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Publications 2007 Hudelson, Matthew G., Ketkar, Nikhil S., Holder, Lawrence B., Carlson, Timothy J., Peng, Chi-Chi, Waldher, Benjamin J., and Jones, Jeffrey P., High Confidence Predictions of DrugāDrug Interactions: Predicting Affinities for Cytochrome P450 2C9 with Multiple Computational Methods, Appearing in J. Med. Chem., 2008. W. Eberle and L. Holder, Anomaly Detection in Data Represented as Graphs, Intelligent Data Analysis, Volume 11, Number 6, 2007. J. Kukluk, L. Holder and D. Cook, Inference of Node Replacement Graph Grammars, Intelligent Data Analysis, Volume 11, Number 4, 2007. J. Kukluk, L. Holder and D. Cook, Inference of Node and Edge Replacement Graph Grammars, International Conference on Machine Learning (ICML) Workshop on Challenges and Applications of Grammar Induction, June 2007. W. Eberle and L. Holder, Mining for Structural Anomalies in Graph-Based Data, International Conference on Data Mining (DMIN-07), June 2007. J. Kukluk, C. You, L. Holder and D. Cook, Learning Node Replacement Graph Grammars in Metabolic Pathways, International Conference on Bioinformatics and Computational Biology (BIOCOMP-07), June 2007. J. Kukluk, L. Holder and D. Cook, Inference of Edge Replacement Graph Grammars, Twentieth International Conference of the Florida AI Research Society (FLAIRS), May 2007. 2006 D. Cook and L. Holder (editors), Mining Graph Data, John Wiley and Sons, 2006. J. Coble, D. Cook and L. Holder, Structure Discovery in Sequentially-Connected Data Streams, International Journal on Artificial Intelligence Tools, Volume 15, Number 6, 2006. C. You, L. Holder and D. Cook, Application of Graph-based Data Mining to Metabolic Pathways, Workshop on Data Mining in Bioinformatics, IEEE International Conference on Data Mining, December 2006. K. Ates, J. Kukluk, L. Holder, D. Cook and K. Zhang, Graph Grammar Induction on Structural Data for Visual Programming, 18th IEEE International Conference on Tools with Artificial Intelligence, November 2006. N. Ketkar, L. Holder and D. Cook, Mining in the Proximity of Subgraphs, ACM KDD Workshop on Link Analysis, August 2006. W. Eberle and L. Holder, Detecting Anomalies in Cargo Shipments Using Graph Properties, IEEE Intelligence and Security Informatics Conference, May 2006. J. Kukluk, L. Holder and D. Cook, Inference of Node Replacement Recursive Graph Grammars, SIAM Conference on Data Mining, April 2006. 2005 N. Ketkar, L. Holder and D. Cook, Comparison of Graph-based and Logic-based MRDM, ACM SIGKDD Explorations Special Issue on Link Mining, Volume 7, Issue 2, December 2005. J. Coble, D. J. Cook, R. Rathi, and L. B. Holder, Iterative Structure Discovery in Graph-Based Data, International Journal of Artificial Intelligence Techniques, 14(1-2): 101-124 (2005) L. Holder, D. Cook, J. Coble and M. Mukherjee, Graph-based Relational Learning with Application to Security, Fundamenta Informaticae Special Issue on Mining Graphs, Trees and Sequences, 6(1-2):83-101, March 2005. J. Kukluk, L. B. Holder, and D. J. Cook, Algorithm and Experiments in Testing Planar Graphs for Isomorphism, Journal of Graph Algorithms and Applications, Volume 8, Number 3, 2004. L. B. Holder and D. J. Cook, Graph-based Data Mining, J. Wang (ed.), Encyclopedia of Data Warehousing and Mining, Idea Group Publishing, 2005. N. Ketkar, L. Holder and D. Cook, Qualitative Comparison of Graph-based and Logic-based Multi-Relational Data Mining: A Case Study, Proceedings of the ACM KDD Workshop on Multi-Relational Data Mining, August 2005. N. Ketkar, L. Holder, D. Cook, R. Shah and J. Coble, Subdue: Compression-based Frequent Pattern Discovery in Graph Data, Proceedings of the ACM KDD Workshop on Open-Source Data Mining, August 2005. J. Potts, L. B. Holder, D. J. Cook, and J. Coble, Learning Concepts from Intelligence Data Embedded in a Supervised Graph, Proceedings of the International Conference on Intelligence Analysis, 2005. J. Coble and D. J. Cook, Structure Discovery in Sequentially Connected Data, Proceedings of the Florida Artificial Intelligence Research Symposium, 2005. Recipient of the best paper award. R. Rathi and D. J. Cook, A Serial Partitioning Approach to Scaling Graph-Based Knowledge Discovery, Proceedings of the Florida Artificial Intelligence Research Symposium, 2005. 