News

 

James Reecy and Vasant Honavar Receive an USDA Grant to Develop Bioinformatics Tools for Comparative Animal Genomics

21 Jan, 2008

The United States Department of Agriculture has awarded a 3-year, $1,000,000 grant to a team led by Professor Vasant Honavar of the Department of Computer Science and Professor James Reecy of the Department of Animal Science at Iowa State University and Professor Anne Kwitek of the Department of Internal Medicine at the University of Iowa to develop bioinformatics tools for integrative and comparative annotation, analysis, and visualization of quantitative trait loci (QTL) data across multiple animal species. Recent advances in high-throughput sequencing have led to the mapping and sequencing of whole genomes of multiple vertebrate and non-vertebrate species. This offers unprecedented opportunities for comparative studies that leverage data from large numbers of sequenced genomes for developing improved methods for gene identification and genome annotation, and for advancing our understanding of evolution of species, as well as the principles that govern gene function, and genetic interactions that orchestrate processes such as cellular development, differentiation, aging and disease. However, the paucity of computational tools that help integrate animal trait information across species is a major hurdle to realizing such opportunities. This research aims to overcome this hurdle by developing an animal trait ontology for integrative cross-species analysis of trait data, along with software tools for annotation and visualization of QTL and phenotype data across multiple animal species, including humans, livestock species, and model organisms. This work will leverage as well as drive advances in the theoretical foundations of, and software tools for, collaborative ontology development and ontology-based federated approaches to information integration in the ISU Artificial Intelligence Laboratory. The project will offer research opportunities in Computer Science and Bioinformatics and Computational Biology for Ph.D., Masters, and undergraduate students.

ISO Analytics Appoints ISU Computer Science Alumnus Karthik Balakrishnan as the Vice President of Analytics

31 Oct, 2007

Dr. Karthik Balakrishnan, an alumnus of the Iowa State University Artificial Intelligence Research Laboratory and the Department of Computer Science, has recently accepted a position as the Vice President of Analytics at ISO Analytics (iiA) in San Francisco. A unit of Insurance Services Office(ISO), a leading provider of data, analytics and decision support to the Property and Casualty Insurance industry, iiA's mission is to leverage advanced data mining techniques to create innovative and value-generating products and solutions for the insurance industry. In his role, Karthik oversees all of iiA's analytical activities.

Prior to joining iiA, Karthik led the Analytical Services organization at Fireman's Fund Insurance Company (a company of Allianz), where his team had notable successes through initiatives such as claim fraud detection, and underwriting rules analysis (among others), leading to increases in annual financial savings or profits in excess of $5Million. Karthik has also had stints building and running a Data Mining/Web mining group at Obongo Inc. (an eCommerce startup), and developing claim fraud prediction models at Allstate Research and Planning Center.

Karthik received his Ph.D. degree in Computer Science in 1998, specializing in machine learning and data mining, under the supervision of Professor Vasant Honavar. Karthik has over 20 publications on topics spanning neural networks, evolutionary algorithms, spatial learning, and cognitive modelling. He co-edited a book (with Vasant Honavar and Mukesh Patel) on Evolutionary Synthesis of Intelligent Agents (MIT Press, 2001). Karthik is especially proud of his work on the computational modeling of the Hippocampal formation and its role in spatial learning, localization, and navigation, which was carried out as part of his Ph.D. Research in the ISU Artificial Intelligence Research Laboratory. For his doctoral research, Karthik was awarded the Iowa State University Research Excellence Award in 1998.

Vasant Honavar Receives an NSF Grant to Develop Algorithms and Software for Collaborative, Integrative, Analysis of Large, Distributed, Semantically Heterogeneous Data Sets

