Refereed Journal Articles

Books

Refereed Book Chapters

Refereed Conference Papers

Invited Conference Papers

Refereed Workshop Papers

Refereed Extended Abstracts in Conferences

Technical Reports

Tutorials

Posters and Presentations

See also: Publications by Year or by Topic, DBLP, Google Scholar

Refereed Journal Articles

• Caragea, D., Silvescu, A., and Honavar, V. (2004). Invited Paper. A Framework for Learning from Distributed Data Using Sufficient Statistics and its Application to Learning Decision Trees. In: International Journal of Hybrid Intelligent Systems. Vol. 1, No. 2, pp. 80-89.

Books

• Das, S., Caragea, D., Hsu, W.H., and Welch, S.M. (Eds.) Computational Methodologies in Gene Regulatory Networks, IGI Publishers, New York. To appear, 2009.
• Honavar, V. and Caragea, D. Collaborative Knowledge Acquisition from Semantically Disparate, Distributed Data Sources. Springer UK. To appear, 2008.

• Caragea, D. and Honavar, V. (2008). Learning Classifiers from Distributed Data Sources. In: Encyclopedia of Database Technologies and Applications, 2nd Ed. Ferraggine, V.E., Doorn, J.H., and Rivero, L.C. (Eds.). To Appear, 2008.
• Honavar, V. and Caragea, D. (2008). Invited Chapter. Towards Semantics-Enabled Infrastructure for Knowledge Acquisition from Distributed Data. In: Next Generation of Data Mining. Eds.: Kargupta, H., Han, J., Yu, P., Motwani, R., and Kumar, V. CRC Press. To appear, 2008.
• Paradesi, M.S.R., Caragea, D., and Hsu, W.H. (2008). Incorporating Graph Features for Predicting Protein-Protein Interactions. In: Biological Data Mining in Protein Interaction Networks. Eds.: X.-L. Li and S.-K. Ng. IGI Publishers. To appear, 2008.
• Caragea, D. and Honavar, V. (2008). Knowledge Acquisition from Semantically Heterogeneous Data. In: Encyclopedia of Data Warehousing and Mining, Second Edition, Wang, J. (Ed.). IGI Publishers.
• Caragea, D., Cook, D., Wickham, H., and Honavar, V. (2008). Invited Chapter. Visual Methods for Examining SVM Classifiers. In: Visual Data Mining: Theory, Techniques, and Tools for Visual Analytics. Springer, LNCS Volume 4404.
• Caragea, D., Silvescu, A., and Honavar, V. (2001). Invited Chapter. Towards a Theoretical Framework for Analysis and Synthesis of Agents That Learn from Distributed Dynamic Data Sources. In: Emerging Neural Architectures Based on Neuroscience. Pp. 547-559. Berlin: Springer-Verlag.

• Xia, J., Caragea, D. and Brown, S.J. (2008). Exploring Alternative Splicing Features using Support Vector Machines. In: Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM’08), Philadelphia, PA. [Regular Paper. Acceptance rate: 24%]

• Koul, N., Bahirwani, V., Caragea, C., Caragea, D., and Honavar, V. (2008). Learning from Large Autonomous Data Sources using Sufficient Statistics. Short Paper. In: Proceedings of the International Conference on Web Intelligence (WI 2008), Sydney, Australia. [Short Paper. Acceptance rate: 39%]

• Harmon, S., DeLoach, S., Robby, Caragea, D. (2008). Leveraging Organizational Guidance Policies with Learning to Self-Tune Multiagent Systems. In: Proceedings of the Second IEEE International Conference on Self-Adaption and Self-Organization (SASO’08). Venice, Italy. [Regular Paper. Acceptance rate: 27%]

• Aljandal, W.A., Bahirwani, V., Caragea, D., Hsu, W.H. and Weninger, T. (2008). Validation-based normalization and selection of interestingness measures for association rules. In: Proceedings of ANNIE 2008.

