Sophia Ananiadou

Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Paul Thompson, Sophia Ananiadou: Deploying and sharing U-Compare workflows as web services. J. Biomedical Semantics 4: 7 (2013)

Claudiu Mihaila, Tomoko Ohta, Sampo Pyysalo, Sophia Ananiadou: BioCause: Annotating and analysing causality in the biomedical domain. BMC Bioinformatics 14: 2 (2013)

Raheel Nawaz, Paul Thompson, Sophia Ananiadou: Negated bio-events: analysis and identification. BMC Bioinformatics 14: 14 (2013)

Sophia Ananiadou, Paul Thompson, Raheel Nawaz: Enhancing Search: Events and Their Discourse Context. CICLing (2) 2013: 318-334

Riza Theresa Batista-Navarro, Georgios Kontonatsios, Claudiu Mihaila, Paul Thompson, Rafal Rak, Raheel Nawaz, Ioannis Korkontzelos, Sophia Ananiadou: Facilitating the Analysis of Discourse Phenomena in an Interoperable NLP Platform. CICLing (1) 2013: 559-571

Makoto Miwa, Paul Thompson, Sophia Ananiadou: Boosting automatic event extraction from the literature using domain adaptation and coreference resolution. Bioinformatics 28(13): 1759-1765 (2012)

Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Junichi Tsujii, Sophia Ananiadou: Event extraction across multiple levels of biological organization. Bioinformatics 28(18): 575-581 (2012)

Makoto Miwa, Paul Thompson, John McNaught, Douglas B. Kell, Sophia Ananiadou: Extracting semantically enriched events from biomedical literature. BMC Bioinformatics 13: 108 (2012)

Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou: Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011. BMC Bioinformatics 13(S-11): S2 (2012)

Tingting Mu, John Yannis Goulermas, Jun'ichi Tsujii, Sophia Ananiadou: Proximity-Based Frameworks for Generating Embeddings from Multi-Output Data. IEEE Trans. Pattern Anal. Mach. Intell. 34(11): 2216-2232 (2012)

Rafal Rak, BalaKrishna Kolluru, Sophia Ananiadou: Building Trainable Taggers in a Web-based, UIMA-Supported NLP Workbench. ACL (System Demonstrations) 2012: 121-126

Min Song, Doheon Lee, Hua Xu, Sophia Ananiadou: DTMBIO 2012: international workshop on data and text mining in biomedical informatics. CIKM 2012: 2766-2767

Pontus Stenetorp, Sampo Pyysalo, Goran Topic, Tomoko Ohta, Sophia Ananiadou, Jun'ichi Tsujii: brat: a Web-based Tool for NLP-Assisted Text Annotation. EACL 2012: 102-107

Sophia Ananiadou: Extracting Semantically Enriched Events from the Literature. KDIR 2012

Sophia Ananiadou: Biomedical text mining for semantic search and knowledge discovery. IHI 2012: 1-2

Ioannis Korkontzelos, Sophia Ananiadou: ASCOT: assisting search and creation of clinical trials. IHI 2012: 855-858

Anita de Waard, Sophia Ananiadou, Maryann E. Martone, Ágnes Sándor, Hagit Shatkay: Detecting and using document structure in scientific text. IHI 2012: 883-884

Xinkai Wang, Paul Thompson, Jun'ichi Tsujii, Sophia Ananiadou: Biomedical Chinese-English CLIR Using an Extended CMeSH Resource to Expand Queries. LREC 2012: 1148-1155

William J. Black, Rob Procter, Steven Gray, Sophia Ananiadou: A data and analysis resource for an experiment in text mining a collection of micro-blogs on a political topic. LREC 2012: 2083-2088

Rafal Rak, Andrew Rowley, Sophia Ananiadou: Collaborative Development and Evaluation of Text-processing Workflows in a UIMA-supported Web-based Workbench. LREC 2012: 2971-2976

Raheel Nawaz, Paul Thompson, Sophia Ananiadou: Identification of Manner in Bio-Events. LREC 2012: 3505-3510

Georgios Kontonatsios, Ioannis Korkontzelos, Sophia Ananiadou: Developing Multilingual Text Mining Workflows in UIMA and U-Compare. NLDB 2012: 82-93

Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun'ichi Tsujii: AGRA: analysis of gene ranking algorithms. Bioinformatics 27(8): 1185-1186 (2011)

Yoshimasa Tsuruoka, Makoto Miwa, Kaisei Hamamoto, Jun'ichi Tsujii, Sophia Ananiadou: Discovering and visualizing indirect associations between biomedical concepts. Bioinformatics [ISMB/ECCB] 27(13): 111-119 (2011)

