Publications by Mohammed Javeed Zaki


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Papers by Topic

Bioinformatics

Mining Complex Patterns: Tree Mining, Graph Mining, etc.

Social Networks

Classification

Clustering

Sequence Mining

Web Mining

Association Rules: Itemset Mining

Intrusion Detection

Data Mining Overview

Load Balancing, Network of Workstations

Misc.


Edited Books

  1. Jason Wang, Mohammed J. Zaki, Hannu Toivonen, Dennis Shasha (Eds.), Data Mining in Bioinformatics, Springer London Ltd., September 2004.

  2. Mohammed J. Zaki, Shinichi Morishita and Isidore Rigoutsos (editors), BIOKDD04: 4th Workshop on Data Mining in Bioinformatics (with SIGKDD04) , Seattle, WA, August 2004.

  3. Bart Goethals and Mohammed J. Zaki (Eds.), Proceedings of the Workshop on Frequent Itemset Mining Implementations (with ICDM'03), CEUR Workshop Proceedings, Vol. 90, November 2003 (also RPI Tech Report 03-14).

  4. Mohammed J. Zaki, Jason T.L. Wang, and Hannu T.T. Toivonen (editors), BIOKDD03: 3rd Workshop on Data Mining in Bioinformatics (with SIGKDD03) , Washington, DC, August 2003 (also RPI Technical Report 03-11).

  5. Mohammed J. Zaki, Charu C. Aggarwal (editors), Proceedings of the 8th ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery, San Diego, CA, June 2003 (also RPI Technical Report 03-05).

  6. Mohammed J. Zaki, Jason T.L. Wang, and Hannu T.T. Toivonen (editors), BIOKDD02: 2nd Workshop on Data Mining in Bioinformatics (with SIGKDD02) , Edmonton, Canada, July 2002. ISBN: 1-58113-568-8, ACM KDD 2002 Digital Proceedings on CD-ROM, ACM Press.

  7. Mohammed J. Zaki, Hannu T.T. Toivonen, and Jason T.L. Wang (editors), BIOKDD01 Workshop on Data Mining in Bioinformatics (with SIGKDD01) , San Francisco, CA, August 2001.

  8. Mohammed J. Zaki, Vipin Kumar and David Skillicorn (editors), Parallel and Distributed Data Mining, CD-ROM Workshop Proceedings, IEEE Computer Society Press, Los Alamitos, CA, April 2001.

  9. Mohammed J. Zaki and Ching-Tien Ho (editors), Large-scale Parallel Data Mining, Lecture Notes in Artificial Intelligence, State-of-the-Art-Survey, Volume 1759, Springer-Verlag, 2000.

  10. Jose Rolim et al. (including Mohammed J. Zaki, Vipin Kumar and David B. Skillicorn) (editors), Parallel and Distributed Processing, Lecture Notes in Computer Science, Vol. 1800, Springer-Verlag, 2000. (Proceedings of the 3rd Workshop on High Performance Data Mining).

  11. Mohammed J. Zaki and Ching-Tien Ho (editors), KDD99 Workshop on Large-scale Parallel KDD Systems, Technical Report 99-8, RPI, August 1999.


Book Chapters

  1. Mohammed J. Zaki, A Unified Approach to Rooted Tree Mining: Algorithms and Applications, in Larry Holder and Diane Cook (eds.), Mining Graph Data, John Wiley and Sons, Inc., 2006 (to appear).

  2. Mohammed J. Zaki, TreeMiner: An Efficient Algorithm for Mining Embedded Ordered Frequent Trees, in Larry Holder, Sanghamitra Bandyopadhyay, Ujjwal Maulik, and Diane Cook (eds.), Advanced Methods for Knowledge Discovery from Complex Data, Springer-Verlag, 2006 (to appear).

  3. Mohammed J. Zaki, Mining Data in Bioinformatics, in Srinivas Aluru (ed.), Handbook of Computational Molecular Biology, Computer and Information Science Series, Chapman \& Hall/CRC Press, 2005 (to appear).

  4. Mohammed J. Zaki, Mining Closed and Maximal Frequent Itemsets, in Jozef Zurada and Mehmet Kantardzic (eds.), New Generation of Data Mining Applications, IEEE/Wiley Press, 2005 (to appear).