• Paradesi, M.S.R., Caragea, D., and Hsu, W.H. (2007). Structural Prediction of Protein-Protein Interactions in Saccharomyces cerevisiae. In: Proceedings of the 2007 IEEE 7th International Symposium on BioInformatics and BioEngineering (BIBE'07). Boston, MA. [Short Paper]
• Bao, J., Caragea, D., and Honavar, V. (2006). A Tableau-based Federated Reasoning Algorithm for Modular Ontologies. In: Proceedings of the 2006 IEEE / WIC / ACM International Conference on Web Intelligence. pp. 404-410. Hong Kong. [Acceptance rate: 18%]
• Bao, J., Caragea, D., and Honavar, V. (2006). On the Semantics of Linking and Importing in Modular Ontologies. In: Proceedings of the International Semantic Web Conference (ISWC 2006). I. Cruz et al. (Eds.) LNCS 4273, pages 72-86. Athens, Georgia, USA. [Acceptance rate: 23%]

• Caragea, D., Zhang, J., Pathak, J., and Honavar, V. (2006). Learning Classifiers from Distributed, Ontology-Extended Data Sources. In: Proceedings of the 8th International Conference on Data Warehousing and Knowledge Discovery (DaWaK 2006). Krakov, Poland. In presss. Lecture Notes in Computer Science. Berlin: Springer. To appear. [Acceptance rate: 35%]

• Bao, J., Caragea, D., and Honavar, V. (2006). Modular Ontologies - A Formal Investigation of Semantics and Expressivity. Best Paper Award. In: Proceedings of the First Asian Semantic Web Conference (ASWC 2006). September 2-7, 2006, Beijing, China. R. Mizoguchi, Z. Shi, and F. Giunchiglia (Eds.)  LNCS 4185, pp. 616–631, Springer-Verlag. [Acceptance rate: 18%]

• Wickham, H., Caragea, D. and Cook, D. (2006). Exploring High-Dimensional Classification Boundaries. In: Proceedings of the 38^th Symposium on the Interface of Statistics, Computing Science, and Applications  - Interface 2006: Massive Data Sets and Streams. May 24-27, 2006, Pasadena, CA, USA.

• Bao, J., Caragea, D., and Honavar, V. (2006) Towards Collaborative Environments for Ontology Construction and Sharing. In: Proceedings of the 2006 International Symposium on Collaborative Technologies and Systems (CTS 2006). May 14-17, 2006 Las Vegas, Nevada, USA.

• Zhang, J., Caragea, D., and Honavar, V. (2005). Learning Ontology-Aware Classifiers. In: Proceedings of the Eight International Conference on Discovery Science (DS 2005), Springer-Verlag Lecture Notes in Computer Science. October 8-11, 2005, Singapore. Vol. 3735, pp. 308-321. Berlin: Springer-Verlag. [Acceptance rate: 21%]
• Caragea, D., Pathak, J., and Honavar, V. (2004). Learning Classifiers from Semantically Heterogeneous Data. In: Proceedings of the Third International Conference on Ontologies, DataBases and Applications of Semantics for Large Scale Information Systems (ODBASE 2004), Springer-Verlag Lecture Notes in Computer Science. October 25-29, 2004, Agia Napa, Cyprus. LNCS #3291, pp. 963-980. Springer-Verlag. [Acceptance rate: 25%]

• Cook, D., Caragea, D., and Honavar, V. (2004). Visualization for Classification Problems, with Examples Using Support Vector Machines.  In: Proceedings of Computational Statistics (COMPSTAT 2004), 16th Symposium of IASC, August 23-27, 2004, Prague, Czech Republic. Pp. 799-806. Springer-Verlag.

• Caragea, D., Cook, D. and Honavar, V. (2003). Towards Simple, Easy-to-Understand, but Accurate Classifiers. In: Proceedings of the Third IEEE International Conference on Data Mining (ICDM 2003), November 19-22, 2003, Melbourne, FL, USA. Pp. 497-500. IEEE Press. [Acceptance rate: 23%]

• Reinoso J., Silvescu, A., Caragea, D., Pathak, J., and Honavar, V. (2003). A Federated Query-Centric Approach to Information Extraction and Integration from Heterogeneous, Distributed and Autonomous Data Sources.  In: Proceedings of the 2003 IEEE International Conference on Information Reuse and Integration (IRI 2003), October 27-29, 2003, Las Vegas, NV, USA. Pp. 183-191. IEEE Press.

• Caragea, D., Silvescu, A., and Honavar, V. (2003). Decision Tree Induction from Distributed Data Sources. In: Proceedings of the Conference on Intelligent Systems Design and Applications (ICDA 2003), August 10-13, 2004, Tulsa, OK, USA. Pp. 341-350. Springer-Verlag.