Xinglong Wang, Iain McKendrick, Ian Barrett, Ian Dix, Tim French, Jun'ichi Tsujii, Sophia Ananiadou: Automatic extraction of angiogenesis bioprocess from text. Bioinformatics 27(19): 2730-2737 (2011)

Paul Thompson, Raheel Nawaz, John McNaught, Sophia Ananiadou: Enriching a biomedical event corpus with meta-knowledge annotation. BMC Bioinformatics 12: 393 (2011)

Paul Thompson, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo Del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, Valeria Quochi, C. J. Rupp, Yutaka Sasaki, Giulia Venturi, Dietrich Rebholz-Schuhmann, Sophia Ananiadou: The BioLexicon: a large-scale terminological resource for biomedical text mining. BMC Bioinformatics 12: 397 (2011)

Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii: U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics 12: 481 (2011)

Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, C. J. Rupp, Riza Theresa Batista-Navarro, Raheel Nawaz, Sophia Ananiadou: Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature. BMC Bioinformatics 12(S-8): S11 (2011)

Yutaka Sasaki, Xinglong Wang, Sophia Ananiadou: Extracting Secondary Bio-Event Arguments with Extraction Constraints. Computational Intelligence 27(4): 702-721 (2011)

Yoshinobu Kano, Makoto Miwa, K. Bretonnel Cohen, Lawrence Hunter, Sophia Ananiadou, Jun'ichi Tsujii: U-Compare: A modular NLP workflow construction and evaluation system. IBM Journal of Research and Development 55(3): 11 (2011)

BalaKrishna Kolluru, Sirintra Nakjang, Robert P. Hirt, Anil Wipat, Sophia Ananiadou: Automatic extraction of microorganisms and their habitats from free text using text mining workflows. J. Integrative Bioinformatics 8(2) (2011)

Johanna R. McEntyre, Sophia Ananiadou, Stephen Andrews, William J. Black, Richard Boulderstone, Paula Buttery, David Chaplin, Sandeepreddy Chevuru, Norman Cobley, Lee-Ann Coleman, Paul Davey, Bharti Gupta, Lesley Haji-Gholam, Craig Hawkins, Alan Horne, Simon J. Hubbard, Jee-Hyub Kim, Ian Lewin, Vic Lyte, Ross MacIntyre, Sami Mansoor, Linda Mason, John McNaught, Elizabeth Newbold, Chikashi Nobata, Ernest Ong, Sharmila Pillai, Dietrich Rebholz-Schuhmann, Heather Rosie, Rob Rowbotham, C. J. Rupp, Peter Stoehr, Philip Vaughan: UKPMC: a full text article resource for the life sciences. Nucleic Acids Research 39(Database-Issue): 58-65 (2011)

Sophia Ananiadou, Doheon Lee, Shamkant B. Navathe, Min Song: DTMBIO 2011: international workshop on data and textmining in biomedical informatics. CIKM 2011: 2617-2618

Simon Kocbek, Rune Sætre, Gregor Stiglic, Jin-Dong Kim, Igor Pernek, Yoshimasa Tsuruoka, Peter Kokol, Sophia Ananiadou, Jun'ichi Tsujii: Poster: Analysis of gene ranking algorithms with extraction of relevant biomedical concepts from PubMed publications. ICCABS 2011: 249

Georgios Kontonatsios, Ioannis Korkontzelos, BalaKrishna Kolluru, Sophia Ananiadou: Adding text mining workflows as web services to the BioCatalogue. SWAT4LS 2011: 50-57

Xinglong Wang, Jun'ichi Tsujii, Sophia Ananiadou: Disambiguating the species of biomedical named entities using natural language parsers. Bioinformatics 26(5): 661-667 (2010)

Naoaki Okazaki, Sophia Ananiadou, Jun'ichi Tsujii: Building a high-quality sense inventory for improved abbreviation disambiguation. Bioinformatics 26(9): 1246-1253 (2010)

Brian Kemper, Takuya Matsuzaki, Yukiko Matsuoka, Yoshimasa Tsuruoka, Hiroaki Kitano, Sophia Ananiadou, Jun'ichi Tsujii: PathText: a text mining integrator for biological pathway visualizations. Bioinformatics [ISMB] 26(12): 374-381 (2010)

