Partner Organizations:
Center for Genomics & Bioinformatics -IU: Collaborative Research

source for bioinformatics problems

ISO Technical Comm 184/SubComm 5/Working Group 1 provides both
motivation and a sounding board for research in high-level modeling.
Richard Martin (see collaborators) is convenor of TC 184/SC 5/WG 1.

Other collaborators:

Chris Giannella and Edward Robertson have worked with
Jaiwei Han of University of Illinios Urbana-Champaign

Edward Robertson and John Springer have worked with Richard 
A Martin, private consultant of Bloomington IN., on enterprise
architecture frameworks.

Dirk Van Gucht and his students have worked with Jan Paradaens, Marc
Gyssens, and Nele Dexters of the University of Antwerp, Belgium
and Jan Van den Bussche and Stijn Vansummerin of Univ. Hasselt.
Van Gucht has also collaborated with Hari Bercovici of the IU
Mathematics Department.

Edward Robsertson is working with Cathy Wyss of Indiana University
and her student George Fletcher on metadata formalisms.

Memhet Dalikic is working with Sun Kim of Indiana University
and students L. Do Hoon and J.H. Choi on bioinformatics.
He is also working with Arijit Sengupta, now of Wright State
University, and students H. Kim and M. Fox on Ontologies.
.

Activities and findings:

Research and Education Activities: 

1. conceptual and theoretical analysis of the basic principles
   of information and measurement in a database context

2. simulation experiments relating to the the application of
   Information Dependencies and information theory in general
   to query optimization, histogram construction, etc.

3. weekly seminar series

Findings:

1. a better understanding of the strengths and weaknesses of
   the InD approach

2. placing the InD approach in a theoretical context and generalizing
   the InD measure to other measures, approximation results, and
   meassure constraint inferencing

3. promising applications in query optimization and histogram 
   construction

4. understanding that issues involving metadata were inherent in
   the Information Dependency, with the additional understanding
   that metadata concerns had a much wider range, from implementation
          through querying to modeling.  Thus additional work in these
area
   has been undertaken, producing an elegant algebra for relational
   metadata querying and initiating work on enterprise-level
modeling.

5. a very broad approach to measures in databases, relating to such
   things as level of support as well as the information theoretic
   measures which initiated this work.

Training and Development:

1. incorporation of information theory in information systems
    courses (surprisingly, there has been essentially no connection
    between these areas up to this point)

Outreach Activities:

working with ISO on various metamodeling standards

Journal Publications:

Catharine M. Wyss, Chris M. Giannella, and Edward Robertson, "FastFDs: A Heuristic-Driven Depth-First Algorithm for Mining Functional Dependencies from Relation Instances", Proceedings of the 3rd International Conference on Data Warehousing and Knowledge Discovery, vol. , (2002), p. . Accepted

Chris Giannella and Edward Robertson, "On an Information Theoretic Approximation Measure for Functional Dependencies", Information Processing Letters, vol. 85, (2003), p. 153. Published

Dennis P. Groth and Edward L. Robertson, "Discovering Frequent Itemsets in the Presence of Highly Frequent Items", 14th International Conference on Applications of Prolog, vol. , (2002), p. . Accepted

Dennis P. Groth and Edward L. Robertson, "An Integrated System for Database Visualization", The Sixth International Conference on Information Visualization, vol. , (2002), p. 462. Published

Chris M. Giannella, Mehmet M. Dalkilic, Dennis P. Groth, Edward L. Robertson, "Improving Query Evaluation with Approximate Functional Dependency Based Decompositions", Proceedings of the 19th British National Conference on Databases, vol. , (2002), p. 26. Published

Dennis P. Groth and Edward L. Robertson, "An Entropy-Based Approach to Visualizing Database Structure", Sixth IFIP Working Conference on Visual Database Systems, vol. , (2002), p. 157. Published

Dennis P. Groth and Edward L. Robertson, "An Integrated Approach to Database Visualization", Advanced Visual Interfaces 2002, vol. , (2002), p. 365. Published

Dennis P. Groth and Edward L. Robertson, "Discovering Frequent Itemsets in the Presence of Highly Frequent Items", Rule Based Data Mining 2001, vol. , (2002), p. 237. Published

Edward L. Robertson, Lawrence Saxton, and Dirk Van Gucht, "Polynomial-Time Query Languages for Untyped Lists", International Conference on Database Theory, vol. , (2002), p. . Submitted

Chris M. Giannella and Edward L. Robertson, "A Comparison of Three Approximation Measures for Functional Dependencies in Relational Databases", IPL, vol. , (2002), p. . Submitted

Chris M. Giannella and Edward L. Robertson, "A Note on Approximation Measures for Multi-valued Dependencies in Relational Databases", Information Processsing Letters, vol. 85, (2003), p. 153. Published

Chris M. Giannella and Edward L. Robertson, "What's Been Lost in a Lossy Join Decomposition?", SIGMOD Record, vol. , (2002), p. . Submitted

Chris M. Giannella, "An Axiomatic Approach to Defining Approximation Measures for Functional Dependencies", Lecture Notes in Computer Science, vol. 2435, (2002), p. 37. Published

Edward Robertson and Catharine Wyss, "Optimal Tuple Merge is NP-complete", Information Processing Letters, vol. , (), p. . Submitted

Catharine Wyss and Edward Robertson, "Relational Interoperability", TODS, vol. , (), p. . Submitted

Chris Gianella, Memhet Dalkilc, Dennis Groth, and Edward Robertson, "Using Horizontal-Vertical Decompositions to Improve Query Evaluation", Lecture Notes in Computer Science, vol. 2405, (2002), p. 26. Published