  5. Mohammed J. Zaki, Efficiently Mining Frequent Embedded Unordered Trees, in Luc De Raedt, Takashi Washio, and Joost N. Kok (eds.), Advances in Mining Graphs, Trees and Sequences, Vol. 124, Frontiers in Artificial Intelligence and Applications, IOS Press, June 2005.

  6. Mohammed J. Zaki, Directions in Protein Contact Map Mining, in H. Kargupta, A. Joshi, K. Sivakumar and Y. Yesha (eds.), Data Mining: Next Generation Challenges and Future Directions, pp 291-314, AAAI/MIT Press, 2004.

  7. Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff, Predicting Protein Folding Pathways, in Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha (Eds.), Data Mining in Bioinformatics, pp 127-141, Springer-Verlag London Ltd., 2005.

  8. Mohammed J. Zaki, Data Mining, in William S. Bainbridge (ed.), The Encyclopedia of Human-Computer Interaction, pp. 149-152, Berkshire Publishing Group, 2004.

  9. Mohammed J. Zaki and Limsoon Wong, Data Mining Techniques, in Limsoon Wong (ed.), Post-Genome Knowledge Discovery, pp. 125-163, World Scientific Publishers, 2004.

  10. Mohammed J. Zaki, Mining Data in Bioinformatics, in Nong Ye (ed.), Handbook of Data Mining, pp 573-596, Lawrence Earlbaum Associates, 2003.

  11. J. Punin, M. Krishnamoorthy, M. J. Zaki, Web Usage Mining: Languages and Algorithms, in O. Opitz, M. Schwaiger (editors), Explanatory Data Analysis in Empirical Research (series Studies in Classification, Data Analysis, and Knowledge Organization), pp 266-281, Springer-Verlag, 2002.

  12. Mohammed J. Zaki and Chris Bystroff, Mining Residue Contacts in Proteins, in R. Grossman, C. Kamath, P. Kegelmeyer, V. Kumar and R. Namburu (eds.), Data Mining for Scientific and Engineering Applications, Kluwer Academic Publishers, Boston, MA, 2001.

  13. Mohammed J. Zaki, Neal Lesh and Mitsunori Ogihara, Predicting Failures in Event Sequences, in R. Grossman, C. Kamath, P. Kegelmeyer, V. Kumar and R. Namburu (eds.), Data Mining for Scientific and Engineering Applications, Kluwer Academic Publishers, Boston, MA, 2001.

  14. Mohammed J. Zaki, Sequence Mining in Categorical Domains: Algorithms and Applications, in Ron Sun and Lee Giles (eds.), Sequence Learning: Paradigms, Algorithms, and Applications , LNAI State-of-the-Art-Survey, Vol. 1828, pp 163-187, Springer-Verlag, 2001.

  15. S. Parthasarathy, M. J. Zaki, M. Ogihara, S. Dwarkadas, Sequence Mining in Dynamic and Interactive Environments, in W. Abramowicz and J. Zurada (eds.), Knowledge Discovery for Business Information Systems, Chapter 16, pp 377-396, Kluwer Academic Publishers, 2001.

  16. Mohammed J. Zaki, Ching-Tien Ho, Rakesh Agrawal, Parallel Classification on Shared-Memory Systems, in Hillol Kargupta and Philip Chan (eds.), Advances in Distributed and Parallel Knowledge Discovery , Chapter 14, pp 377-407, AAAI Press, 2000.

  17. Mohammed J. Zaki, Hierarchical Parallel Algorithms for Association Mining , in Hillol Kargupta and Philip Chan (eds.), Advances in Distributed and Parallel Knowledge Discovery , Chapter 13, pp 339-376, AAAI Press, 2000.

  18. W. A. Maniatty, Mohammed J. Zaki, A Requirement Analysis for Parallel KDD Systems, in Jose Rolim et al. (including Mohammed J. Zaki, Vipin Kumar and David B. Skillicorn) (editors), Parallel and Distributed Processing, LNCS, Vol. 1800, pp 358-265, Springer-Verlag, 2000.

