Vasant Honavar

Vasant Honavar
Nationality	USA
Fields	Computer science, Artificial Intelligence, Machine Learning, Data Mining, Bioinformatics, Big Data, Data science, Computational Biology, Cognitive Science, Health Informatics, Neuroinformatics, Network Science
Institutions	Iowa State University National Science Foundation Pennsylvania State University
Alma mater	University of Wisconsin, Madison (Ph.D., M.S.), Drexel University (M.S.), B.M.S. College of Engineering, Bangalore University (B.E).
Doctoral advisor	Leonard Uhr
Doctoral students	Chun-Hsien Chen, Computer Science, Iowa State University, 1997; Karthik Balakrishnan, Computer Science, Iowa State University,1998; Rajesh Parekh, Computer Science, Iowa State University, 1998; Jihoon Yang, Computer Science, Iowa State University, 1999; Doina Caragea, Computer Science, Iowa State University, 2004; Changhui Yan, Bioinformatics and Computational Biology, Iowa State University, 2005; Jun Zhang, Computer Science, Iowa State University, 2005; Dae-Ki Kang, Computer Science, Iowa State University, 2006; Jie Bao, Computer Science, Iowa State University, 2007; Tyra Dunn, Bioinformatics and Computational Biology, Iowa State University, 2007; Jyotishman Pathak, Computer Science, Iowa State University, 2007; Yasser El-Manzalawy, Computer Science, Iowa State University, 2008; LaRon Hughes, Bioinformatics and Computational Biology, Iowa State University, 2008; Adrian Silvescu, Computer Science, Iowa State University, 2008; Michael Terribilini, Bioinformatics and Computational Biology, Iowa State University, 2008; Feihong Wu, Bioinformatics and Computational Biology, Iowa State University, 2008; Cornelia Caragea, Iowa State University, 2009; Kent Vander Velden, Bioinformatics and Computational Biology, Iowa State University, 2009; Oksana Yakhnenko, Computer Science, Iowa State University, 2009; Ganesh Ram Santhanam Computer Science, , Iowa State University, 2010; George Voutsadakis, Iowa State University, 2010; Neeraj Koul, Iowa State University, 2011; Fadi Towfic, Bioinformatics and Computational Biology, Iowa State University, 2011; Rafael Jordan, Computer Science, Iowa State University, 2012; Jia Tao, Computer Science, Iowa State University, 2012; Kewei Tu, Computer Science, Iowa State University, 2012; Li Xue, Bioinformatics and Computational Biology, Iowa State University, 2012; Carson Andorf, Computer Science, Iowa State University, 2013; Harris Lin, Computer Science, Iowa State University, 2013; Rasna Walia, Bioinformatics and Computational Biology, Iowa State University, 2014; Ngot Bui, Information Sciences and Technology, Pennsylvania State University, 2016.
Other notable students	Sushain Pandit, IBM Master Inventor, MS, Computer Science, Iowa State University, 2010.
Known for	Artificial Intelligence, Machine Learning, Bioinformatics, Big Data, Knowledge Representation, Neural Networks, Grammar Induction, Causal inference, Informatics

Vasant G. Honavar is an Indian born American computer scientist, Artificial Intelligence, Machine Learning, Bioinformatics and Health Informatics researcher and educator. In 2013, he joined the faculty of Penn State College of Information Sciences and Technology^[1] at Pennsylvania State University where he holds the Edward Frymoyer endowed professorship and serves on the faculty of graduate programs in Computer Science, Information Sciences and Technology, Bioinformatics and Genomics, Neuroscience, and of Operations Research. Honavar also serves as the Director of the Artificial Intelligence Research Laboratory, Associate Director of the Institute for Cyberscience^[2] and the Director of the Center for Big Data Analytics and Discovery Informatics^[3] at Pennsylvania State University. Honavar serves on the Executive Board of the Northeast Big Data Innovation Hub.^[4] Honavar serves on the Computing Research Association's Computing Community Consortium Council.^[5][6] In 2015, Honavar was elected to the Electorate Nominating Committee of the Information, Computing, and Communication Section of the American Association for the Advancement of Science.^[7] In 2016, Honavar was selected as the first Sudha Murty Distinguished Visiting Chair of Neurocomputing and Data Science by the Indian Institute of Science, Bangalore, India.

Honavar is known for his research contributions in artificial intelligence, machine learning, data mining, knowledge representation, neural networks, semantic web, big data analytics, and bioinformatics and computational biology. He has published over 250 research articles, including many highly cited ones,^[8][9] as well as several books on these topics.^[10] His recent work has focused on scalable algorithms for constructing predictive models from large, semantically disparate distributed data, learning predictive models from linked open data, big data analytics, analysis and prediction of protein-protein, protein-RNA, and protein-DNA interfaces and interactions, social network analytics, health informatics, secrecy-preserving query answering, representing and reasoning about preferences, and causal inference and meta analysis.

Honavar is a highly sought after mentor of Ph.D. students. He has directly supervised the dissertation research of 32 Ph.D. students,^[11] all of whom have gone onto pursue successful research careers in academia, industry, or government.

During 1990–2013, Honavar was a professor of computer science at Iowa State University where he led the Artificial Intelligence Research Laboratory which he founded in 1990. From 2006 to 2013, he served as the director of the Iowa State University Center for Computational Intelligence, Learning and Discovery which he founded in 2006. He was instrumental in establishing the Iowa State University interdepartmental graduate program in Bioinformatics and Computational Biology (and served as its Chair during 2003–2005).

During 2010–2013, Honavar served as a Program Director in the Information Integration and Informatics program in the Information and Intelligent Systems Division of the Computer and Information Science and Engineering Directorate of the US National Science Foundation where he led the Big Data Program^[12] and contributed to several core and cross-cutting programs.

He has held visiting professorships at Carnegie Mellon University and at the University of Wisconsin–Madison.

