Publications

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Ananiadou, S. and Thompson, P. (2017). Supporting Biological Pathway Curation Through Text Mining. In: Kalinichenko, L., Kuznetsov, S. and Manolopoulos, Y.(Eds.) Data Analytics and Management in Data Intensive Domains, Springer (DOI) (URL)
Batista-Navarro, R. and Ananiadou, S. (2017). A text mining-based approach to graph database curation in support of metabolic pathway model reconstruction. In: Proceedings of Biocuration 2017
Batista-Navarro, R., Zerva, C., Nguyen, N. T. H. and Ananiadou, S. (2017). A Text Mining-Based Framework for Constructing an RDF-Compliant Biodiversity Knowledge Repository, Springer, Communications in Computer and Information Science, volume 656 (DOI)
Brockmeier, A. J., Mu, T., Ananiadou, S. and Goulermas, J. Y (2017). Quantifying the Informativeness of Similarity Measurements. In: Journal of Machine Learning Research, 18 (URL)
Kontonatsios, G., Brockmeier, A. J., Przybyła, P., McNaught, J., Mu, T., Goulermas, J. Y and Ananiadou, S. (2017). A semi-supervised approach using label propagation to support citation screening. In: Journal of Biomedical Informatics, 72 (DOI) (URL)
Mu, T., Goulermas, J. Y and Ananiadou, S. (2017). Data Visualization with Structural Control of Global Cohort and Local Data Neighborhoods. In: IEEE Transactions on Pattern Analysis and Machine Intelligence, 99 (DOI) (URL)
Nguyen, N. T. H., Soto, A., Kontonatsios, G., Batista-Navarro, R. and Ananiadou, S. (2017). Constructing a Biodiversity Terminological Inventory. In: PLOS ONE, 12(4) (DOI) (URL)
Sato, M., Brockmeier, A. J., Kontonatsios, G., Mu, T., Goulermas, J. Y, Tsujii, J. and Ananiadou, S. (2017). Distributed Document and Phrase Co-embeddings for Descriptive Clustering. In: Proceedings of EACL (URL)
Swainston, N., Batista-Navarro, R., Carbonel, P., Dobson, P., Dunstan, M., Jervis, A., Vinaixa, M., Williams, A., Ananiadou, S., Faulon, J. L., Mendes, P., Kell, D. B., Scrutton, N. and Breitling, R. (2017). biochem4j: integrated and extensible biochemical knowledge through graph databases. In: PLOS ONE, 12(7) (DOI) (URL)
Thompson, P. and Ananiadou, S. (2017). Extracting Gene-Disease Relations from Text to Support Biomarker Discovery. In: Proceedings of the 7th International conference on Digital Health (DOI) (URL)
Thompson, P., Ananiadou, S. and Tsujii, J. (2017). The GENIA Corpus: Annotation Levels and Applications. In: Ide, N. and Pustejovsky, J.(Eds.) Handbook of Linguistic Annotation, Springer (DOI) (URL)
Thompson, P., Boylan, K., Freemont, A. and Ananiadou, S. (2017). Supporting biomarker discovery using text mining. In: Proceedings of Informatics for Health 2017
Zerva, C., Batista-Navarro, R., Day, P. J. R. and Ananiadou, S. (2017). Using uncertainty to link and rank evidence from biomedical literature for model curation. In: Bioinformatics (DOI) (URL)