  19. Mohammed J. Zaki, Parallel and Distributed Data Mining: An Introduction, in Mohammed Zaki and Howard Ho (eds.), Large-Scale Parallel Data Mining , LNAI State-of-the-Art-Survey, Vol. 1759, pp 1-23, Springer-Verlag, 2000.

  20. Mohammed J. Zaki, Parallel Sequence Mining on Shared-Memory Machines, in Mohammed Zaki and Howard Ho (eds.), Large-Scale Parallel Data Mining , LNAI State-of-the-Art-Survey, Vol. 1759, pp 161-189, Springer-Verlag, 2000.

  21. Mohammed J. Zaki, Srinivasan Parthasarathy, Wei Li, Customized Dynamic Load Balancing for Cluster Computing, Rajkumar Buyya (ed.), High Performance Cluster Computing: Architectures and Systems, volume 1, chapter 24, pp 582-607, Prentice Hall, 1999.

  22. Vineet Gupta, Srinivasan Parthasarathy, Mohammed J. Zaki, Arithmetic and Logic Operations with DNA, Harvey Rubin and David H. Wood (eds.), DNA Based Computers III (DIMACS Workshop), Series in Discrete Mathematics and Theoretical Computer Science, pp 149-160, Volume 48, American Mathematical Society, 1999.

  23. Mohammed J. Zaki, Srinivasan Parthasarathy, Mitsunori Ogihara, Wei Li, Parallel Algorithms for Discovery of Association Rules, Paul Stolorz and Ron Musick (eds.), Scalable High Performance Computing for Knowledge Discovery and Data Mining, Kluwer Academic Publishers, 1998.


Journals

  1. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, Mohammed J. Zaki, An integrated, generic approach to pattern mining: data mining template library, Data Mining and Knowledge Discovery , Published Online: DOI:10.1007/s10618-008-0098-x, June 2008.

  2. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, Jeremy Besson, Mohammed J. Zaki, ORIGAMI: A Novel and Effective Approach for Mining Representative Orthogonal Graph Patterns, Statistical Analysis and Data Mining, Vol. 1, Issue 2, pp. 67-84, (DOI: 10.1002/sam.10004) June 2008.

  3. Zujun Shentu, Mohammad Al Hasan, Christopher Bystroff and Mohammed J. Zaki, Context Shapes: Efficient Complementary Shape Matching for Protein-Protein Docking, in Proteins: Structure, Function and Bioinformatics, , Vol. 70, Issue 3, pp. 1056-1073, February 2008.

  4. Feng Gao and Mohammed J. Zaki, PSIST: A Scalable Approach to Indexing Protein Structures using Suffix Trees, in Journal of Parallel and Distributed Computing, special issue on Parallel Techniques for Information Extraction, Sanguthevar Rajasekaran (ed.), Vol. 68, pp. 54-63, 2008

  5. Mohammed J. Zaki, Markus Peters, Ira Assent, Thomas Seidl, CLICKS: An Effective Algorithm for Mining Subspace Clusters in Categorical Datasets, in Data and Knowledge Engineering special issue on Intelligent Data Mining, Fernando Berzal and Juan Carlos Cubero (eds.), Vol. 60, Issue 1, pp. 51-70, January 2007.

  6. Mohammed J. Zaki, Akifumi Makinouchi, Shunsuke Uemura, Editorial: special issue on Biomedical Data Engineering, in International Journal of Bioinformatics Research and Applications, Volume 3, No. 1, pp 1-3, 2007.

  7. Yongqiang Zhang, Mohammed J. Zaki, sMOTIF: Efficient structured pattern and profile motif search, in Algorithms for Molecular Biology, Vol. 1, 22, November 2006.

  8. Yongqiang Zhang, Mohammed J. Zaki, ExMOTIF: Efficient Structured Motif Extraction, in Algorithms for Molecular Biology, Vol. 1, 21, November 2006.

  9. Mohammed J. Zaki, Charu C. Aggarwal, XRules: An Effective Structural Classifier for XML Data, in Machine Learning Journal special issue on Statistical Relational Learning and Multi-Relational Data Mining, Hendrik Blockeel, David Jensen, Stefan Kramer (eds.), Vol. 62, No. 1-2, pp. 137-170, Feb. 2006.