16 Aug, 2007

The US National Science Foundation has awarded a 3-year, $449,999 grant to a team led by Professor Vasant Honavar of Computer Science to develop algorithms and software for collaborative, integrative analysis of large, semantically heterogeneous data sets. Advances in networks, sensors, storage, computing, and high throughput data acquisition, have led to a proliferation of autonomous, distributed data sources in many areas of human activity. New discoveries in biological, physical, and social sciences and engineering are being driven by our ability to discover, share, integrate and analyze disparate types of data. Statistically-based machine learning algorithms offer some of the most cost-effective approaches to discovery of experimentally testable predictive models and hypotheses from data. However, the large size, distributed nature, and autonomy of the data sources (and the attendant differences in access, queries allowed, processing capabilities, structure, organization, and underlying data models and data semantics) present hurdles to effective utilization of machine learning. This research aims to overcome these hurdles by developing efficient, resource-aware distributed algorithms and software services to support collaborative, integrative knowledge acquisition such a setting. This project builds on the results of collaboration involving Dr. Honavar's former Ph.D. students Dr. Jie Bao (currently a postdoctoral research associate at the Center for Computational Intelligence, Learning, and Discovery at Iowa State University), Dr. Doina Caragea (currently an assistant professor of Computer Science at Kansas State University), Dr. Jun Zhang (currently a research scientist at Fair Isaac), Dr. Jyotishman Pathak (currently a research scientist at Mayo Clinic). The project will provide enhanced opportunities for research-based training of several Ph.D. students in the Artificial Intelligence Research Laboratory including Cornelia Caragea, Oksana Yakhnenko, Neeraj Koul, and Kewei Tu. The project will also provide research opportunities for MS and undergraduate students. The research team led by Professor Vasant Honavar at Iowa State University and Professor Doina Caragea at Kansas State University will implement, deploy, and evaluate the resulting algorithms using benchmark data sets, associated data models and ontologies, and user-specified inter-ontology mappings on a distributed test-bed of networked databases and services at the two institutions. The resulting open-source software can potentially transform collaborative e-science in the same way that Web has transformed information sharing. The project web site provides access to additional information about the project.

Dr. Rajesh Parekh Promoted to Director of Data Mining and Research at Yahoo!

July 30, 2007

Dr. Rajesh Parekh, an alumnus of the Iowa State University Artificial Intelligence Research Laboratory and the Department of Computer Science, has recently been promoted to the position of Director of Data Mining and Research at Yahoo! Inc. Dr. Parekh received his Ph.D. degree in Computer Science in 1998, specializing in machine learning and data mining, under the supervision of Professor Vasant Honavar. His Ph.D. thesis focused on the constructive learning algorithms for grammar induction and pattern classification, and included one of the first positive results in the literature on efficient learning of regular languages from labeled examples.

In his new position, Dr. Parekh will continue to work on applications of data mining and machine learning to solve challenging problems in user personalization, web-page real-estate optimization, and balancing user experience with ad monetization. Dr. Parekh joined the Data Mining Research group at Yahoo! in October 2004, where he was promoted to the position of Data Mining Engineering Manager in 2006. Prior to joining Yahoo, Dr. Parekh was a Senior Data Mining Research Engineer at Blue Martini Software and a Senior Research Associate in Data Mining at Allstate Research and Planning Center.

Dr. Parekh has published over 25 research papers in refereed conferences and journals. Dr. Parekh has received several professional awards and honors including the Yahoo! Data Wizard Award (2005), KDD Cup Honorable Mention (2001), Iowa State University Research Excellence Award (1998), John Vincent Atanasoff Graduate Award (1996), and Iowa State University Teaching Excellence Award (1993). The Iowa State University Artificial Intelligence Research Laboratory and the Department of Computer Science are proud to count Rajesh Parekh among their alumni and wish him continued success in his career.

CCILD Faculty help establish new Bioinformatics and Computational Biology Undergraduate Major

July 7, 2007.

The Board of Regents, State of Iowa, approved the new undergraduate major in Bioinformatics and Computational Biology (BCB) this summer. The program, to be offered by by Iowa State University's College of Liberal Arts and Sciences, will be administered jointly by the Departments of Computer Science; Genetics, Development and Cell Biology; and Mathematics, and is one of the few such undergraduate academic programs in the United States.

Several members of the Center for Computational Intelligence, Learning, and Discovery, including Dr. Drena Dobbs, Dr. David Fernandez-Baca, and Dr. Vasant Honavar were instrumental in establishing the BCB undergraduate major.

According to Dr. Vasant Honavar, Professor of Computer Science and director of the Center for Computational Intelligence, Learning, and Discovery, Biology is undergoing a major transformation, from a data-poor science into an increasingly data-rich science

With increased availability of data, come challenges in organizing, analyzing, integrating, and interpreting data and unprecedented opportunities for accelerating scientific discovery. Virtually every area of human endeavor has been transformed by advances in computing and information sciences leading to the birth of new informatics-enabled disciplines such as Bioinformatics and Computational Biology, leading some to suggest that all sciences are morphing into computer science.

