Publications

Books

Honavar, V., D. Caragea, J. (2008). Knowledge Acquisition from Semantically Heterogeneous Distributed Data. Springer-Verlag. In press.

 

Patel, M., Honavar, V. and Balakrishnan, K. (Ed). (2001). Advances in Evolutionary Synthesis of Intelligent Agents. MIT Press.

 

 

Refereed Research Publications

2009

Xiaoyang Gu, Jack H. Lutz, and Elvira Mayordomo (2009). Curves That Must Be Retraced. In: Sixth International Conference on Computability and Complexity in Analysis. Ljubljana, Slovenia (August 18--22, 2009). To appear.

 

James I. Lathrop, Jack H. Lutz, Matthew J. Patitz, and Scott M. Summers (2009). Computability and Complexity in Self-Assembly. In: Theory of Computing Systems. To appear.

 

Yakhnenko, O. and Honavar, V. (2009). Multi-Modal Hierarchical Dirichlet Process Model for Predicting Image Annotation and Image-Object Label Correspondence. In: Proceedings of the SIAM Conference on Data Mining. SIAM Press. To appear.

 

Jack H. Lutz (2009). A Divergence Formula for Randomness and Dimension. In: Computability in Europe: Mathematical Theory and Computational Practice (Fifth Annual Conference). Heidelberg, Germany (July 19-24, 2009). To appear.

 

Mukul S. Bansal and David Fernandez-Baca (2009). Computing Distances Between Partial Rankings. In: Information Processing Letters. Vol. 109. No. 4. pp. 238-241. Elsevier.

 

James I. Lathrop, Jack H. Lutz, and Scott M. Summers (2009). Strict Self-Assembly of Discrete Sierpinski Triangles. In: Theoretical Computer Science. Vol. 410. pp. 384-405.

 

2008

Santhanam, G., Basu, S., and Honavar, V. (2008). TCP-Compose* - A TCP-net based Algorithm for Efficient Composition of Web Services Based on Qualitative Preferences. In: Proceedings of the 6th International Conference on Service Oriented Computing. Sydney, Australia. Vol. 5254. pp. 453-467. Springer-Verlag Lecture Notes in Computer Science. To appear.

 

Voutsadakis, G., Bao, J., Slutzki, G., and Honavar, V. (2008). F-ALCI: A Fully Contextualized, Federated Logic for the Semantic Web. In: Proceedings of the ACM/IEEE/WIC Conference on Web Intelligence. Sydney, Australia. pp. 575-578.

 

Koul, N., Caragea, C., Bahirwani, V., Caragea, D., and Honavar, V. (2008). Using Sufficient Statistics to Learn Predictive Models from Massive Data Sets. In: Proceedings of the ACM/IEEE/WIC Conference on Web Intelligence. Sydney, Australia. pp. 923-926. IEEE Computer Society.

 

Xiaoyang Gu and Jack H. Lutz (2008). Dimension Characterizations of Complexity Classes. In: Computational Complexity. Vol. 17. pp. 459-474.

 

Peto M., Kloczkowski A., Honavar V., Jernigan R.L. (2008). Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable. In: BMC Bioinformatics. Vol. 9. pp. 487-.

 

Jo, H., Na, Y-C.,, Oh, B., Yang, J., and Honavar, V. (2008). Attribute Value Taxonomy Generation through Matrix Based Adaptive Genetic Algorithm. In: IEEE Conference on Tools with Artificial Intelligence. Dayton, OH. pp. 393-400. IEEE Press.

 

Caragea D., Cook, D., Wickham H. and Honavar, V. (2008). Visual Methods for Examining SVM Classifiers. In: Visual Data Mining - Theory, Techniques and Tools for Visual Analytics. Vol. 4404. pp. 136-153. Springer-Verlag.

 

Tu, K., and Honavar, V. (2008). Unsupervised Learning of Probabilistic Context-Free Grammar using Iterative Biclustering. In: 9th International Colloquium on Grammatical Inference (ICGI 2008). St . Malo, France. In press. To appear.

 

El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008). On Evaluating MHC-II Binding Peptide Prediction Methods. In: PLoS One. Vol. 3. No. 9. pp. e3268. http://dx.plos.org/10.1371/journal.pone.0003268.

 

El-Manzalawy, Y., Dobbs, D., and Honavar, V (2008). Predicting Flexible Length Linear B-cell Epitopes. In: 7th Annual International Conference on Computational Systems Bioinformatics. Stanford, CA. World Scientific.

 

Yakhnenko, O. and Honavar, V. (2008). Annotating Images and Image Objects using a Hierarchical Dirichlet Process Model. In: 9th International Workshop on Multimedia Data Mining (SIGKDD MDM 2008). Las Vegas. ACM.

 

Caragea, C., Sinapov, J., Dobbs, D., and Honavar, V. (2008). Using Global Sequence Similarity to Enhance Macromolecular Sequence Labeling. In: IEEE Conference on Bioinformatics and Biomedicine. In press. To appear.

 

El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008). Predicting Protective Linear B-cell Epitopes using Evolutionary Information. In: IEEE Conference on Bioinformatics and Biomedicine. In press. To appear.

 

Y. Wang, W. Tavanapong, J. Wong, J. Oh, and P. C. de Groen (2008). Edge Cross-Section Features for Detection of Appendiceal Orifice Appearance in Colonoscopy Videos. In: International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). Vancouver, British Columbia, Canada. pp. 3000-3003.

 

S. Hwang, J. Oh, W. Tavanapong, J. Wong, J. Oh, and P. C. de Groen (2008). Stool Detection in Colonoscopy Videos. In: International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). Vancouver, British Columbia, Canada. pp. 3004-3007.

 

Jack H. Lutz and Elvira Mayordomo (2008). Dimensions of Points in Self-Similar Fractals. In: SIAM Journal on Computing. Vol. 38. pp. 1080-1112.

 

Pathak, J., Basu, S., and Honavar, V. (2008). Composing Web Services through Automatic Reformulation of Service Specifications. In: IEEE International Conference on Services Computing. Vol. In press.. IEEE. To appear.