  10. Lizhuang Zhao, Mohammed J. Zaki, MicroCluster: An Efficient Deterministic Biclustering Algorithm for Microarray Data, in IEEE Intelligent Systems, special issue on Data Mining for Bioinformatics, Jinyan Li, Limsoon Wong, Qiang Yang (eds.), Vol. 20, No. 6, pp. 40-49, Nov-Dec 2005.

  11. Mohammed J. Zaki, Efficiently Mining Frequent Trees in a Forest: Algorithms and Applications, in IEEE Transaction on Knowledge and Data Engineering, special issue on Mining Biological Data, Wei Wang and Jiong Yang (eds.), Vol. 17, No. 8, pp 1021-1035, 2005.

  12. Karam Gouda and Mohammed J. Zaki, GenMax: An Efficient Algorithm for Mining Maximal Frequent Itemsets, Data Mining and Knowledge Discovery: An International Journal, Vol. 11, pp 1-20, 2005.

  13. Karlton Sequeira, Mohammed J. Zaki, SCHISM: A New Approach to Interesting Subspace Mining, International Journal of Business Intelligence and Data Mining, Invited paper, Vol. 1, No. 2, pp. 137-160, 2005.

  14. Lane Hemaspaandra, Mitsunori Ogihara, Mohammed J. Zaki, Marius Zimand, The Complexity of Finding Top-Toda-Equivalence-Class Members, Theory of Computing Systems, 2005 (to appear).

  15. Mohammed J. Zaki, Efficiently Mining Frequent Embedded Unordered Trees, Fundamenta Informaticae, special issue on Advances in Mining Graphs, Trees and Sequences, Luc De Raedt, Takashi Washio, and Joost N. Kok (eds.), Vol. 65, No. 1-2, pp. 33-52, March/April 2005.

  16. Mohammed J. Zaki, Ching-Jui Hsiao, Efficient Algorithms for Mining Closed Itemsets and Their Lattice Structure, IEEE Transaction on Knowledge and Data Engineering, Vol 17, No. 4, pp. 462-478, April 2005.

  17. Mohammed J. Zaki, Mining Non-Redundant Association Rules, Data Mining and Knowledge Discovery: An International Journal, Vol. 9, Issue 3, pp. 223-248, Nov 2004.

  18. Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff, Predicting Protein Folding Pathways, Bioinformatics, Volume 20, Suppl 1, pp i386-i393, Aug 2004.

  19. Mohammed J. Zaki, Shinichi Morishita, Isidore Rigoutsos, Report on BIOKDD04: Workshop on Data Mining in Bioinformatics, in SIGKDD Explorations, Volume 6. Issue 2, pp. 153-154, December 2004.

  20. Bart Goethals and Mohammed J. Zaki, Advances in Frequent Itemset Mining Implementations: Report on FIMI'03, in SIGKDD Explorations, Vol. 6, Issue 1, pp. 109-117, June 2004.

  21. Vinay Nadimpally and Mohammed J. Zaki, A Novel Approach to Determine Normal Variation in Gene Expression Data, in SIGKDD Explorations, special issue on Microarray Data Analysis, Gregory Piatetsky-Shapiro and Pablo Tamayo (eds.), Vol. 5, Issue 2, pp 4-13, December 2003.

  22. Mohammed J. Zaki, Hannu Toivonen, and Jason Wang, Data Mining in Bioinformatics: Report on BIOKDD'03, in SIGKDD Explorations, Volume 5. Issue 2, pp. 119-120, December 2003.

  23. Mohammed J. Zaki, Shan Jin and Chris Bystroff, Mining Residue Contacts in Proteins Using Local Structure Predictions, in IEEE Transactions on Systems, Man and Cybernetics -- Part B, special issue on Bio-imaging and Bio-informatics, N. Bourbakis (ed.), Vol. 33, No. 5, pp. 789-801, October 2003.

  24. Mohammed J. Zaki and Jason T.L. Wang (Eds.), Data Management in Bioinformatics in Information Systems: An International Journal, guest editorial for special issue on Data Management in Bioinformatics, Volume 28, No. 4, pp. 241-242, June, 2003.