Alnazzawi, N., Thompson, P. and Ananiadou, S. (2016). Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain-Specific Terminological Resource. In: PLOS ONE, 11(9) (DOI) (URL)
Batista-Navarro, R., Carter, J. and Ananiadou, S. (2016). Argo: Enabling the development of bespoke workflows and services for disease annotation. In: Database: The Journal of Biological Databases and Curation, 2016 (DOI) (URL)
Batista-Navarro, R., Hammock, J., Ulate, W. and Ananiadou, S. (2016). A Text Mining Framework for Accelerating the Semantic Curation of Literature. In: Proceedings of the 20th International Conference on Theory and Practice of Digital Libraries (TPDL 2016), Springer (URL)
Batista-Navarro, R., Soto, A., Ulate, W. and Ananiadou, S. (2016). Text Mining Workflows for Indexing Archives with Automatically Extracted Semantic Metadata. In: Proceedings of the 20th International Conference on Theory and Practice of Digital Libraries (TPDL 2016), Springer (URL)
Batista-Navarro, R., Zerva, C. and Ananiadou, S. (2016). 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) (URL)
Black, W.J., Rowley, A., Miwa, M., McNaught, J. and Ananiadou, S. (2016). Text Mining for Semantic Search in Europe PubMed Central Labs. In: Working with Text: Tools, Techniques and Approaches for Text Mining, Elsevier (URL)
Espinosa, K., Batista-Navarro, R. and Ananiadou, S. (2016). Learning to recognise named entities in Tweets by exploiting weakly labelled data. In: Proceedings of the 2nd Workshop on Noisy User-generated Text (W-NUT 2016)
Hashimoto, K., Kontonatsios, G., Miwa, M. and Ananiadou, S. (2016). Topic Detection Using Paragraph Vectors to Support Active Learning in Systematic Reviews. In: Journal of Biomedical Informatics, 62 (DOI) (URL)
Haynes, C., Kay, N., Harrison, K., McLeod, C., Shaw, B., Leng, G., Kontonatsios, G. and Ananiadou, S. (2016). Using text mining to facilitate study identification in public health systematic reviews. In: Guidelines International Network (G-I-N) conference
Korkontzelos, I., Nikfarjam, A., Shardlow, M., Sarker, A., Ananiadou, S. and Gonzalez, G. (2016). Analysis of the effect of sentiment analysis on extracting adverse drug reactions from tweets and forum posts. In: Journal of Biomedical Informatics, 62 (DOI) (URL)
Korkontzelos, I., Thomas, B., Miwa, M. and Ananiadou, S. (2016). Ensemble Classification of Grants using LDA-based features. In: Proceedings of LREC 2016 (URL)
Korkontzelos, I., Thompson, P. and Ananiadou, S. (2016). Identifying content types of messages related to Open Source Software projects. In: Proceedings of LREC 2016 (URL)
Mu, T., Goulermas, J. Y, Korkontzelos, I. and Ananiadou, S. (2016). Descriptive Clustering via Discriminant Learning in a Coembedded Space of Multi-level Similarities. In: Journal of the Association for Information Science and Technology, 67(1) (DOI) (URL)
Przybyła, P., Nguyen, N. T. H., Shardlow, M., Kontonatsios, G. and Ananiadou, S. (2016). 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 (SemEval 2016) (URL)
Przybyła, P., Shardlow, M., Aubin, S., Bossy, R., {Eckart de Castilho}, R., Piperidis, S., McNaught, J. and Ananiadou, S. (2016). Text Mining Resources for the Life Sciences. In: Database: The Journal of Biological Databases and Curation (DOI) (URL)
Rehm, G., Uszkoreit, H., Ananiadou, S., Bel, N., Bieleviciene, A., Borin, L., Branco, A., Budin, G., Calzolari, N., Daelemans, W., Garabik, R., Grobelnik, M., Garcia-Mateo, C., Van Genabith, J., Hajic, J., Hernaez, I., Judge, J., Koeva, S., Krek, S., Krstev, C., Linden, K., Magnini, B., Mariani, J., McNaught, J., Melero, M., Monachini, M., Moreno, A., Odijk, J., Ogrodniczuk, M., Pezik, P., Piperidis, S., Przepiorkowski, A., Rognvaldsson, E., Rosner, M., Pedersen, B., Skadina, I., De Smedt, K., Tadic, M., Thompson, P., Tufis, D., Varadi, T., Vasiljevs, A., Vider, K. and Zabarskaite, J. (2016). The strategic impact of META-NET on the regional, national and international level. In: Language Resources and Evaluation, 50(2) (DOI) (URL)
Shardlow, M., Przybyła, P., Batista-Navarro, R., Carter, J., McNaught, J. and Ananiadou, S. (2016). Facilitating and promoting web annotation with Argo. In: Proceedings of I Annotate 2016
Thompson, P., Batista-Navarro, R., Kontonatsios, G., Carter, J., Toon, E., McNaught, J., Timmermann, C., Worboys, M. and Ananiadou, S. (2016). Text Mining the History of Medicine. In: PLOS One, 11(1) (DOI) (URL)
Thompson, P., Nawaz, R., McNaught, J. and Ananiadou, S. (2016). Enriching News Events with Meta-knowledge Information. In: Language Resources and Evaluation (DOI) (URL)
Venkatesan, A., Kim, J. -H., Talo, F., Ide-Smith, M., Gobeill, J., Carter, J., Batista-Navarro, R., Ananiadou, S., Ruch, P. and McEntyre, J. R. (2016). SciLite: a platform for displaying text-mined annotations as a means to link research articles with biological data [version 1; referees: 3 approved with reservations].. In: Wellcome Open Res, 1(25) (DOI) (URL)

