College of Information Sciences & Technology

Ph.D. Thesis

"Abstraction-based Probabilistic Models for Sequence Classification." Iowa State University, 2009. [pdf]

Journal Papers

Cornelia Caragea, Adrian Silvescu, and Prasenjit Mitra. "Protein Sequence Classification using Feature Hashing." Proteome Science, 2012. [pdf]

Rasna Walia, Cornelia Caragea, Benjamin Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, and Vasant Honavar. "Protein-RNA Interface Residue Prediction Using Machine Learning: An Assessment of the State of the Art." BMC Bioinformatics, 2012. [pdf]

Cornelia Caragea, Doina Caragea, Adrian Silvescu, and Vasant Honavar. "Semi-Supervised Prediction of Protein Subcellular Localization Using Abstraction Augmented Markov Models." BMC Bioinformatics, Special Issue on Machine Learning in Computational Biology (MLCB), 2010. [pdf]

Cornelia Caragea, Jivko Sinapov, Drena Dobbs, and Vasant Honavar. "Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling." BMC Bioinformatics, 2009, doi:10.1186/1471-2105-10-S4-S4. [pdf]

Fadi Towfic, Cornelia Caragea, David Gemperline, Drena Dobbs, and Vasant Honavar. "Struct-NB: Predicting protein-RNA binding sites using structural features." International Journal of Data Mining and Bioinformatics, 2008. [pdf]

Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, and Vasant Honavar. "Glycosylation site prediction using ensembles of Support Vector Machine classifiers." BMC Bioinformatics, 2007, 8:438. [pdf]

Conference Papers

Cornelia Caragea, Adrian Silvescu, and Prasenjit Mitra. "Combining Hashing and Abstraction in Sparse High Dimensional Feature Spaces." In: Proceedings of the American Association for Artificial Intelligence, Toronto, Ontario, Canada, 2012. [pdf]

Kang Zhao, Baojun Qiu, Cornelia Caragea, Dinghao Wu, Prasenjit Mitra, John Yen, Greta E. Greer, Kenneth Portier. "Identifying Leaders in an Online Cancer Survivor Community." In: Proceedings of the 21st Annual Workshop on Information Technologies and Systems, Shanghai, China, 2011. [pdf]

Cornelia Caragea, Adrian Silvescu, and Prasenjit Mitra. "Protein Sequence Classification Using Feature Hashing." In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, Atlanta, GA, USA, 2011. [pdf]

Baojun Qiu, Kang Zhao, Prasenjit Mitra, Dinghao Wu, Cornelia Caragea, John Yen, Greta E. Greer, Kenneth Portier. "Get Online Support, Feel Better-Sentiment Analysis and Dynamics in an Online Cancer Survivor Community." In: Proceedings of the Third IEEE International Conference on Social Computing, Boston, Massachusetts, USA, 2011. [pdf]

Cornelia Caragea, Adrian Silvescu, Saurabh Kataria, Doina Caragea, and Prasenjit Mitra. "Classifying Scientific Publications Using Abstract Features." In: Proceedings of the Symposium on Abstraction, Reformulation, and Approximation, Parador de Cardona, Spain, 2011. [pdf]

Saurabh Kataria, Prasenjit Mitra, Cornelia Caragea, and C. Lee Giles. "Context Sensitive Topic Models for Author Influence in Document Networks." In: Proceedings of the 22nd International Joint Conference on Artificial Intelligence, Barcelona, Spain, 2011. [pdf]

Sujatha Das, C. Lee Giles, Prasenjit Mitra, and Cornelia Caragea. "On Identifying Academic Homepages for Digital Libraries." In: Proceedings of the ACM/IEEE Joint Conference on Digital Libraries, Ottawa, Canada, 2011. [pdf]

Cornelia Caragea, Nathan McNeese, Anuj Jaiswal, Greg Traylor, Hyun-Woo Kim, Prasenjit Mitra, Dinghao Wu, Andrea H. Tapia, C. Lee Giles, Bernard J. Jansen, John Yen. "Classifying Text Messages for the Haiti Earthquake." In: Proceedings of the 8th International Conference on Information Systems for Crisis Response and Management, Lisbon, Portugal, 2011. [pdf]

Cornelia Caragea, Adrian Silvescu, Doina Caragea, and Vasant Honavar. "Abstraction Augmented Markov Models." In: Proceedings of the 10th IEEE International Conference on Data Mining, Sydney, Australia, 2010. [pdf]

Cornelia Caragea, Adrian Silvescu, Doina Caragea, and Vasant Honavar. "Semi-Supervised Sequence Classification Using Abstraction Augmented Markov Models." In: Proceedings of the ACM Conference on Bioinformatics and Computational Biology, Niagara Falls, New York, USA, 2010. [pdf]

Adrian Silvescu, Cornelia Caragea, and Vasant Honavar. "Combining Super-Structuring and Abstraction on Sequence Classification." In: Proceedings of the 9th IEEE International Conference on Data Mining, Miami, Florida, USA, 2009. [pdf]