I. Gunduz, S. Zhao, M. Dalkilic and S. Kim, "Motif Discovery from Large Number of Sequences: A Case Study with Disease Resistance Genes in Arabidopsis thaliana", The 2003 International Multiconference in Computer Science and Computer Engineering, vol. , (2003), p. 0. Published

Bassem Sayrafi and Chris Giannella, "An Information Theoretic Histogram for Single Dimentional Selectivity Estimation", ICDE, vol. , (2003), p. . Submitted

Paul Purdom, Dirk Van Gucht and Dennis Groth, "Average Case Performance of the Apriori Algorithm", SIAM Journal of Computing, vol. , (2003), p. . Accepted

Bassem Sayrafi, Dirk Van Gucht and Marc Gyssens, "Measures in Databases and Data Mining", Information Sciences, vol. , (), p. . Submitted

Bassem Sayrafi and Dirk Van Gucht, "Applications of Tsallis entropies in databases", Information Sciences, vol. , (2003), p. . Submitted

Chris Giannella and Edward Robertson, "On an Information Theoretic Approximation Measure for Functional Dependencies", Information Systems, vol. , (), p. . Accepted

Richard Martin, Edward Robertson, and John Springer, "Architectural Principles for Enterprise Frameworks", EMMSAD '04, vol. , (), p. . Accepted

Zhiping Wang, Mehmet Dalkilic, and Sun Kim, "Guiding Motif Discovery by Iterative Pattern Refinement", 2004 ACM Symposium on Applied Computing Bioinformatics Track (Nicosia, Cyprus) , vol. , (2004), p. 162. Published

Irfan Gunduz, Sihui Zhao, Mehmet Dalkilic and Sun Kim, "Motif Discovery from Large Number of Sequeces: A Case Study with Disease Resistance Genes in Arabidopsis thaliana", Medicine and Biological Sciences (METMBS'03: Las Vegas, Nevada), vol. , (2003), p. 29. Published

Catharine M. Wyss and Edward L. Robertson, "Relational Languages for Metadata Integration", ACM Trans. on Database Systems, vol. 29, (2005), p. 624. Published

George Fletcher, Catharine Wyss, Edward Robertson, and Dirk Van Gucht, "A Calculus for Data Mapping", Proc. Int'l Conf. on Database Interoperability, Elsevier Notes in Theoretical Computer Science,, vol. , (), p. . Accepted

Catharine Wyss and Edward Robertson, "A Formal Characterization of PIVOT/UNPIVOT", Proc. ACM Conf. on Information and Knowledge Management, vol. , (), p. . Accepted

Edward Robertson and Richard Martin, "Views in the Enterprise Domain", Views, Aspects, and Roles 05, workshop at European Conf. on Object Oriented Programming, vol. n.a., (2005), p. electroni. Published

Edward L. Robertson, "Triadic Relations: an Algebra for the Semantic Web", Semantic Web and Databases, C. Bussler, V. Tannen, and I. Fundulaki (eds), Lecture Notes in Computer Science, vol. 3372, (2004), p. 91. Published

Dexters, N., Purdom, P.W. and Van Gucht, D, "A Probability Analysis of Candidate-Based Frequent Item Set Mining Algorithms", Proc. of the 21st ACM Symposium on Applied Computing Special Track on Data Mining, vol. , (), p. . Accepted

Sayrafi, B., Van Gucht, D., and Purdom, P.W., "On the Effectiveness and Efficiency of Computing Bounds on the Support of Item Sets in the Frequent Item Set Mining Problem", Proc. First International Workshop on Open Source Data Mining, vol. n.a., (2005), p. 46. Published

Sayrafi, B. and Van Gucht, D., "Differential Constraints", Proc. of the 24th ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, vol. 24, (2005), p. 348. Published

Bercovici, H. and Van Gucht, D., "An Inequality for Mixed L^p-Norms", Mathematical Inequalities & Applications, vol. 8, (2005), p. 1223. Published

Van den Bussche, J., Van Gucht, D., and Vansummeren, S., "Well-definedness and semantic type-checking in the nested relational calculus and XQuery", Proc. of the 2005 International Conference on Database Theory (ICDT '05), vol. n.a., (2005), p. 99. Published

Dexters, N., Purdom, P.W., Van Gucht, D., "A Probability Analysis of Candidate-Based Frequent Item Set Mining Algorithms", SIAM J. on Computing, vol. , (), p. . Submitted

Edward Robertson, "Explicitly Modeling Metadata", CACM, vol. , (), p. . Submitted

L. Do Hoon, J.H. Choi, M.M. Dalkilic, S. Kim, "COMPAM : Visualization of Combining Pairwise Alignment", Bioinformatics, vol. , (), p. . Accepted

H. Kim, A. Sengupta, M. Fox, M.M. Dalkilic, "A Measurement Ontology Generalizable for Emerging Domain Applications on the Semantic Web", Journal of Database Management, vol. , (), p. . Accepted

Book(s) of other one-time publications(s):

Memhet Dalkilic, "PFA: The Protein Family Annotator" , bibl. Boston, MA, (2003). workshop Published of Collection: , "Executive IT Life Sciences Forum"

Richard Martin and Edward Robertson, "A Comparison of Frameworks for Enterprise Architecture Modeling" , bibl. ISBN: 3-540-20299-4, (2003). Book Published of Collection: Song, I.-Y.; Liddle, S.W.; Ling, T.W.; Scheuermann, P., "Conceptual Modeling -- ER 2003"

Other Specific Products:


Internet Dissemination:

http://www.cs.indiana.edu/database/InD/index.html

Contributions to Other Disciplines:

 Memhet Dalkilic's work with the Center for Genomics and
Bioinformatics
has resulted in the development of the Protein Family Annotator,
as well as other bioinformatics results.

We welcome comments on this system