Yoshinobu Kano, Paul Dobson, Mio Nakanishi, Jun'ichi Tsujii, Sophia Ananiadou: Text mining meets workflow: linking U-Compare with Taverna. Bioinformatics 26(19): 2486-2487 (2010)

Yutaka Sasaki, John McNaught, Sophia Ananiadou: The Value of an in-Domain Lexicon in genomics QA. J. Bioinformatics and Computational Biology 8(1): 147-161 (2010)

Tingting Mu, Xinglong Wang, Jun'ichi Tsujii, Sophia Ananiadou: Imbalanced Classification Using Dictionary-based Prototypes and Hierarchical Decision Rules for Entity Sense Disambiguation. COLING (Posters) 2010: 851-859

Tingting Mu, Sophia Ananiadou: Proximity-based Graph Embeddings for Multi-label Classification. KDIR 2010: 74-84

Sophia Ananiadou, John McNaught, James Thomas, Mark Rickinson, Sandy Oliver: Evaluating a Text Mining Based Educational Search Portal. LREC 2010

Yoshinobu Kano, Ruben Dorado, Luke McCrohon, Sophia Ananiadou, Jun'ichi Tsujii: U-Compare: An Integrated Language Resource Evaluation Platform Including a Comprehensive UIMA Resource Library. LREC 2010

Raheel Nawaz, Paul Thompson, John McNaught, Sophia Ananiadou: Meta-Knowledge Annotation of Bio-Events. LREC 2010

Yoshinobu Kano, William A. Baumgartner Jr., Luke McCrohon, Sophia Ananiadou, K. Bretonnel Cohen, Lawrence Hunter, Jun'ichi Tsujii: U-Compare: share and compare text mining tools with UIMA. Bioinformatics 25(15): 1997-1998 (2009)

Paul Thompson, Syed A. Iqbal, John McNaught, Sophia Ananiadou: Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics 10: 349 (2009)

Yutaka Sasaki, Brian Rea, Sophia Ananiadou: Clinical text classification under the Open and Closed Topic Assumptions. IJDMB 3(3): 299-313 (2009)

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: Stochastic Gradient Descent Training for L1-regularized Log-linear Models with Cumulative Penalty. ACL/IJCNLP 2009: 477-485

Alberto Barrón-Cedeño, Gerardo Sierra, Patrick Drouin, Sophia Ananiadou: An Improved Automatic Term Recognition Method for Spanish. CICLing 2009: 125-136

Giulia Venturi, Simonetta Montemagni, Simone Marchi, Yutaka Sasaki, Paul Thompson, John McNaught, Sophia Ananiadou: Bootstrapping a Verb Lexicon for Biomedical Information Extraction. CICLing 2009: 137-148

Yutaka Sasaki, Paul Thompson, John McNaught, Sophia Ananiadou: Three BioNLP Tools Powered by a Biological Lexicon. EACL (Demos) 2009: 61-64

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: Fast Full Parsing by Linear-Chain Conditional Random Fields. EACL 2009: 790-798

Xinglong Wang, Jun'ichi Tsujii, Sophia Ananiadou: Classifying Relations for Biomedical Named Entity Disambiguation. EMNLP 2009: 1513-1522

Scott Songlin Piao, Brian Rea, John McNaught, Sophia Ananiadou: Improving Full Text Search with Text Mining Tools. NLDB 2009: 301-302

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: FACTA: a text search engine for finding associated biomedical concepts. Bioinformatics 24(21): 2559-2560 (2008)

Dina Demner-Fushman, Sophia Ananiadou, K. Bretonnel Cohen, John Pestian, Jun'ichi Tsujii, Bonnie L. Webber: Themes in biomedical natural language processing: BioNLP08. BMC Bioinformatics 9(S-11) (2008)

Yutaka Sasaki, Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou: How to make the most of NE dictionaries in statistical NER. BMC Bioinformatics 9(S-11) (2008)

Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: Accelerating the annotation of sparse named entities by dynamic sentence selection. BMC Bioinformatics 9(S-11) (2008)

Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou: Normalizing biomedical terms by minimizing ambiguity and variability. BMC Bioinformatics 9(S-3) (2008)

Farid Meziane, Nikos Athanasakis, Sophia Ananiadou: Generating Natural Language specifications from UML class diagrams. Requir. Eng. 13(1): 1-18 (2008)

Naoaki Okazaki, Sophia Ananiadou, Jun'ichi Tsujii: A Discriminative Alignment Model for Abbreviation Recognition. COLING 2008: 657-664

