Artificial Intelligence Research Laboratory: Faculty, Students, Alumni, and Collaborators

Faculty

Dr. Vasant Honavar, Professor of Computer Science and of Bioinformatics and Computational Biology; Director, Artificial Intelligence Research Laboratory, Director, Center for Computational Intelligence, Learning, and Discovery. Dr. Honavar works on Artificial Intelligence; Bioinformatics and Computational Systems Biology, Data Mining, Information Integration, Semantic Web, and applications in Bioinformatics, Security Informatics, Materials Informatics, and Engineering Informatics.
Dr. Dimitris Margaritis, Assistant Professor of Computer Science. Dr. Margaritis works on Bayesian Networks, Machine Learning, and Very Large Databases.
Dr. Jin Tian, Assistant Professor of Computer Science. Dr. Tian works on Computational models of Causal Inference.

Students

Current Ph.D. Students

Tim Alcon (Honavar, Greenlee). Interests: Computational Systems Biology, Proteomics, Transcriptomics, Bioinformatics. Tim is supported by a Multi-disciplinary Graduate Education and Training (MGET) award funded by the USDA. Expected graduation: Summer 2008.
Carson Andorf (Honavar). Ph.D. Student in Computer Science. Interests: Data Mining, Bioinformatics, Machine Learning, Distributed Knowledge Networks, Intelligent Agents and Multi-agent systems, Gene Expression Analysis. Carson is supported by an IGERT fellowship funded by the National Science Foundation and a research assistantship funded by the National Institutes of Health. Expected Graduation: Fall 2007.
Cornelia Caragea (Honavar). Ph.D. Student in Computer Science. Interests: Machine Learning, Data Mining, Probabilistic Relational Models. Cornelia is being supported by a teaching assistantship in Computer Science. Expected Graduation: Spring 2008.
Yasser El-Manzalawy (Honavar). Ph.D. Student in Computer Science. Interests: Machine Learning, Data Mining, Probabilistic Relational Models, Semantic Web. Yasser is supported by a fellowship from the Egyptian Government. Expected graduation: Summer 2009.
Neeraj Koul (Honavar). Ph.D. Student in Computer Science. Interests: Information Integration, Query Planning, Query Decomposition, Query Optimization. Neeraj is a progammer/analyst for Center for Computational Intelligence, Learning, and Discovery. Expected Graduation: Summer 2009.
Rafael Jordan (Honavar). Ph.D. Student in Computer Science. Interests: Information Integration, Bioinformatics, Data Mining. Raphael is supported by a Fulbright Fellowship.
Adrian Silvescu (Honavar). Interests: Machine Learning, Data Mining, Ontology Learning, Probabilistic Relational Models, Computational Biology and Bioinformatics. Adrian has been supported through a teaching assistantship from the Department of Computer Science and research assistantships funded by Pioneer Hi-Bred and the National Science Foundation. Expected Graduation: Fall 2007.
Jivko Sinapov (Stoytchev, Honavar). Ph.D. Student in Computer Science. Interests: Machine Learning, Developmental Robotics.
Fadi Towfic (Honavar, Greenlee). Ph.D. Student in Bioinformatics and Computational Biology. Interests: Computational Systems Biology; Genomics; Gene and Protein Networks. Machine Learning. Fadi is supported by a fellowship funded by an Integrative Graduate Education and Research Training (IGERT) grant from the National Science Foundation. Expected Graduation: Spring 2010.
Kewei Tu (Honavar), Ph.D. Student in Computer Science. Interests: Machine Learning, Data Mining, Probabilistic Relational Models. Kewei is supported by a teaching assistantship in Computer Science. Expected Graduation: Spring 2010.
Flavian Vasile (Honavar). Interests: Machine Learning, Human-Computer Interaction, and the Semantic Web. Flavian is being supported by a teaching assistantship in Computer Science. Expected Graduation: Spring 2009.
Oksana Yakhnenko (Honavar). Interests: Machine Learning, Multi-relational learning, Learning from Semantically Heterogeneous data, Probabilistic Relational Models, Data Visualization, Learning from Sequence Data. Oksana is funded by a graduate teaching assistantship in Computer Science and a research assistantship funded by the National Science Foundation. Expected Graduation: Spring 2009.

