuk, M., Pęzik, P., Bel, N., Piperidis, S., Przepiórkowski, A., Rögnvaldsson, E., Rosner, M., Pedersen, B. S., Skadiņa, I., De Smedt, K., Tadíc, M., Thompson, P., Tufiș, D., Bielevičiené, A., Váradi, T., Vasiļjevs, A., Vider, K., Zabarskaitė, J., Borin, L., Branco, A., Budin, G., Calzolari, N. & Daelemans, W., Jun 2016, In : Language Resources and Evaluation. 50, 2, p. 351-374 24 p.

    Research output: Contribution to journalArticle

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