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. (2015). 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) (URL)
Alnazzawi, N., Thompson, P., Batista-Navarro, R. and Ananiadou, S. (2015). Using text mining techniques to extract phenotypic information from the PhenoCHF corpus. In: BMC Medical Informatics and Decision Making, 15(Suppl. 2) (DOI) (URL)
Batista-Navarro, R. and Ananiadou, S. (2015). Adapting ChER for the recognition of chemical mentions in patents. In: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain (URL)
Batista-Navarro, R. and Ananiadou, S. (2015). Augmenting the Medical Subject Headings vocabulary with semantically rich variants to improve disease mention normalisation. In: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain (URL)
Batista-Navarro, R., Carter, J. and Ananiadou, S. (2015). Development of bespoke machine learning and biocuration workflows in a BioC-supporting text mining workbench. In: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain (URL)
Batista-Navarro, R., Carter, J. and Ananiadou, S. (2015). Semi-automatic curation of chronic obstructive pulmonary disease phenotypes using Argo. In: Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Seville, Spain (URL)
Batista-Navarro, R., Nawaz, R., Zerva, C. and Ananiadou, S. (2015). Bridging text-mined biomolecular events to pathway models using approximate subgraph matching techniques. In: Proceedings of the 16th International Conference on Systems Biology, Singapore
Batista-Navarro, R., Rak, R. and Ananiadou, S. (2015). Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics. In: Journal of Cheminformatics, 7(Suppl 1) (DOI) (URL)
Batista-Navarro, R., Ulate, W., Hammock, J., Kontonatsios, G., Rose-Sandler, T. and Ananiadou, S. (2015). Unlocking knowledge in biodiversity legacy literature through automatic semantic metadata extraction. In: Proceedings of the TDWG 2015 Annual Conference (URL)
Bollegala, D., Kontonatsios, G. and Ananiadou, S. (2015). A Cross-lingual Similarity Measure for Detecting Biomedical Term Translations. In: PLOS ONE, 10(6) (DOI) (URL)
Korkontzelos, I., Piliouras, D., Dowsey, A. and Ananiadou, S. (2015). Boosting Drug Named Entity Recognition using an Aggregate Classifier. In: Artificial Intelligence in Medicine (AIIM), Special issue of ICHI 2013 conference (DOI) (URL)
Mihăilă, C., Batista-Navarro, R., Alnazzawi, N., Kontonatsios, G., Korkontzelos, I., Rak, R., Thompson, P. and Ananiadou, S. (2015). Mining the biomedical literature. In: Healthcare Data Analytics, CRC Press (URL)
Miwa, M. and Ananiadou, S. (2015). Adaptable, high recall, event extraction system with minimal configuration. In: BMC Bioinformatics, 16(Suppl 10.) (DOI) (URL)
Mo, Y., Kontonatsios, G. and Ananiadou, S. (2015). Supporting Systematic Reviews Using LDA-based Document Representations. In: Systematic Reviews, 4 (DOI) (URL)
O’Mara-Eves, A., Thomas, J., McNaught, J., Miwa, M. and Ananiadou, S. (2015). Using text mining for study identification in systematic reviews: A systematic review of current approaches. In: Systematic Reviews, 4(1) (DOI) (URL)
Pyysalo, S., Ohta, T., Rak, R., Rowley, A., Chun, H.-W., Jung, S. -J., Choi, S. -P., Tsujii, J. and Ananiadou, S. (2015). Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. In: BMC BioInformatics, 16(Suppl 10)(Suppl 10) (DOI) (URL)
Thompson, P., Carter, J., McNaught, J. and Ananiadou, S. (2015). Semantically Enhanced Search System for Historical Medical Archives. In: Proceedings of DigitalHeritage 2015 (DOI) (URL)
Thompson, P., McNaught, J. and Ananiadou, S. (2015). Customised OCR Correction for Historical Medical Text. In: Proceedings of DigitalHeritage 2015 (DOI) (URL)
Xu, Y., Chen, L., Wei, J., Ananiadou, S., Fan, Y., Qian, Y., Chang, E. I-C. and Tsujii, J. (2015). Bilingual term alignment from comparable corpora in English discharge summary and Chinese discharge summary. In: BMC Bioinformatics, 16 (DOI) (URL)
Zerva, C. and Ananiadou, S. (2015). Event Extraction in pieces: Tackling the partial event identification problem on unseen corpora. In: Proceedings of the 2015 Workshop on Biomedical Natural Language Processing (BioNLP 2015) (URL)

Alnazzawi, N., Thompson, P. and Ananiadou, S. (2014). 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), Gothenburg, Sweden, Association for Computational Linguistics (URL)
Ananiadou, S., Thompson, P., Nawaz, R., McNaught, J. and Kell, D. B. (2014). Event Based Text Mining for Biology and Functional Genomics. In: Briefings in Functional Genomics, 14(3) (DOI) (URL)
Batista-Navarro, R., Islam, A., Ulate, W., Hammock, J., Soto, A., Ananiadou, S. and Milios, E. (2014). Enriching the legacy literature with OCR corrections and text-mined semantic metadata. In: Proceedings of the TDWG 2014 Annual Conference (URL)
Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S. (2014). 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, Association for Computational Linguistics, Gothenburg, Sweden, Association for Computational Linguistics (URL)
Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S. (2014). 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), Doha, Qatar, Association for Computational Linguistics (URL)
Kontonatsios, G., Mihăilă, C., Korkontzelos, I., Thompson, P. and Ananiadou, S. (2014). A hybrid approach to compiling bilingual dictionaries of medical terms from parallel corpora. In: Statistical Language and Speech Processing, Second International Conference, SLSP 2014, Springer (DOI)
Korkontzelos, I. and Ananiadou, S. (2014). Locating Requests among Open Source Software Communication Messages. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC’14), Reykjavik, Iceland, European Language Resources Association (ELRA) (URL)
Korkontzelos, I. and Ananiadou, S. (2014). Term Extraction. In: Oxford Handbook of Computational Linguistics (2nd Ed.) (DOI) (URL)
Mihăilă, C. and Ananiadou, S. (2014). The Meta-knowledge of Causality in Biomedical Scientific Discourse. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC’14), Reykjavik, Iceland, European Language Resources Association (ELRA) (URL)
Mihăilă, C. and Ananiadou, S. (2014). Semi-supervised learning of causal relations in biomedical scientific discourse. In: BioMedical Engineering OnLine, 13(Suppl 2) (DOI) (URL)
Miwa, M., Thomas, J., O’Mara-Eves, A. and Ananiadou, S. (2014). Reducing systematic review workload through certainty-based screening. In: Journal of Biomedical Informatics (DOI) (URL)
Miwa, M., Thompson, P., Korkontzelos, I. and Ananiadou, S. (2014). Comparable Study of Event Extraction in Newswire and Biomedical Domains. In: Proceedings of Coling 2014 (URL)
Pyysalo, S. and Ananiadou, S. (2014). Anatomical Entity Mention Recognition at Literature Scale. In: Bioinformatics, 30(6) (DOI) (URL)
Rak, R., Batista-Navarro, R., Carter, J., Rowley, A. and Ananiadou, S. (2014). Processing Biological Literature with Customisable Web Services Supporting Interoperable Formats. In: Database: The Journal of Biological Databases and Curation (DOI) (URL)
Rak, R., Batista-Navarro, R., Rowley, A., Carter, J. and Ananiadou, S. (2014). Text Mining-assisted Biocuration Workflows in Argo. In: Database: The Journal of Biological Databases and Curation (DOI) (URL)
Rak, R., Rowley, A., Carter, J., Batista-Navarro, R. and Ananiadou, S. (2014). Interoperability and Customisation of Annotation Schemata in Argo. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC’14), Reykjavik, Iceland, European Language Resources Association (ELRA) (URL)
Rehm, G., Uszkoreit, H., Ananiadou, S., Bel, N., Bieleviciene, A., Borin, L., Branco, A., Budin, G., Calzolari, N., Daelemans, W., Garabik, R., Grobelnik, M., Garcia-Mateo, C., Van Genabith, J., Hajic, J., Hernaez, I., Judge, J., Koeva, S., Krek, S., Krstev, C., Linden, K., Magnini, B., Mariani, J., McNaught, J., Melero, M., Monachini, M., Moreno, A., Odijk, J., Ogrodniczuk, M., Pezik, P., Piperidis, S., Przepiorkowski, A., Rognvaldsson, E., Rosner, M., Pedersen, B., Skadina, I., De Smedt, K., Tadic, M., Thompson, P., Tufis, D., Varadi, T., Vasiljevs, A., Vider, K. and Zabarskaite, J. (2014). 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), European Language Resources Association (URL)
Rosner, M., Attard, A., Thompson, P., Gatt, A. and Ananiadou, S. (2014). Extending a Tool Resource Framework with U-Compare. In: Human Language Technology Challenges for Computer Science and Linguistics, Springer (URL)
Stenetorp, P., Pyysalo, S., Ananiadou, S. and Tsujii, J. (2014). Generalising semantic category disambiguation with large lexical resources for fun and profit. In: Journal of Biomedical Semantics, 5 (DOI) (URL)
Williams, J., Matragkas, N., Kolovos, D. S., Korkontzelos, I., Ananiadou, S. and Paige, R. F. (2014). Software Analytics for MDE Communities. In: Proceedings of the Open Source Software for Model Driven Engineering Workshop (OSS4MDE’14) (URL)
Xu, Y., Hua, J., Ni, Z., Chen, Q., Fan, Y., Ananiadou, S., Chang, E. I-C. and Tsujii, J. (2014). Anatomical entity recognition with a hierarchical framework augmented by external resources. In: PLOS ONE, 9(10) (DOI) (URL)