Cornelia Caragea, Doina Caragea, and Vasant Honavar. "Learning Link-Based Classifiers from Ontology-Extended Textual Data." In: Proceedings of the 21st International Conference on Tools with Artificial Intelligence, Newark, New Jersey, USA, 2009. [pdf]

Cornelia Caragea, Doina Caragea, and Vasant Honavar. "Learning Link-Based Naive Bayes Classifiers from Ontology-Extended Distributed Data." In: Proceedings of the 8th International Conference on Ontologies, DataBases, and Applications of Semantics, Vilamoura, Algarve-Portugal, 2009. [pdf]

Neeraj Koul, Vikas Bahirwani, Cornelia Caragea, Doina Caragea, and Vasant Honavar. "Learning Classifiers from Large Databases Using Statistical Queries." In: Proceedings of the International Conference on Web Intelligence, Sydney, Australia, 2008. [pdf]

Cornelia Caragea, Jivko Sinapov, Drena Dobbs, and Vasant Honavar. "Using Global Sequence Similarity to Enhance Biological Sequence Labeling." In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, Philadelphia, Pennsylvania, USA, pp. 104-111, 2008. [pdf]

Jae-Hyung Lee, Michael Hamilton, Colin Gleeson, Cornelia Caragea, Peter Zaback, Jeffry Sander, Xue Li, Feihong Wu, Michael Terribilini, Vasant Honavar, and Drena Dobbs. "Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches." In: Proceedings of the Pacific Symposium on Biocomputing, The Big Island of Hawaii, Vol. 13., pp. 501-512, 2008. [pdf]

Cornelia Caragea, Jivko Sinapov, Drena Dobbs, and Vasant Honavar. "Assessing the Performance of Macromolecular Sequence Classifiers." In: Proceedings of IEEE 7th International Conference on Bioinformatics and Bioengineering, Boston, Massachusetts, USA, pp. 320-326, 2007. [pdf]

Workshop Papers

Cornelia Caragea, Hyun-Woo Kim, Prasenjit Mitra, and John Yen. "Classifying Text Messages for Emergency Response." In Machine Learning for Social Computing Workshop, Co-located with NIPS. Whistler, Canada, 2010. [pdf] [poster]

Rasna Walia, Cornelia Caragea, Drena Dobbs, and Vasant Honavar. "Improving the State of the Art in Machine Learning Methods for Protein-RNA Interface Prediction." In: Workshop for Women in Machine Learning, Co-located with NIPS, Vancouver, BC, Canada, 2010. [pdf]

Cornelia Caragea, Adrian Silvescu, Doina Caragea, and Vasant Honavar. "Abstraction Augmented Markov Models." In: Machine Learning in Computational Biology Workshop, Co-located with NIPS., Whistler, Canada, 2009. [pdf] [talk]

Cornelia Caragea, Adrian Silvescu, and Vasant Honavar. "Designing Abstract Features for Sequence Classification Tasks." In: Workshop for Women in Machine Learning, Co-located with NIPS, Vancouver, BC, Canada, 2009. [pdf]

Fadi Towfic, David Gemperline, Cornelia Caragea, Feihong Wu, Drena Dobbs, and Vasant Honavar. "Structural Characterization of RNA-Binding Sites of Proteins: Preliminary Results." In: Computational Structural Bioinformatics Workshop, Co-located with BIBM, Silicon Valley, CA, USA, 2007. [pdf]

Book Chapters

Cornelia Caragea, and Vasant Honavar. "Machine Learning in Computational Biology." In: Encyclopedia of Database Systems, 2008. [pdf]

Student Abstracts and Poster Programs

Adrian Silvescu, Cornelia Caragea, and Vasant Honavar. "Combining Abstraction and Super-Structuring on Macromolecular Sequence Classication." The 13th Annual International Conference on Research in Computational Molecular Biology, Poster Program, Tucson, AZ, USA, 2009. [pdf] [poster]

Cornelia Caragea, Michael Terribilini, Jivko Sinapov, Jae-Hyung Lee, Fadi Towfic, Drena Dobbs, and Vasant Honavar. "Predicting Protein-RNA Binding Sites Using Structural Information." The 16th Annual International Conference On Intelligent Systems For Molecular Biology, Poster Program, Toronto, Canada, 2008. [pdf] [poster]

Cornelia Caragea, Jivko Sinapov, Michael Terribilini, Drena Dobbs, and Vasant Honavar. "Assessing the Performance of Macromolecular Sequence Classifiers." The 15th Annual International Conference On Intelligent Systems For Molecular Biology, Poster Program, Vienna, Austria, 2007. [pdf] [poster]

Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, and Vasant Honavar. "Glycosylation Site Prediction using Machine Learning Approaches." The 11th Annual International Conference on Research in Computational Molecular Biology, Poster Program, Oakland, California, USA, 2007. [pdf] [poster]

Cornelia Caragea, Doina Caragea, and Vasant Honavar. "Learning Support Vector Machine Classifiers from Distributed Data Sources." In: Proceedings of the 20th National Conference on Artificial Intelligence, pp. 1602-1603. AAAI Press, Student Abstract and Poster Program, Pittsburgh, Pennsylvania, USA, 2005. [pdf] [poster]

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