  25. Mohammed J. Zaki, Hannu Toivonen, and Jason Wang, BIOKDD02: Recent Advances in Data Mining in Bioinformatics, in SIGKDD Explorations, Volume 4. Issue 2, pp. 112-114, December 2002.

  26. Mohammed J. Zaki and Yi Pan (Eds.), Introduction: Recent Developments in Parallel and Distributed Data Mining, in Distributed and Parallel Databases: An International Journal, guest editorial for special issue on Parallel and Distributed Data Mining, Volume 11, No. 2, pp. 123-137, March, 2002.

  27. Mohammed J. Zaki, Online, Interactive and Anytime Data Mining, guest editorial for special issue of SIGKDD Explorations, Volume 3, Issue 2, pp. i-ii, January, 2002.

  28. Mohammed J. Zaki, Hannu Toivonen, and Jason Wang, BIOKDD01: Workshop on Data Mining in Bioinformatics, in SIGKDD Explorations, Volume 3, Issue 2, pp 71-73, January, 2002.

  29. Mohammed J. Zaki, Parallel Sequence Mining on Shared-Memory Machines, in Journal of Parallel and Distributed Computing, special issue on High Performance Data Mining (Vipin Kumar, Sanjay Ranka, Vineet Singh, eds.), Volume 61, No. 3, pp. 401-426, March 2001.

  30. Srinivasan Parthasarathy, Mohammed Zaki, Mitsunori Ogihara, Wei Li, Parallel Data Mining for Association Rules on Shared-memory Systems, in Knowledge and Information Systems, Volume 3, Number 1, pp 1-29, Feb 2001.

  31. Mohammed J. Zaki, SPADE: An Efficient Algorithm for Mining Frequent Sequences, in Machine Learning Journal, special issue on Unsupervised Learning (Doug Fisher, ed.), pp 31-60, Vol. 42 Nos. 1/2, Jan/Feb 2001.

  32. William A. Maniatty, Mohammed J. Zaki, Systems Support for Scalable Data Mining, in SIGKDD Explorations, Volume 2, Issue 2, pp 56-65, December, 2000.

  33. Mohammed J. Zaki, Neal Lesh, Mitsunori Ogihara, PlanMine: Predicting Plan Failures using Sequence Mining, to appear in Artificial Intelligence Review, special issue on the Application of Data Mining, Volume 14, No. 6, pp 421-446, December 2000.

  34. Mohammed J. Zaki, Scalable Algorithms for Association Mining, in IEEE Transactions on Knowledge and Data Engineering, Vol. 12, No. 3, pp 372-390, May/June 2000.

  35. Neal Lesh, Mohammed J. Zaki, Mitsunori Ogihara, Scalable Feature Mining for Sequential Data, in IEEE Intelligent Systems and their Applications, special issue on Data Mining, Vol. 15, No. 2, pp 48-56, March/April 2000.

  36. Mohammed J. Zaki, Ching-Tien Ho, Workshop Report: Large-Scale Parallel KDD Systems, in SIGKDD Explorations, Volume 1, Issue 2, pp 112-114, January, 2000.

  37. Mohammed J. Zaki, Parallel and Distributed Association Mining: A Survey, in IEEE Concurrency, special issue on Parallel Mechanisms for Data Mining, Vol. 7, No. 4, pp14-25, December, 1999.

  38. Mohammed J. Zaki, Srinivasan Parthasarathy, Mitsunori Ogihara, Wei Li, Parallel Algorithms for Discovery of Association Rules, Data Mining and Knowledge Discovery: An International Journal, special issue on Scalable High-Performance Computing for KDD, pp 343-373, Vol. 1, No. 4, December 1997.

  39. Michal Cierniak, Mohammed J. Zaki, and Wei Li, Compile-time Scheduling Algorithms for Heterogeneous Network of Workstations, The Computer Journal , special issue on Automatic Loop Parallelization, Vol. 40, No. 6, pp 356-372, December 1997.

  40. Mohammed J. Zaki, Wei Li, and Srinivasan Parthasarathy, Customized Dynamic Load Balancing for a Network of Workstations, Journal of Parallel and Distributed Computing, special issue on Workstation Clusters and Network-based Computing (Performance Evaluation, Scheduling, and Fault-Tolerance), Vol. 43, No. 2, pp 156-162, June 1997.