• Caragea, D., Cook, D., and Honavar, V. (2001). Gaining Insights into Support Vector Machine Classifiers Using Projection-Based Tour Methods. In: Proceedings of the Conference on Knowledge Discovery and Data Mining (KDD 2001),  August 26-29, San Francisco, CA, USA. Pp. 251-256. ACM Press. [Acceptance rate: 25%]

• Agapie, A. and Caragea, D. (1997). Genetic Algorithms, Schemata Construction and Statistics. In: Proceedings of the International Conference on Computational Intelligence, Theory and Applications, 5th Fuzzy Days, Dortmund, Germany. Pp. 16-23.

Invited Conference Papers

• Caragea, D., Zhang, J., Bao, J., Pathak, J., and Honavar, V. (2005). Algorithms and Software for Collaborative Discovery from Autonomous, Semantically Heterogeneous Information Sources (Invited paper). In: Proceedings of the 16th International Conference on Algorithmic Learning Theory (ALT 2005). Lecture Notes in Computer Science. Singapore. Vol. 3734, pp. 13-44. Berlin: Springer-Verlag.

Refereed Workshop Papers

• Bahirwani, V., Caragea, D., Aljandal, W. and Hsu, H.W. (2008). Ontology Engineering and Feature Construction for Predicting Friendship Links in the Live Journal Social Network. In: Proceedings of the KDD 2008 Second Workshop on Social Network Mining and Analysis (SNA-KDD).  Las Vegas, NV, August 2008. ACM Digital Library. [Regular paper. Acceptance rate: 35%]

• Bao, J., Caragea, D. and Honavar, V. (2007). Query Translation for Ontology-Extended Data Sources. In: Proceedings of the AAAI 2007 Workshop on Semantic e-Science, Vancouver, Canada. [Acceptance rate: 33%]

• Caragea, D., Bao, J. and Honavar, V. (2007). Learning Relational Bayesian Classifiers on the Semantic Web. In: Proceedings of the IJCAI 2007 Workshop on Semantic Web for Collaborative Knowledge Acquisition (SWeCKa 2007). In conjunction with the Twentieth International Joint Conference on Artificial Intelligence, Hyderabad, India, January 2007.

• Bao, J., Hu, Z., Caragea, D., Reecy, J., and Honavar, V. (2006). A Tool for Collaborative Construction of Large Biological Ontologies. In: Fourth International Workshop on Biological Data Management (BIDM 2006), pp. 191-195. Krakov, Poland. IEEE Press

• Bao, J., Caragea, D., and Honavar, V. (2006). A Distributed Tableau Algorithm for Package-based Description Logics. In: Proceedings of the Second International Workshop on Context Representation and Reasoning (CRR 2006). Riva del Garda, Italy.  CEUR.

• Pathak, J., Koul, N., Caragea, D. and Honavar, V. (2005). A Framework for Semantic Web Services Discovery. In: Proceedings of the 7th ACM International Workshop on Web Information and Data Management (WIDM-2005), Bremen, Germany. Pp. 45-50. ACM press. [Acceptance rate: 27%]
• Caragea, D., Pathak, J., Bao, J., Silvescu, A., Andorf., C., Dobbs, D., and Honavar, V. (2005). Information Integration from Semantically Heterogeneous Biological Data Sources. In: Proceedings of the 3rd International Workshop on Biological Data Management (BIDM 2005), DEXA Workshops 2005, Copenhagen, Denmark. Pp. 580-584. IEEE Computer Society.
• Caragea, D., Pathak, J., Bao, J., Silvescu, A., Andorf., C., Dobbs, D. and Honavar, V. (2005). Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources. In: Proceedings of the 2nd International Workshop on Data Integration in Life Sciences (DILS 2005), San Diego, CA. Vol. 3615, pp. 175-190. Berlin: Springer-Verlag. [Acceptance rate: 35%]
• Pathak, J., Caragea, D. and Honavar, V. (2004). Ontology Extended Component-Based Workflows: A Framework for Constructing Complex Workflows from Semantically Heterogeneous Software Components. In: Proceedings of the VLDB-04 Second International Workshop on Semantic Web and Databases (SWDB 2004), August 29 – September 3, 2004, Toronto, Canada. Vol. 3372, pp. 41-56. Springer-Verlag.

• Caragea, D., Reinoso, J., Silvescu, A. and Honavar, V. (2003). Statistics Gathering for Learning from Distributed, Heterogeneous and Autonomous Data Sources. In: Proceedings of the IJCAI International Workshop on Information Integration on the Web (IIWeb 2003). August 9-15, 2003, Acapulco, Mexico. Pp. 99-104.