Ananiadou, S., Friburger, N. and Rosset, S.(Eds.) Entités Nommées, ATALA, Traitement Automatique des Langues, volume 54 (URL)
Ananiadou, S., Thompson, P. and Nawaz, R. (2013). Enhancing Search: Events and their Discourse Context. In: Computational Linguistics and Intelligent Text Processing, Springer (DOI) (URL)
Ananiadou, S., Thompson, P. and Nawaz, R. (2013). Mining events from the literature for bioinformatics applications. In: ACM SIGWEB Newsletter, Autumn 2013 (URL)
Batista-Navarro, R., Kontonatsios, G., Mihăilă, C., Thompson, P., Rak, R., Nawaz, R., Korkontzelos, I. and Ananiadou, S. (2013). Facilitating the Analysis of Discourse Phenomena in an Interoperable NLP Platform. In: Computational Linguistics and Intelligent Text Processing, Springer Berlin Heidelberg (DOI) (URL)
Batista-Navarro, R., Rak, R. and Ananiadou, S. (2013). Chemistry-specific Features and Heuristics for Developing a CRF-based Chemical Named Entity Recogniser. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA (URL)
Batista-Navarro, R., Rak, R. and Ananiadou, S. (2013). NaCTeM CTD Web Services. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA
Kontonatsios, G., Korkontzelos, I., Kolluru, B., Thompson, P. and Ananiadou, S. (2013). Deploying and Sharing U-Compare Workflows as Web Services. In: Journal of Biomedical Semantics, 4 (DOI) (URL)
Kontonatsios, G., Korkontzelos, I., Tsujii, J. and Ananiadou, S. (2013). Using Random Forest to recognise translation equivalents of biomedical terms across languages. In: Proceedings of the Sixth Workshop on Building and Using Comparable Corpora, Sofia, Bulgaria, Association for Computational Linguistics (URL)
Kontonatsios, G., Thompson, P., Batista-Navarro, R., Mihăilă, C., Korkontzelos, I. and Ananiadou, S. (2013). Extending an interoperable platform to facilitate the creation of multilingual and multimodal NLP applications. In: Proceedings of the 51st Annual Meeting of the Association for Computational Linguistics: System Demonstrations, Association for Computational Linguistics, Sofia, Bulgaria (URL)
Mihăilă, C. and Ananiadou, S. (2013). 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, Sofia, Bulgaria, Association for Computational Linguistics (URL)
Mihăilă, C. and Ananiadou, S. (2013). Recognising Discourse Causality Triggers in the Biomedical Domain. In: Journal of Bioinformatics and Computational Biology, 11(6) (DOI)
Mihăilă, C. and Ananiadou, S. (2013). A Hybrid Approach to Recognising Discourse Causality in the Biomedical Domain. In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2013, Shanghai, China, IEEE
Mihăilă, C., Kontonatsios, G., Batista-Navarro, R., Thompson, P., Korkontzelos, I. and Ananiadou, S. (2013). 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, Association for Computational Linguistics, Sofia, Bulgaria (URL)
Mihăilă, C., Ohta, T., Pyysalo, S. and Ananiadou, S. (2013). BioCause: Annotating and Analysing Causality in the Biomedical Domain. In: BMC Bioinformatics, 14(1) (DOI) (URL)
Miwa, M. and Ananiadou, S. (2013). NaCTeM EventMine for BioNLP 2013 CG and PC tasks. In: Proceedings of BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, Association for Computational Linguistics (URL)
Miwa, M., Ohta, T., Rak, R., Rowley, A., Kell, D. B., Pyysalo, S. and Ananiadou, S. (2013). A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text. In: Bioinformatics, 29(13) (DOI) (URL)
Miwa, M., Pyysalo, S., Ohta, T. and Ananiadou, S. (2013). Wide coverage biomedical event extraction using multiple partially overlapping corpora. In: BMC Bioinformatics, 14(175) (DOI) (URL)
Nawaz, R., Thompson, P. and Ananiadou, S. (2013). Negated BioEvents: Analysis and Identification. In: BMC Bioinformatics, 14(1) (DOI) (URL)
Nawaz, R., Thompson, P. and Ananiadou, S. (2013). Something old, something new: identifying knowledge source in bio-events. In: International Journal of Computational Linguistics and Applications, 4(1) (URL)
Nawaz, R., Thompson, P. and Ananiadou, S. (2013). Towards Event-based Discourse Analysis of Biomedical Text. In: International Journal of Computational Linguistics and Applications, 4(2) (URL)
Ohta, T., Pyysalo, S., Rak, R., Rowley, A., Chun, H.-W., Jung, S. -J., Choi, S. -P. and Ananiadou, S. (2013). Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013. In: Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, Association for Computational Linguistics (URL)
Piliouras, D., Korkontzelos, I., Dowsey, A. and Ananiadou, S. (2013). Dealing with data sparsity in Drug Named Entity Recognition. In: Proceedings of IEEE International Conference on Healthcare Informatics, Philadelhia, PA (DOI)
Pyysalo, S., Ginter, F., Moen, H., Salakoski, T. and Ananiadou, S. (2013). Distributional Semantics Resources for Biomedical Text Processing. In: Proceedings of LBM 2013 (URL)
Pyysalo, S., Ohta, T. and Ananiadou, S. (2013). Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013. In: Proceedings of the BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, Association for Computational Linguistics (URL)
Rak, R. and Ananiadou, S. (2013). Making UIMA Truly Interoperable with SPARQL. In: Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse, Sofia, Bulgaria (URL)
Rak, R., Batista-Navarro, R., Rowley, A., Carter, J. and Ananiadou, S. (2013). Customisable Curation Workflows in Argo. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA
Rak, R., Batista-Navarro, R., Rowley, A., Miwa, M., Carter, J. and Ananiadou, S. (2013). NaCTeM’s BioC Modules and Resources for BioCreative IV. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA
Rak, R., Rowley, A., Carter, J. and Ananiadou, S. (2013). Development and Analysis of NLP Pipelines in Argo. In: Proceedings of the 51st Annual Meeting of the Association for Computational Linguistics: System Demonstrations, Association for Computational Linguistics, Sofia, Bulgaria (URL)
Restificar, A., Korkontzelos, I. and Ananiadou, S. (2013). A method for discovering and inferring appropriate eligibility criteria in clinical trial protocols without labeled data. In: BMC Medical Informatics and Decision Making, 13(Suppl 1) (DOI) (URL)
Thompson, P., Nawaz, R., Korkontzelos, I., Black, W.J., McNaught, J. and Ananiadou, S. (2013). News Search Using Discourse Analytics. In: Proceedings of the 2013 Digital Heritage International Congress, Marseille, France, IEEE (DOI) (URL)
Van Landeghem, S., Björne, J., Wei, C-. H, Hakala, K., Pyysalo, S., Ananiadou, S., Kao, H. -Y., Lu, Z., Salakoski, T., Van de Peer, Y. and Ginter, F. (2013). Large-scale event extraction from literature with multi-level gene normalization. In: PLOS ONE, 8(4) (DOI) (URL)