Advances in sequencing have resulted in a wealth of genomic sequences. The genomic sequence can be viewed as a genetic program that orchestrates an organism's development, its behavior, and its responses to its environment. We now have the ability to measure the expression levels of tens of thousands of genes during development, onset and progression of disease, and in response to environmental factors. These data contain a wealth of information about how organisms function. Comparative genomics can provide us insights into how organisms came to be what they are. There is a growing need for tools, primarily computational tools, for integrating, analyzing, interpreting, and gaining scientific insights from exponentially increasing amounts of biological data, and for individuals with the background and training needed to develop and apply such tools to solve real-world problems

On a scientific level, there is a growing realization that biology is fundamentally an information science. Large scale use of algorithms - precise recipes for information processing developed with the advent of Computer Science nearly 60 years ago is transforming biology from a descriptive science into a predictive science, much like physics was transformed by the development and use of calculus by Newton and Leibnitz more than 200 years ago.

Today there are great opportunities for discovering the nature of biological information and for using this knowledge to create tools that will advance our ability to create disease-resistant crops, develop new therapies and drugs, develop biofuels, and mitigate environmental disasters. There is a growing demand in industry - e.g., in pharmaceutical, agribusiness, and biotechnology companies for individuals who can combine knowledge of biological and computational sciences to exploit these opportunities.

The undergraduate major in Bioinformatics and Computational Biology (BCB) is a natural outgrowth of the highly successful interdepartmental BCB graduate program at Iowa State University (ISU). It builds on ISU's strengths in Computer Science, Biological Sciences (including in particular, Plant and Animal Sciences), Statistics, and related areas. The BCB graduate program was initiated at ISU in 2000, with support provided by the National Science Foundation (NSF), through a 5-year, $2.57 million Integrative Graduate Education and Research Training (IGERT) grant. In 2005, the program received an additional $3 million in IGERT funding, to expand the training opportunities in new areas such as systems biology. The BCB program has also received approximately $1 million in two 5-year awards from NSF to organize a Summer Institute in Bioinformatics to introduce undergraduates from around the country to bioinformatics.

The ISU BCB graduate program is currently one of the largest and strongest BCB Ph.D. programs in the country. The BCB graduate program has over 80 faculty affiliated with the BCB graduate program, of whom about 30 are extremely active in core areas of BCB while the rest provide expertise in related areas of biological and computational sciences. BCB Ph.D. graduates have been extremely sought after by academia and industry. BCB faculty collectively have tens of millions of dollars of research support from NSF, NIH, and USDA. The Laurence H. Baker Center for Bioinformatics and Biological Statistics, the Center for Integrative Animal Genomics, and the Center for Computational Intelligence, Learning, and Discovery support a broad range of BCB research at ISU.

Because of ISU's research strengths in BCB, Computational and Biological Sciences, and the wealth of research-based training opportunities available to BCB undergraduates, the depth and breadth of BCB faculty expertise, we are well-positioned to offer one of the strongest BCB undergraduate programs in the United States.

The BCB undergraduate major will prepare students for careers at the interfaces of biological, informational and computational sciences. The required course work and associated electives provide students with the foundation in biological sciences, computer science, mathematics, statistics, chemistry, and physics. Strong analytical skills, inquisitive personality, willingness and ability to learn mathematics and computer science in addition to biology, are critical for student success in the BCB major. BCB undergraduate major will offer a challenging, but extremely rewarding undergraduate experience.

Professor Vasant Honavar part of an NIH-Funded International Collaboration on Improved Methods for Protein Structure Prediction

July 5, 2007

Accurate knowledge of protein structures is important for predicting protein function, and structure-based drug design for therapeutics. The gap between the number of experimentally determined structures and the number of known sequences continues to increase at a rapid rate. Hence, there is an urgent need for accurate and computationally efficient methods for protein structure prediction. The National Institutes of Health has awarded a 3-year, $744,725 grant to a team of researchers from Biochemistry, Biophysics, and Molecular Biology (Andrzej Kloczkowski , Robert Jernigan) Chemistry (Mark Gordon), Computer Science (Vasant Honavar), and Mathematics (Zhijun Wu) from Iowa State University in the United States and Janusz Bujnicki, Krzysztof Ginalski and Andrzej Kolinski from the International Institute of Molecular and Cell Biology and the Warsaw University in Poland to improve the accuracy of structures predicted by homology modeling, fold recognition, and de novo modeling. The resulting algorithms and software will significantly advance the current state-of-the-art in protein structure prediction.