Collaborating Ph.D. Students

Oliver Couture (Tuggle, Honavar). Interests: Animal Genomics, Bioinformatics. Oliver is an USDA MGET Fellow. Expected Graduation: Summer 2008.
Laron Hughes (Reecy, Honavar). Interests: Phenotype ontologies, Comparative Genomics. Expected Graduation: LaRon is an IGERT Fellow. Expected Graduation: Summer 2008.
Michael Terribilini (Dobbs, Honavar). Interests: Macromolecular Structure-Function, Bioinformatics. Michael is an USDA MGET Fellow. Expected Graduation: Spring 2008.
Peter Zaback (Dobbs, Honavar). Interests: Bioinformatics and Computational Biology, Protein-DNA interaction. Expected Graduation: Spring 2009.
Kent Vander Velden (Reilley and Honavar). Interests: Systems Biology, Metabolic Networks, Computational Biology. Kent is an NSF IGERT fellow. He is at present a research scientist at Pioneer Hi-Bred and his doctoral work is supported by Pioneer Hi-Bred. Expected Graduation: Fall 2007.

Current M.S. Students

None at present.

Rotation Students (Graduate)

None at present

Undergraduates and Summer Research Students

Remy Younes. Topics in Semantic Web and Data Integration.

Alumni

Postdoctoral Fellows

Dr. Doina Caragea (Honavar). Postdoctoral research associate, 2004-2006. Current Position: Assistant Professor of Computer Science, Kansas State University.
Dr. Byron Olson (Honavar). Postdoctoral research associate, 2005-2006. Current Position: Research Assistant Professor, Arizona State University.

Ph.D. Graduates

Jie Bao (Honavar). Ph.D., Computer Science, 2007. Thesis: Representing and Reasoning with Modular Ontologies. Jie Bao was supported by a research assistantship in Computer Science funded in part by the National Science Foundation, the Iowa State University Center for Integrative Animal Genomics, and the Center for Computational Intelligence, Learning, and Discovery. Current Position: Research Associate, Center for Computational Intelligence, Learning, and Discovery, Iowa State University.
Tyra Dunn (Greenlee, Honavar). Ph.D., Bioinformatics and Computational Biology, 2007. Thesis: Characterizing and Influencing Differentiation of Retinal Progenitor Cells. Tyra was supported in part by an Integrative Graduate Education and Research Training (IGERT) fellowship from the National Science Foundation.
Jyotishman Pathak (Honavar). Ph.D., Computer Science, 2007. Thesis: Interactive and Verifiable Web Service Composition, Reformulation, and Adaptation. Jyotish was supported by a graduate research assistantship in Computer Science funded in part by grants from the National Science Foundation. Initial Employment: Research Scientist, Informatics, Mayo Clinic.
Dae-Ki Kang (Honavar). Ph.D., Computer Science, 2006. Thesis: Abstraction, Aggregation and Recursion for Generating Accurate and Simple Classifiers. Dae-Ki was supported in part by a Teaching assistantship from the Department of Computer Science and a Research assistantship funded by the Center for Computational Intelligence, Learning, and Discovery. Initial Employment: Senior Member of Technical Staff, National Security Research Institute, Korea. Dae-Ki is funded by a Teaching assistantship from the Department of Computer Science and a Research assistantship funded by the National Science Foundation.
Changhui Yan (Honavar and Dobbs). Ph.D., Bioinformatics and Computational Biology, 2005. Thesis: Analysis and Computational Prediction of Protein-Protein and Protein-DNA Interfaces. Changhui was supported by a Plant Sciences Fellowship and a research assistantships funded by the ISU Graduate College and a grant from the National Institutes of Health. Current Position: Assistant Professor of Computer Science, Utah State University.
Jun Zhang (Honavar). Ph.D., Computer Science, 2005. Thesis: Learning Ontology Aware Classifiers. Jun was supported by a teaching assistantship in Computer Science and research assistantships funded by the Iowa State University Graduate College and the National Science Foundation. Current Position: Data Mining Research Scientist, Fair Isaac, San Diego.
Doina Caragea (Honavar). Ph.D., Computer Science, 2004. Thesis: Learning Classifiers From Distributed, Semantically Heterogeneous, Autonomous Data Sources. Doina was supported through research assistantships funded by the ISU Graduate College and the National Science Foundation. Doina also received the IBM Research Fellowship during 2002-2003 and 2003-2004. Initial Employment: Research Fellow, Computational Intelligence, Learning, and Discovery Program, Iowa State University.
Jihoon Yang (Honavar) Ph.D., Computer Science, 1999. Thesis: Intelligent Information Retrieval and Knowledge Discovery Agents.. Jihoon has been supported by a CS Teaching Assistantship and Research Assistantships funded by the ISU Graduate College and the John Deere Foundation. Initial Employment: Research Scientist, Information Sciences Laboratory, Hughes Research Laboratory, Malibu, CA. Current Position: Assistant Professor, Computer Science, Sogang University, Korea.
Karthik Balakrishnan, Ph.D., Computer Science, 1998. Thesis: Biologically Inspired Information Processing Structures for Autonomous Agents and Robots. Karthik was supported through CS Teaching assistantship, Research assistantships funded by the National Science Foundation and the John Deere Foundation. Karthik received an IBM Research Fellowship during 1997-1998, and a Research Excellence Award from the Iowa State University Graduate College. Initial Employment: Research Scientist, Allstate Research and Planning Center, Menlo Park, CA. Current Position: Director of Analytics, Fireman's Fund Insurance, Novato, CA.
Rajesh Parekh, Ph.D., Computer Science, 1998. Constructive Learning Algorithms: Inducing Grammars and Neural Networks. Rajesh was supported by a CS teaching assistantship, and a research assistantship funded by the National Science Foundation. . Rajesh received a Graduate Research Excellence award from the Iowa State University graduate college. Initial Employment: Research Scientist, Allstate Research and Planning Center, Menlo Park. Current Position: Senior Data Mining Engineer, Blue Martini Software, San Mateo, CA.
Chun-Hsien Chen, Ph.D., Computer Science, 1997. Thesis: Neural Architectures for Associative Memory, Syntax Analysis, Knowledge Representation, and Inference. Chun-Hsien was funded by a project assistantship at the Division of Extended and Continuing Education. Initial Employment: Research Scientist, Computer and Communications Research Laboratories, Industrial Technology Research Institute, Taiwan. Current Position: Assistant Professor, Department of Information Management, Chang Gung University, Taiwan.
Armin Mikler, Ph.D., Computer Science, 1995. (Co-advised with Johnny Wong). Thesis: Quo-Vadis - A Framework for Intelligent Routing in Large Communication Networks. Armin was supported by a CS teaching assistantship and a project assistantship at the Center for Agricultural and Rural Development. Initial Employment: Postdoctoral Research Fellow, Scalable Computation Laboratory, DOE Ames Laboratory, Ames, IA. Current Position: Associate Professor, Department of Computer Science, University of North Texas, Denton.