Early life

Honavar received a B.E. in Electronics Engg. from B.M.S. College of Engineering in Bangalore, India in 1982, when it was affiliated with Bangalore University, an M.S. in Electrical and Computer Engg. in 1984 from Drexel University, and an M.S. in Computer Science in 1989, and a Ph.D. in 1990, respectively, from the University of Wisconsin–Madison, where he worked with Leonard Uhr.

Selected Books and Articles

Books

• Vasant Honavar and Leonard Uhr. (Ed.) Artificial Intelligence and Neural Networks: Steps Toward Principled Integration. New York: Academic Press. 1994. ISBN 0-12-355055-6
• Vasant Honavar and Giora Slutzki (Ed). Grammatical Inference. Berlin: Springer-Verlag. 1998. ISBN 3-540-64776-7
• Mukesh Patel, Vasant Honavar and Karthik Balakrishnan (Ed). Advances in the Evolutionary Synthesis of Intelligent Agents. Cambridge, MA: MIT Press. 2001. ISBN 0-262-16201-6
• Ganesh Ram Santhanam, Samik Basu, and Vasant Honavar. Representing and Reasoning with Qualitative Preferences: Tools and Applications. Lecture #31, Synthesis Lectures on Artificial Intelligence and Machine Learning. Morgan & Claypool Publishers. 2016. DOI 10.2200/S00689ED1V01Y201512AIM031, ISBN 978-1-62705-839-1

Selected Research Articles

Discovery Informatics

• Honavar, V., Hill, M. Yelick, K. (2016). Accelerating Science: A Computing Research Agenda, Computing Community Consortium.
• Honavar, V. (2014). Honavar, V. (2014). The Promise and Potential of Big Data: A Case for Discovery Informatics Review of Policy Research 31:4 10.1111/ropr.12080.

Causality

• Lee, S. and Honavar, V. (2016). A Characterization of Markov Equivalence Classes of Relational Causal Models Under Path Semantics. In: Proceedings of the Conference on Uncertainty in Artificial Intelligence (UAI-16).
• Bui, N., Yen, J., and Honavar, V. (2016). Temporal Causality Analysis of Sentiment Change in a Cancer Survivor Network. IEEE Transactions on Computational Social Systems. DOI: 10.1109/TCSS.2016.2591880
• Lee, S. and Honavar, V. (2016). On learning causal models from relational data. In: Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (AAAI-16).
• Bui, N., Yen, J. and Honavar, V. (2015). Temporal Causality of Social Support in an Online Community for Cancer Survivors In: International Conference on Social Computing, Behavioral-Cultural Modeling, and Prediction (SBP15). Springer-Verlag Lecture Notes in Computer Science, Vol. 9021, pp. 13–23.
• Lee, S., and Honavar, V. (2015). Lifted Representation of Relational Causal Models Revisited: Implications for Reasoning and Structure Learning In: Workshop on Advances in Causal Inference, Conference on Uncertainty in Artificial Intelligence, 2015.
• Bareinboim, E., Lee, S., Honavar, V. and Pearl, J. (2013). Transportability from Multiple Environments with Limited Experiments. In: Advances in Neural Information Systems (NIPS) 2013. pp. 136–144.
• Lee, S. and Honavar, V. (2013). Transportability of a Causal Effect from Multiple Environments. In: Proceedings of the 27th Conference on Artificial Intelligence (AAAI 2013).
• Lee, S. and Honavar, V. (2013). Causal Transportability of Experiments on Controllable Subsets of Variables: z-Transportability. In: Proceedings of the 29th Conference on Uncertainty in Artificial Intelligence (UAI 2013).