Yutaka Sasaki, Paul Thompson, Philip Cotter, John McNaught, Sophia Ananiadou: Event Frame Extraction Based on a Gene Regulation Corpus. COLING 2008: 761-768

Naoaki Okazaki, Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii: A Discriminative Candidate Generator for String Transformations. EMNLP 2008: 447-456

Kenji Hirohata, Naoaki Okazaki, Sophia Ananiadou, Mitsuru Ishizuka: Identifying Sections in Scientific Abstracts using Conditional Random Fields. IJCNLP 2008: 381-388

Yoshinobu Kano, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Keiichiro Fukamachi, Yusuke Miyao, Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii: Towards Data and Goal Oriented Analysis: Tool Inter-operability and Combinatorial Comparison. IJCNLP 2008: 859-864

Scott Songlin Piao, John McNaught, Sophia Ananiadou: Clustering Related Terms with Definitions. LREC 2008

Rune Sætre, Brian Kemper, Kanae Oda, Naoaki Okazaki, Yukiko Matsuoka, Norihiro Kikuchi, Hiroaki Kitano, Yoshimasa Tsuruoka, Sophia Ananiadou, Jun'ichi Tsujii: Connecting Text Mining and Pathways using the PathText Resource. LREC 2008

Paul Thompson, Philip Cotter, John McNaught, Sophia Ananiadou, Simonetta Montemagni, Andrea Trabucco, Giulia Venturi: Building a Bio-Event Annotated Corpus for the Acquisition of Semantic Frames from Biomedical Corpora. LREC 2008

Yoshinobu Kano, Ngan Nguyen, Rune Sætre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiroh Matsubayashi, Sophia Ananiadou, Jun'ichi Tsujii: Filling the Gaps Between Tools and Users: A Tool Comparator, Using Protein-Protein Interactions as an Example. Pacific Symposium on Biocomputing 2008: 616-627

Chikashi Nobata, Philip Cotter, Naoaki Okazaki, Brian Rea, Yutaka Sasaki, Yoshimasa Tsuruoka, Jun'ichi Tsujii, Sophia Ananiadou: Kleio: a knowledge-enriched information retrieval system for biology. SIGIR 2008: 787-788

Yoshimasa Tsuruoka, John McNaught, Jun'ichi Tsujii, Sophia Ananiadou: Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. Bioinformatics 23(20): 2768-2774 (2007)

Yutaka Sasaki, Brian Rea, Sophia Ananiadou: Multi-topic Aspects in Clinical Text Classification. BIBM 2007: 62-70

Naoaki Okazaki, Sophia Ananiadou: Building an abbreviation dictionary using a term recognition approach. Bioinformatics 22(24): 3089-3095 (2006)

Sophia Ananiadou, Juliane Fluck: Proceedings of the Second International Symposium for Semantic Mining in Biomedicine. BMC Bioinformatics 7(S-3) (2006)

Goran Nenadic, Sophia Ananiadou: Mining semantically related terms from biomedical literature. ACM Trans. Asian Lang. Inf. Process. 5(1): 22-43 (2006)

Hideki Mima, Sophia Ananiadou, Katsumori Matsushima: Terminology-based knowledge mining for new knowledge discovery. ACM Trans. Asian Lang. Inf. Process. 5(1): 74-88 (2006)

Naoaki Okazaki, Sophia Ananiadou: A Term Recognition Approach to Acronym Recognition. ACL 2006

Irena Spasic, Sophia Ananiadou, John McNaught, Anand Kumar: Text mining and ontologies in biomedicine: Making sense of raw text. Briefings in Bioinformatics 6(3): 239-251 (2005)

Irena Spasic, Sophia Ananiadou, Jun'ichi Tsujii: MaSTerClass: a case-based reasoning system for the classification of biomedical terms. Bioinformatics 21(11): 2748-2758 (2005)

Jun'ichi Tsujii, Sophia Ananiadou: Thesaurus or Logical Ontology, Which One Do We Need for Text Mining? Language Resources and Evaluation 39(1): 77-90 (2005)

Yoshimasa Tsuruoka, Yuka Tateishi, Jin-Dong Kim, Tomoko Ohta, John McNaught, Sophia Ananiadou, Jun'ichi Tsujii: Developing a Robust Part-of-Speech Tagger for Biomedical Text. Panhellenic Conference on Informatics 2005: 382-392

Irena Spasic, Sophia Ananiadou: A Flexible Measure of Contextual Similarity for Biomedical Terms. Pacific Symposium on Biocomputing 2005