M.S. Graduates

Oksana Kohutyuk (Honavar). M.S. 2007. Thesis: The Retina Workbench. Oksana was supported by a research assistantship funded in part by a grant from the National Institutes of Health and a teaching assistantship in Computer Science.
Charles Gieseler (Honavar, Tesfatsion). M.S. 2005. Thesis: A Java Reinforcement Learning Module for the Recursive Porous Agent Simulation Toolkit. Current Position: Lawrence Livermore Labs.
Anna Atramentov (Honavar). Thesis: Multi-Relational Decision Tree Learning Algorithm - Implementation and Experiments. Anna was supported by a Teaching Assistantship in Computer Science and Research Assistantship funded by the Graduate College. Current position: Ph.D. Student, Computer Science, University of Illinois at Urbana-Champaign.
Zhong Gao (Honavar and Ho). Thesis: Genome wide recognition of tumor necrosis factor (TNF) like ligands in human and Arabidopsis genomes: A structural Threading Approach. Current position: Post-doctoral Associate, The Center for Cardiovascular Bioinformatics and Modeling, Johns Hopkins University.
Hector Leiva (Honavar). 2002. Thesis: Multi-Relational Decision Tree Learning. Hector was supported by a Fullbright Fellowship and a Graduate Teaching Assistantship in Computer Science. Current Position: Research Scientist, Universidad Nacional de San Luis. Argentina.
Jaime Reinoso-Castillo (Honavar). Thesis: Ontolgy-Driven Information Extraction and Integration from Autonomous, Heterogeneous, Distributed Data Sources -- A Federated Query-Centric Approach. Thesis. Jaime was supported by a Fullbright Scholarship and a research assistantship funded by the National Science Foundation. Current Position: Universidad Javeriana, Colombia.
Xiaosi Zhang. 2002. Interests: Bioinformatics and Computational Biology. Gene Expression Analysis. Xiaosi was supported by a graduate assistantship funded by a grant from the Carver Foundation. Current Position: Papajohn Center for Entreprenuership.
Xiangyun Wang (Honavar). 2002. Interests: Bioinformatics and Computational Biology. Gene Expression Analysis. Macromolecular Structure-Function Prediction from Sequence Data. Xiangyun was supported by a fellowship from the ISU graduate college and a teaching assistantship in Computer Science. Current Position: Research Scientist, Astra Zeneca, Inc.
Kent Vander Velden 2002. (Gavin Naylor's lab). Interests: Bioinformatics and Computational Biology, Characterization of Molecular Structure-Function relationships, Phylogenetics. Kent was supported by an NSF IGERT Fellowship in Computational Molecular Biology. Current Status: Member of Research Staff, Pioneer Hi-Bred, Inc.
Neeraj Koul. 2001. Thesis: Clustering with Semi-Metrics. Neeraj was supported by a research assistantship in Computer Science funded by the Carver Foundation and a Teaching Assistantship in Computer Science. Current Position: Motorola.
Rushi Bhatt. 2001. Thesis: Spatial Learning and Localization. Rushi was supported by the ISU Neuroscience Graduate Fellowship and a Teaching Assistantship in Computer Science. Current Status: Ph.D. Student, Boston University.
Dake Wang. 2001. Dake was supported by a teaching assistantship in Computer Science and a research assistantship funded by the Carver Foundation. Initial Employment: Lumicyte Inc.
Asok Tiyyagura. Project: Mutual Information Based Association Rule Mining. Asok has been supported through a research assistantship funded by the ISU Council on International Programs and EPRI and a teaching assistantship in Computer Science. Initial Employment: Cisco Systems.