  41. Lane A. Hemaspaandra, Mohammed J. Zaki and Marius Zimand, Polynomial-Time Semi-Rankable Sets, Journal of Computing and Information, special issue on 8th International Conference of Computing and Information Vol. 2, No. 1, pp. 50-67, June 1996.


Conferences and Workshops

  1. Benjarath Phoophakdee and Mohammed J. Zaki, TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences using Suffix Trees, 13th Pacific Symposium on Biocomputing (PSB), Hawaii, January 2008.

  2. Mohammad Hasan, Vineet Chaoji, Saeed Salem, jeremy Besson, and Mohammed J. Zaki, ORIGAMI: Mining Representative Orthogonal Graph Patterns, 7th IEEE International Conference on Data Mining, Omaha, NE, October 2007.

  3. Karam Gouda, Mosab Hassaan, and Mohammed J. Zaki, PRISM: A Prime-Encoding Approach for Frequent Sequence Mining, 7th IEEE International Conference on Data Mining, Omaha, NE, October 2007.

  4. Adriano Veloso, Wagner Meira, Jr, Marcos Golcalves and Mohammed J. Zaki, Multi-Label Lazy Associative Classification , 11th European Conference on Principles and Practice of Knowledge Discovery (PKDD), Warsaw, Poland, September 2007.

  5. Charu A. Aggarwal, Na Ta, Jianyong Wang, Jianhua Feng, Mohammed J. Zaki, XProj: A Framework for Projected Structural Clustering of XML Documents, 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Diego, CA, August 2007.

  6. Benjarath Phoophakdee and Mohammed J. Zaki, Genome-scale Disk-based Suffix Tree Indexing, ACM SIGMOD International Conference on Management of Data, Beijing, China, June 2007.

  7. Adriano Veloso, Wagner Meira Jr, and Mohammed J. Zaki, Lazy Associative Classification , 6th IEEE International Conference on Data Mining, Hong Kong, December 2006.

  8. Adriano Veloso, Wagner Meira, Jr, Marco Cristo, Marcos Golcalves and Mohammed J. Zaki, Multi-Evidence, Multi-Criteria, Lazy Associative Document Classification , 15th ACM Conference on Information and Knowledge Management, Arlington, VA, November 2006.

  9. Bouchra Bouqata, Christopher D. Carothers, Boleslaw K. Szymanski and Mohammed J. Zaki, VOGUE: A Novel Variable Order-Gap State Machine for Modeling Sequences, 10th European Conference on Principles and Practice of Knowledge Discovery (PKDD), Berlin, Germany, September 2006.

  10. Lizhuang Zhao, Mohammed J. Zaki and Naren Ramakrishnan, BLOSOM: A Framework for Mining Arbitrary Boolean Expressions, 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Philadelphia, PA, August 2006.

  11. Yongqiang Zhang and Mohammed J. Zaki, ExMotif: Efficient Structured Motif Extraction, 6th SIGKDD Workshop on Data Mining in Bioinformatics, Philadelphia, PA, August 2006.

  12. Jeffery Baumes, Mark Goldberg, Mykola Hayvanovych, Malik Magdon-Ismail, William Wallace, Mohammed J. Zaki, Finding Hidden Group Structure in a Stream of Communications, IEEE International Conference on Intelligence and Security Informatics, San Diego, CA, May 2006. Honorable Mention for Best Paper Award (best 3 papers at ISI'06) .

  13. Mohammad Hasan, Vineet Chaoji, Saeed Salem, Mohammed J. Zaki, Link Prediction using Supervised Learning, Workshop on Link Analysis, Counter-terrorism and Security (with SIAM Data Mining Conference), Bethesda, MD, April 2006.

  14. Mohammad Hasan, Vineet Chaoji, Saeed Salem, Nagender Parimi, and Mohammed Zaki, DMTL: A Generic Data Mining Template Library, in Workshop on Library-Centric Software Design (LCSD'05), with Object-Oriented Programming, Systems, Languages and Applications (OOPSLA'05) conference, San Diego, California, October 2005.