Samik Basu, Vasant Honavar, and Robyn Lutz Recieve an NSF Grant to Develop New Tools for Specification-Based Service Composition

June 25, 2007

The US National Science Foundation has awarded a 3-year, $335,000 grant to Computer Science professors Samik Basu, Vasant Honavar, and Robyn Lutz. The Web services are beginning to play an increasingly important role in scientific, engineering, government, health-care, and business applications. Complex applications, e.g., in e-science cyberinfrastructure, call for tools that support users to assemble composite services from independently developed component services to achieve the desired functionality. This research aims to address this need by developing powerful interactive methods for service composition with provable guarantees with respect to user-specified functional and non-functional requirements. It will also provide enhanced opportunities for research-based training of graduate students. This research builds on the results of collaboration involving Jyotishman Pathak, a Ph.D. student in the Artificial Intelligence Research Laboratory, and the team of faculty with complementary expertise in formal methods, artificial intelligence, and software engineering, initiated with seed funds from the Iowa State University Center for Computational Intelligence, Learning, and Discovery.

Prof. Vasant Honavar receives a Regents Faculty Excellence Award

April 16, 2007.

The Regents faculty excellence award, given by the Board of Regents, State of Iowa, "recognizes commitment to excellence, outstanding academic work, leadership and service to the community, and the high regard with which Professor Honavar is held by colleagues and co-workers."

Dr. Vasant Honavar received his M.S. and Ph.D. in Computer Science from the University of Wisconsin, Madison, USA in 1989 and 1990 respectively. He is a professor of Computer Science and of Bioinformatics and Computational Biology at Iowa State University (ISU) where he has been a member of the faculty since 1990. He is the founder and director of the Artificial Intelligence Research Laboratory and the Center for Computational Intelligence, Learning, and Discovery at ISU. He served as associatechair (2001-2003) and chair (2003-2005) of the ISU Bioinformatics and Computational Biology progam. He has also held visiting professorships at the Carnegie Mellon University and the University of Wisconsin-Madison. Honavar's primary research areas include machine learning, knowledge representation, data and service integration, semantic web, and bioinformatics and computational systems biology. Honavar has published over 160 refereed articles (between 1990 and 2006) in journals and conferences (including two that received the best paper awards- at ASWC 2006 and ICTAI 2006), 10 book chapters, and a research monograph to be published by Springer in 2008. Honavar's research has been supported by several grants from the National Science Foundation, the National Institutes of Health, and the Department of Agriculture (USA). Honavar currently serves on the editorial boards of the International Journal of Semantic Web and Information Systems, the Journal of Cognitive Systems Research, and the International Journal of Bioinformatics and Data Mining, and has served on the editorial board of the Machine Learning Journal. He regularly serves on the program committees of several major conferences in Artificial Intelligence, Bioinformatics, Data Mining, and Machine Learning. Honavar has co-chaired the 2006 AAAI Fall Symposium and the 2007 IJCAI workshops on Semantic Web for Collaborative Knowledge Acquisition, and will co-chair the 2007 WI/IAT workshop on e-Science Cyberinfrastructure. Honavar is a senior member of IEEE, ACM, and a member of AAAI, AMIA, and AAAS.

Prof. Jack Lutz receives an LAS Research Excellence Award

April 16, 2007.

The LAS Research Excellence award, given by the Iowa State University College of Liberal Arts and Sciences recognizes faculty members for excellence in research.

Dr. Jack Lutz received his Ph.D. in Mathematics from the California Institute of Technology in 1987, and Bachelors and Masters degrees in Mathematics and a Masters degree in Computer Science from the University of Kansas in 1976, 1979, and 1981 (respectively). He is a professor of Computer Science at Iowa State University where he has been a faculty member since 1986. He is also a core faculty member of the ISU Center for Computational Intelligence, Learning, and Discovery. Dr. Lutz received the NSF presidential young investigator award in 1991. His research interests include computational complexity, algoruthmic information and randomness, and nanoscale self-assembly. Dr. Lutz has published over 50 refereed research papers in journals and conferences during 1987 through 2006. Lutz's research has been supported in part by several grants from the National Science Foundation.