Fajun Chen. 2000. Thesis: Learning Information Extraction Patterns. Fajun has been supported through a research assistantship funded by the ISU Graduate College and a Teaching Assistantship in Computer Science. Initial Employment: Ericsson.
Tarkeshwari (Taru) Trivedi. 2000. Thesis: An Agent Toolkit for Distributed Knowledge Networks. Taru was supported through a teaching assistantship in Computer Science and a research assistantship funded by the John Deere Foundation. Initial Employment: Motorola.
Di Wang, 1998. Project: Mobile Agents for Information Retrieval. Initial Employment: Consultant, Canada.
Shane Konsella, 1997. Thesis: Trie Compaction Using Genetic Algorithms. Shane was supported by a teaching assistantship in Computer Science. Initial Employment: Hewlett-Packard.
Karthik Balakrishnan, 1993. Project: Faster Learning Approximations of Backpropagation by Handling Flat-Spots. Karthik was supported by a teaching assistantship in Computer Science and a research assistantship funded by the ISU graduate College. (Stayed on as a Ph.D. Student).
Rajesh Parekh, 1993. Project: Efficient Learning of Regular Languages Using Teacher-Supplied Positive Examples and Learner-Generated Queries. Rajesh was suported by a teaching assistantship in Computer Science. (Stayed on as a Ph.D. Student).
Jayathi Janakiraman, 1993. Project: Adaptive Learning Rate for Increasing Learning Speed in Backpropagation Networks. Jayathi was supported by a teaching assistantship in Computer Science. Initial Employment: Motorola.
Priyamvadha Thambu, 1993. Thesis: Automated Knowledge-Base Consistency Maintenan ce in an Evolving Intelligent Advisory System. Priya was supported by a research assistantship funded by Iowa Department of Housing and Urban Development. Initial Employment: Inference Corporation.
Richard Spartz, 1992. Project: Speeding Up Backpropagation Using Expected Source Values. Rich was supported by a teaching assistantship in Computer Science. Initial Employment: IBM Rochester.

Undergraduates and Summer Research Students

David Gemperline, Participant, Summer Institute in Bioinformatics and Computational Systems Biology, 2007.
Keith Callenberg, Participant, Summer Institute in Bioinformatics and Computational Systems Biology, 2007.
John Leacox, Undergraduate Research Assistant, 2006.
Matt Miller, Undergraduate Research Assistant, 2006.
Peter Wong, Undergraduate Research Assistant, 2006.
Ryan Bruce, Undergraduate Research Assistant. Interests: Machine Learning, Bioinformatics. 2004.
Tim Goodman, Duke University, Participant, Summer Institute in Bioinformatics and Computational Biology, 2004.
Oksana Yakhnenko. 2004. Interests: Artificial Intelligence, Machine Learning, Data Mining, Data and Knowledge Visualization. Undergraduate Researcher, 2003-2004. Oksana is now pursuing a Ph.D. in Computer Science at Iowa State University.
Amy Nienaber, Participant, Summer Institute in Bioinformatics and Computational Biology Summer 2003. Interests: Computational Biology.
Matthew Beard, Participant, Summer Institute in Bioinformatics and Computational Biology Summer 2003. Interests: Compuational Biology.
Diane Schroeder. 2002. Undergraduate research assistant 2000-2002. Interests: Bioinformatics and Computational Biology; Data Mining. Diane is now pursuing a Ph.D. at Stanford University.
Carl Pecinovsky, 1997. Undergraduate Research Assistant 1996-1997. Employed at IBM Rochester, MN.
Jeremy Ludwig, 1997. Undergraduate Research Assistant 1996-97. Graduate School: University of Pittsburgh.
Todd Lindsey, 1996. Undergraduate Research Assistant, 1995-1996.
Eric Barsness, 1993. Employed at IBM Rochester, MN.