Ananiadou, S., McNaught, J. and Thompson, P. (2012). The English Language in the Digital Age. In: Rehm, G. and Uszkoreit, H.(Eds.) White Paper Series, Springer (URL)
Ananiadou, S., Ohta, T. and Rutter, M. (2012). Text Mining supporting Search for Knowledge Discovery in Diabetes. In: Current Cardiovascular Risk Reports (URL)
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Liakata, M., Thompson, P., de Waard, A., Nawaz, R., Pander Maat, H. and Ananiadou, S. (2012). A three-way perspective on scientific discourse annotation for knowledge extraction. In: Proceedings of the ACL Workshop on Detecting Structure in Scholarly Discourse (DSSD) (URL)
Mihăilă, C., Batista-Navarro, R. and Ananiadou, S. (2012). Analysing Entity Type Variation across Biomedical Subdomains. In: Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012), Istanbul, Turkey (URL)
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Miwa, M., Thompson, P., McNaught, J., Kell, D. B. and Ananiadou, S. (2012). Extracting semantically enriched events from biomedical literature. In: BMC Bioinformatics, 13 (DOI) (URL)
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Ananiadou, S., Sullivan, D., Black, W.J., Levow, G., Gillespie, J., Mao, C., Pyysalo, S., Kolluru, B., Tsujii, J. and Sobral, B. (2011). Named Entity Recognition for Bacterial Type IV Secretion Systems. In: PLoS ONE, 6(3) (DOI) (URL)
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Sasaki, Y., McNaught, J. and Ananiadou, S. (2010). The value of an in-domain lexicon in genomics qa. In: Journal of bioinformatics and computational biology, 8(1) (URL)
Wang, X. and Ananiadou, S. (2010). A Task-Oriented Extension of the Chinese MeSH Concepts Hierarchy. In: Proceedings of the Second Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM), LREC 2010 (URL)
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Ananiadou, S., Okazaki, N., Procter, R., Rea, B. and Thomas, J. (2009). Supporting Systematic Reviews using Text Mining. In: Social Science Computer Review, 27(4) (DOI) (URL)
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Lyte, V., Jones, S., Ananiadou, S. and Kerr, L. (2009). UK Institutional Repository Search: Innovation and Discovery. In: Ariadne, 61 (URL)
Matsuoka, Y., Ghosh, S., Kikuchi, N., Sætre, R., Kemper, B., Okazaki, N., Ananiadou, S., Tsujii, J. and Kitano, H. (2009). Community Platform for Pathway Model Building. In: 10th International Conference on Systems Biology, Stanford University (URL)
Nobata, C., Sasaki, Y., Okazaki, N., Rupp, C. J., Tsujii, J. and Ananiadou, S. (2009). Semantic Search on Digital Document Repositories based on Text Mining Results. In: International Conferences on Digital Libraries and the Semantic Web 2009 (ICSD2009)
Piao, S., Rea, B., McNaught, J. and Ananiadou, S. (2009). Improving Full Text Search With Text Mining Tools. In: Proceedings of the 14th International Conference on Applications of Natural Language to Information Systems
Piao, S., Tsuruoka, Y. and Ananiadou, S. (2009). Sentiment Analysis with Knowledge Resource and NLP Tools. In: The International Journal of Interdisciplinary Social Sciences, 4(5) (URL)
Sasaki, Y., McNaught, J. and Ananiadou, S. (2009). The Value of an In-Domain Lexicon in Genomics QA. In: Proceedings of 3rd International Symposium on Languages in Biology and Medicine (LBM-2009) (URL)
Sasaki, Y., Rea, B. and Ananiadou, S. (2009). Clinical Text Classification under the Open and Closed Topic Assumptions. In: International Journal on Data Mining and Bioinformatics (IJDMB), 3(3) (URL)
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Tekiner, F., Ananiadou, S., Tsuruoka, Y. and Tsujii, J. (2009). Highly Scalable Text Mining Parallel Tagging Application. In: Proceedings of ICSSCW2009, Famgusta, Cyprus (URL)
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Hirohata, K., Okazaki, N., Ananiadou, S. and Ishizuka, M. (2008). Identifying Sections in Scientific Abstracts using Conditional Random Fields. In: Proceedings of the 3rd International Joint Conference on Natural Language Processing (IJCNLP 2008)
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Nobata, C., Cotter, P., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y., Tsujii, J. and Ananiadou, S. (2008). 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
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Piao, S., McNaught, J. and Ananiadou, S. (2008). Clustering Related Terms with Definitions. In: Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC 2008), European Language Resources Association (ELRA)
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Sasaki, Y., Thompson, P., Cotter, P., McNaught, J. and Ananiadou, S. (2008). Event Frame Extraction Based on a Gene Regulation Corpus. In: Proceedings of the 22nd International Conference on Computational Linguistics (Coling 2008), Coling 2008 Organizing Committee
Sasaki, Y., Tsuruoka, Y., McNaught, J. and Ananiadou, S. (2008). How to make the most of NE dictionaries in statistical NER. In: BMC Bioinformatics, 9(Suppl 11)
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Splendiani, A., Piao, S., Sasaki, Y., Ananiadou, S., McNaught, J. and Burgun, A (2008). Compositional Enrichment of Bio-Ontologies. In: Proceedings of 11th Annual Bio-Ontologies Meeting, at the Intelligent Systems for Molecular Biology 2008 Conference (ISMB-2008)
Thompson, P., Cotter, P., McNaught, J., Ananiadou, S., Montemagni, S., Trabucco, A. and Venturi, G. (2008). 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), European Language Resources Association (ELRA)
Thompson, P., Venturi, G., McNaught, J., Montemagni, S. and Ananiadou, S. (2008). Categorising Modality in Biomedical Texts. In: Proceedings of the LREC 2008 Workshop on Building and Evaluating Resources for Biomedical Text Mining.
Tsuruoka, Y., McNaught, J. and Ananiadou, S. (2008). Normalizing biomedical terms by minimizing ambiguity and variability. In: BMC Bioinformatics, 9(Suppl 3)
Tsuruoka, Y., Tsujii, J. and Ananiadou, S. (2008). FACTA: a text search engine for finding associated biomedical concepts. In: Bioinformatics, 24(21)
Tsuruoka, Y., Tsujii, J. and Ananiadou, S. (2008). Accelerating the annotation of sparse named entities by dynamic sentence selection. In: BMC Bioinformatics, 9(Suppl 11)
Tsuruoka, Y., Tsujii, J. and Ananiadou, S. (2008). 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