Sophia Ananiadou, Carol Friedman, Jun'ichi Tsujii: Introduction: named entity recognition in biomedicine. Journal of Biomedical Informatics 37(6): 393-395 (2004)

Irena Spasic, Sophia Ananiadou: Using automatically learnt verb selectional preferences for classification of biomedical terms. Journal of Biomedical Informatics 37(6): 483-497 (2004)

Goran Nenadic, Sophia Ananiadou, John McNaught: Enhancing automatic term recognition through recognition of variation. COLING 2004

Irena Spasic, Goran Nenadic, Sophia Ananiadou: Learning to Classify Biomedical Terms Through Literature Mining and Genetic Algorithms.. IDEAL 2004: 345-351

Sophia Ananiadou, Jong C. Park: Introduction (Thematic Session: Text Mining in Biomedicine). IJCNLP 2004: 776-776

Goran Nenadic, Irena Spasic, Sophia Ananiadou: Mining Biomedical Abstracts: What's in a Term? IJCNLP 2004: 797-806

Goran Nenadic, Irena Spasic, Sophia Ananiadou: Terminology-driven Mining of Biomedical Literature. Bioinformatics 19(8): 938-943 (2003)

Kostas Manios, Goran Nenadic, Irena Spasic, Sophia Ananiadou: An Integrated Term-Based Corpus Query System. EACL 2003: 243-250

Goran Nenadic, Irena Spasic, Sophia Ananiadou: Terminology-driven Mining of Biomedical Literature. SAC 2003: 83-87

Sophia Ananiadou: Spotting and Discovering Terms through Natural Language Processing by Christian Jacquemin. Computational Linguistics 28(2): 217-220 (2002)

Goran Nenadic, Hideki Mima, Irena Spasic, Sophia Ananiadou, Jun'ichi Tsujii: Terminology-driven literature mining and knowledge acquisition in biomedicine. I. J. Medical Informatics 67(1-3): 33-48 (2002)

Hideki Mima, Sophia Ananiadou, Goran Nenadic, Jun'ichi Tsujii: A Methodology for Terminology-based Knowledge Acquisition and Integration. COLING 2002

Irena Spasic, Goran Nenadic, Kostas Manios, Sophia Ananiadou: Supervised Learning of Term Similarities. IDEAL 2002: 429-434

Goran Nenadic, Irena Spasic, Sophia Ananiadou: Automatic Acronym Acquisition and Term Variation Management within Domain-Specific Texts. LREC 2002

Irena Spasic, Goran Nenadic, Sophia Ananiadou: Tuning Context Features with Genetic Algorithms. LREC 2002

Goran Nenadic, Irena Spasic, Sophia Ananiadou: Term Clustering Using a Corpus-Based Similarity Measure. TSD 2002: 151-154

Hideki Mima, Sophia Ananiadou, Goran Nenadic: The ATRACT Workbench: Automatic Term Recognition and Clustering for Terms. TSD 2001: 126-133

Katerina T. Frantzi, Sophia Ananiadou, Hideki Mima: Automatic recognition of multi-word terms: the C-value/NC-value method. Int. J. on Digital Libraries 3(2): 115-130 (2000)

Diana Maynard, Sophia Ananiadou: Identifying Terms by their Family and Friends. COLING 2000: 530-536

Diana Maynard, Sophia Ananiadou: Creating and Using Domain-specific Ontologies for Terminological Applications. LREC 2000

Katerina T. Frantzi, Sophia Ananiadou, Jun'ichi Tsujii: Classifying Technical Terms. ELPUB 1999

Katerina T. Frantzi, Sophia Ananiadou, Jun'ichi Tsujii: The C-value/NC-value Method of Automatic Recognition for Multi-Word Terms. ECDL 1998: 585-604

Katerina T. Frantzi, Sophia Ananiadou: Extracting Nested Collocations. COLING 1996: 41-46

Jutta Frense, Sophia Ananiadou: Book review. Machine Translation 10(3): 259-267 (1995)

Sophia Ananiadou: A Methodology For Automatic Term Recognition. COLING 1994: 1034-1038

Satoshi Sekine, Jeremy J. Carroll, Sophia Ananiadou, Jun'ichi Tsujii: Automatic Learning for Semantic Collocation. ANLP 1992: 104-110

Satoshi Sekine, Sophia Ananiadou, Jeremy J. Carroll, Jun'ichi Tsujii: Linguistic Knowledge Generator. COLING 1992: 560-566

Sophia Ananiadou: On the definition of word. Machine Translation 4(4): 313-317 (1990)