srpski   Research   Projects   Publications   Teaching   Personal   Groups   Contact   srpski  Goran Nenadic - selected bio-NLP bibliography* School of Computer Science University of Manchester             Journal papers Yang, H., Spasic, I., Keane, J., Nenadic, G.: A Text Mining Approach to the Prediction of a Disease Status from Clinical Discharge Summaries, J. of American Medical Informatics Association (in press) (link) Yang, H., Keane, J., Bergman, C., Nenadic, G.: Assigning Roles to Protein Mentions: the Case of Transcription Factors, Journal of Biomedical Informatics (link) Yang, H., Nenadic, G., Keane, J.: Identification of transcription factor contexts in literature using machine learning approaches, BMC Bioinformatics 2008, 9(Suppl 3):S11 Yang, H., Nenadic, G., Keane, J.: A cascaded approach to normalizing gene mentions in biomedical literature, Bioinformation 2(5), 197-206 (2007) Nenadic, G., Ananiadou, S.: Mining Semantically Related Terms from Biomedical Literature, ACM Transactions on ALIP (Special Issue on “Text Mining and Management in Biomedicine”) Vol. 5, No. 1, pp.1-22. Rice, S., Nenadic, G., Stapley, B.: Mining protein function from text using term-based support vector machines, BMC Bioinformatics 2005, 6(Suppl 1):S22, "Critical assessment of text mining methods in molecular biology" (full text) Krauthammer, M., Nenadic, G.: Term Identification in the Biomedical Literature, Journal of Biomedical Informatics (Special Issue on Named Entity Recognition in Biomedicine), Vol. 37(6):512-526, 2004 (pre-print) Nenadic, G., Spasic, I., Ananiadou, S.: Mining Term Similarities from Corpora, Terminology 10:1 (2004) Nenadic, G., Spasic, I., Ananiadou, S.: Terminology-Driven Mining of Biomedical Literature, in Bioinformatics Vol. 13, 2003, pp.1-6 (link) Nenadic, G., Mima, H., Spasic, I., Ananiadou, S., Tsujii, J.: Terminology-driven Literature Mining and Knowledge Acquisition in Biomedicine, International Journal of Medical Informatics, Vol.67 (1-3)(2002), 2002, pp. 33-48 (pdf)             Book chapters Ananiadou, S., Nenadic, G: Automatic Terminology Management in Biomedicine (Chapter 4), “Text Mining for Biology and Biomedicine”, S. Ananiadou and J. McNaught (Eds.), Artech House Books, London, pp. 67-98. Ananiadou, S., Nenadic, G., Mima, H., Tsujii, J.: Mining Biomedical Terminology from Literature, Chapter in “Terminology, Computing and Translation”, P. ten Hacken (Ed.), Gunther Narr Verlag, Tübingen, 2006, pp. 117-140 Mima, H., Ananiadou, S., Nenadic, G.: Improving Knowledge Acquisition Through Automatic Term Recognition, in Avouris, N. and Fakotakis, N (Eds.): Advances in Human-Computer Interaction I (PC-HCI 2001), Typorama, Patras, Greece, 2001, pp. 177-182 Ananiadou, S., Mima, H., Nenadic, G.: A Terminology Management Workbench for Molecular Biology, in van der Vet, P. et al. (Eds.): Information Extraction in Molecular Biology, TWLT 19, Twente, The Netherlands, 2001, pp. 7-12             Conference proceedings Afzal, H, Stevens, R., Nenadic, G.: Mining Semantic Descriptions of Bioinformatics Web Resources from the Literature, Proc. of European Semantic Web Conference (ESWC) 2009, LNCS 5554, Springer-Verlag, pp. 535–549, 2009. Afzal, H, Stevens, R., Nenadic, G.: Towards Semantic Network of Bioinformatics Resources, ISMB/ECCB 2009 (in