Publications

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2013

  1. Thomas, J. M., O'Mara-Eves, A., Mcnaught, J., & Ananiadou, S. (2013). Re: The automation of systematic reviews. British Medical Journal, 346. . Publication link: 5b2df045-65aa-4a16-ae2f-7c97b102beba
  2. Alhazmi, S., Black, W., & McNaught, J. (2013). Arabic SentiWordNet in Relation to SentiWordNet 3.0. International Journal of Computational Linguistics, 4(1), 1-11. . Publication link: acaa87af-fa6c-4c61-9d22-7516203a1a81
  3. Thompson, P., Nawaz, R., Korkontzelos, I., Black, W., McNaught, J., & Ananiadou, S. (2013). 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.|Proc. Digit. Herit. Int. Congr., DigitalHeritage - Fed. Int. VSMM, Eurographics GCH, UNESCO Mem. World Conf., Plus Spec. Ses. (Vol. 1, pp. 597-604). Piscataway, NJ: IEEE. DOI: 10.1109/DigitalHeritage.2013.6743801. Publication link: c234c92d-a12b-489b-835d-61ef14cee0d8
  4. Thomas, J., O'Mara-Eves, A., McNaught, J., & Ananiadou, S. (2013). The potential of text mining to reduce screening workload in systematic reviews: a retrospective evaluation. 5-5. Poster session presented at 21st Cochrane Colloquium, Quebec, .. Publication link: fc5da96d-54a7-40b5-b41b-571c413eeebb
  5. Thompson, P., Nawaz, R., Korkontzelos, I., Black, W., McNaught, J., & Ananiadou, S. (2013). 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.|Proc. Digit. Herit. Int. Congr., DigitalHeritage - Fed. Int. VSMM, Eurographics GCH, UNESCO Mem. World Conf., Plus Spec. Ses. (Vol. 1, pp. 597-604). Piscataway, NJ: IEEE. DOI: 10.1109/DigitalHeritage.2013.6743801. Publication link: c234c92d-a12b-489b-835d-61ef14cee0d8
  6. Mih{\u{a}}il{\u{a}}, C., & Ananiadou, S. (2013). What causes a causal relation? Detecting causal triggers in biomedical scientific discourse. In I. Nikolova, E. Vecchi, A. Dey, & S. Krause (Eds.), 51st Annual Meeting of the Association for Computational Linguistics Proceedings of the Student Research Workshop. (pp. 38-45). Association for Computational Linguistics. . Publication link: b32bb001-a687-489f-93fc-192d52794cf8
  7. Mihǎilǎ, C., Ohta, T., Pyysalo, S., & Ananiadou, S. (2013). BioCause: Annotating and analysing causality in the biomedical domain. BMC Bioinformatics, 14, [2]. DOI: 10.1186/1471-2105-14-2. Publication link: ac0972fc-0710-465d-8d95-390b308ae18c
  8. Ohta, T., Pyysalo, S., Rak, R., Rowley, A., Chun, H-W., Jung, S. -J., ... Ananiadou, S. (2013). Overview of the Pathway Curation (PC) task of BioNLP Shared Task 2013. In Proceedings of the BioNLP Shared Task 2013 Workshop. (pp. 67-75). Association for Computational Linguistics. . Publication link: 9f4307bb-ed2d-444e-a21b-9933b961f4b3
  9. Ananiadou, S., Thompson, P., & Nawaz, R. (2013). Mining events from the literature for bioinformatics applications. ACM SIGWEB Newsletter, Autumn 2013. . Publication link: a133e6bc-0db0-4e85-89d1-d26772c5c687
  10. Ananiadou, S., Thompson, P., & Nawaz, R. (2013). Enhancing search: Events and their discourse context. 318-334. 14th Annual Conference on Intelligent Text Processing and Computational Linguistics, CICLing 2013, Samos, .DOI: 10.1007/978-3-642-37256-8_27. Publication link: e1bf77df-5d06-4e5f-98c8-50e19158a2b2
  11. Batista-Navarro, R. T., Kontonatsios, G., Mihaila, C., Thompson, P., Nawaz, R., Korkontzelos, I., & Ananiadou, S. (2013). Supporting Discourse Phenomena in an Interoperable NLP Framework. In host publication.. Publication link: cd8dcfd4-6be7-41a3-a0b5-134362040738
  12. Rak, R., & Ananiadou, S. (2013). Making UIMA Truly Interoperable with SPARQL. In Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse. (pp. 88-97). Publication link: d468c3dc-044e-4f28-9bab-f8beacdb0c59
  13. Kontonatsios, G., Korkontzelos, I., Tsujii, J., & 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. (pp. 95-104). Association for Computational Linguistics. . Publication link: fd594c3d-7d75-4263-bd06-8de9da305cee
