PI: Dejing Dou
We propose to advance biomedical natural language processing by combining ontology-based reasoning, semantic search, and embedding-driven methods to improve information extraction, representation, and consistency detection in biomedical texts.
PI: Dejing Dou
We propose to advance methods for semantic oppositeness detection in natural language, focusing on embedding-based models and contextual representations to improve reasoning and error detection in text.
Dissertations
Book chapters
N. H. Nisansa D de Silva, "Relational Databases and Biomedical Big Data", Bioinformatics in MicroRNA Research, pp. 69--81, 2017. doi: 10.1007/978-1-4939-7046-9_5
Journal Papers
Jingshan Huang, Fernando Gutierrez, Harrison J Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A Blake, Karen Eilbeck, Darren A Natale, Yu Lin, Bin Wu, Nisansa de Silva, and others, "OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data", Journal of biomedical semantics, vol. 7, no. 1, pp. 25, 2016. doi: 10.1186/s13326-016-0064-2
Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A Blake, Dejing Dou, Weili Huang, Darren A Natale, Alan Ruttenberg, Jun Huan, Michael T Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Nisansa de Silva, and others, "The development of non-coding RNA ontology", International journal of data mining and bioinformatics, vol. 15, no. 3, pp. 214--232, 2016. doi: 10.1504/IJDMB.2016.077072
Conference Papers
Nisansa de Silva, Dejing Dou, and Jingshan Huang, "Discovering Inconsistencies in PubMed Abstracts Through Ontology-Based Information Extraction", in Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, New York, NY, USA: ACM, 2017, pp. 362--371. doi: 10.1145/3107411.3107452