 

J. Tian (2008). Identifying Dynamic Sequential Plans. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (UAI). Helsinki, Finland. pp. 554-561. AUAI Press.

 

Xiaoyang Gu and Jack H. Lutz (2008). Effective Dimensions and Relative Frequencies. In: Computability in Europe: Logic and Theory of Algorithms (Fourth Annual Conference). Athens, Greece (June 15-20, 2008). pp. 231-240. Springer.

 

El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008). Predicting linear B-cell epitopes using string kernels. In: Journal of Molecular Recognition. Vol. 21. No. 4. pp. 243-255. 10.1002/jmr.893.

 

Hughes, LaRon, Bao, J., Honavar, V., and Reecy, J. (2008). Animal Trait Ontology (ATO): the importance and usefulness of a unified trait vocabulary for animal species. In: Journal of Animal Science. Vol. 86. pp. 1485-1491.

 

Towfic, F., Caragea, C., Dobbs, D., and Honavar, V. (2008). Struct-NB: Predicting protein-RNA binding sites using structural features. In: International Journal of Data Mining and Bioinformatics. In press. To appear.

 

Bao, J., Voutsadakis, G., Slutzki, G., and Honavar, V. (2008). On the Decidability of Role Mappings between Modular Ontologies. In: Proceedings of the 23nd Conference on Artificial Intelligence (AAAI-2008). Chicago, USA. AAAI. To appear.

 

Kihwan Kim, Ying Cai, Wallapak Tavanapong (2008). Safe Time: Distributed Real-time Monitoring of cKNN in Mobile Peer-to-Peer Networks. In: Mobile Data Management. Beijing China.

 

Pathak, J., Basu, S., Lutz, R., and Honavar, V. (2008). MoSCoE: An Approach for Composing Web Services through Iterative Reformulation of Functional Specifications. In: International Journal on Artificial Intelligence Tools. Vol. 17. No. 1. pp. 109-138.

 

Dunn-Thomas, T., Dobbs, D.L., Sakaguchi, D. Young, M.J. Honavar, V. Greenlee, H. M. W. (2008). Proteomic Differentiation Between Murine Retinal and Brain Derived Progenitor Cells. In: Stem Cells and Development. Vol. 17. No. 1. pp. 119-131.

 

1. S. Stanek, W. Tavanapong, J. Wong, J. Oh, and P. C. de Groen (2008). Automatic Real-Time Capture and Segmentation of Endoscopy Video. In: SPIE Medical Imaging. San Diego. Vol. 6919. pp. 69190X-69190X-10.

 

Yan, C., Dobbs, D., Jernigan, R., and Honavar, V. (2008). Characterization of Protein-Protein Interfaces. In: The Protein Journal. Vol. 27. No. 1. pp. 59-70.

 

Alcon, T., Hecker, L., Honavar, V., and Greenlee, H. (2008). Analysis and Interpretation of Large-Scale Gene Expression Data Sets Using a Seed Network. In: Journal of Bioinformatics and Biology Insights. Vol. 2. pp. 91-102.

 

Lee, J-H., Hamilton, M., Gleeson, C., Caragea, C., Zaback, P., Sander, J.D., Li, X., Wu, F., Terribilini, M., Honavar, V., and Dobbs, D. (2008). Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches. In: Pacific Symposium on Bioinformatics. Vol. 13. pp. 501-512.

 

Jack H. Lutz and Klaus Weihrauch (2008). Connectivity Properties of Dimension Level Sets. In: Mathematical Logic Quarterly. Vol. 54. pp. 483-491.

 

J. Oh, S. Hwang, Y. Cao, W. Tavanapong, J. Wong, and P. C. de Groen. Measuring Objective Quality of Colonoscopy. Accepted to appear in IEEE Transactions on Biomedical Engineering (2008). Measuring Objective Quality of Colonoscopy. In: IEEE Transactions on Biomedical Engineering. To appear.

 

W. Putthividhya, A. Ghosh, and W. Tavanapong (2008). Modeling of End-to-End Available Bandwidth in Wide Area Network. In: Int’l Symposium on Parallel and Distributed Processing with Applications. Sydney, Australia.

 

2007

David Fernández-Baca and Balaji Venkatachalam (2007). Parametric Analysis for Ungapped Markov Models of Evolution. In: ACM Transactions on Algorithms. Under review.

 

Pathak, J., Basu, S., and Honavar, V. (2007). On Context-Specific Substitutability of Web Services. In: Proceedings of the IEEE International Conference on Web Services. pp. 192-199. IEEE.

 

Wu, F., Towfic, F., Dobbs, D. and Honavar, V. (2007). Analysis of Protein Protein Dimeric Interfaces. In: IEEE International Conference on Bioinformatics and Biomedicine. San Jose. IEEE.

 

Bao, J., Slutzki, G. and Honavar, V. (2007). Privacy-Preserving Reasoning on the Semantic Web. In: ACM/WIC/IEEE International Conference on Web Intelligence. San Jose, CA. pp. 791-797. IEEE.

 

Towfic, F., Gemperline, D., Caragea, C., Wu, F., Dobbs, D., and Honavar, V. (2007). Structural Characterization of RNA-Binding Sites of Proteins: Preliminary Results. In: IEEE BIBM Computational Structural Bioinformatics Workshop.

 

David Doty, Jack H. Lutz, and Satyadev Nandakumar (2007). Finite-State Dimension and Real Arithmetic. In: Information and Computation. Vol. 205. pp. 1640-1651.

 

Caragea, C., Sinapov, J., Terribilini, M., Dobbs, D. and Honavar, V. (2007). Assessing the Performance of Macromolecular Sequence Classifiers. In: IEEE Conference on Bioinformatics and Bioengineering. Boston, MA. pp. 320-326. IEEE.

 

3. S. Hwang, J. Oh, W. Tavanapong, J. Wong, and P. C. de Groen (2007). Polyp Detection in Colonoscopy Video Using Elliptical Shape Feature. In: IEEE Int'l Conf. on Image Processing. San Antonio, Texas,.

