Publications

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2009

  1. Thompson, P., Iqbal, S. A., McNaught, J., & Ananiadou, S. (2009). Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics, 10, [349]. DOI: 10.1186/1471-2105-10-349. Publication link: 7fbe472f-ae7d-48ea-b90d-84e21b4b41d9
  2. Venturi, G., Montemagni, S., Marchi, S., Sasaki, Y., Thompson, P., McNaught, J., & Ananiadou, S. (2009). Bootstrapping a verb lexicon for biomedical information extraction. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. (Vol. 5449, pp. 137-148). Heidelberg: Springer Verlag. DOI: 10.1007/978-3-642-00382-0_11. Publication link: 2f5107ee-df3e-4c23-b7e8-21ae939f9c9d
  3. Sasaki, Y., Thompson, P., McNaught, J., & Ananiadou, S. (2009). Biological event recognition with textual induction. In Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM-2009). (pp. 91-96). Publication link: 33aab968-bdc2-4736-989a-e674790fab34
  4. Algahtani, S., Black, W., & McNaught, J. (2009). Arabic part of speech tagging using Tranformation-Based Learning. In Proceedings of the 2nd International Conference on Arabic Language Resources and Tools. (pp. -5pp). Publication link: c568fcf7-ad48-4930-9ef5-a3ba2d09be57
  5. Piao, S., Rea, B., McNaught, J., & Ananiadou, S. (2009). Improving full text search with text mining tools. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. (Vol. 5723, pp. 301-302). DOI: 10.1007/978-3-642-12550-8_29. Publication link: cf06ab8d-b1a0-4de1-8fe6-5b45c0987278
  6. Thew, S., Sutcliffe, A., Procter, R., de Bruijn, O., McNaught, J., Venters, C., & Buchan, I. (2009). Requirements engineering for E-science: Experiences in epidemiology. IEEE Software, 26(1), 80-87. DOI: 10.1109/MS.2009.19. Publication link: ea545bcf-b25f-4af4-953d-9e0385a0ea2f
  7. Sasaki, Y., Thompson, P., McNaught, J., & Ananiadou, S. (2009). Three BioNLP Tools Powered by the BioLexicon. In Proceeedings of EACL 2009 : Demonstration Session. (pp. 61-64). Publication link: f1842e1c-3d51-4925-97c0-c19574b18500
  8. Lyte, V., Jones, S., Ananiadou, S., & Kerr, L. (2009). UK Institutional Repository Search: Innovation and Discovery. Ariadne, (61). . Publication link: f944e196-e058-46ba-ac5c-cbde0da61590
  9. Sasaki, Y., Thompson, P., McNaught, J., & Ananiadou, S. (2009). Three BioNLP Tools Powered by the BioLexicon. In Proceeedings of EACL 2009 : Demonstration Session. (pp. 61-64). Publication link: f1842e1c-3d51-4925-97c0-c19574b18500
  10. Ananiadou, S., Rea, B., Okazaki, N., Procter, R., & Thomas, J. (2009). Supporting systematic reviews using text mining. Social Science Computer Review, 27(4), 509-523. DOI: 10.1177/0894439309332293. Publication link: c84fa55b-0e31-4933-9bab-fb303e59c5fc
  11. Tekiner, F., Tsuruoka, Y., Tsujii, J., & Ananiadou, S. (2009). Highly scalable text mining - Parallel tagging application. In ICSCCW 2009 - 5th International Conference on Soft Computing, Computing with Words and Perceptions in System Analysis, Decision and Control|ICSCCW - Int. Conf. Soft Comput., Comput. Words Percept. Syst. Anal., Decis. Control. DOI: 10.1109/ICSCCW.2009.5379432. Publication link: ca929ed7-1e01-47e3-8135-3e7d605ce22b
  12. Kano, Y., Baumgartner, W. A., McCrohon, L., Ananiadou, S., Cohen, K. B., Hunter, L., & Tsujii, J. (2009). U-Compare: Share and compare text mining tools with UIMA. Bioinformatics, 25(15), 1997-1998. DOI: 10.1093/bioinformatics/btp289. Publication link: ced41bac-7839-45a6-a860-34f8af02eeac
  13. Piao, S., Rea, B., McNaught, J., & Ananiadou, S. (2009). Improving full text search with text mining tools. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. (Vol. 5723, pp. 301-302). DOI: 10.1007/978-3-642-12550-8_29. Publication link: cf06ab8d-b1a0-4de1-8fe6-5b45c0987278
  14. Barrón-Cedeño, A., Sierra, G., Drouin, P., & Ananiadou, S. (2009). An improved automatic term recognition method for spanish. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. (Vol. 5449, pp. 125-136). Proceedings of the 10th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing 2009): Springer Verlag. DOI: 10.1007/978-3-642-00382-0_10. Publication link: ea2ef5da-be16-4dc7-9c57-8ffb476dfe41
