Publications

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2012

  1. Miwa, M., Thompson, P., McNaught, J., Kell, D., & Ananiadou, S. (2012). Extracting semantically enriched events from biomedical literature.BMC Bioinformatics, 13(1), [108]. DOI: 10.1186/1471-2105-13-108. Publication link: c670d5bd-a7d1-40d2-8623-ce1e5b03bce1 | PubMed:22621266
  2. Ananiadou, S., McNaught, J., & Thompson, P. (2012). The English Language in the Digital Age. (META-NET White Paper Series). Heidelberg: Springer Verlag. DOI: 10.1007/978-3-642-30684-6. Publication link: a224bb13-6e2e-47e3-818b-ed2ef3f466af
  3. Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., ... Ananiadou, S. (2012). Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.BMC Bioinformatics, 13, S2. DOI: 10.1186/1471-2105-13-S11-S2. Publication link: 4c4bb3b9-d8df-4514-b89c-27107f99b14b
  4. Rak, R., Kolluru, B., & Ananiadou, S. (2012). Building trainable taggers in a web-based, UIMA-supported NLP workbench. In Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics (ACL 2012). (pp. 121-126). Publication link: 3479af6b-423c-4fc1-b289-6aaacff96e17
  5. Nawaz, R., Thompson, P., & Ananiadou, S. (2012). Meta-Knowledge Annotation at the Event Level: Comparison between Abstracts and Full Papers. In Proceedings of the Third Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2012). (pp. 24-31). Publication link: 007640dd-e86a-4de5-a5f4-cb4d302372b0
  6. Ananiadou, S., McNaught, J., Thompson, P., Rehm, G. (Ed.), & Uszkoreit, H. (Ed.) (2012). The English Language in the Digital Age. In White Paper Series. Springer Verlag. . Publication link: 12e7d880-0439-450d-8532-13ee534ba03d
  7. Stenetorp, P., Pyysalo, S., Ohta, T., Ananiadou, S., & Tsujii, J. (2012). Bridging the Gap Between Scope-based and Event-based Negation/Speculation Annotations: A Bridge Not Too Far. In Proceedings of ExProM 2012. (pp. 47-56). Publication link: 21517439-af5c-4ea7-97e7-46c0895f91db
  8. Kontonasios, G., Korkontzelos, I., Ananiadou, S., & Kontonatsios, G. (2012). Developing multilingual text mining workflows in UIMA and U-compare. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)|Lect. Notes Comput. Sci.. (Vol. 7337, pp. 82-93). (Lecture Notes in Computer Science). Berlin, Heidelberg: Springer Berlin / Heidelberg. DOI: 10.1007/978-3-642-31178-9_8. Publication link: 19e752cf-42dc-4f2f-8ab4-975899f54e1b
  9. Kim, J-D., Pyysalo, S., Nédellec, C., Ananiadou, S., & Tsujii, J. (Eds.) (2012). Selected articles from the BioNLP Shared Task 2011. In host publication. (Vol. 13). Publication link: 9af2a029-d0f6-4cc2-bc53-206a62f4ab5c
  10. Rak, R., Rowley, A., & Ananiadou, S. (2012). Collaborative Development and Evaluation of Text-processing Workflows in a UIMA-supported Web-based Workbench. In Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012). (pp. 2971-2976). Publication link: 88561180-1ddc-4959-9b2a-bdd92c92c437
  11. Mihaila, C., Batista-Navarro, R. T., & 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). (pp. 1-7). Publication link: 878ac435-6710-4274-9e4a-98ba1ccdbc67
  12. Miwa, M., Thompson, P., & Ananiadou, S. (2012). Boosting automatic event extraction from the literature using domain adaptation and coreference resolution. Bioinformatics, 28(13), 1759-1765. [bts237]. DOI: 10.1093/bioinformatics/bts237. Publication link: 52f0d697-b455-4566-82e7-b0b415cfb7f2
  13. Nawaz, R., Thompson, P., & Ananiadou, S. (2012). Identification of Manner in Bio-Events. In Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012). (pp. 3505-3510). Publication link: 511da710-b6c9-4da2-9032-a63a76338098
  14. Liakata, M., Thompson, P., de Waard, A., Nawaz, R., Pander Maat, H., & 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). (pp. 37-46). Publication link: 5692535a-15ff-4cf2-bf86-ee267385e5e8
  15. Pyysalo, S., Stenetorp, P., Ohta, T., Kim, J-D., & Ananiadou, S. (2012). New Resources and Perspectives for Biomedical Event Extraction. In Proceedings of BioNLP 2012. (pp. 100-108). Publication link: 602aacc3-cf8b-44b2-96ef-a4fe086593ea