Dr. Honavar and colleagues receive support to develop e-science Cyberinfrastructure for life sciences

26 Feb, 2007

The Center for Integrative Animal Genomics (CIAG) recently awarded a  $50,000, 2-year grant to the Center for Computational Intelligence, Learning, and Discovery (CCILD) which, together with an additional $50,000 in matching funds  from CCILD, will be used to support a CCILD Research Associate. The research associate will work with CCILD and CIAG faculty including Dr. Vasant Honavar  (Computer Science), Dr. Chris Tuggle (Animal Science), Dr. Heather Greenlee (Biomedical Sciences), and Dr. Drena Dobbs (Genetics, Cell, and Developmental Biology),  along with their colleagues, to develop data mining, database, and semantic data integration components of  software for collaborative, distributed e-science cyberinfrastructure.This work leverages research  on Algorithms and Software for Knowledge Acquisition from Heterogeneous Distributed Data, Modular Ontologies supported by the National Science Foundation, research on Integration Integrating Functional Genomics and Quantitative Genetics supported by the US Department of Agriculture, and research on Discovery of Macromolecular Sequence-Structure Function Relationships and Discovery and Modelling of Genetic Networks involved in Retinal Development, funded by the National Institutes of Health. The resulting software will, by enabling scientists to flexibly integrate, analyze, and interpret data from disparate sources to explore specific scientific questions,  significantly expedite several aspects of data-driven discovery in the life sciences.

IJCAI 2007 Workshop on Semantic Web for Collaborative Knowledge Acquisition Co-Chaired by Professor Vasant Honavar

31 Jan, 2007

Professor Vasant Honavar co-chaired (with Prof. Tim Finin of UMBC) the IJCAI 2007 Workshop on Semantic Web for Collaborative Knowledge Acquisition (SWeCKa 2007), held in conjunction with the Twentieth International Joint Conference on Artificial Intelligence (IJCAI 2007) at Hyderabad, India on January 7, 2007. The workshop brought together researchers from academic and industrial research laboratories from around the world that are working in the relevant areas of artificial intelligence, databases, knowledge bases, machine learning, information integration, ontologies, semantic web, web services, and relevant application areas (e.g., bioinformatics, environmental informatics, enterprise informatics e-science, e-government, medical informatics, security informatics, social informatics, among others). The symposium participants shared recent advances in the state of the art in semantic web technologies for knowledge acquisition from semantically disparate, autonomous, distributed information sources for such applications. They also discussed open research problems and areas for collaboration.

Professor Honavar delivers keynote talk on Semantic Web for Collaborative e-Science at ICISIP 2006

21 Dec, 2006

Professor Vasant Honavar delivered a keynote lecture titled "Semantic Web for Collaborative e-Science" in the Fourth International Conference on Intelligent Sensing and Signal Processing (ICISIP 2006) which was held at Bangalore, India during December 15 through December 18, 2006. Other keynote speakers included Professor Ramesh Jain, Dr. Nevenka Dimitrova, Professor Mohan Kankanhalli, and Professor Cauligi Raghavendra. Honavar also gave an invited tutorial on Bioinformatics and Computational Systems Biology - a Machine Learning approach at ICISIP 2006. He also gave an invited tutorial on Semantic Web for Collaborative Knowledge Acquisition at the First International Conference on Digital Information Management (ICDIM 2006) which was also held in Bangalore, India during December 6 through December 8, 2006.

Jyotishman Pathak, Samik Basu, Robyn Lutz, and Vasant Honavar receive the Best Paper Award at IEEE ICTAI 2006

14 Nov, 2006

The paper "Selecting and Composing Web Services Through Iterative Reformulation of Functional Specifications" authored by Computer Science Ph.D. student  Jyotishman Pathak and Computer Science faculty  Dr. Samik Basu, Dr. Robyn Lutz and Dr. Vasant Honavar received the C.V. Ramamoorthy award for the best paper at the IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2006), held at Washington, DC, during November 13-15, 2006. The paper proposes a specification-driven approach to Web service composition. Web services are playing an increasingly important role in applications such as e-Science, e-Government, and e-Commerce. The authors' approach allows users to specify an abstract and possibly incomplete specification of the desired service (goal) that can be realized by selecting and composing a set of pre-existing services. In the event that such a composition is unrealizable, i.e. the composition is not functionally equivalent to the goal or the non-functional requirements are violated, the proposed system provides the user with the causes for the failure, that can be used to appropriately reformulate the functional and/or non-functional requirements of the goal specification. The authors have recently extended the approach to consider both functional and non-functional specifications in service composition. This project is the result of a collaboration between  the Artificial Intelligence Research Laboratory, the Laboratory for Software Safety, and the Software Systems Specification and Verification Group  at Iowa State University and is supported in part by grants from the National Science Foundation.