• Caragea, D., Silvescu, A., and Honavar, V. (2000). Agents that Learn from Distributed Dynamic Data Sources. In: Proceedings of the Workshop on Learning Agents, Agents 2000/ECML 2000. Stone, P. and Sen, S. (Eds.) June 3, Barcelona, Spain.

• Caragea, D., Silvescu, A., and Honavar, V. (2000). Towards a Theoretical Framework for Analysis and Synthesis of Distributed and Incremental Learning Agents. In: Proceedings of the Workshop on Distributed and Parallel Knowledge Discovery. ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2000).  August 20, Boston, MA, U.S.A.

Refereed Extended Abstracts in Conferences

• Paradesi, M.S.R., Caragea, D., and Hsu, W.H. (2007). Structural Prediction of Protein-Protein Interactions in Saccharomyces cerevisiae. In: Proceedings of the  Annual Meeting of the International Society for Computational Biology (ISMB 2007), Poster Program, Vienna, Austria.
• Bao, J., Caragea, D., and Honavar, V. (2006). Package-based Description Logics - Preliminary Results (full paper). In: International Semantic Web Conference - Doctoral Consortium (ISWC-DC 2006). Athens, Georgia, USA. [Acceptance rate: 26%]
• Caragea, D. and Honavar, V. (2006). Knowledge Discovery from Disparate Earth Data Sources. Second NASA Data Mining Workshop: Issues and Applications in Earth Sciences. Poster Session. Pasadena, CA, May 23-24, 2006.
• Caragea, D., Bao, J., Pathak, J. and Honavar, V. (2005). Ontology-based Information Integration using INDUS System. In: The Program of the Eight Annual Bio-Ontologies Meeting (Bio-Ont SIG 2005). Poster Session. Detroit, Michigan.
• Caragea, D., Silvescu, A., Pathak, J., Bao, J., Andorf., C., Yan, C., Dobbs, D. and Honavar, V. (2005). Knowledge Acquisition from Autonomous, Distributed, Semantically Heterogeneous Data Sources. In: Proceedings of the  Annual Meeting of the International Society for Computational Biology (ISMB 2005), Poster Program, Detroit, Michigan.
• Pathak, J., Bao, J., Caragea, D., Silvescu, A., Andorf., C., Yan, C., Dobbs, D. and Honavar, V. (2005). INDUS: A System for Information Integration and Knowledge Acquisition from Autonomous, Distributed, and Semantically Heterogeneous Data Sources. In: The Program of the  Annual Meeting of the International Society for Computational Biology (ISMB 2005), Demo Program, Detroit, Michigan.
• Caragea, C., Caragea, D. and Honavar, V. (2005). Learning Support Vector Machine Classifiers from Distributed Data Sources. In: Proceedings of the Twentieth National Conference on Artificial Intelligence (AAAI 2005), Student Abstract and Poster Program, Pittsburgh, Pennsylvania. Pp. 1602-1603. AAAI Press.
• Caragea, D., Syeda-Mahmood, T. (2004). Semantic API Matching for Automatic Service Composition. In: Proceedings of the 13th International World Wide Web conference on Alternate track papers & posters, Poster session (WWW 2004), May 17-22, 2004, New York, NY, USA. Pp. 436-437. ACM Press.
• Caragea, D. (2002). Learning in Open-Ended Dynamic Distributed Environments. In: Proceedings of the 18th National Conference on Artificial Intelligence (AAAI 2002), Doctoral Consortium Program. Edmonton, Alberta, Canada. Pp. 980. AAAI Press.
• Caragea, D., Silvescu, A., and Honavar, V. (2000). Incremental and Distributed Learning Using Support Vector Machines. In: Proceedings of the17th National Conference on Artificial Intelligence (AAAI 2000), Student Abstract and Poster Program. Austin, TX. Pp. 1067. AAAI Press.

Technical Reports

• Caragea, D., Cook, D., and Honavar, V. (2005). Visual Methods for Examining Support Vector Machine Results, with Applications to Gene Expression Data Analysis. ISU Technical Report, December 2005.

• Silvescu A., Caragea D., Atramentov A. (2002). Graph Databases. Technical Report. May 2002. [ slides ]

Tutorials

• Honavar, V. and Caragea, D. (2006). Semantic Web Technologies for Collaborative Knowledge Acquisition. In conjunction with the 2006 1^st  International Conference on Digital Information Management (ICDIM), December 06-08, 2006, Christ College, Bangalore, India.

• Honavar V. and Caragea, D. (2006). Collaborative Knowledge Acquisition on the Semantic Web. In conjunction with the 2006 International Multi-Conference on Computing in the Global Information Technology (ICCGI). August 1-3, 2006, Bucharest, Romania.