  14. Thomas, J., O'Mara-Eves, A., McNaught, J., & Ananiadou, S. (2013). The potential of text mining to reduce screening workload in systematic reviews: a retrospective evaluation. 5-5. Poster session presented at 21st Cochrane Colloquium, Quebec, .. Publication link: fc5da96d-54a7-40b5-b41b-571c413eeebb
  15. Nawaz, R., Thompson, P., & Ananiadou, S. (2013). Towards Event-based Discourse Analysis of Biomedical Text. International Journal of Computational Linguistics and Applications, 4(2), 101-120. . Publication link: f55e9056-4229-4b62-baf4-95af59501c1e
  16. Rutter, M., Ananiadou, S., Ohta, T., & Rutter, M. K. (2013). Text Mining Supporting Search for Knowledge Discovery in Diabetes. Current Cardiovascular Risk Reports, 7(1), 1-8. DOI: 10.1007/s12170-012-0288-3. Publication link: 157385a7-8973-4876-bdd3-1ccd60107927
  17. Ananiadou, S., Thompson, P., & Nawaz, R. (2013). Enhancing Search: Events and their Discourse Context. In Computational Linguistics and Intelligent Text Processing. (Vol. 7817, pp. 318-334). (Lecture Notes in Computer Science). Springer Verlag. DOI: 10.1007/978-3-642-37256-8_27. Publication link: 18ea668e-394f-4a00-8897-74595f479029
  18. Miwa, M., Pyysalo, S., Ohta, T., & Ananiadou, S. (2013). Wide coverage biomedical event extraction using multiple partially overlapping corpora. BMC Bioinformatics, 14(175). DOI: 10.1186/1471-2105-14-175. Publication link: 22fd4ab9-980c-42d5-92c0-9587fe0b2c51
  19. Rak, R., Batista-Navarro, R. T., Rowley, A., Miwa, M., Carter, J., & Ananiadou, S. (2013). NaCTeM’s BioC Modules and Resources for BioCreative IV. In Proceedings of the Fourth BioCreative Challenge Evaluation Workshop. (Vol. 1, pp. 61-67). Publication link: 07d8ae4b-470b-43e9-8572-798c3f64f83c
  20. Rak, R., Batista-Navarro, R. T., Rowley, A., Carter, J., & Ananiadou, S. (2013). Customisable Curation Workflows in Argo. In Proceedings of the Fourth BioCreative Challenge Evaluation Workshop. (Vol. 1, pp. 270-278). Publication link: 12b1457a-63e5-46fc-9ede-15998bc17f4f
  21. Mihǎilǎ, C., & 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. (pp. 361-366). IEEE. DOI: 10.1109/BIBM.2013.6732519. Publication link: 11d26261-1a3b-44bd-b69a-1b683a13a459
  22. Batista-Navarro, R. T., Rak, R., & Ananiadou, S. (2013). NaCTeM CTD Web Services. In Proceedings of the Fourth BioCreative Challenge Evaluation Workshop. (Vol. 1, pp. 85-89). Publication link: 34d6062d-6f23-4a40-8232-250f68f2b745
  23. Van Landeghem, S., Björne, J., Wei, C. H., Hakala, K., Pyysalo, S., Ananiadou, S., ... Ginter, F. (2013). Large-scale event extraction from literature with multi-level gene normalization. PLoS ONE, 8(4). DOI: 10.1371/journal.pone.0055814. Publication link: 32ea34e0-fe1f-4786-adb9-53687c139ba5
  24. Miwa, M., & Ananiadou, S. (2013). NaCTeM EventMine for BioNLP 2013 CG and PC tasks. In Proceedings of BioNLP Shared Task 2013 Workshop. (pp. 94-98). Association for Computational Linguistics. . Publication link: 3ac4b36f-5c1b-4684-ab0b-9079430abdd8
  25. Mihaila, C., Kontonatsios, G., Thompson, P., Batista-Navarro, R. T., Mihaila, C., Korkontzelos, I., ... Hussain, S. (Ed.) (2013). Extending an interoperable platform to facilitate the creation of multilingual and multimodal NLP applications. In M. Butt, & S. Hussain (Eds.), Proceedings of the System Demonstration Session at The 51st Annual Meeting of the Association for Computational Linguistics. (pp. 43-48). Association for Computational Linguistics. . Publication link: 3d66b057-6d0e-452d-9adf-51d48c1997e9
  26. Nawaz, R., Thompson, P., & Ananiadou, S. (2013). Negated BioEvents: Analysis and Identification. BMC Bioinformatics, 14(1). DOI: doi:10.1186/1471-2105-14-14. Publication link: 3d881840-2bb1-48ad-8bfc-6d1a04645fe0