First International Workshop on Modular Ontologies Chaired by Professor Vasant Honavar

13 Nov, 2006

Professor Vasant Honavar co-chaired the First International Workshop on Modular Ontologies, held in conjunction with the Fifth International Semantic Web Conference at Athens, Georgia on November 5, 2006. The workshop brought together researchers from around the world that are working on syntax, semantics, proof theory, and algorithms for linking, using, and reasoning with modular ontologies in Semantic Web applications. The workshop organizers included Peter Haase and York Sure (Karlsruhe), Oliver Kutz (Manchester) and Andrei Tamilin (Trento), in addition to Vasant Honavar (ISU). The symposium included several contributed papers as well as invited lectures (by Professor Alex Borgida of Rutgers University and Professor Frank Wolter from the University of Liverpool).

AAAI Fall Symposium on Semantic Web for Collaborative Knowledge Acquisition chaired by Professor Vasant Honavar

18 Oct, 2006

Professor Vasant Honavar, co-chaired, with professor Tim Finin of UMBC, the AAAI Fall Symposium on Semantic Web for Collaborative Knowledge Acquisition, held at Washington, DC during October 13-15, 2006. The symposium, sponsored by the American Association for Artificial Intelligence, brought together researchers from academic and industrial research laboratories from around the world that are working in the relevant areas of artificial intelligence, databases, knowledge bases, machine learning, information integration, ontologies, semantic web, web services, and relevant application areas (e.g., bioinformatics, environmental informatics, enterprise informatics e-science, e-government, medical informatics, security informatics, social informatics, among others). The symposium participants shared recent advances in the state of the art in semantic web technologies for knowledge acquisition from semantically disparate, autonomous, distributed information sources for such applications. They also discussed open research problems, and areas for collaboration. In addition to contributed papers, the symposium included invited lectures by Professor Henry Lieberman of MIT and Dr. Todd Hughes of DARPA.

NSF grant awarded for BBSI Bioinformatics and Computational Systems Biology Summer Institute at Iowa State University

12 Oct, 2006

The US National Science Foundation has awarded a 3-year, $450,000 grant to support the Summer Institute in Bioinformatics and Computational Systems Biology at Iowa State University. The summer institute, first organized in 2002, includes a 2-week intensive course covering topics in Genomics, Bioinformatics, and Computational Biology followed by a 6-week research experience in one of the participating laboratories for 10-12 undergraduate students from around the country. The institute, led by Dr. Brendel (Genetics, Development, and Cell Biology), Dr. Dickerson (Electrical and Computer Engineering) Dr. Dorman (Statistics), Dr. Honavar (Computer Science), and Dr. Jernigan (Biochemistry, Biophysics, and Molecular Biology) offers interdisciplinary training spanning biological and computational sciences.

Iowa State University has one of the strongest graduate programs in the US in the field of Bioinformatics and Computational Biology, supported in part by an Integrative Graduate Education and Research Training Award from the National Science Foundation. Plans are currently underway to offer an undergraduate degree in Bioinformatics and Computational Biology.

Jie Bao, Doina Caragea, and Vasant Honavar Receive the Best Paper Award at the Asian Semantic Web Conference

September 7, 2006

The paper Modular Ontologies - A Formal Investigation of Semantics and Expressivity by Jie Bao, Doina Caragea, and Vasant Honavar received the best paper award, sponsored by the Knowledge Web project of the European Network of Excellence and the Japanese Society for Artificial Intelligence at the First Asian Semantic Web Conference (ASWC 2006), held in Beijing, China, during September 3 through September 7, 2006. The paper introduced an abstract modular ontology Language to analyze the expressivity requirements, semantics, and reasoning procedures for modular ontologies and to compare several existing modular ontology language proposals. It also shows that P-DL, a new modular ontology language proposed by the authors, by relaxing the strict domain disjointedness assumed by distributed description logics (DDL) and E-connections, can overcome some of the known semantic difficulties of both DDL and E-connections. The paper appears in the conference proceedings published by Springer-Verlag (Lecture Notes in Computer Science, Voll 4185, pp. 616-631, 2006). The results presented in this paper form the basis of research on modular distributed ontologies being pursued in the Artificial Intelligence Research Laboratory in the Center for Computational Intelligence, Learning, and Discovery at Iowa State University. This work builds on other ongoing research in the lab on knowledge acquisition from semantically heterogeneous, distributed information sources. Modular ontologies and the associated distributed reasoning algorithms constitute some of the key ingredients for the emerging semantic information integration, knowledge acquisition, and semantic web technolologies.