Machine Learning and Big Data Analytics

• Bui, N., Le, T., and Honavar, V. (2016). Labeling Actors in Multi-view Social Networks by Integrating Information From Within and Across Multiple Views. In: Proceedings of the IEEE Conference on Big Data.
• Lin, H., Bui, N., and Honavar, V. (2015). Learning Classifiers from Remote RDF Data Stores Augmented with RDFS Subclass Hierarchies. In: 2nd International Workshop on High Performance Big Graph Data Management, Analysis,and Mining (BigGraph 2015), The IEEE International Conference on Big Data.
• Bui, N. and Honavar, V. (2014). Labeling Actors in Social Networks Using a Heterogeneous Graph Kernel. In: International Conference on Social Computing, Behavioral-Cultural Modeling, and Prediction (SBP14). pp. 27–34.
• Lin, H. and Honavar, V. (2013). Learning Classifiers from Chains of Multiple Interlinked RDF Data Stores. In: IEEE Big Data Congress. Best Student Paper Award.
• Lin, H., Lee, S., Bui, N. and Honavar, V. (2013). Learning Classifiers from Distributional Data. In: IEEE Big Data Congress.
• Bui, N. and Honavar, V. (2013). On the Utility of Abstraction in Labeling Actors in Social Networks. In: The 2013 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining.
• Silvescu, A. and Honavar, V. (2013). Abstraction Super-structuring Normal Forms: Towards a Theory of Structural Induction. In: Algorithmic Probability and Friends. Bayesian Prediction and Artificial Intelligence (pp. 339–350). Springer Berlin Heidelberg.
• Tu, K. and Honavar, V. (2012). Unambiguity Regularization for Unsupervised Learning of Probabilistic Grammars. In: Proceedings of EMNLP-CoNLL 2012 : Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning. pp. 1324–1334.
• Lin, H., Koul, N., and Honavar, V. (2011). Learning Relational Bayesian Classifiers from RDF Data. In: Proceedings of the International Semantic Web Conference (ISWC 2011). Springer-Verlag Lecture Notes in Computer Science Vol. 7031 pp. 389–404.
• Tu, K. and Honavar, V. (2011). On the Utility of Curricula in Unsupervised Learning of Grammars. In: Proceedings of the Twenty-Second International Joint Conference on Artificial Intelligence (IJCAI 2011) pp. 1523–1528.
• Tu, K., Ouyang, X., Han, D., Yu, Y., and Honavar, V. (2011). Exemplar-based Robust Coherent Biclustering. In: Proceedings of the SIAM Conference on Data Mining (SDM 2011). pp. 884–895.
• Yakhnenko, O., and Honavar, V. (2011). Multi-Instance Multi-Label Learning for Image Classification with Large Vocabularies. In: Proceedings of the British Machine Vision Conference.
• Caragea, C., Silvescu, A., Caragea, D. and Honavar, V. (2010). Abstraction-Augmented Markov Models. In: Proceedings of the IEEE Conference on Data Mining (ICDM 2010). IEEE Press. pp. 68–77.
• Koul, N. and Honavar, V. (2010). Learning in the Presence of Ontology Mapping Errors. In: Proceedings of the IEEE/WIC/ACM International Conference on Web Intelligence and Intelligent Agent Technology. pp. 291–296. ACM Press.
• Bromberg, F., Margaritis, D., and Honavar, V. (2009). Efficient Markov Network Structure Discovery from Independence Tests. Journal of Artificial Intelligence Research. Vol. 35. pp. 449–485.
• El-Manzalawi, Y. and Honavar, V. (2009). MICCLLR: Multiple-Instance Learning using Class Conditional Log Likelihood Ratio. In: Proceedings of the 12th International Conference on Discovery Science (DS 2009). Springer-Verlag Lecture Notes in Computer Science Vol. 5808, pp. 80–91, Berlin: Springer.
• Silvescu, A., Caragea, C. and Honavar, V. (2009). Combining Super-structuring and Abstraction on Sequence Classification. IEEE Conference on Data Mining (ICDM 2009).
• 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. pp. 281–294
• Tu, K., and Honavar, V. (2008). Unsupervised Learning of Probabilistic Context-Free Grammar using Iterative Biclustering. . In: International Colloquium on Grammatical Inference (ICGI-2008). Springer-Verlag Lecture Notes in Computer Science vol. 5278 pp. 224–237.
• Yakhnenko, O. and Honavar, V. (2008). Annotating Images and Image Objects using a Hierarchical Dirichlet Process Model. 9th International Workshop on Multimedia Data Mining (SIGKDD MDM 2008), Las Vegas, ACM.
• Zhang, J.; Kang, D.K.; Silvescu, A.; Honavar, V. (2006). "Learning accurate and concise naïve Bayes classifiers from attribute value taxonomies and data". Knowledge and Information Systems. 9 (2): 157–179. doi:10.1007/s10115-005-0211-z.
• 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). Proceedings of the 16th International Conference on Algorithmic Learning Theory. Lecture Notes in Computer Science, Singapore, Berlin: Springer-Verlag. Vol. 3734. pp. 13–44
• Zhang, J., Caragea, D. and Honavar, V. Learning Ontology-Aware Classifiers. Proceedings of the 8th International Conference on Discovery Science. Springer-Verlag Lecture Notes in Computer Science, Singapore, Berlin: Springer-Verlag. Vol. 3735. pp. 308–321, 2005.
• Yakhnenko, O., Silvescu, A., and Honavar, V. (2005) Discriminatively Trained Markov Model for Sequence Classification. IEEE Conference on Data Mining (ICDM 2005), Houston, Texas, IEEE Press
• Kang, D-K., Zhang, J., Silvescu, A., and Honavar, V. (2005) Multinomial Event Model Based Abstraction for Sequence and Text Classification. Proceedings of the Symposium on Abstraction, Reformulation, and Approximation (SARA 2005), Edinburgh, UK, Berlin: Springer-Verlag. Vol. 3607. pp. 134–148.
• Wu. F., Zhang, J., and Honavar, V. (2005) Learning Classifiers Using Hierarchically Structured Class Taxonomies. Proceedings of the Symposium on Abstraction, Reformulation, and Approximation (SARA 2005), Edinburgh, Berlin, Springer-Verlag. Vol. 3607. pp. 313–320.
