Professor Karin Verspoor

  • Room: Level: 03 Room: 3.12
  • Building: Doug McDonell Building
  • Campus: Parkville

Research interests

  • Bioinformatics and Computational Bioscience
  • Biomedical Natural Language Processing (Text Mining)
  • Health informatics (Biomedical ontologies)

Personal webpage

http://www.textminingscience.com

Recent publications

  1. Bouadjenek, MR.; Zobel, J.; Verspoor, K. Automated assessment of biological database assertions using the scientific literature. BMC Bioinformatics. BMC. 2019, Vol. 20, Issue 1, pp. 1-22. DOI: 10.1186/s12859-019-2801-x
  2. Lopez-campos, G.; Kiossoglou, P.; Borda, A.; Hawthorne, C.; Gray, K.; Verspoor, K. Characterizing the Scope of Exposome Research Through Topic Modeling and Ontology Analysis.. Studies in Health Technology and Informatics. 2019, Vol. 264, pp. 1530-1531. DOI: 10.3233/SHTI190519
  3. Nguyen, DQ.; Verspoor, K. End-to-end neural relation extraction using deep biaffine attention. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). SpringerLink. 2019, Vol. 11437 LNCS, pp. 729-738. DOI: 10.1007/978-3-030-15712-8_47
  4. Al Bkhetan, Z.; Zobel, J.; Kowalczyk, A.; Verspoor, K.; Goudey, B. Exploring effective approaches for haplotype block phasing.. BMC Bioinformatics. BioMed Central. 2019, Vol. 20, Issue 1, pp. 540-540. DOI: 10.1186/s12859-019-3095-8
  5. Dat, QN.; Verspoor, K. From POS tagging to dependency parsing for biomedical event extraction. BMC Bioinformatics. BMC. 2019, Vol. 20, Issue 1. DOI: 10.1186/s12859-019-2604-0
  6. Zhai, Z.; Nguyen, DQ.; Akhondi, S.; Thorne, C.; Druckenbrodt, C.; Cohn, T.; Gregory, M.; Verspoor, K. Improving Chemical Named Entity Recognition in Patents with Contextualized Word Embeddings. Proceedings of the 18th BioNLP Workshop and Shared Task. Association for Computational Linguistics. 2019, pp. 328-338. DOI: 10.18653/v1/W19-5035
  7. Dogan, RI.; Kim, S.; Chatr-aryamontri, A.; Wei, C-H.; Comeau, DC.; Antunes, R.; Matos, S.; Chen, Q.; Elangovan, A.; Panyam, NC.; Verspoor, K.; Liu, H.; Wang, Y.; Liu, Z.; Altinel, B.; Husunbeyi, ZM.; Ozgur, A.; Fergadis, A.; Wang, C-K.; Dai, H-J.; Tran, T.; Kavuluru, R.; Luo, L.; Steppi, A.; Zhang, J.; Qu, J.; Lu, Z. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database. Oxford University Press. 2019, Vol. 2019. DOI: 10.1093/database/bay147
  8. Névéol, A.; Yepes, AJ.; Neves, M.; Verspoor, K. Parallel corpora for the biomedical domain. LREC 2018 - 11th International Conference on Language Resources and Evaluation. European Language Resources Association. 2019, pp. 286-291.
  9. Chen, Q.; Britto, R.; Erill, I.; J. Jeffery, C.; Liberzon, A.; Magrane, M.; Onami, J-I.; Robinson-rechavi, M.; Sponarova, J.; Zobel, J.; Verspoor, K. Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. . Cold Spring Harbor Laboratory. 2019. DOI: 10.1101/788034
  10. Hassanzadeh, H.; Nguyen, A.; Verspoor, K. Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis.. Journal of Biomedical Informatics. Elsevier. 2019, Vol. 100, pp. 103321-103321. DOI: 10.1016/j.jbi.2019.103321
  11. Valentine, JC.; Hall, L.; Verspoor, KM.; Worth, LJ. The current scope of healthcare-associated infection surveillance activities in hospitalized immunocompromised patients: a systematic review.. International Journal of Epidemiology. Oxford University Press (OUP). 2019. DOI: 10.1093/ije/dyz162
  12. Hur, B.; Hardefeldt, LY.; Verspoor, K.; Baldwin, T.; Gilkerson, JR. Using natural language processing and VetCompass to understand antimicrobial usage patterns in Australia. Australian Veterinary Journal. Wiley. 2019, Vol. 97, Issue 8, pp. 298-300. DOI: 10.1111/avj.12836
  13. Hameed, PN.; Verspoor, K.; Kusljic, S.; Halgamuge, S. A two-tiered unsupervised clustering approach for drug repositioning through heterogeneous data integration. BMC Bioinformatics. BMC. 2018, Vol. 19, Issue 1. DOI: 10.1186/s12859-018-2123-4
  14. Nguyen, DQ.; Verspoor, K. An Improved Neural Network Model for Joint POS Tagging and Dependency Parsing. Proceedings of the. Association for Computational Linguistics. 2018, pp. 81-91. DOI: 10.18653/v1/K18-2008
  15. Downie, LE.; Makrai, E.; Bonggotgetsakul, Y.; Dirito, LJ.; Kristo, K.; Pham, M-AN.; You, M.; Verspoor, K.; Pianta, MJ. Appraising the Quality of Systematic Reviews for Age-Related Macular Degeneration Interventions A Systematic Review. JAMA Ophthalmology. AMER MEDICAL ASSOC. 2018, Vol. 136, Issue 9, pp. 1051-1061. DOI: 10.1001/jamaophthalmol.2018.2620
  16. Chen, Q.; Panyam, NC.; Elangovan, A.; Verspoor, K. BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics. Database. OXFORD UNIV PRESS. 2018, Vol. 2018. DOI: 10.1093/database/bay122
  17. Verspoor, K.; Ofoghi, B.; Robles Granda, M. CommViz: Visualization of semantic patterns in large social communication networks. Information Visualization. SAGE PUBLICATIONS LTD. 2018, Vol. 17, Issue 1, pp. 66-88. DOI: 10.1177/1473871617693039
  18. Chen, Q.; Wan, Y.; Zhang, X.; Lei, Y.; Zobel, J.; Verspoor, K. Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases. Journal of Data and Information Quality. ASSOC COMPUTING MACHINERY. 2018, Vol. 9, Issue 3. DOI: 10.1145/3131611
  19. Nguyen, DQ.; Verspoor, K. Convolutional neural networks for chemical-disease relation extraction are improved with character-based word embeddings. Proceedings of the BioNLP 2018 workshop. Association for Computational Linguistics. 2018, pp. 129-136.
  20. Pianta, MJ.; Makrai, E.; Verspoor, KM.; Cohn, TA.; Downie, LE. Crowdsourcing critical appraisal of research evidence (CrowdCARE) was found to be a valid approach to assessing clinical research quality. Journal of Clinical Epidemiology. ELSEVIER SCIENCE INC. 2018, Vol. 104, pp. 8-14. DOI: 10.1016/j.jclinepi.2018.07.015

View a full list of publications on the University of Melbourne’s ‘Find An Expert’ profile