 

Andorf, C., Silvescu, A., Dobbs, D., and Honavar, V. (2007). Exploring Inconsistencies in Genome Wide Protein Function Annotations: A Machine Learning Approach. In: BMC Bioinformatics. Vol. 8. pp. doi:10.1186/1471-210.

 

3. D. Liu, Y. Cao. W. Tavanapong, J. Wong, J. Oh, and P. C. de Groen, Quadrant Coverage Histogram (2007). A New Method for Measuring Quality of Colonoscopy Procedures. In: IEEE EMBC 2007. Lyon, France.

 

Bao, J., Slutzki, G., and Honavar, V. (2007). A Semantic Importing Approach to Knowledge Reuse from Multiple Ontologies. In: In: Proceedings of the 22nd Conference on Artificial Intelligence (AAAI-2007). Vancouver, Canada. AAAI.

 

Y. Cao, D. Liu, W. Tavanapong, J. Wong, J. Oh, and P. C. de Groen (2007). Computer-aided Detection of Diagnostic and Therapeutic Operations in Colonoscopy Videos. In: IEEE Transactions on Biomedical Engineering. Vol. 54. No. 7. pp. 1268-1279.

 

Bao, J., Slutzki, G., and Honavar, V. (2007). Distributed Reasoning with Modular ALC Ontologies (ALCP). In: Web Intelligence and Agent Systems. Vol. In press.. To appear.

 

Terribilini, M., Sander, J.D., Lee, J-H., Zaback, P., Jernigan, R.L., Honavar, V. and Dobbs, D. (2007). RNABindR: A Server for Analyzing and Predicting RNA Binding Sites in Proteins. In: Nucleic Acids Research. Vol. 35. No. 9. pp. doi:10.1093/nar/gkm2.

 

Mukul S. Bansal1 Contact Information, Jianrong Dong1 Contact Information and David Fernández-Baca (2007). Comparing and Aggregating Partially Resolved Trees. In: LATIN 2008: Theoretical Informatics. Buzios, Brazil. Vol. 4957. pp. 72-83. Springer LNCS.

 

S. Hwang, J. Oh, J. Lee, W. Tavanapong, P. C. de Groen, and J. Wong (2007). Informative Frame Classification for Endoscopy Video. In: Medical Image Analysis. Vol. 11. No. 2. pp. 110-127.

 

D. Liu, Y. Cao. W. Tavanapong, J. Wong, J. Oh, and P. C. de Groen (2007). Mining Colonoscopy Videos to Measure Quality of Colonoscopic Procedures. In: IASTED Int'l Conf. on Biomedical Engineering, 2007.. Innsbruck, Austria.

 

6. S. Hwang, J. Oh, W. Tavanapong, P. C. de Groen, and J. Wong (2007). Automatic Polyp Segmentation for Colonoscopy Image using Watershed Algorithm and Ellipse Fitting Method. In: SPIE Medical Imaging. San Diego, CA.

 

Facundo Bromberg, Dimitris Margaritis (2007). Efficient and Robust Independence-Based Markov Network Discovery. In: International Joint Conference on Artificial Intelligence (IJCAI). Hyderabad, India.

 

Duhong Chen, J. Gordon Burleigh, and David Fernández-Baca (2007). Spectral Partitioning of Phylogenetic Data Sets Based on Compatibility. In: Systematic Biology. Vol. 56. No. 4. pp. 623 – 632. Under review.

 

Helmer, G., Wong, J., Slagell, M., Honavar, V., Miller, L., Wang, Y., Wang, X., and Stakhanova, N. (2007). Software Fault Tree and Colored Petri Net Based Specification, Design, and Implementation of Agent-Based Intrusion Detection Systems. In: International Journal of Information and Computer Security. Vol. 1. No. 1. pp. 09-142.

 

Pathak, J., Li, Y., Honavar, V., McCalley , J. (2007). A Service-Oriented Architecture for Electric Power Transmission System Asset Management. In: Second International Workshop on Engineering Service-Oriented Applications: Design and Composition, Lecture Notes in Computer Science. Berlin: Springer-Verlag.

 

J. McCalley, V. Honavar, S. Ryan, W. Meeker, D. Qiao, R. Roberts, Y. Li, J. Pathak, M. Ye, Y. Hong (2007). Integrated Decision Algorithms for Auto-steered Electric Transmission System Asset Management. In: 7th Intl. Conference on Computational Science. Vol. 4487. pp. 1066-1073. Berlin: Springer-Verlag.

 

Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D. and Honavar, V. (2007). Glycosylation Site Prediction Using Ensembles of Support Vector Machine Classifiers. In: BMC Bioinformatics. Vol. 8. doi:10.1186/1471-2105-8-438.

 

Krishna B. Athreya, John M. Hitchcock, Jack H. Lutz, and Elvira Mayordomo (2007). Effective Strong Dimension in Algorithmic Information and Computational Complexity. In: SIAM Journal on Computing. Vol. 37. No. 3. pp. 671-705.

 

John M. Hitchcock, Jack H. Lutz, and Sebastiaan Terwijn (2007). The Arithmetical Complexity of Dimension and Randomness. In: ACM Transactions on Computational Logic. Vol. 8. No. 2. pp. article no. 13.

 

Xiaoyang Gu, Jack H. Lutz, and Philippe Moser (2007). Dimensions of Copeland-Erdos Sequences. In: Information and Computation. Vol. 205. pp. 1317-1333.

 

2006

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.

 

Bao, J., Caragea, D., and Honavar, V. (2006). A Tableau-based Federated Reasoning Algorithm for Modular Ontologies. In: ACM/IEEE/WIC Conference on Web Intelligence. Hong Kong. pp. 404-410. IEEE.

 

Pathak, J., Basu, S., and Honavar, V. (2006). Modeling Web Services by Iterative Reformulation of Functional and Non-Functional Requirements. In: Proceedings of the International Conference on Service-Oriented Computing, Lecture Notes in Computer Science. Chicago. Vol. 4294. pp. 314-326. Springer-Verlag Lecture Notes in Computer Science.