• Caragea, D.; Silvescu, A.; Honavar, V. (2004). "A Framework for Learning from Distributed Data Using Sufficient Statistics and its Application to Learning Decision Trees". International Journal of Hybrid Intelligent Systems. 1 (2): 80–89.
• Kang, D-K., Silvescu, A., Zhang, J. and Honavar, V. Generation of Attribute Value Taxonomies from Data for Accurate and Compact Classifier Construction. IEEE International Conference on Data Mining, IEEE Press. pp. 130–137, 2004.
• R. Polikar, L. Udpa, S. Udpa, and V. Honavar (2004). An Incremental Learning Algorithm with Confidence Estimation for Automated Identification of NDE Signals. IEEE Transactions of Ultrasonics, Ferroelectrics, and Frequency Control. Vol. 51. pp. 990–1001, 2004.
• Atramentov, A., Leiva, H., and Honavar, V. (2003). A Multi-Relational Decision Tree Learning Algorithm – Implementation and Experiments.. In: Proceedings of the Thirteenth International Conference on Inductive Logic Programming. Berlin: Springer-Verlag.
• Zhang, J. and Honavar, V. (2003). Learning Decision Tree Classifiers from Attribute Value Taxonomies and Partially Specified Data. In: Proceedings of the International Conference on Machine Learning (ICML-03).
• 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: Springer-Verlag.
• Polikar, R., Udpa, L., Udpa, S., and Honavar, V. (2001). Learn++: An Incremental Learning Algorithm for Multi-Layer Perceptron Networks. IEEE Transactions on Systems, Man, and Cybernetics. Vol. 31, No. 4. pp. 497–508.
• Parekh, R. and Honavar, V. (2001). DFA Learning from Simple Examples. Machine Learning. Vol. 44. pp. 9–35.
• Silvescu, A., and Honavar, V. (2001). Temporal Boolean Network Models of Genetic Networks and Their Inference from Gene Expression Time Series. Complex Systems.. Vol. 13. No. 1. pp. 54-.
• Balakrishnan, K., Bousquet, O. and Honavar, V. (2000). Spatial Learning and Localization in Animals: A Computational Model and Its Implications for Mobile Robots, Adaptive Behavior. Vol. 7. no. 2. pp. 173–216.
• Caragea, D., Silvescu, A., and Honavar, V. (2000). Agents That Learn from Distributed Dynamic Data Sources. In: Proceedings of the ECML 2000/Agents 2000 Workshop on Learning Agents. Barcelona, Spain.
• Parekh, R. and Honavar, V. (2000). On the Relationships between Models of Learning in Helpful Environments. In: Proceedings of the Fifth International Conference on Grammatical Inference. Lisbon, Portugal.
• Parekh, R., Yang, J., and Honavar, V. (2000). Constructive Neural Network Learning Algorithms for Multi-Category Pattern Classification. IEEE Transactions on Neural Networks. Vol. 11. No. 2. pp. 436–451.
• Polikar, R., Udpa, L., Udpa, S., and Honavar, V. (2000). Learn++: An Incremental Learning Algorithm for Multilayer Perceptron Networks. In: Proceedings of the IEEE Conference on Acoustics, Speech, and Signal Processing (ICASSP) 2000. Istanbul, Turkey.
• Yang, J., Parekh, R. & Honavar, V. (2000). Comparison of Performance of Variants of Single-Layer Perceptron Algorithms on Non-Separable Data. Neural, Parallel, and Scientific Computation. Vol. 8. pp. 415–438.
• Yang, J. and Honavar, V. (1999). DistAl: An Inter-Pattern Distance Based Constructive Neural Network Learning Algorithm.. Intelligent Data Analysis. Vol. 3. pp. 55–73.
• Parekh, R. and Honavar, V. (1999). Simple DFA are Polynomially Probably Exactly Learnable from Simple Examples. In: Proceedings of the International Conference on Machine Learning. Bled, Slovenia.
• Bousquet, O., Balakrishnan, K. and Honavar, V. (1998). Is the Hippocampus a Kalman Filter?. In: Proceedings of the Pacific Symposium on Biocomputing. Singapore: World Scientific. pp. 655–666.
• Parekh, R., Nichitiu, C., and Honavar, V. (1998). A Polynomial Time Incremental Algorithm for Learning DFA. In: Proceedings of the Fourth International Colloquium on Grammatical Inference (ICGI'98), Ames, IA. Lecture Notes in Computer Science vol. 1433 pp. 37–49. Berlin: Springer-Verlag.
• Yang, J. and Honavar, V. (1998). Feature Subset Selection Using a Genetic Algorithm. IEEE Intelligent Systems (Special Issue on Feature Transformation and Subset Selection). vol. 13. pp. 44–49.
• Parekh, R.G., Yang, J., and Honavar, V. (1997). MUPStart – A Constructive Neural Network Learning Algorithm for Multi-Category Pattern Classification. In: Proceedings of IEEE International Conference on Neural Networks (ICNN'97). Houston, TX. pp. 1924–1929.
• Parekh, R.G., Yang, J., and Honavar, V. (1997). Pruning Strategies for Constructive Neural Network Learning Algorithms. In: Proceedings of IEEE International Conference on Neural Networks (ICNN'97). Houston, TX. pp. 1960–1965. June 9–12, 1997.
• Parekh, R.G. and Honavar, V. (1997) Learning DFA from Simple Examples. In: Proceedings of the International Workshop on Algorithmic Learning Theory. (ALT 97). Sendai, Japan. Lecture notes in Computer Science. Vol. 1316 pp. 116–131.
• Chen, C-H., Parekh, R., Yang, J., Balakrishnan, K. and Honavar, V. (1995). Analysis of Decision Boundaries Generated by Constructive Neural Network Learning Algorithms. In: Proceedings of the World Congress on Neural Networks (WCNN'95). Washington, D.C. July 17–21, 1995. pp. 628–635.
• Honavar, V.; Uhr, L. (1993). "Generative Learning structures for Generalized Connectionist Networks". Information Sciences. 70 (1–2): 75–108. doi:10.1016/0020-0255(93)90049-r.
• Honavar, V. (1992). Some Biases for Efficient Learning of Spatial, Temporal, and Spatio-Temporal Patterns. In: Proceedings of International Joint Conference on Neural Networks. Beijing, China.