2004 I. Jonyer, L. B. Holder and D. J. Cook, MDL-Based Context-Free Graph Grammar Induction and Applications, International Journal of Artificial Intelligence Tools, March 2004. A. Rakhshan, L. B. Holder and D. J. Cook, Structural Web Search Engine, International Journal of Artificial Intelligence Tools, March 2004. 2003 L. B. Holder and D. J. Cook, Graph-Based Relational Learning: Current and Future Directions SIGKDD Explorations special issue on Multirelational Data Mining, 2003. C. Noble and D. J. Cook, Graph-Based Anomaly Detection, Proceedings of the Ninth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2003. D. J. Cook, N. Manocha, and L. B. Holder, Using a Graph-Based Data Mining System to Perform Web Search, International Journal of Pattern Recognition and Artificial Intelligence 17(5), 2003. I. Jonyer, L. Holder, and D. J. Cook, MDL-Based Context-Free Graph Grammar Induction, Proceedings of the Sixteenth International Conference of the Florida AI Research Society, May 2003. A. Rakhshan, L. B. Holder, and D. J. Cook, Structural Web Search Engine, Proceedings of the Sixteenth International Conference of the Florida AI Research Society, May 2003. 2002 L. B. Holder, D. J. Cook, J. Gonzalez, and I. Jonyer, Structural Pattern Recognition in Graphs, Pattern Recognition and String Matching (D. Chen and X. Cheng, eds.), Kluwer Academic Publishers, 2002. I. Jonyer, L. B. Holder, and D. J. Cook, Concept Formation Using Graph Grammars, Proceedings of the KDD Workshop on Multi-Relational Data Mining, 2002. J. Gonzalez, L. B. Holder, and D. J. Cook, Experimental Comparison of Graph-Based Relational Concept Learning with Inductive Logic Programming Systems, Proceedings of the Inductive Logic Programming Conference, 2002. J. Gonzalez, L. B. Holder, and D. J. Cook, Graph-Based Relational Concept Learning, Proceedings of the International Machine Learning Conference, 2002. S. Bandyopadhyay, U. Maulik, D. J. Cook, L. B. Holder, and Y. Ajmerwala, Enhancing Structure Discovery for Data Mining in Graphical Databases Using Evolutionary Programming, Proceedings of the Florida Artificial Intelligence Research Symposium, pages 232-236, 2002. 2001 I. Jonyer, D. J. Cook, and L. B. Holder, Discovery and Evaluation of Graph-Based Hierarchical Conceptual Clusters, Journal of Machine Learning Research, 2, pages 19-43, 2001. D. J. Cook, L. B. Holder, S. Su, R. Maglothin, and I. Jonyer, Structural Mining of Molecular Biology Data, IEEE Engineering in Medicine and Biology special issue on Advances in Genomics, 20(4), pages 67-74, 2001. I. Jonyer, L. B. Holder, and D. J. Cook, Hierarchical Conceptual Structural Clustering, International Journal on Artificial Intelligence Tools, 10(1-2), pages 107-136, 2001. D. J. Cook, L. B. Holder, G. Galal, and R. Maglothin, Approaches to Parallel Graph-Based Knowledge Discovery, Journal of Parallel and Distributed Computing, 61(3), pages 427-446, 2001. J. Gonzalez, L. B. Holder, and D. J. Cook, Application of Graph-Based Concept Learning to the Predictive Toxicology Domain, Proceedings of the Predictive Toxicology Challenge Workshop, 2001. J. Gonzalez, L. B. Holder, and D. J. Cook, Graph-Based Concept Learning, Proceedings of the Florida Artificial Intelligence Research Symposium, 2001. D. J. Cook and L. B. Holder, Graph-Based Data Mining, IEEE Intelligent Systems, 15(2), pages 32-41, 2000. 2000 J. Gonzalez, I. Jonyer, L. B. Holder and D. J. Cook, Efficient Mining of Graph-Based Data." AAAI Workshop on Learning Statistical Models from Relational Data, 2000. J. A. Gonzalez, L. B. Holder, and D. J. Cook, Graph Based Concept Learning, In the Proceedings of the Seventeenth National Conference on Artificial Intelligence, 2000. I. Jonyer, L. B.