 

Minh Tran and Wallapak Tavanapong (2006). On the Design, Analysis, and Implementation of a Periodic Broadcast Server. In: IEEE Transactions on Broadcasting. Vol. 52. No. 4. pp. 515-528.

 

J. Pathak, S. Basu, R. Lutz, and V. Honavar (2006). MoSCoE: A Framework for Modeling Web Service Composition and Execution. In: IEEE Conference on Data Engineering Ph.D. Workshop. Atlanta, GA.

 

Bao, J., Caragea, D., and Honavar, V. (2006). On the Semantics of Linking and Importing in Modular Ontologies. In: International Semantic Web Conference. Athens, Georgia, USA. Vol. 4273. pp. 72-86. Springer-Verlag Lecture Notes in Computer Science.

 

Pathak, J., Basu, S., Lutz, R., and Honavar, V. (2006). Applying Tabled-Logic Programming to Web Service Development using Abstraction, Composition and Refinement. In: Proceedings of the IEEE International Conference on Tools With Artificial Intelligence (ICTAI 2006). Washington, DC. pp. 445-454. IEEE Press.

 

Pathak, J., Basu, S., Lutz, R., and Honavar, V. (2006). Parallel Web Service Composition in MoSCoE: A Choreography Based Approach. In: Proceedings of the IEEE European Conference on Web Services (ECOWS 2006). Zurich, Switzerland. pp. 3-12. IEEE.

 

S. Shetty, P. Galdames, W. Tavanapong, and Y. Cai (2006). Detecting Malicious Peers in Overlay Multicast Streaming. In: Proc. of IEEE Conf. on Local Area Networks (LCN). Florida, USA.

 

Xiaoyang Gu, Jack H. Lutz, and Elvira Mayordomo (2006). Points on Computable Curves. In: IEEE Symposium on Foundations of Computer Science (October 22-24, 2006). Berkeley, CA. pp. 469-474. IEEE Computer Society Press.

 

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). Krakov, Poland. IEEE Press.

 

Bao, J., Caragea, D., and Honavar, V. (2006). Modular Ontologies - A Formal Investigation of Semantics and Expressivity. In: In Proceedings of the First Asian Semantic Web Conference. Beijing, China. pp. 616-631. Springer-Verlag.

 

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. Vol. 4081. pp. 363-373. Lecture Notes in Computer Science. Berlin: Springer.

 

Terribilini, M., Lee, J.-H., Yan, C., Jernigan, R. L., Honavar, V. and Dobbs, D. (2006). Predicting RNA-binding Sites from Amino Acid Sequence. In: RNA Journal.. Vol. 12. pp. 1450-1462.

 

Y. Cao, D. Liu, W. Tavanapong, J. Wong, J. Oh, and P. C. de Groen (2006). Automatic Classification of Images with Appendiceal Orifice in Colonoscopy Videos. In: In Proc. of IEEE Engineering in Medicine and Biology Conference. New York City, New York. pp. 2349-2352.

 

Pathak, J., Basu, S., and Honavar, V. (2006). Modeling Web Service Composition Using Symbolic Transition Systems. In: AAAI '06 Workshop on AI-Driven Technologies for Services-Oriented Computing (AI-SOC). Boston, MA. AAAI Press.

 

C. Kang and J. Tian (2006). Inequality Constraints in Causal Models with Hidden Variables. In: Conference on Uncertainty in Artificial Intelligence (UAI). Cambridge, Massachusetts. pp. 233-240. AUAI Press.

 

John M. Hitchcock and Jack H. Lutz (2006). Why Computational Complexity Requires Stricter Martingales. In: Theory of Computing Systems. Vol. 39. pp. 277-296.

 

Yan, C., Terribilini, M., , Wu, F., Jernigan, R.L., Dobbs, D. and Honavar, V (2006). Identifying amino acid residues involved in protein-DNA interactions from sequence. In: BMC Bioinformatics. Vol. 7. pp. 262-.

 

Facundo Bromberg, Dimitris Margaritis and Vasant Honavar (2006). Efficient Markov Network Structure Discovery from Independence Tests. In: SIAM International Conference on Data Mining (SDM). Bethesda, MD. To appear.

 

D. Chen, O. Eulenstein, D. Fernández-Baca, and M.J. Sanderson (2006). Minimum-flip supertrees: complexity and algorithms. In: IEEE Transactions on Bioinformatics and Computational Biology.

 

Kang, D-K., Silvescu, A. and Honavar, V. (2006). RNBL-MN: A Recursive Naive Bayes Learner for Sequence Classification. In: Proceedings of the Tenth Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2006). Lecture Notes in Computer Science.. pp. 45-54. Berlin: Springer-Verlag.

 

Bao, J., Caragea, D., and Honavar, V. (2006). Towards Collaborative Environments for Ontology Construction and Sharing. In: Proceedings of the International Symposium on Collaborative Technologies and Systems.. Las Vegas.

 

S. Sheu, W. Tavanapong, and K. A. Hua (2006). A Scalable Cost Effective Video Broadcasting System for On-Demand Video Services. In: Journal of Multimedia Tools and Applications. Vol. 8. No. 3. pp. 321-345. Springer-Verlag.

 

Wang, Y., Behera, S., Wong, J., Helmer, G., Honavar, V., Miller, L., and Lutz, R. (2006). Towards Automatic Generation of Mobile Agents for Distributed Intrusion Detection Systems. In: Journal of Systems and Software. Vol. 79. pp. 1-14.

 

Zhang, J., Kang, D-K., Silvescu, A. and Honavar, V. (2006). Learning Compact and Accurate Naive Bayes Classifiers from Attribute Value Taxonomies and Data. In: Knowledge and Information Systems. Vol. 9. No. 2. pp. 157-179.

 

Bromberg, F., Margaritis, D., and Honavar, V. (2006). Efficient Markov Network Structure Discovery from Independence Tests. In: SIAM Conference on Data Mining (SDM 06). pp. 141-152. SIAM Press.