Knowledge Representation and Semantic Web

• Tao, J.; Slutzki, G.; Honavar, V. (2015). "A Conceptual Framework for Secrecy-preserving Reasoning in Knowledge Bases". ACM Transactions on Computational Logic. 16: 1–32. doi:10.1145/2637477.
• Santhanam, G.R., Basu, S. and Honavar, V. (2013) Verifying preferential equivalence and subsumption via model checking. In International Conference on Algorithmic DecisionTheory (pp. 324–335). Springer Berlin Heidelberg.
• Tao, J., Slutzki, G., and Honavar, V. (2012). PSpace Tableau Algorithms for Acyclic Modalized ALC. Journal of Automated Reasoning. Vol. 49. pp. 551–582
• Santhanam, G.; Basu, S.; Honavar, V. (2011). "Representing and Reasoning with Qualitative Preferences for Compositional Systems". Journal of Artificial Intelligence Research. 42: 211–274.
• Santhanam, G., Suvorov, Y., Basu, S., and Honavar, V. (2011). Verifying Intervention Policies for Countering Infection Propagation over Networks: A Model Checking Approach. In: Proceedings of the Twenty-Fifth Conference on Artificial Intelligence (AAAI-2011). pp. 1408–1414.
• Sanghvi, B., Koul, N., and Honavar, V. (2010). Identifying and Eliminating Inconsistencies in Mappings across Hierarchical Ontologies. In: Springer-Verlag Lecture Notes in Computer Science Vol. 6427, pp. 999–1008. Berlin: Springer.
• Santhanam, G., Basu, S., and Honavar, V. (2010). Efficient Dominance Testing for Unconditional Preferences. In: Proceedings of the Twelfth International Conference on the Principles of Knowledge Representation and Reasoning (KR 2010). pp. 590–592. AAAI Press.
• Santhanam, G., Basu, S., and Honavar, V. (2010). Dominance Testing Via Model Checking. In: Proceedings of the 24th AAAI Conference on Artificial Intelligence (AAAI-10). pp. 357–362. AAAI Press.
• Bao, J., Voutsadakis G., Slutzki, G. Honavar:, V. (2009). Package-Based Description Logics. In: Modular Ontologies: Concepts, Theories and Techniques for Knowledge Modularization. Lecture Notes in Computer Science Vol. 5445, pp. 349–371
• 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), Menlo Park, CA: AAAI Press, pp. 400–405
• Bao, J., Slutzki, G., and Honavar, V. (2007). A Semantic Importing Approach to Knowledge Reuse from Multiple Ontologies.. In: Proceedings of the 22nd Conference on Artificial Intelligence (AAAI-2007). Vancouver, Canada. Semantic Importing Approach to Knowledge Reuse from Multiple Ontologies. pp. 1304–1309. AAAI Press.
• Bao, J., Slutzki, G., and Honavar, V. (2007). Privacy-Preserving Reasoning on the Semantic Web. IEEE/WIC/ACM Conference on Web Intelligence. IEEE. pp. 791–797
• 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), Lecture Notes in Computer Science, Berlin: Springer. Lecture Notes in Computer Science Vol. 4273, pp. 72–86.
• Bao, J., Caragea, D., and Honavar, V. (2006). A Tableau Based Federated Reasoning Algorithm for Modular Ontologies. In: Proceedings of the ACM/IEEE/WIC Conference on Web Intelligence. IEEE Press. pp. 404–410.
• Bao, J., Caragea, D., and Honavar, V. A Distributed Tableau Algorithm for Package-based Description Logics. Proceedings of the Second International Workshop on Context Representation and Reasoning (CRR 2006), Riva del Garda, Italy, CEUR. 2006.
• Bao, J., Caragea, D., and Honavar, V. Modular Ontologies – A Formal Investigation of Semantics and Expressivity. In Proceedings of the First Asian Semantic Web Conference, Beijing, China, Springer-Verlag. Vol. Vol. 4185, pp. 616–631, 2006. Best Paper Award
• Silvescu, A. and Honavar, V. Independence, Decomposability and functions which take values into an Abelian Group. Proceedings of the Ninth International Symposium on Artificial Intelligence and Mathematics, http://anytime.cs.umass.edu/aimath06/proceedings.html, 2006.

Software Composition

• Santhanam, G.R., Basu, S. and Honavar, V. (2013). Preference based service adaptation using service substitution. In Proceedings of the 2013 IEEE/WIC/ACM International Joint Conferences on Web Intelligence (WI) and Intelligent Agent Technologies (IAT)-Volume 01 (pp. 487–493). IEEE Computer Society.
• Sun, H., Basu, S., Honavar, V., and Lutz, R. (2010). Automata-Based Verification of Security Requirements of Composite Web Services. In: Proceedings of the IEEE International Symposium on Software Reliability Engineering (ISSRE-2010). pp. 348–357, IEEE Press.
• Santhanam, G.R., Basu, S., and Honavar, V. (2009). Web Service Substitution Based on Preferences Over Non-functional Attributes. In: Proceedings of the IEEE International Conference on Services Computing (SCC 2009).
• Pathak, J., Basu, S., and Honavar, V. (2008). Composing Web Services through Automatic Reformulation of Service Specifications. Proceedings of the IEEE International Conference on Services Computing, IEEE, pp. 361–369.
• Pathak, J.; Basu, S.; Lutz, R.; Honavar, V. (2008). "MoSCoE: An Approach for Composing Web Services through Iterative Reformulation of Functional Specifications". International Journal of Artificial Intelligence Tools. 17 (1): 109–138. doi:10.1142/s0218213008003807.
• 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. Proceedings of the 6th International Conference on Service Oriented Computing, Springer-Verlag Lecture Notes in Computer Science, Vol. 5254. pp. 453–467
• 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 Press.
• Pathak, J., Li, Y., Honavar, V., McCalley, J. (2007). A Service-Oriented Architecture for Electric Power Transmission System Asset Management. Second International Workshop on Engineering Service-Oriented Applications: Design and Composition, Lecture Notes in Computer Science, Berlin: Springer-Verlag, 2007.
• Pathak, J., Basu, S., Lutz, R., and Honavar, V. (2006). Selecting and Composiing Web Services through Iterative Reformulation of Functional Specifications. Proceedings of the IEEE International Conference on Tools With Artificial Intelligence (ICTAI 2006), Washington, DC, IEEE Press. Best Paper Award. pp. 445–454.
• Pathak, J., Basu, S., and Honavar, V. (2006). Modeling Web Services by Iterative Reformulation of Functional and Non-Functional Requirements. Proceedings of the International Conference on Service Oriented Computing. Lecture Notes in Computer Science, Berlin: Springer, Vol. 4294, pp. 314–326.
• Pathak, J., Yuan, L., Honavar, V., and McCalley, J. (2006). A Service-Oriented Architecture for Electric Power Transmission System Asset Management, In: Proceedings of the Second International Workshop on Engineering Service-Oriented Applications: Design and Composition (WESOA-2006), Lecture Notes in Computer Science, Berlin: Springer-Verlag.
• Pathak, J., Basu, S., Lutz, R., and Honavar, V. (2006). Parallel Web Service Composition in MoSCoE: A Choreography Based Approach. Proceedings of the IEEE European Conference on Web Services (ECOWS 2006), Zurich, Switzerland, IEEE. In press.
• Pathak, J., Basu, S., and Honavar, V. Modeling Web Service Composition Using Symbolic Transition Systems. AAAI '06 Workshop on AI-Driven Technologies for Services-Oriented Computing (AI-SOC), Boston, MA, AAAI Press, 2006.
• Pathak, J., Koul, N., Caragea, D., and Honavar, V. A Framework for Semantic Web Services Discovery. Proceedings of the 7th ACM International Workshop on Web Information and Data Management (WIDM 2005)., ACM Press. pp. 45–50, 2005.
• Pathak, J., Caragea, D., and Honavar, V. Ontology-Extended Component-Based Workflows: A Framework for Constructing Complex Workflows from Semantically Heterogeneous Software Components. VLDB-04 Workshop on Semantic Web and Databases. Springer-Verlag Lecture Notes in Computer Science., Toronto, Springer-Verlag. Vol. 3372. pp. 41–56, 2004.