Holder, and D. J. Cook, Graph-Based
Hierarchical Conceptual Clustering in Structural A. Baritchi, D. J. Cook and L. B. Holder, Discovering Structural Patterns in Telecommunications Data In the Proceedings of the Thirteenth Annual Florida AI Research Symposium, 2000. J. A. Gonzalez, L. B. Holder, and D. J. Cook, Structural Knowledge Discovery Used to Analyze Earthquake Activity", In the Proceedings of the Thirteenth Annual Florida AI Research Symposium, 2000. I. Jonyer, L. B. Holder, and D. J. Cook, Graph-Based Hierarchical Conceptual Clustering, In the Proceedings of the Thirteenth Annual Florida AI Research Symposium, 2000. 1999 R.Chittimori, J. Gonzalez, and L. B. Holder, Structural Knowledge Discovery in Chemical and Spatio-Temporal Databases, Proceedings of the Sixteenth National Conference on Artificial Intelligence, 1999. R. Chittimoori, L. B. Holder, and D. J. Cook, Applying the Subdue Substructure Discovery System to the Chemical Toxicity Domain, Proceedings of the Florida AI Research Symposium, 1999. R. Chittimoori, L. B. Holder, and D. J. Cook, Applying the Subdue Substructure Discovery System to the Chemical Toxicity Domain'', Proceedings of the AAAI Spring Symposium on Predictive Toxicology of Chemicals: Experiences and Impact of AI Tools, 1999. S. Su, D. J. Cook, and L. B. Holder, Application of Knowledge Discovery to Molecular Biology: Identifying Structural Regularities in Proteins, Proceedings of the Pacific Symposium on Biocomputing, pages 190--201, 1999. 1998 D. J. Cook, G. Galal, and L. B. Holder, ``Exploiting Parallelism in Knowledge Discovery Systems to Improve Scalability, Proceedings of the Thirty-First Hawaii International Conference on System Sciences, 1998. G. Galal, D.J. Cook, and L.B. Holder, Exploiting Parallelism in a Scientific Discovery System to Improve Scalability, Journal of the American Society for Information Science 1998. D.J. Cook, G. Galal, and L.B. Holder, Improving Scalability of Scientific Discovery Systems by Exploiting Parallelism, Pattern Discovery in Biological Data: Tools, Techniques and Application, Oxford University Press, 1998. 1997 S. Djoko, D. J. Cook, and L. B. Holder. An Empirical Study of Domain Knowledge and Its Benefits to Substructure Discovery". In the IEEE Transactions on Knowledge and Data Engineering, Volume 9, Number 4, 1997. G. Galal and D. J. Cook, Exploiting Papallelism in a Scientefic Discovery System to Improve Scalability, Proceedings of the Tenth Annual Florida AI Research Symposium, 1997. G. Galal, D. J. Cook and L. B. Holder. Improving Scalability in a Knowledge Discovery System by Exploiting Parallelism". In the Proceedings of the Third International Conference on Knowledge Discovery and Data Mining, pages 171-174, 1997. 1996 D. J. Cook, L. B. Holder, and S. Djoko. Scalable Discovery of Informative Structural Concepts Using Domain Knowledge. In IEEE Expert, Volume 11, Number 5, pages 59-68, 1996. 1995 S. Djoko, D. J. Cook and L. B. Holder. Analyzing the Benefits of Domain Knowledge in Substructure Discovery. In the Proceedings of the First International Conference on Knowledge Discovery and Data Mining, pages 75-80, 1995. D. J. Cook, L. B. Holder, and S. Djoko. Knowledge Discovery from Structural Data. Journal of Intelligence and Information Sciences, Volume 5, Number 3, pages 229-245, 1995. Also available as Technical Report TR-95-149, NASA Center of Excellence in Space Data and Information Sciences, 1995. 1994 D. J. Cook and L. B. Holder. Substructure Discovery Using Minimum Description Length and Background Knowledge. In Journal of Artificial Intelligence Research, Volume 1, pages 231-255, 1994. L. B. Holder, D. J. Cook and S. Djoko. Substructure Discovery in the SUBDUE System. In Proceedings of the AAAI Workshop on Knowledge Discovery in Databases, pages 169-180, 1994. 1993 L. B. Holder and D. J. Cook. Discovery of Inexact Concepts from Structural Data. In IEEE Transactions on Knowledge and Data Engineering, Volume 5, Number 6, pages 992-994, 1993. 1992 L. B. Holder, D. J. Cook and H. Bunke, Fuzzy Substructure Discovery In Proceedings of the Ninth International Conference on Machine Learning, pages 218-223, 1992. 1989 L. B. Holder. Empirical Substructre Discovery. In Proceedings of the Sixth International Workshop on Machine Learning, pages 133-136, 1989. 1988 L. B. Holder. Substructure Discovery in Subdue. Technical Report UILU-ENG-88-2220, Department of Computer Science, University of Illinois, Urbana, IL, May 1988. L. B. Holder. Discovering Substructure in Examples. Master's thesis, Department of Computer Science, University of Illinois, Urbana, IL, May 1988. (Available as Technical Report UILU-ENG-88-2223).
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