 

Pathak, J, Yong, J. Honavar, V., McCalley, J. (2006). Condition Data Aggregation for Failure Mode Estimation of Power Transformers. In: Hawaii International Conference on Systems Sciences. pp. 241a. IEEE Computer Society.

 

Terribilini, M., Lee. J-H., Yan, C., Carpenter, S., Jernigan, R., Honavar, V. and Dobbs, D. (2006). Identifying interaction sites in recalcitrant proteins: predicted protein and rna binding sites in HIV-1 and EIAV agree with experimental data. In: Pacific Symposium on Biocomputing. Hawaii. Vol. 11. pp. 415-426. World Scientific.

 

Silvescu, A. and Honavar, V. (2006). Independence, Decomposability and functions which take values into an Abelian Group. In: Proceedings of the Ninth International Symposium on Artificial Intelligence and Mathematics. http://anytime.cs.umass.edu/aimath06/proceedings.html.

 

Vasile, F., Silvescu, A., Kang, D-K., and Honavar, V. (2006). TRIPPER: An Attribute Value Taxonomy Guided Rule Learner. In: Proceedings of the Tenth Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD). pp. 55-59. Berlin: Springer-Verlag.

 

Wu, F., Olson, B., Dobbs, D., and Honavar, V. (2006). Using Kernel Methods to Predict Protein-Protein Interaction Sites from Sequence. In: IEEE Joint Conference on Neural Networks. Vancouver, Canada. IEEE Press.

 

2005

Minh Tran and Wallapak Tavanapong (2005). Peer-assisted Content Distribution Networks. In: IEEE Local Computer Networks. Australia.

 

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).. pp. 45-50. ACM Press.

 

Yakhnenko, O., Silvescu, A., and Honavar, V. (2005). Discriminatively Trained Markov Model for Sequence Classification. In: IEEE Conference on Data Mining (ICDM 2005). Houston, Texas. IEEE Press.

 

. Hwang, J. Oh, J. Lee, P. C. de Groen, Y. Cao, W. Tavanapong, D. Liu, and J. Wong (2005). Automatic Measurement of Quality Metrics for Colonoscopy Videos. In: ACM Multimedia. Singapore.

 

Minh Tran and Wallapak Tavanapong (2005). On Using a CDN's Infrastructure to Improve File Transfer Among Peers. In: Int’l Conf. on Management of Multimedia Networks and Services (MMNS) 2005. Barcelona, Spain.

 

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. Lecture Notes in Computer Science. Singapore. Vol. 3734. pp. 13-44. Berlin: Springer-Verlag.

 

Zhang, J., Caragea, D. and Honavar, V. (2005). Learning Ontology-Aware Classifiers. In: Proceedings of the 8th International Conference on Discovery Science. Springer-Verlag Lecture Notes in Computer Science. Singapore. Vol. 3735. pp. 308-321. Berlin: Springer-Verlag.

 

Ying Cai, Zhan Chen, Wallapak Tavanapong (2005). Video Management in Peer-to-Peer Systems. In: IEEE International Conference on Peer-to-Peer Computing. Germany.

 

Caragea, D., Bao, J., Pathak, J., Andorf, C,., Dobbs, D., and Honavar, V. (2005). Information Integration from Semantically Heterogeneous Biological Data Sources. In: Proceedings of the Sixteenth International Workshop on Databases and Expert Systems Applications (DEXA 05). Copenhagen. pp. 580-584. IEEE Computer Society.

 

David Doty, Xiaoyang Gu, Jack H. Lutz, Elvira Mayordomo, and Philippe Moser (2005). Zeta-Dimension. In: Thirtieth International Symposium on Mathematical Foundations of Computer Science (August 29 - September 2, 2005). Gdansk, Poland. pp. 283-294. Springer-Verlag.

 

Dimitris Margaritis (2005). Distribution-Free Learning of Bayesian Network Structure in Continuous Domains. In: National Conference on Artificial Intelligence (AAAI). Pittsburgh, PA. AAAI Press / The MIT Press.

 

Kang, D-K., Fuller, D., and Honavar, V. (2005). Learning Misuse and Anomaly Detectors from System Call Frequency Vector Representation. In: IEEE International Conference on Intelligence and Security Informatics. Springer-Verlag Lecture Notes in Computer Science. Vol. 3495. pp. 511-516. Springer-Verlag.

 

Kang, D-K., Zhang, J., Silvescu, A., and Honavar, V. (2005). Multinomial Event Model Based Abstraction for Sequence and Text Classification. In: Proceedings of the Symposium on Abstraction, Reformulation, and Approximation (SARA 2005). Edinburgh, UK. Vol. 3607. pp. 134-148. Berlin: Springer-Verlag.

 

Wu. F., Zhang, J., and Honavar, V. (2005). Learning Classifiers Using Hierarchically Structured Class Taxonomies. In: Proceedings of the Symposium on Abstraction, Reformulation, and Approximation (SARA 2005). Edinburgh. Vol. 3607. pp. 313-320. Berlin, Springer-Verlag.

 

J. Tian (2005). Identifying Direct Causal Effects in Linear Models. In: the National Conference on Artificial Intelligence (AAAI). Pittsburgh, Pennsylvania. pp. 346-352. AAAI Press.

 

Kang, D-K., Fuller, D., and Honavar, V. (2005). Learning Classifiers for Misuse and Anomaly Detection Using a Bag of System Calls Representation. In: Proceedings of the 6th IEEE Systems, Man, and Cybernetics Workshop (IAW 05). West Point, NY. pp. 118-125. IEEE.

 

Caragea, D., Silvescu, A., Pathak, J., Bao, J., Andorf, C., Dobbs, D., and Honavar, V. (2005). Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources. In: Data Integration in Life Sciences (DILS 2005) Springer-Verlag Lecture Notes in Computer Science. San Diego. Vol. 3615. pp. 175-190. Berlin: Springer-Verlag.

 

Lance Fortnow and Jack H. Lutz (2005). Prediction and Dimension. In: Journal of Computer and System Sciences. Vol. 70. pp. 570-589.