Bioinformatics and Computational Biology

• El-Manzalawy, Y., Munoz, E., Lindner, S.E., and Honavar, V. (2016). PlasmoSEP: Predicting surface-exposed proteins on themalaria parasite using semisupervised self-training and expert-annotated data. Proteomics. doi: DOI 10.1002/pmic.201600249.
• El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2016). In silico prediction of linear B-cell epitopes on proteins. In: Y. Zhou, E. Faraggi, A. Kloczkowski and Y. Yang (Eds.), Prediction of Protein Secondary Structure, Methods in Molecular Biology, vol. 1484, DOI:10.1007/978-1-4939-6406-2_17.
• Walia, R., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2016). Sequence-based Prediction of RNA-binding Residues in Proteins. In: Y. Zhou, E. Faraggi, A. Kloczkowski and Y. Yang (Eds.), Prediction of Protein Secondary Structure, Methods in Molecular Biology, vol. 1484, DOI:10.1007/978-1-4939-6406-2_15.
• El-Manzalawy, Y., Abbas, M., Malluhi, Q., and Honavar, V. (2016). FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues. PLoS One 11(7): e0158445. doi:10.1371/journal.pone.0158445
• Xue, L., Rodrigues, J.P.L.M., Dobbs, D., Honavar, V., and Bonvin, A. (2016). Template-Based Protein-Protein Docking Improved Using Pairwise Interfacial Residue Restraints. Briefings in Bioinformatics, doi:10.1093/bib/bbw027.
• Xue, L., Dobbs, D., Bonvin, A., and Honavar, V. (2015). Computational Prediction of Protein Interfaces: A Review of Data Driven Methods. FEBS Letters. Vol. 589, No. 23, pp. 3516–3526.
• El-Manzalawy. Y. and Honavar, V. (2014). Building Classifier Ensembles for B-Cell Epitope Prediction. In: De, R.K. and Tomar, N. (Ed). Immunoinformatics, Springer Protocols Methods in Molecular Biology, Vol. 1184. pp. 285–294.
• Walia, RR., Xue, LC., Wilkins, K., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2014). RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins, PloS one 9 (5), e97725
• Xue, L., Jordan, R., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2014) DockRank: Ranking Docked Conformations Using Partner-Specific Sequence Homology Based Protein Interface Prediction. Proteins: Structure, Function and Bioinformatics. Vol. 82, pp. 250–267. DOI: 10.1002/prot.24370.
• Andorf, C., Honavar, V. and Sen, T. (2013). Predicting the Binding Patterns of Proteins: A Study Using Yeast Protein Interaction Networks. PLOS One 8(2): e56833, doi: 10.1371/journal.pone.0056833
• El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2012). Predicting protective bacterial antigens using random forest classifiers.. ACM Conference on Bioinformatics and Computational Biology. pp. 426–433, 2012.
• Jordan, R., El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2012). Predicting protein-protein interface residues using local surface structural similarity" BMC Bioinformatics 2012, 13:41 doi:10.1186/1471-2105-13-41. Highly Accessed.
• Towfic, F., Gupta, S., Honavar, V., and Subramaniam, S. (2012). B-Cell Ligand Processing Pathways Detected by Large-Scale Gene Expression Analysis. Genomics, Proteomics, and Bioinformatics. Vol. 10. pp. 142–152.
• Towfic, F., Kohutyuk, O., Greenlee, MHW., and Honavar, V. (2012). Bionetworkbench: Database and Software for Storage, Query, and Interactive Analysis of Gene and Protein Networks. Bioinformatics and Biology Insights. Vol. 6. pp. 235–246.
• Walia, R.; Caragea, C.; Lewis, B.; Towfic, F.; Terribilini, M.; El-Manzalawy, Y.; Dobbs, D.; Honavar, V. (2012). "Protein-RNA Interface Residue Prediction Using Machine Learning: An Assessment of the State of the Art". BMC Bioinformatics. 13: 89. doi:10.1186/1471-2105-13-89.
• El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2011). Predicting MHC-II binding affinity using multiple instance regression. IEEE/ACM Transactions on Computational Biology and Bioinformatics. DOI: 10.1109/TCBB2010.94
• Lewis, B.A., Walia, R.R., Terribilini, M., Ferguson, J., Zheng, C., Honavar, V., and Dobbs, D. (2011). PRIDB: A Protein-RNA Interface Database. Nucleic Acids Research. D277-282. DOI: 10.1093/nar/gkq1108.
• Muppirala, U., Honavar, V., and Dobbs, D. (2011). Predicting RNA-Protein Interactions Using Only Sequence Information" BMC Bioinformatics 2011, 12:489, doi:10.1186/1471-2105-12-489
• Tuggle, C. K., Towfic, F. and Honavar, V. G. (2011) Introduction to Systems Biology for Animal Scientists, in Systems Biology and Livestock Science (eds M. F. W. te Pas, H. Woelders and A. Bannink), Wiley-Blackwell, Oxford, UK. doi: 10.1002/9780470963012.ch1
• Xue, L.; Dobbs, D.; Honavar (2011). "HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods". BMC Bioinformatics. 12: 244. doi:10.1186/1471-2105-12-244.
• Barnhill, A.E., Hecker, L.A., Kohutyuk, O., Buss, J.E., Honavar, V. and Greenlee, H.W. (2010) Characterization of the Retinal Proteome During Rod Photoreceptor Genesis. BMC Research Notes 3:25.
• Caragea, C. Silvescu, A., Caragea, D., and Honavar, V. (2010). Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models. BMC Bioinformatics. doi: 10.1186/1471-2105-11-S8-S6.
• El-Manzalawy, Y. and Honavar, V. (2010). Recent Advances in B-Cell Epitope Prediction Methods. Immunome Research Suppl. 2:S2.
• Towfic, F.; Caragea, C.; Dobbs, D.; Honavar, V. (2010). "Struct-NB: Predicting protein-RNA binding sites using structural features". International Journal of Data Mining and Bioinformatics. 4: 21–43. doi:10.1504/ijdmb.2010.030965.