  15. Ananiadou, S., Sasaki, Y., & McNaught, J. (2009). The Value of an In-Domain Lexicon in Genomics QA. In host publication. (pp. 47-55). Publication link: 69061eaa-6ff3-44b0-9131-2080e91dc7df
  16. Matsuoka, Y., Ghosh, S., Kikuchi, N., Sætre, R., Kemper, B., Okazaki, N., ... Kitano, H. (2009). Community Platform for Pathway Model Building. In 10th International Conference on Systems Biology. (pp. 139-140). Publication link: 77003d05-43df-4c10-ad94-c225b33957cd
  17. Nobata, C., Sasaki, Y., Okazaki, N., Rupp, C. J., Tsujii, J., & 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). (pp. 34-48). Publication link: 74687ed7-ec1f-4aa5-b17b-ff62aa997c99
  18. Ananiadou, S. (2009). Text mining for biomedicine. In Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration|Info. Retr. in Biomed.: Nat. Lang. Proc. for Knowledge Intgn.. (pp. 1-9). IGI Global. DOI: 10.4018/978-1-60566-274-9.ch001. Publication link: 5475d3f5-926b-4e9c-8861-08b2c26737f9
  19. Rea, B., Weissenbacher, D., Sasaki, Y., Thomas, J., & Ananiadou, S. (2009). ASSIST: Education Evidence Portal. In Proceedings of the UK e-Science All Hands Meeting 2009.. Publication link: 5c68597b-8668-4f20-98fc-6bf7629ec0b8
  20. Tsuruoka, Y., Tsujii, J., & Ananiadou, S. (2009). Fast full parsing by linear-chain conditional random fields. In EACL 2009 - 12th Conference of the European Chapter of the Association for Computational Linguistics, Proceedings|EACL - Conf. Eur. Chapter Assoc. Comput. Linguist., Proc.. (pp. 790-798). Publication link: 8796c4a1-ebce-4e14-988c-02286248ea5a
  21. Thompson, P., Iqbal, S. A., McNaught, J., & Ananiadou, S. (2009). Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics, 10, [349]. DOI: 10.1186/1471-2105-10-349. Publication link: 7fbe472f-ae7d-48ea-b90d-84e21b4b41d9
  22. Piao, S., Tsuruoka, Y., & Ananiadou, S. (2009). Sentiment analysis with knowledge resource and NLP tools. International Journal of Interdisciplinary Social Sciences, 4(5), 17-28. . Publication link: 8e72cdf5-f64b-457c-bb7e-5eccf2c8b6ae
  23. Ananiadou, S., Weissenbacher, D., Rea, B., Pieri, E., Lin, Y., Vis, F., ... Halfpenny, P. (2009). Supporting Frame Analysis using Text Mining. In Proceedings of the 5th International Conference on e-Social Science.. Publication link: 26dd5fc9-5ab0-4392-9a36-704f739f0835
  24. Wang, X., Tsujii, J., & Ananiadou, S. (2009). Classifying relations for biomedical named entity disambiguation. In EMNLP 2009 - Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: A Meeting of SIGDAT, a Special Interest Group of ACL, Held in Conjunction with ACL-IJCNLP 2009|EMNLP - Proc. Conf. Empir. Methods Nat. Lang. Process.: Meet. SIGDAT, Spec. Interest Group ACL, Held Conjunction ACL-IJCNLP. (pp. 1513-1522). Publication link: 134d55cf-e519-4377-b749-07496bd1604a
  25. Sasaki, Y., Thompson, P., McNaught, J., & Ananiadou, S. (2009). Biological event recognition with textual induction. In Proceedings of the 3rd International Symposium on Languages in Biology and Medicine (LBM-2009). (pp. 91-96). Publication link: 33aab968-bdc2-4736-989a-e674790fab34
  26. Venturi, G., Montemagni, S., Marchi, S., Sasaki, Y., Thompson, P., McNaught, J., & Ananiadou, S. (2009). Bootstrapping a verb lexicon for biomedical information extraction. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. (Vol. 5449, pp. 137-148). Heidelberg: Springer Verlag. DOI: 10.1007/978-3-642-00382-0_11. Publication link: 2f5107ee-df3e-4c23-b7e8-21ae939f9c9d
  27. Kano, Y., McCrochon, L., Ananiadou, S., & Tsujii, J. (2009). Integrated NLP Evaluation System for Pluggable Evaluation Metrics with Extensive Interoperable Toolkit. In Proceedings of the NAACL HLT Workshop on Software Engineering, Testing, and Quality Assurance for Natural Language Processing. (pp. 22-30). Publication link: 3c2c7b56-40bb-4656-8686-b49638de6bed
  28. Sasaki, Y., Rea, B., & Ananiadou, S. (2009). Clinical text classification under the open and closed topic assumptions. International Journal of Data Mining and Bioinformatics, 3(3), 299-313. DOI: 10.1504/IJDMB.2009.026703. Publication link: 414cb7b0-9ef6-4378-ae83-1957f0fb2dfc