 

Y.-H. An, S. Hwang, J. Oh, W. Tavanapong, P. C. de Groen, J. Wong, and JeongKyu Lee (2005). Informative Frame Filtering in Endoscopy Videos. In: SPIE Medical Imaging. San Diego, CA, USA.

 

Stephen A. Fenner, Jack H. Lutz, Elvira Mayordomo, and Patrick Reardon (2005). Weakly Useful Sequences. In: Information and Computation. Vol. 197. pp. 41-54.

 

Jack H. Lutz (2005). Effective Fractal Dimensions. In: Mathematical Logic Quarterly. Vol. 51. pp. 62-72.

 

2004

Sen, T.Z., Kloczkowski, A., Jernigan, R.L., Yan, C., Honavar, V., Ho, K-M., Wang, C-Z., Ihm, Y., Cao, H., Gu, X., and Dobbs, D. (2004). Predicting Binding Sites of Protease-Inhibitor Complexes by Combining Multiple Methods. In: BMC Bioinformatics. Vol. 5. pp. 205.

 

Y. Cao, D. Li, W. Tavanapong, J. Wong, J. Oh, and P. C. de Groen (2004). Parsing and Browsing Tools for Colonoscopy videos. In: Proc. of ACM Multimedia. pp. 844-851.

 

K. A. Hua, M. A. Tantaoui, W. Tavanapong (2004). Video Delivery Technologies for Large-Scale Deployment of Multimedia Applications. In: Proceedings of the IEEE. Vol. 92. No. 9. pp. 1439-1451.

 

F. Sun, D. Fernández-Baca, and W. Yu (2004). Inverse parametric sequence alignment. In: Journal of Algorithms. Vol. 53. No. 1. pp. 36--54. Elsevier.

 

R. Polikar, L. Udpa, S. Udpa, and V. Honavar (2004). An Incremental Learning Algorithm with Confidence Estimation for Automated Identification of NDE Signals. In: IEEE Transactions of Ultrasonics, Ferroelectrics, and Frequency Control. Vol. 51. pp. 990-1001.

 

Cook, D., Caragea, D., and Honavar, V. (2004). Visualization in Classification Problems. In: Proceedings in Computational Statistics (COMPSTAT 2004). pp. 799-806. Springer-Verlag.

 

Zhang, J. and Honavar, V. (2004). Learning Compact and Accurate Classifiers from Attribute Value Taxonomies and Partially Specified Data. In: IEEE International Conference on Data Mining. pp. 289-298. IEEE Press.

 

Bao, J. and Honavar, V. (2004). Collaborative Ontology Building With Wiki@nt. In: Third International Workshop on Evaluation of Ontology Building Tools. Hiroshima.

 

Yan, C., Dobbs, D., and Honavar, V. (2004). A Two-Stage Classifier for Identification of Protein-Protein Interface Residues. In: Bioinformatics. Vol. 20. pp. i371-378.

 

J. Tian (2004). Identifying Linear Causal Effects. In: Proceedings of the National Conference on Artificial Intelligence (AAAI). San Jose, California. pp. 104-110. AAAI Press.

 

M. Tran, W. Tavanapong, W. Putthividhya (2004). OCS: An Effective Caching Scheme for Video Streaming on Overlay Networks. In: Journal of Multimedia Tools and Applications. To appear.

 

Bao, J., Cao, Y., Tavanapong, W., and Honavar, V. (2004). Integration of Domain-Specific and Domain-Independent Ontologies for Colonoscopy Video Database Annotation. In: International Conference on Information and Knowledge Engineeringl (IKE 04). Las Vegas, Nevada, USA. pp. 82-88. CSREA Press.

 

O. Eulenstein, D. Chen, J.G. Burleigh, D. Fernández-Baca, and M.J. Sanderson (2004). Performance of flip supertrees with a heuristic algorithm. In: Systematic Biology. Vol. 53. No. 2. pp. 299--308.

 

Lonosky, P., Zhang, X., Honavar, V., Dobbs, D., Fu, A., and Rodermel, S. (2004). A Proteomic Analysis of Chloroplast Biogenesis in Maize. In: Plant Physiology. Vol. 134. pp. 560-574.

 

Caragea, D., Silvescu, A., and Honavar, V. (2004). 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.

 

JungHwan Oh, Sae Hwang, Wallapak Tavanapong, Piet C. de Groen, and Johnny Wong (2004). Blurry Frame Detection and Shot Segmentation for Colonoscopy Videos. In: Proc. of SPIE Conf. on Storage and Retrieval. San Jose, CA, USA. pp. 531-542.

 

D. Fernández-Baca, T. Seppäläinen, and G. Slutzki (2004). Parametric multiple sequence alignment and phylogeny construction. In: Journal of Discrete Algorithms. Vol. 2. No. 2. pp. 271---287.

 

Yan, C., Dobbs, D., and Honavar, V. (2004). Identifying Protein-Protein Interaction Sites from Surface Residues – A Support Vector Machine Approach. In: Neural Computing Applications. Vol. 13. pp. 123-129.

 

Kang, D-K., Silvescu, A., Zhang, J. and Honavar, V. (2004). Generation of Attribute Value Taxonomies from Data for Accurate and Compact Classifier Construction. In: IEEE International Conference on Data Mining. pp. 130-137. IEEE Press.

 

Andorf, C., Silvescu, A., Dobbs, D. and Honavar, V. (2004). Learning Classifiers for Assigning Protein Sequences to Gene Ontology Functional Families. In: Fifth International Conference on Knowledge Based Computer Systems (KBCS 2004). India. pp. 256-255. New Delhi, India: Allied Publishers.

 

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: VLDB-04 Workshop on Semantic Web and Databases. Springer-Verlag Lecture Notes in Computer Science.. Toronto. Vol. 3372. pp. 41-56. Springer-Verlag.

 

Caragea, D., Pathak, J. and Honavar, V. (2004). Learning Classifiers from Semantically Heterogeneous Data. In: International Conference on Ontologies, Databases, and Applications of Semantics (ODBASE 2004). Springer-Verlag Lecture Notes in Computer Science. Cyprus, Greece. Vol. 3291. pp. 963-980. Springer-Verlag.