  16. Rak, R., Rowley, A., Black, W., & Ananiadou, S. (2012). Argo: An integrative, interactive, text mining-based workbench supporting curation. Database, 2012, [bas010]. DOI: 10.1093/database/bas010. Publication link: 6b9c364d-29f4-4913-aa6d-dc9c88bbb472
  17. Miwa, M., Thompson, P., McNaught, J., Kell, D., & Ananiadou, S. (2012). Extracting semantically enriched events from biomedical literature.BMC Bioinformatics, 13(1), [108]. DOI: 10.1186/1471-2105-13-108. Publication link: c670d5bd-a7d1-40d2-8623-ce1e5b03bce1 | PubMed:22621266
  18. Pyysalo, S., Ohta, T., Miwa, M., Cho, H. C., Tsujii, J., & Ananiadou, S. (2012). Event extraction across multiple levels of biological organization. Bioinformatics, 28(18), 575-581. [bts407]. DOI: 10.1093/bioinformatics/bts407. Publication link: d6cd8757-d66d-4019-adc2-3f0360c3436d
  19. Batista-Navarro, R. T., & Ananiadou, S. (2012). What's in a Name? Entity Type Variation across Two Biomedical Subdomains. In Proceedings of the Student Research Workshop at the 13th Conference of the European Chapter of the Association for Computational Linguistics. (pp. 38-45). Publication link: d49f1568-68e2-4858-9def-2c6190c402cd
  20. Mu, T., Goulermas, J. Y., Tsujii, J. I., & Ananiadou, S. (2012). Proximity-based frameworks for generating embeddings from multi-output data. IEEE Transactions on Pattern Analysis and Machine Intelligence, 34(11), 2216-2232. [6127879]. DOI: 10.1109/TPAMI.2012.20. Publication link: d58279cf-7ce4-4e1e-a75b-e97cc168fece
  21. Björne, J., Van Landeghem, S., Pyysalo, S., Ohta, T., Ginter, F., Van de Peer, Y., ... Salakoski, T. (2012). PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. In Proceedings of BioNLP 2012. (pp. 82-90). Publication link: e6157ac9-c553-466a-9782-1e789cc4251b
  22. Ohta, T., Pyysalo, S., Tsujii, J., & Ananiadou, S. (2012). Open-domain Anatomical Entity Mention Detection. In Proceedings of the ACL Workshop on Detecting Stucture in Scholarly Discourse (DSSD). (pp. 27-36). Publication link: ecb610a9-4d86-44d5-867d-c715945fb81e
  23. Wang, X., Thompson, P., & Ananiadou, S. (2012). Biomedical Chinese-English CLIR Using an Extended CMeSH Resource to Expand Queries. In Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012). (pp. 1148-1155). Publication link: ea4a37c6-c164-499c-921e-76543e917c77
  24. Stenetorp, P., Pyysalo, S., Topi{\'{c}}, G., Ohta, T., Ananiadou, S., & Tsujii, J. (2012). brat: a Web-based Tool for NLP-Assisted Text Annotation. In Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics. (pp. 102-107). Association for Computational Linguistics. . Publication link: e0d2124f-935d-42ad-bb78-994df83ae540
  25. Korkontzelos, I., & Ananiadou, S. (2012). ASCOT: Assisting search and creation of clinical trials. In IHI'12 - Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium|IHI - Proc. ACM SIGHIT Int. Health Informatics Symp.. (pp. 855-858). (IHI '12). ACM. DOI: 10.1145/2110363.2110472. Publication link: 9e145614-6223-4159-b2bb-43f268e7001a
  26. Korkontzelos, I., Mu, T., & Ananiadou, S. (2012). ASCOT: A text mining-based web-service for efficient search and assisted creation of clinical trials. BMC Medical Informatics and Decision Making, 12(1), [S3]. DOI: 10.1186/1472-6947-12-S1-S3. Publication link: c24c4fbd-b38f-4791-a8df-a7ac807110ab
  27. Black, W. J., Procter, R., Gray, S., & Ananiadou, S. (2012). A data and analysis resource for an experiment in text mining a collection of micro-blogs on a political topic. In Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC 2012). (pp. 2083-2088). European Language Resources Association (LREC). . Publication link: bc41a305-b5e9-4b01-9128-97026ac68310
  28. Pyysalo, S., Ohta, T., Miwa, M., Cho, H. C., Tsujii, J., & Ananiadou, S. (2012). Event extraction across multiple levels of biological organization. Bioinformatics, 28(18), 575-581. [bts407]. DOI: 10.1093/bioinformatics/bts407. Publication link: d6cd8757-d66d-4019-adc2-3f0360c3436d
  29. Mu, T., Goulermas, J. Y., Tsujii, J. I., & Ananiadou, S. (2012). Proximity-based frameworks for generating embeddings from multi-output data. IEEE Transactions on Pattern Analysis and Machine Intelligence, 34(11), 2216-2232. [6127879]. DOI: 10.1109/TPAMI.2012.20. Publication link: d58279cf-7ce4-4e1e-a75b-e97cc168fece