Ananiadou, S. (2007). The National Centre for Text Mining: a Vision for the Future. In: Ariadne, 53 (URL)
Ananiadou, S., Cotter, P., Nobata, C., Okazaki, N., Rea, B., Sasaki, Y., Tsuruoka, Y. and Tsujii, J. (2007). SemText: a semantically enriched information retrieval system for biology. In: Proceedings of the 8th International Conference on Systems Biology (ICSB 2007)
Ananiadou, S., Procter, R., Rea, B., Sasaki, Y. and Thomas, J. (2007). Supporting Systematic Reviews using Text Mining. In: Proceedings of the 3rd International Conference on e-Social Science
Frantzi, K. and Ananiadou, S. (2007). C-value for Authorship Identification. In: Proceedings of the 8th Conference on Forensic Linguistics, Language and Law, International Association of Forensic Linguistics
Hahn, U., Buyko, E., Tomanek, K., Piao, S., McNaught, J., Tsuruoka, Y. and Ananiadou, S. (2007). An Annotation Type System for a Data-Driven NLP Pipeline. In: Proceedings of the Linguistic Annotation Workshop, Association for Computational Linguistics
Piao, S., Ananiadou, S. and McNaught, J. (2007). Integrating Annotation Tools into UIMA for Interoperability. In: Proceedings of the UK e-Science AHM Conference 2007
Piao, S., Ananiadou, S., Tsuruoka, Y., Sasaki, Y. and McNaught, J. (2007). Mining Opinion Polarity Relations of Citations. In: Proceedings of the 7th International Workshop on Computational Semantics
Piao, S., Buyko, E., Tsuruoka, Y., Tomanek, K., Kim, J.-D., McNaught, J., Hahn, U., Su, J. and Ananiadou, S. (2007). BOOTStrep Annotation Scheme: Encoding Information for Text Mining. In: Proceedings of the 4th Corpus Linguistics Conference (CL2007)
Rea, B. and Ananiadou, S. (2007). Text Mining Services to Support E-Research. In: UK e-Science All Hands Meeting
Sasaki, Y., Rea, B. and Ananiadou, S. (2007). Multi-topic Aspects in Clinical Text Classification. In: BIBM ’07: Proceedings of the 2007 IEEE International Conference on Bioinformatics and Biomedicine, IEEE Computer Society
Tsuruoka, Y., McNaught, J., Tsujii, J. and Ananiadou, S. (2007). Learning string similarity measures for gene/protein name dictionary look-up using logistic regression. In: Bioinformatics, 23(20)