• Towfic, F.; VanderPlas, S.; Oliver, C.A.; Couture, O.; Tuggle, C.K.; Greenlee, M.H.W.; Honavar, V. (2010). "Detection of gene orthology from gene co-expression and protein interaction networks". BMC Bioinformatics. 11 (Suppl 3): S7. doi:10.1186/1471-2105-11-s3-s7.
• Tuggle, C.K.; Bearson, S.M.D; Huang, T.H.; Couture, O.; Wang, Y.; Kuhar, D.; Lunney, J.K.; Honavar, V. (2010). "Methods for transcriptomic analyses of the porcine host immune response: Application to Salmonella infection using microarrays". Veterinary Immunology and Immunopathology. 138: 282–291. doi:10.1016/j.vetimm.2010.10.006.
• Caragea, C.; Sinapov, J.; Dobbs, D.; Honavar, V. (2009). "Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling". BMC Bioinformatics. 10: S4. doi:10.1186/1471-2105-10-S4-S4.
• Couture, O.; Callenberg, K.; Koul, N.; Pandit, S.; Younes, J.; Hu, Z-L.; Dekkers, J.; Reecy, J.; Honavar, V.; Tuggle, C. (2009). "ANEXdb: An Integrated Animal ANnotation and Microarray EXpression Database". Mammalian Genome. 20: 768–777. doi:10.1007/s00335-009-9234-1.
• Towfic, F., Greenlee, H., and Honavar, V. (2009). Aligning Biomolecular Networks Using Modular Graph Kernels. In: Proceedings of the 9th Workshop on Algorithms in Bioinformatics (WABI 2009). Berlin: Springer-Verlag: LNBI Vol. 5724, pp. 345–361.
• Towfic, F., Greenlee, H., and Honavar, V. (2009). Detecting Orthologous Genes Based on Protein-Protein Interaction Networks. In: Proceedings of the IEEE Conference on Bioinformatics and Biomedicine (BIBM 2009). IEEE Press.
• 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. Stem Cells and Development. 17:119–131.
• El-Manzalawy, Y.; Dobbs, D.; Honavar, V. (2008). "On Evaluating MHC-II Binding Peptide Prediction Methods". PLOS ONE. 3 (9): e3268. doi:10.1371/journal.pone.0003268.
• El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008). Predicting Flexible Length Linear B-cell Epitopes, 7th International Conference on Computational Systems Bioinformatics, Stanford, CA. Singapore: World Scientific.
• El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008). Predicting linear B-cell epitopes using string kernels. Journal of Molecular Recognition, DOI: 10.1002/jmr.893
• El-Manzalawy, Y., Dobbs, D., and Honavar, V. (2008). Predicting Protective Linear B-cell Epitopes using Evolutionary Information. IEEE Conference on Bioinformatics and Biomedicine, pp. 289–292, IEEE Press.
• Hecker, L., Alcon, T., Honavar, V., and Greenlee, H. Analysis and Interpretation of Large-Scale Gene Expression Data Sets Using a Seed Network. Journal of Bioinformatics and Biology Insights. Vol. 2. pp. 91–102, 2008.
• Hughes, LaRon; Bao, J.; Honavar, V.; Reecy, J. (2008). "Animal Trait Ontology (ATO): the importance and usefulness of a unified trait vocabulary for animal species". Journal of Animal Science. 86: 1485–1491. doi:10.2527/jas.2008-0930.
• Lee. J-H., Hamilton, M., Gleeson, C., Caragea, C., Zaback, P., Sander, J., Lee, X., Wu, F., Terribilini, M., Honavar, V. and Dobbs, D. Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches.. In Proceedings of the Pacific Symposium on Biocomputing (PSB 2008). Vol. 13. pp. 501–512, 2008.
• 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". BMC Bioinformatics. 9: 487. doi:10.1186/1471-2105-9-487.
• Yan, C.; Wu, F.; Jernigan, R.L.; Dobbs, D.; Honavar, V. (2008). "Characterization of protein–protein interfaces". The protein journal. 27 (1): 59–70. doi:10.1007/s10930-007-9108-x.
• Andorf, C.; Dobbs, D.; Honavar, V. (2007). "Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach". Bmc Bioinformatics. 8 (1): 284. doi:10.1186/1471-2105-8-284.
• Caragea, C., Sinapov, J., Dobbs, D., and Honavar, V. (2007). Assessing the Performance of Macromolecular Sequence Classifiers, In: Proceedings of the IEEE Conference on Bioinformatics and Bioengineering (BIBE 2007). pp. 320–326, 2007.
• Caragea, C., Sinapov, J., Silvescu, A., Dobbs, D. And Honavar, V. (2007). Glycosylation Site Prediction Using Ensembles of Support Vector Machine Classifiers. BMC Bioinformatics doi:10.1186/1471-2105-8-438.
• 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. Nucleic Acids Research. doi:10.1093/nar/gkm294
• Bao, J., Hu, Z., Caragea, D., Reecy, J., and Honavar, V. A Tool for Collaborative Construction of Large Biological Ontologies. Fourth International Workshop on Biological Data Management (BIDM 2006), Krakov, Poland, IEEE Press. pp. 191–195.
• 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. BMC Bioinformatics, 2006.
• Lonosky, P., Zhang, X., Honavar, V., Dobbs, D., Fu, A., and Rodermel, S. (2004) A Proteomic Analysis of Chloroplast Biogenesis in Maize. Plant Physiology Vol. 134. pp. 560–574, 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. Predicting Binding Sites of Protease-Inhibitor Complexes by Combining Multiple Methods. BMC Bioinformatics. Vol. 5. pp. 205, 2004.
• Yan, C., Dobbs, D., and Honavar, V. A Two-Stage Classifier for Identification of Protein-Protein Interface Residues. Bioinformatics. Vol. 20. pp. i371-378, 2004.
• Yan, C., Dobbs, D., and Honavar, V. Identifying Protein-Protein Interaction Sites from Surface Residues – A Support Vector Machine Approach. Neural Computing Applications. Vol. 13. pp. 123–129, 2004.
• Wang, X.; Schroeder, D.; Dobbs, D.; Honavar, V. (2003). "Automated data-driven discovery of motif-based protein function classifiers". Information Sciences. 155 (1): 1–18. doi:10.1016/s0020-0255(03)00067-7.
• Silvescu, A., and Honavar, V. (2001). Temporal Boolean Network Models of Genetic Networks and Their Inference from Gene Expression Time Series. Complex Systems. Vol. 13. No. 1. pp. 54-.