 

Zhang, Z.; McCalley, J.D.; Vishwanathan, V.; Honavar, V. (2004). Multiagent system solutions for distributed computing, communications, and data integration needs in the power industry. In: Proceedings of the General Meeting of the IEEE Power Engineering Society. pp. 45-49. IEEE Press.

 

John M. Hitchcock, Jack H. Lutz, and Elvira Mayordomo (2004). Scaled Dimension and Nonuniform Complexity. In: Journal of Computer and System Sciences. Vol. 69. pp. 97-122.

 

Josef M. Breutzmann, David W. Juedes, and Jack H. Lutz (2004). Baire Category and Nowhere Differentiability for Feasible Real Functions. In: Mathematical Logic Quarterly. Vol. 50. pp. 460-472.

 

Jack J. Dai, James I. Lathrop, Jack H. Lutz, and Elvira Mayordomo (2004). Finite-State Dimension. In: Theoretical Computer Science. Vol. 310. pp. 1-33.

 

Jack H. Lutz (2004). Computability versus Exact Computability of Martingales. In: Information Processing Letters. Vol. 92. pp. 235-237.

 

W. Tavanapong and J. Zhou (2004). Shot Clustering Techniques for Story Browsing. In: IEEE Transactions on Multimedia. Vol. 6. No. 4. pp. 517-527. To appear.

 

2003

Caragea, D., Cook, D., and Honavar, V. (2003). Toward Simple, Easy-to-Understand Classifiers. In: Proceedings of the IEEE International Conference on Data Mining. pp. 497-500. IEEE Press.

 

Wang, X., Schroeder, D., Dobbs, D., and Honavar, V. (2003). Data-Driven Discovery of Rules for Protein Function Classification Based on Sequence Motifs. In: Information Sciences. Vol. 155. pp. 1-18.

 

Reinoso-Castillo, J., Silvescu, A., Caragea, D., Pathak, J. and Honavar, V. (2003). Information Extraction and Integration from Heterogeneous, Distributed, Autonomous Information Sources: A Federated, Query-Centric Approach. In: Proceedings of the IEEE International Conference on Information Integration and Reuse.. Las Vegas. pp. 183-191. IEEE Press.

 

Zhang, J. and Honavar, V. (2003). Learning from Attribute Value Taxonomies and Partially Specified Data. In: Proceedings of the International Conference on Machine Learning. Washington, DC. pp. 880-887. AAAI Press.

 

Caragea, D., Silvescu, A., and Honavar, V. (2003). Decision Tree Induction from Distributed, Heterogeneous, Autonomous Data Sources. In: Proceedings of the International Conference on Intelligent Systems Design and Applications (ISDA 2003). Springer Verlag.

 

Atramentov, A., Leiva, H., and Honavar, V. (2003). A Multi-Relational Decision Tree Learning Algorithm - Implementation and Experiments. In: Proceedings of the Conference on Inductive Logic Programming. Springer-Verlag.

 

Helmer, G., Wong, J., Honavar, V., and Miller, L. (2003). Lightweight Agents for Intrusion Detection. In: Journal of Systems and Software. Vol. 67. No. 2. pp. 109-122.

 

K. Vu, K. A. Hua, and W. Tavanapong (2003). Image Retrieval Based on Region of Interest. In: IEEE Transactions on Knowledge and Data Engineering.

 

D. Fernández-Baca and J. Lagergren (2003). A polynomial-time algorithm for near-perfect phylogeny. In: SIAM Journal on Computing. Vol. 32. No. 5. pp. 1115-1127.

 

Caragea, D., Reinoso-Castillo, J., Silvescu, A., and Honavar, V. (2003). Statistics Gathering for Learning from Heterogeneous, Distributed, Autonomous Data Sources. In: Proceedings of the Workshop on Information Integration on the Web. International Joint Conference on Artificial Intelligence. Acapulco, Mexico.

 

Z. Zhong, V. Vishwanathan, J. McCalley, V. Honavar (2003). Multiagent System Solutions for Distributed Computing, Communications, and Data Integration Needs in the Power Industry. In: Proc. of the 2003 IEEE PES Summer Meeting. Toronto.

 

Caregea, D., Cook, D., & Honavar, V. (2003). Visualizing Ensemble of Hyperplane Classifiers. In: IEEE International Conference on Data Mining. Melbourne, Florida. Springer Verlag.

 

Jack H. Lutz (2003). Dimension in Complexity Classes. In: SIAM Journal on Computing. Vol. 32. No. 5. pp. 1236-1259.

 

Jack H. Lutz (2003). The Dimensions of Individual Strings and Sequences. In: Information and Computation. Vol. 187. pp. 49-79.

 

M. Tran and W. Tavanapong (2003). Overlay Caching Schemes for Overlay Networks. In: Proc. of SPIE/ACM Multimedia Computing and Networking. San Jose, CA, USA. pp. 150-161.

 

2002

Helmer, G., Wong, J., Honavar, V., and Miller, L. (2002). Automated Discovery of Concise Predictive Rules for Intrusion Detection. In: Journal of Systems and Software. Vol. 60. No. 3. pp. 165-175.

 

J. Tian and J. Pearl (2002). On the Testable Implications of Causal Models with Hidden Variables. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (UAI). Edmonton, Alberta, Canada.. pp. 519-527. Morgan Kaufmann Publishers.

 

J. Tian and J. Pearl (2002). A general identification condition for causal effects. In: Proceedings of the National Conference on Artificial Intelligence (AAAI). Edmonton, Alberta, Canada. pp. 567-573. AAAI Press.

 

Helmer, G., Wong, J., Slagell, M., Honavar, V., Miller, L., and Lutz, R. (2002). A Software Fault Tree Approach to Requirements Specification of an Intrusion Detection System. In: Requirements Engineering. Vol. 7. No. 4. pp. 207-220.

 

D. Fernández-Baca, T. Seppäläinen, and G. Slutzki (2002). Bounds for parametric sequence comparison. In: Discrete Applied Mathematics.