Ananiadou, S. and Fluck, J.(Eds.) Second International Symposium on Semantic Mining in Biomedicine (SMBM) (URL)
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Kim, J.-D., Ananiadou, S. and Tsujii, J. (2006). Ontology based Semantic Annotation for Knowledge Extraction. In: 2nd International Digital Curation Conference
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Mima, H., Ananiadou, S. and Matsushima, K. (2006). Terminology-Based Knowledge Mining for New Knowledge Discovery. In: ACM Transactions on Asian Language Information Processing (TALIP), 5(1)
Nenadić, G. and Ananiadou, S. (2006). Mining Semantically Related Terms from Biomedical Literature. In: ACM Transactions on Asian Language Information Processing (TALIP), 5(1)
Okazaki, N. and Ananiadou, S. (2006). Clustering Acronyms in Biomedical Text for Disambiguation. In: Proceedings of Fifth International conference on Language Resources and Evaluation (LREC 2006)
Okazaki, N. and Ananiadou, S. (2006). Building an Abbreviation Dictionary using a Term Recognition Approach. In: Bioinformatics, 22(24)

Ananiadou, S., Chruszcz, J., Keane, J., McNaught, J. and Watry, P. (2005). The National Centre for Text Mining: Aims and Objectives. In: Ariadne, 42 (URL)
Nenadić, G., Spasić, I. and Ananiadou, S. (2005). Mining Biomedical Abstracts: What’s in a Term?. In: Su, K.-Y., Tsujii, J., Lee, J.-H. and Kwong, O. Y.(Eds.) Natural Language Processing – IJCNLP 2004, Springer-Verlag
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Tsujii, J. and Ananiadou, S. (2005). Thesaurus or Logical Ontology, Which One Do We Need for Text Mining?. In: Language Resources and Evaluation, 39(1)
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Tsuruoka, Y., Tateisi, Y., Kim, J.-D., Ohta, T., McNaught, J., Ananiadou, S. and Tsujii, J. (2005). Developing a Robust Part-of-Speech Tagger for Biomedical Text. In: Advances in Informatics – 10th Panhellenic Conference on Informatics, Springer-Verlag

Ananiadou, S., Friedman, C. and Tsujii, J. (2004). Introduction: named entity recognition in biomedicine. In: Journal of Biomedical Informatics, 37(6) (URL)
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Spasić, I. and Ananiadou, S. (2004). Using automatically learnt verb selectional preferences for classification of biomedical terms. In: Journal of Biomedical Informatics, 37(6)
Spasić, I., Nenadić, G. and Ananiadou, S. (2004). Learning to Classify Biomedical Terms through Literature Mining and Genetic Algorithms. In: Yang, Z. R., Everson, R. and Yin, H.(Eds.) Intelligent Data Engineering and Automated Learning – IDEAL 2004, Springer-Verlag

Nenadic, G., Rice, S., Spasic, I., Ananiadou, S. & Stapley, B. (2003). Selecting Features for Text- based Classification: from Documents to Terms. In: Procs ACL, Workshop on NLP in Biomedicine, Sapporo, Japan, 121-128.
Nenadic, G., Spasic, I. & Ananiadou, S. (2003). Morpho-Syntactic Clues for Terminological Processing in Serbian. In: Procs EACL, Workshop on Morphological Processing of Slavic Languages, Budapest, Hungary, 79-86..
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Spasic, I., Nenadic, G. and Ananiadou, S. (2003). Using Domain-Specific Verbs for Term Classification. In: Procs ACL, Workshop on NLP in Biomedicine, Sapporo, Japan, 17-24