Vasant Honavar and Giora Slutzki Recieve NSF Grant to Study Modular Ontologies

August 29, 2006

Many distributed data and knowledge base applications call for a structured approach to collaborative construction of large ontologies (conceptualizations of objects, properties, and relationships between objects of interest in specific domains). This award from the National Science Foundation to ISU researchers Dr. Vasant Honavar, Dr. Giora Slutzki, and doctoral student Jie Bao working in collaboration with Dr. Doina Caragea (KSU) and Dr. George Voutsadakis (LSSU), provides support for research aimed at addressing the need of such applications for ontology languages, distributed reasoning algorithms, and software tools that support rapid collaborative assembly and use of complex ontologies through partial and selective reuse of independently created ontology modules. The researchers will explore the language features, syntax, and semantics of modular ontology languages, develop a family of description logics (DL) based modular ontology languages, namely Package-Based Description logics (P-DL) as well as open source software tools for collaborative construction and use of ontologies in information integration and knowledge discovery applications (e.g., in comparative genomics). The resulting tools can potentially transform distributed data and knowledgebase applications in the same way that the World-Wide Web has transformed the construction, sharing and use of hyperlinked documents and Wiki has transformed encyclopedia construction. Additional information on the project, publications and prototype software tools can be found here.

Doina Caragea Joins the Computer Science and Engineering Faculty at Kansas State

August 15, 2006

Dr. Doina Caragea, who received her Ph.D. in Computer Science specializing in Artificial Intelligence at Iowa State University in 2004, has joined the faculty of Computer Science and Engineering at Kansas State University as an Assisant Professor. Doina was a postdoctoral research associate at the Center for Computational Intelligence, Learning, and Discovery during 2004-2006. Doina's doctoral and postdoctoral research under the supervision of Dr. Vasant Honavar focused on semantic information integration and knowledge acquisition from distributed, semantically heterogeneous data sources.

Research article authored by CCILD faculty and students among the most highly accessed in BMC Bioinformatics

July 17, 2006

The article Predicting DNA-binding sites of proteins from amino acid sequence by Changhui Yan, Michael Terribilini, Feihong Wu, Robert L. Jernigan, Drena Dobbs, Vasant Honavar, BMC Bioinformatics 2006, 7:262 was among the most highly accessed articles in BMC Bioinformatics.

Byron Olson Joins the Electrical Engineering Faculty at Arizona State

June 15, 2006

Dr. Byron Olson, has joined the faculty of Electrical Engineering at Arizona State University as a Research Assisant Professor after a 1-year postdoctoral research associateship at the Center for Computational Intelligence, Learning, and Discovery during 2005-2006. Byron's postdoctoral research under the supervision of Dr. Vasant Honavar focused on analysis of macromolecular interactions (in collaboration with Dr. Drena Dobbs) and reconstruction of genetic regulatory networks from gene expression data (in collaboration with Dr. Heather Greenlee).

Jun Zhang and Changhui Yan receive Iowa State University Research Excellence Awards

Jun Zhang and Changhui Yan have been awarded the Iowa State University's Graduate Research Excellence Awards. The award honors students whose research accomplishments place them among the top 10 percent of all graduate students at Iowa State University.

Jun Zhang completed his Ph.D. studies in Computer Science under the supervision of Vasant Honavar in the fall of 2005. His work in the Iowa State University Artificial Intelligence Research Laboratory has led to the development of ontology aware learning algorithms that can exploit prior knowledge in the form of taxonomies defined over attribute values to construct concise and accurate classifiers from partially specified data. Jun has published 9 refereed conference or journal publications based on his thesis research. Jun has accepted a position as a data mining research scientist at Fair Isaac at San Diego.

Changhui Yan completed his Ph.D. studies in Bioinformatics and Computational Biology with a co-major in Computer Science under the joint supervision of Vasant Honavar and Drena Dobbs in the fall of 2005.  His work in the Iowa State University Artificial Intelligence Research Laboratory has led to the development and application of machine learning algorithms for characterization and prediction of protein-protein, protein-DNA, and protein-RNA interfaces. Changhui has published 5 refereed conference or journal publications based on his thesis research, and has several journal submissions that are currently under review. Changhui has accepted a position as a tenure-track assistant professor in the Computer Science Department at Utah State University.