 

Zhang, J., Silvescu, A., and Honavar, V. (2002). Ontology-Driven Induction of Decision Trees at Multiple Levels of Abstraction. In: Proceedings of Symposium on Abstraction, Reformulation, and Approximation. Berlin. pp. 316-323. Springer-Verlag.

 

Andorf, C., Dobbs, D., and Honavar, V. (2002). Discovering Protein Function Classification Rules from Reduced Alphabet Representations of Protein Sequences. In: Proceedings of the Conference on Computational Biology and Genome Informatics. Durham, North Carolina.

 

2001

D. Margaritis, C. Faloutsos and S. Thrun (2001). NetCube: A Scalable Tool for Fast Data Mining and Compression. In: 27th Conference on Very Large Databases (VLDB). Rome, Italy.

 

D. Margaritis and S. Thrun (2001). A Bayesian Multiresolution Independence Test for Continuous Variables. In: 17th Conference on Uncertainty in Artificial Intelligence (UAI). Seattle, WA.

 

Parekh, R. and Honavar, V. (2001). DFA Learning from Simple Examples. In: Machine Learning. Vol. 44. pp. 9-35.

 

Polikar, R., Udpa, L., Udpa, S., and Honavar, V. (2001). Learn++: An Incremental Learning Algorithm for Multi-Layer Perceptron Networks. In: IEEE Transactions on Systems, Man, and Cybernetics. Vol. 31. No. 4. pp. 497-508.

 

W. Tavanapong and K. A. Hua (2001). Design and Implementation of a Video Browsing System for the Internet. In: Journal of Software: Practice and Experience. Vol. 31. No. 5. pp. 471-503.

 

D. Fernández-Baca (2001). On nonlinear parametric search. In: Algorithmica.

 

Mikler, A., Honavar, V. and Wong, J. (2001). Autonomous Agents for Coordinated Distributed Parameterized Heuristic Routing in Large Dynamic Communication Networks. In: Journal of Systems and Software. Vol. 56. pp. 231-246.

 

Silvescu, A., and Honavar, V. (2001). Temporal Boolean Network Models of Genetic Networks and Their Inference from Gene Expression Time Series. In: Complex Systems. Vol. 13. No. 1. pp. 54-75.

 

Wong, J., Helmer, G., Naganathan, V. Polavarapu, S., Honavar, V., and Miller, L. (2001). SMART Mobile Agent Facility. In: Journal of Systems and Software. Vol. 56. No. 1. pp. 9-22.

 

Polikar, R., Shinar, R., Honavar, V., Udpa, L., and Porter, M. (2001). Detection and Identification of Odorants Using an Electronic Nose. In: The Sixth IEEE Conference on Acoustics, Speech, and Signal Processing.. Salt Lake City, UT, USA. pp. 3137-3140.

 

Caragea, D., Cook, D., and Honavar, V. (2001). Gaining Insights into Support Vector Machine Classifiers Using Projection-Based Tour Methods. In: ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. San Francisco, CA, USA. pp. 251-256. ACM.

 

Wang, D., Wang, X., Honavar, V., & Dobbs, D. (2001). Data-Driven Generation of Decision Trees for Motif-Based Assignment of Protein Sequences to Functional Families. In: Proceedings of the Atlantic Symposium on Computational Biology, Genome Information Systems & Technology.

 

Vishwanathan, V., McCalley, J., and Honavar, V. (2001). A Multiagent System Infrastructure and Negotiation Framework for Electric Power Systems. In: Proceedings of the IEEE Power Technology Conference. Porto, Portugal.

 

2000

Balakrishnan, K., Bousquet, O. and Honavar, V. (2000). Spatial Learning and Localization in Animals: A Computational Model and Its Implications for Mobile Robots. In: Adaptive Behavior. Vol. 7. No. 2. pp. 173-216.

 

Parekh, R., Yang, J., and Honavar, V. (2000). Constructive Neural Network Learning Algorithms for Multi-Category Pattern Classification. In: IEEE Transactions on Neural Networks. Vol. 11. No. 2. pp. 436-451.

 

Chung, M and Honavar, V. (2000). A Negotiation Model in Agent-Mediated Electronic Commerce. In: Proceedings of the International Symposium on Multimedia Software Engineering. pp. 403-410.

 

Yang, J., Parekh, R. and Honavar, V. (2000). Comparison of Performance of Variants of Single-Layer Perceptron Algorithms on Non-Separable Data. In: Neural, Parallel, and Scientific Computations. Vol. 8. pp. 451-438.

 

Pai, P., Miller, L., Nilakanta, S., Honavar, V., and Wong, J. (2000). Challenges of Information Technology Management in the 21st centure. In: Proceedings of the Eleventh International Conference of the Information Resources Management Association. Anchorage, Alaska. pp. 325-329.

 

Parekh, R. and Honavar, V. (2000). On the Relationships between Models of Learning in Helpful Environments. In: Proceedings of the International Colloquium on Grammatical Inference (ICGI-2000). Lisbon, Portugal. pp. 207-220. Berlin: Springer-Verlag.

 

Polikar, R., Udpa, L., Udpa, S., and Honavar, V. (2000). Learn++: An incremental learning algorithm for multilayer perceptron networks. In: IEEE International Conference on Acoustics, Speech, and Signal Processing. pp. 3414-3417.

 

J. Tian and J. Pearl (2000). Probabilities of causation: bounds and identification. In: Annals of Mathematics and Artificial Intelligence. Vol. 28. pp. 287-313.

 

Jack H. Lutz and Yong Zhao (2000). The Density of Weakly Complete Problems under Adaptive Reductions. In: SIAM Journal on Computing. Vol. 30. pp. 1197-1210.

 

Josef M. Breutzmann and Jack H. Lutz (2000). Equivalence of Measures of Complexity Classes. In: SIAM Journal on Computing. Vol. 29. pp. 302-326.

 

David W. Juedes and Jack H. Lutz (2000). Modeling Time-Bounded Prefix Kolmogorov Complexity. In: Theory of Computing Systems. Vol. 33. pp. 111-123.

 

 

 

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