Ananiadou, S., Nenadic, G., Schuhmann, D. & Spasic, I. (2002). Term based literature mining from biomedical texts. In: Proc. of Intelligent Systems for Molecular Biology, ISMB, Text Data Mining SIG, Edmond, Canada.
Mima, H., Ananiadou, S., Nenadic, G. & Tsujii, J. (2002). A methodology for terminology-based knowledge acquisition and integration. In: Procs 19th Int. Conference on Computational Linguistics, Coling 2002, Taipei, Taiwan, 667-673.
Mima, H., Ananiadou, S., Nenadic, G., Tsujii, J. (2002). An Integrated System for Ontology-based Knowledge Structuring and Discovery. Poster at SOFG 2002 (Standards and Ontologies for Functional Genomics), Hinxton, Cambridge.
Mima, H., Ananiadou, S., Nenadic, G., Spasic, I. and Tsujii, J. (2002). Terminology-based literature mining and knowledge acquisition in biomedicine. In: International Journal of Medical Informatics 67(1-3):33-48
Mima, H., Ananiadou, S., Nenadic, G. & Tsujii, J. (2002). TIMS: A workbench for ontology- based knowledge acquisition and integration. In: Procs. Workshop on Natural Language Processing in Biomedical Applications, Nicosia, Cyprus, 11-15.
Mima, H., Ananiadou, S., Nenadic, G. & Tsujii, J. (2002). XML tag information management system: A workbench for ontology-based knowledge acquisition and integration. In: Procs Human Language Technology Conference (HLT 2002), San Diego, California, USA, 286-292.
Nenadic, G., Spasic, I., & Ananiadou, S. (2002). Automatic acronym acquisition and management with domain specific texts. In: Procs LREC-3, 3rd International Conference on Language, Resources and Evaluation, Las Palmas, Spain, 2155-2162.
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Spasic, I., Nenadic, G. & Ananiadou, S. (2002). Tuning Context Features with Genetic Algorithms. In: Procs LREC-3, 3rd International Conference on Language, Resources and Evaluation, Las Palmas, Spain, 2048-2054.

Maynard, D. and Ananiadou, S. (2001). Term extraction using a similarity-based approach. In: Bourigault, D., Jacquemin, C. & L’Homme, M-C. (Eds.) Recent Advances in Computational Terminology. Natural Language Processing Series Vol. 2. John Benjamins, Amsterdam, 261–279.
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Ananiadou, S., Albert, S. & Schuhmann, D. (2000). Evaluation of automatic term recognition of nuclear receptors from Medline. Genome Informatics Series, vol.11.
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Mima, H. and Ananiadou, S. (2000). An application and evaluation of the C/NC-value approach for the automatic term recognition of multi-word units in Japanese. In: International Journal of Terminology 6(2):175–194

Frantzi, K., Ananiadou, S. and Tsujii, J. (1999). Automatic classification of technical terms using the NC-value method for term recognition. In: Proc. Int. Conf. on Computational Lexicography (COMPLEX ’99). Budapest, Hungary, 57–66.
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Ananiadou, S. (1998). Machine translation trends in Europe and in Japan. In: Proc. Translating and the Computer 20. Aslib, London, ISBN 0 85142 4171.
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Marshall, P., Bandar, Z. and Ananiadou, S. (1998). A connectionist approach to term recognition. In: Proc. 12th Int. Conf. on Artificial Intelligence and Expert Systems Applications. Virginia, USA.
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Mima, H., Frantzi, K. and Ananiadou S. (1998), 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. Held at 5th Pacific Rim Int. Conf. on Artificial IntelligenceI (PRICAI ’98). Singapore, 10–21.

Ananiadou, S. (1997) Term recognition for information retrieval and information extraction. In: Proc. Int. Workshop on NLP and Information Retrieval. Held at Natural Language Processing Pacific Rim Symposium (NLPRS ’97). Phuket, Thailand.
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Ananiadou, S. (1996). Towards a linguistic treatment of compounds in a machine translation environment. In: Journal of Natural Language Processing 3(1), 45–66.
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Ananiadou, S. (1995). Automatic recognition of medical terminology (Immunology). In: Proc. MedInfo ’95. Vancouver, 3–8.
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Frantzi, K. & Ananiadou, S. (1995). Statistical approaches for collocation extraction and term recognition. In: Proc. 16th Ann. Mtng. of the Department of Linguistics. Aristotle University of Thessaloniki, 681-693. Kyriakides pub.
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Ananiadou, S. (1993). A sublanguage approach to automatic term recognition. In: Proc. Natural Language Processing Pacific Rim Symposium (NLPRS ’93). Fukuoka, Japan, 159–164.
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Olivier P., Ananiadou, S. and Tsujii, J. (1992). A visualisation architecture based on the systematicity of language. In: Proc. Pacific Rim International Conference on AI (PRICAI). Seoul, Korea.
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Ananiadou, S. and Antona, M. (1991). Multilingual linguistic aspects of machine translation. In: Proc. 12th Ann. Mtng. of the Department of Linguistics: Studies in Greek Linguistics. Aristotle University of Thessaloniki. Kyriakides pub., 291–305.
Ananiadou, S., Ralli, A. and Villalva, A. (1991). The treatment of derivational morphology in a multilingual transfer-based machine translation system: EUROTRA. In: Language Research 27(4), 627–638.
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