  27. Batista-Navarro, R. T., Kontonatsios, G., Mihǎilǎ, C., Thompson, P., Rak, R., Nawaz, R., ... Ananiadou, S. (2013). 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)|Lect. Notes Comput. Sci.. (Vol. 7816, pp. 559-571). (Lecture Notes in Computer Science). Berlin, Germany: Springer Berlin Heidelberg. DOI: 10.1007/978-3-642-37247-6_45. Publication link: 4a56f75f-ae30-4b93-88af-50cefd4a1169
  28. Pyysalo, S., Ohta, T., & Ananiadou, S. (2013). Overview of the Cancer Genetics (CG) task of BioNLP Shared Task 2013. In Proceedings of the BioNLP Shared Task 2013 Workshop. (pp. 58-66). Association for Computational Linguistics. . Publication link: 4d770228-292e-4a1e-a04c-319351f8b324
  29. Pyysalo, S., Ginter, F., Moen, H., Salakoski, T., & Ananiadou, S. (2013). Distributional Semantics Resources for Biomedical Text Processing. In Proceedings of LBM 2013. (pp. 39-44). Publication link: 8b865ebe-417a-41fb-acb7-241efe6a5490
  30. Mih{\u{a}}il{\u{a}}, C., Ananiadou, S., & Mihǎilǎ, C. (2013). Recognising Discourse Causality Triggers in the Biomedical Domain. Journal of Bioinformatics and Computational Biology, 11(6), [1343008]. DOI: 10.1142/S0219720013430087. Publication link: 868e3424-d42d-4e89-ab87-e8358a0fca86
  31. Batista-Navarro, R. T., Rak, R., & 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. (Vol. 2, pp. 55-59). Publication link: 87835651-2c0b-4dc3-a9b2-4057009a4cb9
  32. Restificar, A., Korkontzelos, I., & Ananiadou, S. (2013). A method for discovering and inferring appropriate eligibility criteria in clinical trial protocols without labeled data. BMC Medical Informatics and Decision Making, 13(Suppl 1). DOI: 10.1186/1472-6947-13-S1-S6. Publication link: 7f225dbc-4440-49f7-a5a5-0afa3b2ca3b4
  33. Rak, R., Rowley, A., Carter, J., & 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. (pp. 115-120). Publication link: 79288ae2-428a-4bfd-b058-6bdeaf3aa8cf
  34. Mihaila, C., Kontonatsios, G., Batista-Navarro, R. T., Thompson, P., Korkontzelos, I., & 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. (pp. 79-88). Publication link: 535590d0-7e51-482c-9963-5fad56c39def
  35. Miwa, M., Ohta, T., Rak, R., Rowley, A., Kell, D. B., Pyysalo, S., & Ananiadou, S. (2013). A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text.Bioinformatics (Oxford, England), 29(13), i44-i52. DOI: 10.1093/bioinformatics/btt227. Publication link: 54206554-9942-4ff4-bded-a6bb9aca5a34 | PubMed:23813008
  36. Hakenberg, J., Nenadic, G., Rebholz-Schuhmann, D., & Kim, J. D. (2013). Literature mining solutions for life science research. Advances in Bioinformatics, 2013, [320436]. DOI: 10.1155/2013/320436. Publication link: 0bb073f7-f745-45d2-9360-b4240798d68c
  37. Tian, D., Gledson, A., Antoniades, A., Aristodimou, A., Dimitrios, N., Sahay, R., ... Keane, J. (2013). A bayesian association rule mining algorithm. In Proceedings - 2013 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2013|Proc. - IEEE Int. Conf. Syst., Man, Cybern., SMC. (pp. 3258-3264). IEEE Xplore. DOI: 10.1109/SMC.2013.555. Publication link: 046f4cec-681b-468a-b0d4-09e1780e4385
  38. Jamieson, D. G., Roberts, P. M., Robertson, D. L., Sidders, B., & Nenadic, G. (2013). Cataloguing the biomedical world of pain through semi-automated curation of molecular interactions. Database, [bat033]. DOI: doi:10.1093/database/bat033. Publication link: 8dc3088c-3e50-43c3-9a45-409cdc068df1
  39. Kovačević, A., Dehghan, A., Filannino, M., Keane, J. A., & Nenadic, G. (2013). Combining rules and machine learning for extraction of temporal expressions and events from clinical narratives. Journal of the American Medical Informatics Association, 20(5), 859-866. DOI: 10.1136/amiajnl-2013-001625. Publication link: 6c459eae-4583-455d-9ec6-80adb154ef39
  40. Duck, G., Nenadic, G., Brass, A., Robertson, D. L., & Stevens, R. (2013). BioNerDS: Exploring bioinformatics' database and software use through literature mining. BMC Bioinformatics, 14(1), [194]. DOI: 10.1186/1471-2105-14-194. Publication link: 705055ba-b73f-4ac1-b434-c91d5dec5042 | PubMed:23768135