Computer and Information Security

• Oster, Z., Santhanam, G., Basu, S. and Honavar, V. (2013). Model Checking of Qualitative Sensitivity Preferences to Minimize Credential Disclosure. International Symposium on Formal Aspects of Component Software. Springer-Verlag Lecture Notes in Computer Science Vol. 7684, pp. 205–223, 2013.
• Helmer, G.; Wong, J.; Slagell, M.; Honavar, V.; Miller, L.; Wang, Y.; Wang, X.; Stakhanova, N. (2007). "Software Fault Tree and Colored Petri Net Based Specification, Design, and Implementation of Agent-Based Intrusion Detection Systems". International Journal of Information and Computer Security. 1 (1/2): 109–142. doi:10.1504/ijics.2007.012246.
• Wang, Y.; Behera, S.; Wong, J.; Helmer, G.; Honavar, V.; Miller, L.; Lutz, R. (2006). "Towards Automatic Generation of Mobile Agents for Distributed Intrusion Detection Systems". Journal of Systems and Software. 79: 1–14. doi:10.1016/j.jss.2004.08.017.
• Kang, D-K., Fuller, D., and Honavar, V. Learning Misuse and Anomaly Detectors from System Call Frequency Vector Representation. IEEE International Conference on Intelligence and Security Informatics. Springer-Verlag Lecture Notes in Computer Science, Springer-Verlag. Vol. 3495. pp. 511–516, 2005.
• Helmer, G.; Wong, J.; Honavar, V.; Miller, L. (2003). "Lightweight Agents for Intrusion Detection". Journal of Systems and Software. 67: 109–122. doi:10.1016/s0164-1212(02)00092-4.
• Helmer, G.; Wong, J.; Slagell, M.; Honavar, V.; Miller, L.; Lutz, R. (2002). "A Software Fault Tree Approach to Requirements Specification of an Intrusion Detection System". Requirements Engineering. 7 (4): 207–220. doi:10.1007/s007660200016.

Honors

• National Science Foundation Director's Award for Superior Accomplishment, 2013^[13]
• National Science Foundation Director's Award for Collaborative Integration, 2012
• Margaret Ellen White Graduate Faculty Award, Iowa State University, 2011^[14]
• Outstanding Career Achievement in Research Award, College of Liberal Arts and Sciences, Iowa State University, 2008^[15]
• Regents Award for Faculty Excellence, Iowa Board of Regents, 2007^[16]
• Senior Faculty Research Excellence Award, Penn State College of Information Sciences and Technology, Pennsylvania State University, 2016
• 125 People of Impact, Department of Electrical and Computer Engineering, University of Wisconsin-Madison, 2016 ^[17]
• Sudha Murty Distinguished (Visiting) Chair of Neurocomputing and Data Science, Indian Institute of Science, 2016 ^[18]

References

1. "Vasant Honavar's Official Web Page at Pennsylvania State University"
2. "Penn State Institute for Cyberscience". Retrieved 29 May 2015.
3. "Interdisciplinary Center Seeks to Leverage the Power of Big Data Analytics
4. "Exploring Big Data's Potential for the Northeast". Retrieved 3 Nov 2015.
5. "Computing Community Consortium Members". Retrieved 29 May 2015.
6. "CCC Announces new members". Retrieved 31 May 2015.
7. "Susan Hockfield Chosen to Serve as AAAS President-Elect". Retrieved 21 December 2015.
8. "ORCID Record for Vasant Honavar".
9. "Vasant Honavar's Google Scholar Page". Retrieved 29 May 2015.
10. "Library of Congress Catalog Search". Retrieved 29 May 2015.
11. "Vasant Honavar's Math Genealogy Record". Retrieved 29 May 2015.
12. "NSF 12-499 Core Techniques and Technologies for Big Data". Retrieved 29 May 2015.
13. "Honavar honored for his leadership of the NSF Big Data Program". Retrieved 29 May 2015.
14. "Inside Iowa State" (PDF). Retrieved 31 May 2015.
15. "Teaching, service and research awards to LAS faculty, staff". Retrieved 31 May 2015.
16. "2007 Fall University Convocation & Awards Ceremony". Retrieved 31 May 2015.
17. "125 People of Impact". Retrieved 25 August 2016.
18. "Sudha Murty' chair launched at IISc". Retrieved 14 October 2016.

External links

• Personal home page