CCILD faculty advance engineering informatics

Professor Vasant Honavar (Computer Science) will lead, together with Professors James McCalley and Daji Qiao (Electrical and Computer Engineering), Sarah Ryan (Industrial and Manufacturing Systems Engineering), and Professor William Meeker (Statistics), a three-year research project funded by the National Science Foundation aimed at aimed at automation of information-decision processes involved in managing the operations, maintenance, and planning of the high-voltage electric power transmission systems. This work will advance the state of the art in management of capital-intensive, geographically distributed physical assets in several areas: (a) Sensing and communications; (b) Data Integration; (c) Transforming  equipment condition measurements to reliability metrics; (d) Developing and linking multi-time scale stochastic decision algorithms; (e) Valuation of information and subsequent sensor deployment. An important impact of this research will be an increased ability to process and use the massive data streams associated with owning and operating transmission equipment, resulting in better investment, maintenance, and operating decisions, and ultimately, more economic and more reliable delivery of electric power. For more information, see the NSF abstract.

CCILD faculty advance research-based graduate training in Bioinformatics

CCILD faculty Vasant Honavar (Computer Science) and Drena Dobbs (GDCB) will lead, together with Professors Dan Voytas (GDCB), the ISU Computational Molecular Biology Training Group funded by an  Integrative Graduate Education and Research Training (IGERT) award from the National Science Foundation. IGERT is an NSF-wide program intended to meet the challenges of educating U.S. Ph.D. scientists and engineers with the interdisciplinary background, deep knowledge in a chosen discipline, and the technical, professional, and personal skills needed for the career demands of the future. The program is intended to catalyze a cultural change in graduate education by establishing innovative new models for graduate education and training in a fertile environment for collaborative research that transcends traditional disciplinary boundaries. Computational biology is an interdisciplinary field which aims to answer complex biological questions by accessing, manipulating and interpreting the rapidly accumulating body of genomic sequence and expression data. The challenge is to understand how genomic information is integrated to create complex biological pathways, processes and systems. Meeting this challenge requires a diverse and broadly trained group of professionals working at the interface of the biological and computational sciences (Computer Science, Mathematics, Statistics). The ISU Computational Molecular Biology Training group will train a diverse group of Ph.D. students to lead computational biology into the next era of discovery. This goal will be achieved through an integrated, inter-institutional training program which involves a partnership between Iowa State University (ISU) - with its established PhD Bioinformatics and Computational Biology program - and New Mexico State University (NMSU) - a strong research institution with a rich tradition in minority student training. This partnership will foster collaborative research in areas of common interest to ISU and NMSU faculty: genome informatics, macromolecular dynamics and interactions, and metabolic and regulatory networks. ISU will share expertise in interdisciplinary graduate training as NMSU establishes a graduate level computational biology program.

The ISU Bioinformatics and Computational Biology graduate program, established in 1999 with support from an earlier five-year IGERT award from the National Science Foundation to the ISU Computational Biology Training Group, has emerged as one of the largest and strongest Bioinformatics programs in the US. For additional information about the current IGERT award, see the NSF abstract.

Dr. Vasant Honavar Delivers Invited Plenary Lecture at the International Conference on Algorithmic Learning Theory

31 Oct, 2005

Dr. Vasant Honavar delivered an invited lecture titled "Algorithms and Software for Collaborative Discovery from Autonomous, Semantically Heterogeneous, Distributed Information Sources" in the 16th International Conference on Algorithmic Learning Theory and the 8th International Conference on Discovery Science held during October 8 through October 12 in Singapore. The invited lecture summerized research carried out in collaboration with students of the Iowa State University Artificial Intelligence Research Laboratory, with support from grants from the National Science Foundation (IIS 0219699) and the National Institutes of Health (GM 0066387) to Dr. Honavar.

CCILD members organize IEEE workshop on knowledge acquisition from distributed, autonomous, semantically heterogeneous data and knowledge sources

Vasant Honavar and Doina Caragea organized the IEEE Workshop on Knowledge Acquisition from Distributed, Autonomous, Semantically Heterogeneous Data and Knowledge Sources in conjunction with the IEEE International Conference on Data Mining at Houston, Texas. The workshop included an invited lecture by Professor Bertram Ludascher on information integration and contributed talks on a number of topics related to collaborative ontology development, information retrieval, inter-ontology mappings, query-driven mining of heterogeneous information sources, and metrics for evaluating ontologies.

 

 

CCILD news archives