Pre-College Students

John Farragher. Summer program for gifted pre-college students 1992.
Stephen Lee. Summer program for gifted pre-college students 1993.
Anna Keyte, Angel Sheriff, Kellan Brumback, Sara Karbeling, 1997. Adventures in Supercomputing (AIS 1997) Team.
Eric Solan, Nic Dayton, Luke Rolfes, and Julian Sheldahl. Adventures in Supercomputing (AIS 1998) Team.

Visiting Researchers

Professor Mokdong Chung, on sabbatical from Pukyong National University, Korea: August 1999 through July 2000.
Olivier Bousquet from Ecole Polytechnique. France: April - July 1997. Olivier is working on biologically inspired computational architectures for intelligent agents during his visit. Olivier's research is funded by Ecole Polytechnique.
Codrin Nichitiu from ENS Lyon, France: June - September 1996. Codrin worked on machine learning of grammars during his visit.
Vadim Kirillov, from Institute of Agricultural Informatics, Kharkov, Ukraine: 1995. Vadim works on temporal and spatial inference under uncertainty.
Brian Walenz (formerly of Iowa State University). Brian is now at Sandia National Lab.

Collaborators

Faculty Collaborators

Dr. Drena Dobbs, Department of Genetics, Cell, and Developmental Biology, Iowa State University. Drena is interested in protein structure prediction, molecular mechanisms of regulation, and bioinformatics.
Dr. Volker Brendel, Department of Genetics, Cell, and Developmental Biology. Interests: Bioinformatics, Genomics.
Dr. Doina Caragea, Department of Computer Science, Kansas State University. Doina is interested in information integration and distributed data mining.
Heather Greenlee, Biomedical Sciences, Iowa State University. Heather is interested in developmental neuroscience of the retina and proteomics.
Robert Jernigan, Director, Laurence H. Baker Center for Bioinformatics and Biological Statistics, Iowa State University. Robert is interested in computational and biophysical characterizations of protein sequence-structure-function relationships.
Dr. Jim McCalley, Electrical and Computer Engineering, Iowa State University. Jim is interested in applications of machine learning in control of large power systems (among other things).
Krishna Rajan, Material Science, Iowa State University. Krishna is interested in Material Informatics.
Don Sakaguchi, Neuroscience Program, Iowa State University. Don is interested in developmental neuroscience.
Dr. Giora Slutzki, Department of Computer Science, Iowa State University. Giora works on graph algorithms, automata theory, logic programming (among other things).
Dr. Leonard Uhr, Computer Sciences Department, University of Wisconsin, Madison. Leonard Uhr, until his untimely death in October 2000, worked on machine learning, neural networks, and parallel architectures for artificial intelligence (among other things).
George Voutsadakis, Department of Mathematics and Computer Science, Lake Superior State University. George is interested in algebraic logic, categorical algebra, algebraic structures, and theoretical computer science.
Dr. Dan Voytas, Department of Genetics, Development, and Cell Biology, Iowa State University. Dan is interested in plant genomics and bioinformatics (among other things).
Dr. Johnny Wong, Department of Computer Science, Iowa State University. Johnny works on communication networks, distributed computing, and distributed multi-media systems.

Industrial Collaborators

Dr. Karthik Balakrishnan, Fireman's Insurance.
Richard Bradford, Rockwell Collins, Cedar Rapids, IA.
Bill Fulkerson, Deere and Company, Moline, IL.
Guy Helmer, Palisade Systems, Ames, IA.
Ellen Maxon, Power Domain, Inc.
Rajesh Parekh, Yahoo!
Jun Zhang, Fair Isaac.

Collaborating Labs and Groups