  29. Kano, Y., Baumgartner, W. A., McCrohon, L., Ananiadou, S., Cohen, K. B., Hunter, L., & Tsujii, J. (2009). U-Compare: Share and compare text mining tools with UIMA. Bioinformatics, 25(15), 1997-1998. DOI: 10.1093/bioinformatics/btp289. Publication link: ced41bac-7839-45a6-a860-34f8af02eeac
  30. Tekiner, F., Tsuruoka, Y., Tsujii, J., & Ananiadou, S. (2009). Highly scalable text mining - Parallel tagging application. In ICSCCW 2009 - 5th International Conference on Soft Computing, Computing with Words and Perceptions in System Analysis, Decision and Control|ICSCCW - Int. Conf. Soft Comput., Comput. Words Percept. Syst. Anal., Decis. Control. DOI: 10.1109/ICSCCW.2009.5379432. Publication link: ca929ed7-1e01-47e3-8135-3e7d605ce22b
  31. Wang, X., Tsujii, J., & Ananiadou, S. (2009). Classifying relations for biomedical named entity disambiguation. In EMNLP 2009 - Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: A Meeting of SIGDAT, a Special Interest Group of ACL, Held in Conjunction with ACL-IJCNLP 2009|EMNLP - Proc. Conf. Empir. Methods Nat. Lang. Process.: Meet. SIGDAT, Spec. Interest Group ACL, Held Conjunction ACL-IJCNLP. (pp. 1513-1522). Publication link: 134d55cf-e519-4377-b749-07496bd1604a
  32. Tsuruoka, Y., Tsujii, J., & Ananiadou, S. (2009). Fast full parsing by linear-chain conditional random fields. In EACL 2009 - 12th Conference of the European Chapter of the Association for Computational Linguistics, Proceedings|EACL - Conf. Eur. Chapter Assoc. Comput. Linguist., Proc.. (pp. 790-798). Publication link: 8796c4a1-ebce-4e14-988c-02286248ea5a
  33. Afzal, H., Stevens, R., & Nenadic, G. (2009). Towards Semantic Network of Bioinformatics Resources. Poster session presented at ISMB/ECCB 2009, Stockholm, Sweden, .. Publication link: f27def94-1f25-4616-835d-9e406aa7b8fe
  34. Afzal, H., Eales, J., Stevens, R., & Nenadic, G. (2009). Mining semantic networks of bioinformatics e-resources from the literature. In CEUR Workshop Proceedings|CEUR Workshop Proc.. (Vol. 559). (CEUR Workshop Proceedings). CEUR-WS.org. . Publication link: c4bd00ad-1830-4819-885d-ea0857852606
  35. Latif, S., Wood, M. M., & Nenadic, G. (2009). Correlation between human assessment of essays and ROUGE evaluation of essays' summaries. In 2009 8th International Symposium on Natural Language Processing, SNLP '09|Int. Symp. Nat. Lang. Process., SNLP. (pp. 122-127). DOI: 10.1109/SNLP.2009.5340933. Publication link: a02d57d9-e5ab-4dd3-b152-b5d07d4c71e7
  36. Yang, H., Spasic, I., Keane, J. A., & Nenadic, G. (2009). A Text Mining Approach to the Prediction of Disease Status from Clinical Discharge Summaries. Journal of the American Medical Informatics Association, 16(4), 596-600. DOI: 10.1197/jamia.M3096. Publication link: df75d334-0f3f-45bb-a7af-ccb95f1e9873
  37. Sarafraz, F., Eales, J., Mohammadi, R., Dickerson, J., Robertson, D., & Nenadic, G. (2009). Biomedical event detection using rules, conditional random fields and parse tree distances. In Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task. (pp. 115-118). Stroudsburg, PA, USA: Association for Computational Linguistics. DOI: 10.3115/1572340.1572359. Publication link: 04018138-4d01-48af-bec7-58ca9909f1c0
  38. Afzal, H., Stevens, R., & Nenadic, G. (2009). Mining semantic descriptions of bioinformatics web resources from the literature. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. (Vol. 5554, pp. 535-549). (Lecture Notes in Computer Science). Springer Verlag. DOI: 10.1007/978-3-642-02121-3_40. Publication link: 22efac89-f703-4f3d-b19f-6c37002e48c3
  39. Mu, T., & Nandi, A. K. (2009). Multiclass classification based on extended support vector data description. IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics), 39(5), 1206-1216. . Publication link: 1bf622b8-2c3e-4b37-8070-d0360e325349
  40. Mu, T., & Nandi, A. K. (2009). Automatic tuning of L2-SVM parameters employing the extended Kalman filter. Expert Systems, 26(2), 160-175. . Publication link: c9d7f570-494f-45eb-b22b-60b2ced34355
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