  41. Wu, C., Schwartz, J-M., & Nenadic, G. (2013). PathNER: A tool for systematic identification of biological pathway mentions in the literature. BMC Systems Biology, 7(Suppl3). DOI: 10.1186/1752-0509-7-S3-S2. Publication link: c18b09b0-894d-42dd-9b15-38e7373e5939 | PubMed:24555844
  42. Rodriguez-Martinez, E., Mu, T., Jiang, J., & Goulermas, J. Y. (2013). Automated induction of heterogeneous proximity measures for supervised spectral embedding. IEEE Transactions on Neural Networks and Learning Systems, 24(10), 1575-1587. . Publication link: 8bfbc46f-61a2-4feb-ad76-c8181d70fee1
  43. Wang, Y., Jiang, J., & Mu, T. (2013). Context-aware and energy-driven route optimization for fully electric vehicles via crowdsourcing. IEEE Transactions on Intelligent Transportation Systems, 14(3), 1331-1345. . Publication link: 8e3911b3-4f66-4d81-ba5a-0bc953ec4b0f
  44. Mu, T., Jiang, J., & Wang, Y. (2013). Heterogeneous delay embedding for travel time and energy cost prediction via regression analysis. IEEE Transactions on Intelligent Transportation Systems, 14(1), 214-224. . Publication link: 85e74ca3-cb0f-43eb-ac67-69dc57e5b36e
  45. Mu, T., & Goulermas, J. Y. (2013). Automatic generation of co-embeddings from relational data with adaptive shaping. IEEE Transactions on Pattern Analysis and Machine Intelligence, 35(10), 2340-2356. . Publication link: ebed5b28-9062-410c-80a0-95f91e5a46a8
  46. Batista-Navarro, R. T., Kontonatsios, G., Mihaila, C., Thompson, P., Nawaz, R., Korkontzelos, I., & Ananiadou, S. (2013). Supporting Discourse Phenomena in an Interoperable NLP Framework. In host publication.. Publication link: cd8dcfd4-6be7-41a3-a0b5-134362040738
  47. Mihaila, C., Kontonatsios, G., Batista-Navarro, R. T., Thompson, P., Korkontzelos, I., & 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. (pp. 79-88). Publication link: 535590d0-7e51-482c-9963-5fad56c39def
  48. Batista-Navarro, R. T., Rak, R., & 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. (Vol. 2, pp. 55-59). Publication link: 87835651-2c0b-4dc3-a9b2-4057009a4cb9
  49. Rak, R., Batista-Navarro, R. T., Rowley, A., Carter, J., & Ananiadou, S. (2013). Customisable Curation Workflows in Argo. In Proceedings of the Fourth BioCreative Challenge Evaluation Workshop. (Vol. 1, pp. 270-278). Publication link: 12b1457a-63e5-46fc-9ede-15998bc17f4f
  50. Rak, R., Batista-Navarro, R. T., Rowley, A., Miwa, M., Carter, J., & Ananiadou, S. (2013). NaCTeM’s BioC Modules and Resources for BioCreative IV. In Proceedings of the Fourth BioCreative Challenge Evaluation Workshop. (Vol. 1, pp. 61-67). Publication link: 07d8ae4b-470b-43e9-8572-798c3f64f83c
  51. Mihaila, C., Kontonatsios, G., Thompson, P., Batista-Navarro, R. T., Mihaila, C., Korkontzelos, I., ... Hussain, S. (Ed.) (2013). Extending an interoperable platform to facilitate the creation of multilingual and multimodal NLP applications. In M. Butt, & S. Hussain (Eds.), Proceedings of the System Demonstration Session at The 51st Annual Meeting of the Association for Computational Linguistics. (pp. 43-48). Association for Computational Linguistics. . Publication link: 3d66b057-6d0e-452d-9adf-51d48c1997e9
  52. Batista-Navarro, R. T., Kontonatsios, G., Mihǎilǎ, C., Thompson, P., Rak, R., Nawaz, R., ... Ananiadou, S. (2013). 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)|Lect. Notes Comput. Sci.. (Vol. 7816, pp. 559-571). (Lecture Notes in Computer Science). Berlin, Germany: Springer Berlin Heidelberg. DOI: 10.1007/978-3-642-37247-6_45. Publication link: 4a56f75f-ae30-4b93-88af-50cefd4a1169
  53. Batista-Navarro, R. T., Rak, R., & Ananiadou, S. (2013). NaCTeM CTD Web Services. In Proceedings of the Fourth BioCreative Challenge Evaluation Workshop. (Vol. 1, pp. 85-89). Publication link: 34d6062d-6f23-4a40-8232-250f68f2b745
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