press) Sarafraz, F., Eales, J., Mohammadi, R., Dickerson, J., Robertson, D., Nenadic, G.: Biomedical Event Detection using Rules, Conditional Random Fields and Parse Tree Distances, Proceedings of the BioNLP shared task 2009 (in press) Yang, H., Spasic, I., Keane, J., Nenadic, G.: Combining Lexical Profiling, Rules and Machine Learning for Disease Prediction from Hospital Discharge Summaries, Proc. of i2b2 Obesity Challenge 2008 Greenwood, M., Nenadic, G.: Lexical Profiling of Existing Web Directories to Support Fine-grained Topic-Focused Web Crawling , Proc. of Corpus Profiling for IR and NLP Workshop, London, p. 42-49 Afzal, H., Stevens, R., Nenadic, G.: Mining bioinformatics services terminology from literature , Proc. of IBRC 2008, Manchester Interdisciplinary Biocentre (pdf) Rebholz-Schuhmann, D., Nenadic, G.: Towards Standardisation of Named Entity Annotations in the Life Science Literature, in Proc. of Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), p. 167-169 Afzal, H., Stevens, R., Nenadic, G.: Towards Semantic Annotation of Bioinformatics Services: Building a Controlled Vocabulary, Proc. of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pp. 5-12 (pdf) Stivaros, S., Nenadic, G., Zeng, X.-J., Keane, J. Jackson, A.: Decision support system for treatment planning and outcome prediction in aneurysmal subarachnoid haemorrhage, Computer Assisted Radiology and Surgery 2008, Barcelona Stivaros, SM., Nenadic, G., Zeng, X., Keane, J., Jackson, A.: Development of a Language-based Bayesian Decision Support System for Treatment Planning and Outcome Prediction in Aneurysmal Subarachnoid Haemorrhage, BSNR 2007, London Rebholz-Schuhmann, D., Kirsch, H., Nenadic, G.: IeXML: towards an annotation framework for biomedical semantic types enabling interoperability of text processing modules, Proceedings of Joint BioLINK and Bio-Ontologies SIG Meeting, ISMB 2006, Fortaleza, Brazil Rebholz-Schuhmann, D., Kirsch, H., Gaudan, S., Arregui, M., Nenadic, G.: Annotation and Disambiguation of Semantic Types in Biomedical Text: a Cascaded Approach to Named Entity Recognition, in Proceedings of NLPXML 2006, EACL 2006, Trente, Italy Nenadic, G., Okazaki, N., Ananiadou, S.: Towards a Terminological Resource for Biomedical Text Mining, LREC 2006, Genoa, Italy Nenadic, G., Spasic, I., Ananiadou, S.: Mining Biomedical Abstracts: What is in a Term?, in K.-Y. Su et al. (Eds.): IJCNLP 2004, Lecture Notes in Artificial Intelligence, Vol. 3248, pp. 797-806, Springer-Verlag, 2005 (pre-print) Nenadic, G., Ananiadou, S., McNaught, J.: Enhancing Automatic Term Recognition through Recognition of Variation, Proceedings of COLING 2004, Geneva, Switzerland, 2004, pp. 604-610 (pdf) Spasic, I., Nenadic, G., Ananiadou, S.: Learning to Classify Biomedical Terms through Literature Mining and Genetic Algorithms, in Yang, ZR et al. (Eds.): Intelligent Data Engineering and Automated Learning (IDEAL'04), Lecture Notes in Computer Science, Vol. 3177, Springer Verlag, pp. 345-351 (pdf) Rice, S., Nenadic, G., Stapley, B.: Protein Function Assignment using Term-based Support Vector Machines: BioCreative Task Two 2003, Workshop on Critical Assessment of Information Extraction systems in Biology (BioCreAtiVe), Granada, Spain (slides) Spasic, I., Nenadic, G., Ananiadou, S.: Using Domain-Specific