• Honavar, V. and Caragea, D. (2006). Collaborative Knowledge Acquisition from Semantically Disparate, Distributed Data Sources. In conjunction with the 2006 International Symposium on Collaborative Technologies and Systems (CTS). May 14-17, 2006, Las Vegas, Nevada, USA.

Posters and Presentations

• Caragea, D., Kallumadi, S., Dittmer, N., Chellapilla, S., Mutti, N., Feng, C., Pierson, M., Heerman, M., Culbertson, C., Reese, J., Edwards, O. and Reeck, G. (2008) Identifying Specialized Salivary Gland Transcripts in Pea Aphid Using Bioinformatics Tools. Second Annual Arthropod Genomics Symposium: New Insights from Arthropod Genomes, April 11 - 13, 2008, in Kansas City.
• Chellapilla, S., Kallumadi^, S., Park, Y., Caragea, D. and Brown, S.J. (2008) ArthropodEST:  A Pipeline for Automated EST Data Analysis. Second Annual Arthropod Genomics Symposium: New Insights from Arthropod Genomes, April 11 - 13, 2008, in Kansas City.
• Cui, F., Dai, H., Hiromasa, Y., Caragea, D., Sheng,C., Reese, J., Edwards, O. and Reeck, G. (2008) Characterization of an endoplasmic reticulum protein from the salivary glands of the pea aphid, Acyrthosiphon pisum. Second Annual Arthropod Genomics Symposium: New Insights from Arthropod Genomes, April 11 - 13, 2008, in Kansas City.
• Steller, M., Kambhampati, S., and Caragea, D. (2008) Bioinformatic Analysis of ESTs from Termite Castes. Second Annual Arthropod Genomics Symposium: New Insights from Arthropod Genomes, April 11 - 13, 2008, in Kansas City.
• Surabhi, G.C., Kumar, S., Alam, N., Caragea, D., Lu, N., Hurt, A., Johnson, L., Shah, J. (2008) Chronic and transient effects of nitrogen saturation on root processes in a dominant prairie grass Andropogon gerardii: Linking gene expression profiles and ecological responses. Submitted for oral presentation at Plant Biology 2008, Mérida, Mexico.

• Honavar, V. and Caragea, D. (2006). Querying Semantically Heterogeneous Data Sources from a User’s Point of View. 2006 Semantic Technology Conference. San Jose, CA, March 6-9, 2006.

• Caragea, D. (2006). Collaborative Knowledge Acquisition from Distributed, Semantically Heterogeneous Data Sources. Technology Screening Panel, New Ventures AgTech Initiative, Eastern Iowa Community College District, Davenport, IA. February 16, 2006. Invited Talk. 

• Caragea, D. (2005). Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources. Division of Biomedical Informatics at Cincinnati Children's Hospital Medical Center, Cincinnati, OH, October 21^st, 2005. Invited Talk.

• Caragea, D. (2004). Learning Classifiers from Distributed, Semantically Heterogeneous, Autonomous Data Sources. Multimedia and Database Research Group, Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, November 5th 2004.

• Caragea, D. and Honavar, V. (2004). Knowledge Acquisition from Semantically Heterogeneous Distributed Data. Demo Presentation at The NSF Information and Data Management Workshop (IDM 2004), Cambridge, Massachusetts, October 10-12, 2004.  

• Caragea, D. (2004). Learning Classifiers from Distributed, Semantically Heterogeneous, Autonomous Data Sources. The IBM Data Analytics Research Group, T.J. Watson Research Center, Yorktown Heights, NY, October 4^th, 2004.

• Caragea, D. (2004). Learning Classifiers from Distributed, Semantically Heterogeneous, Autonomous Data Sources. Colloquium Series Spring 2004, Department of Computer Science, Iowa State University, Ames, IA, July 27^th, 2004. 

• Jie, B., Yan, C., Caragea, D. and Honavar, V. (2004) Integration of Ontology-Extended Biological Data Sources. Poster presented at Standards and Ontologies for Functional Genomics (SOFG 2004), Philadelphia, PA, October 23-26, 2004.
• Caragea, D., Silvescu, A., and Honavar, V. (2000). Multi-Agent Learning from Distributed Data Sources. In: Workshop on Multi-Agent learning: Theory and Practice, organized by Gerry Tesauro and Amy Greenwald. International Conference on Machine Learning (ICML 2000), Stanford University.