  30. Pyysalo, S., Ohta, T., Rak, R., Sullivan, D., Mao, C., Wang, C., ... Ananiadou, S. (2012). Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011.BMC Bioinformatics, 13, S2. DOI: 10.1186/1471-2105-13-S11-S2. Publication link: 4c4bb3b9-d8df-4514-b89c-27107f99b14b
  31. Kovačević, A., Konjović, Z., Milosavljević, B., & Nenadic, G. (2012). Mining methodologies from NLP publications: A case study in automatic terminology recognition. Computer Speech and Language, 26(2), 105-126. DOI: 10.1016/j.csl.2011.09.001. Publication link: 8d2fea3d-2e9a-4804-8092-18f36f93cc44
  32. Kovacevic, A., Dehghan, A., Keane, J., & Nenadic, G. (2012). Topic Categorisation of Statements in Suicide Notes with Integrated Rules and Machine Learning. Biomedical Informatics Insight. . Publication link: 3d55e64f-b852-4a6b-befc-0bbe67f8fbde
  33. Duck, G., Robertson, D., Stevens, R., & Nenadic, G. (2012). Ambiguity and variability of database and software names in bioinformatics. In SMBM 2012 - Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine|SMBM - Proc. Int. Symp. Semantic Min. Biomed.. (pp. 2-9). http://www.zora.uzh.ch/64476/. DOI: 10.5167/uzh-64476. Publication link: ea2ea0a0-da0a-4e8c-b801-2219c3bb5cde
  34. Jamieson, D. G., Gerner, M., Sarafraz, F., Nenadic, G., & Robertson, D. L. (2012). Towards semi-automated curation: Using text mining to recreate the HIV-1, human protein interaction database. Database, 2012, [bas023]. DOI: 10.1093/database/bas023. Publication link: dac4a86a-e696-414e-9c04-5234bbca22bc | PubMed:22529179
  35. Gerner, M., Sarafraz, F., Bergman, C. M., & Nenadic, G. (2012). BioContext: An integrated text mining system for large-scale extraction and contextualization of biomolecular events. Bioinformatics, 28(16), 2154-2161. [bts332]. DOI: 10.1093/bioinformatics/bts332. Publication link: b06cad03-baf4-43d8-8de1-d4491a004881 | PubMed:22711795
  36. Pataky, T. C., Mu, T., Bosch, K., Rosenbaum, D., & Goulermas, J. Y. (2012). Gait recognition: highly unique dynamic plantar pressure patterns among 104 individuals. Journal of The Royal Society Interface, 9(69), 790-800. . Publication link: 24ed1d9c-1ad3-4bd0-9e1e-1fb5c464016c
  37. Rodriguez, E., Nikolaidis, K., Mu, T., Ralph, J. F., & Goulermas, J. Y. (2012). Towards collaborative feature extraction for face recognition. Natural Computing, 11(3), 395-404. . Publication link: 4f049fa5-3412-464c-8994-c638ce8e452b
  38. Mu, T., Jiang, J., Wang, Y., & Goulermas, J. Y. (2012). Adaptive data embedding framework for multiclass classification. IEEE Transactions on Neural Networks and Learning Systems, 23(8), 1291-1303. . Publication link: 70d206a7-2cc4-424d-b172-5e8a3c281214
  39. Romero, E., Mu, T., & Lisboa, P. J. G. (2012). Cohort-based kernel visualisation with scatter matrices. Pattern Recognition, 45(4), 1436-1454. . Publication link: 7a2dc75e-f449-4f04-834d-f87ab393d622
  40. Korkontzelos, I., Mu, T., & Ananiadou, S. (2012). ASCOT: A text mining-based web-service for efficient search and assisted creation of clinical trials. BMC Medical Informatics and Decision Making, 12(1), [S3]. DOI: 10.1186/1472-6947-12-S1-S3. Publication link: c24c4fbd-b38f-4791-a8df-a7ac807110ab
  41. Mu, T., Goulermas, J. Y., Tsujii, J. I., & Ananiadou, S. (2012). Proximity-based frameworks for generating embeddings from multi-output data. IEEE Transactions on Pattern Analysis and Machine Intelligence, 34(11), 2216-2232. [6127879]. DOI: 10.1109/TPAMI.2012.20. Publication link: d58279cf-7ce4-4e1e-a75b-e97cc168fece
  42. Mihaila, C., Batista-Navarro, R. T., & 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). (pp. 1-7). Publication link: 878ac435-6710-4274-9e4a-98ba1ccdbc67
  43. Batista-Navarro, R. T., & Ananiadou, S. (2012). What's in a Name? Entity Type Variation across Two Biomedical Subdomains. In Proceedings of the Student Research Workshop at the 13th Conference of the European Chapter of the Association for Computational Linguistics. (pp. 38-45). Publication link: d49f1568-68e2-4858-9def-2c6190c402cd
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