Verbs for Term Classification, in Proceedings of the ACL 2003 Workshop on NLP in Biomedicine, ACL 2003, Sapporo, Japan, 2003, pp. 17-24 (pdf) Nenadic, G., Rice, S., Spasic, I., Ananiadou, S., Stapley, B.: Selecting Text Features for Gene Name Classification: from Documents to Terms, Proceedings of the ACL 2003 Workshop on NLP in Biomedicine, ACL 2003, Sapporo, Japan, 2003, pp. 121-128 (pdf) Mima, H., Ananiadou, S., Nenadic, G., Tsujii, J.: An Integrated System for Ontology-based Knowledge Structuring and Discovery, poster at SOFG 2002 (Standards and Ontologies for Functional Genomics), Hinxton, Cambridge, 2002 Nenadic, G., Spasic, I., Ananiadou, S.: Automatic Discovery of Term Similarities Using Pattern Mining, in Proceedings of CompuTerm 2002, Taipei, Taiwan, 2002, pp. 43-49 (pdf) Mima, H., Ananiadou, S., Nenadic, G., Tsujii, J.: A Methodology for Terminology-based Knowledge Acquisition and Integration, in Proceedings of COLING 2002, Taipei, Taiwan, 2002, pp. 667-673 (pdf) Nenadic, G., Spasic, I., Ananiadou, S.: Term Clustering using a Corpus-Based Similarity Measure, in P. Sojka et al. (Eds.): Text, Speech and Dialogue (TSD 2002), LNAI Vol. 2448, Springer Verlag, 2002, pp. 151-154 (link) Spasic, I., Nenadic, G., Manios, K., Ananiadou, S.: Supervised Learning of Term Similarities, in H. Yin et al. (Eds.): Intelligent Data Engineering and Automated Learning (IDEAL 2002), LNCS Vol. 2412, Springer Verlag, 2002, pp. 429-434 (link) Ananiadou, S., Nenadic, G., Schuhmann, D., Spasic, I.: Term-based Literature Mining from Biomedical Texts, ISMB Text Data Mining SIG, Edmonton, Canada, 2002 (ppt) Mima, H., Ananiadou, S., Nenadic, G., Tsujii, J.: XML Tag Information Management System - A Workbench for Ontology-based Knowledge Acquisition and Integration, in Proceedings of Human Language Technology Conference (HLT 2002), San Diego, California, USA, 2002, pp. 274-279 Nenadic, G., Spasic, I., Ananiadou, S.: Automatic Acronym Acquisition and Term Variation Management within Domain-Specific Texts, in Proceedings of LREC-3, Las Palmas, Spain, 2002, pp. 2155-2162 (pdf) Spasic, I., Nenadic, G., Ananiadou, S.: Tuning Context Features with Genetic Algorithms, in Proceedings of LREC-3, Las Palmas, Spain, 2002, pp. 2048-2054 Mima, H., Ananiadou, S., Nenadic, G., Tsujii, J.: TIMS - A Workbench for Ontology-based Knowledge Acquisition and Integration, in Proceedings of Workshop on Natural Language Processing in Biomedical Applications, Nicosia, Cyprus, 2002, pp. 11-15 Ananiadou, S., Nenadic, G.: Automatic Term Management in Biology, presentation at Workshop on Natural Language Processing and Ontology Building in Biology, Tokyo, Japan, 2002 (ppt) Spasic, I., Nenadic, G., Ananiadou, S.: A Genetic Algorithm Approach to Unsupervised Learning of Context Features, in Proceedings of 5th National Colloquium for Computational Linguistics in the UK, University of Leeds, UK, 2002, pp. 12-19 Mima, H., Ananiadou, S., Nenadic, G.: The ATRACT Workbench: Automatic Term Recognition and Clustering of Terms, in Matusek, V. et al (Eds.): Text, Speech and Dialogue (TSD 2001), LNAI Vol. 2166, Springer Verlag, 2001, pp. 126-133 (pdf)          srpski   Research   Projects   Publications   Teaching   Personal   Groups   Contact   srpski

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