  15. Feng Gao, Mohammed J. Zaki, PSIST: Indexing Protein Structures using Suffix Trees, in IEEE Computational Systems Bioinformatics Conference, Palo Alto, CA, August 2005.

  16. Mohammed J. Zaki, Naren Ramakrishnan, Reasoning about Sets using Redescription Mining, ACM SIGKDD 11th International Conference on Knowledge Discovery and Data Mining, Chicago, IL, August 2005.

  17. Mohammed J. Zaki, Markus Peters, Ira Assent, Thomas Seidl, CLICKS: An Effective Algorithm for Mining Subspace Clusters in Categorical Datasets, ACM SIGKDD 11th International Conference on Knowledge Discovery and Data Mining, Chicago, IL, August 2005.

  18. Ganesh Ramesh, Mohammed J. Zaki, William A. Maniatty, Distribution-Based Synthetic Database Generation Techniques for Itemset Mining, 9th International Database Engineering and Applications Symposium (IDEAS), Montreal, Canada, July 25-27, 2005.

  19. Lizhuang Zhao, Mohammed J. Zaki, TriCluster: An Effective Algorithm for Mining Coherent Clusters in 3D Microarray Data, ACM SIGMOD International Conference on Management of Data, Baltimore, MD, May 2005.

  20. Markus Peters, Mohammed J. Zaki, CLICKS: Clustering Categorical Data using K-partite Maximal Cliques, IEEE International Conference on Data Engineering, Tokyo, Japan, April 2005 (RPI CS Dept Technical Report 04-11, Jan 2004).

  21. Mohammed J. Zaki, Nagender Parimi, Nilanjana De, Feng Gao, Benjarath Phoophakdee, Joe Urban, Vineet Chaoji, Mohammad Al Hasan, Saeed Salem, Towards Generic Pattern Mining, International Conference on Formal Concept Anaysis (Invited Paper), Lens, France, February 2005 (Also LNCS 3403, Springer-Verlag, and RPI CS Dept Technical Report 04-01, Jan 2004).

  22. Karlton Sequeira, Mohammed J. Zaki, SCHISM: A New Approach for Interesting Subspace Mining, 4th IEEE International Conference on Data Mining, Brighton, UK, November 2004.

  23. Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, Chris Bystroff, Predicting Protein Folding Pathways, 12th International Conference on Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference on Computational Biology, Edinburgh, UK, July 2004.

  24. Amir H. Youssefi, David J. Duke, Mohammed J. Zaki, Ephraim P. Glinert, Visual Web Mining 13th International World Wide Web Conference (poster proceedings), New York, NY, May 2004.

  25. Lane Hemaspaandra, Mitsunori Ogihara, Mohammed J. Zaki, Marius Zimand, The Complexity of Finding Top-Toda-Equivalence-Class Members, Latin American Theoretical Informatics (LATIN) Conference, Buenos Aires, Argentina, April 2004.

  26. Bart Goethals and Mohammed J. Zaki, Introduction: Advances in Frequent Itemset Mining Implementations, Workshop on Frequent Itemset Mining Implementations, (with ICDM'03), Melbourne, FL, November 2003.

  27. Amir H. Youssefi, David Duke, Ephraim P. Glinert, and Mohammed J. Zaki, Toward Visual Web Mining, 3rd International Workshop on Visual Data Mining (with ICDM'03), Melbourne, FL, November 2003.

  28. Mohammed J. Zaki, Charu Aggarwal, XRULES: An Effective Structural Classifier for XML Data, 9th International Conference on Knowledge Discovery and Data Mining, Washington, DC, August 2003.

  29. Mohammed J. Zaki, Karam Gouda, Fast Vertical Mining Using Diffsets, 9th International Conference on Knowledge Discovery and Data Mining, Washington, DC, August 2003.

  30. Karlton Sequeira, Mohammed J. Zaki, Bolek Szymanski, Chris Carothers, Improving Spatial Locality using Data Mining , 9th International Conference on Knowledge Discovery and Data Mining, Washington, DC, August 2003.

  31. Feng Pan, Gao Cong, Anthony K.H. Tung, Joing Yang, Mohammed J. Zaki, CARPENTER: Finding Closed Patterns in Long Biological Datasets, 9th International Conference on Knowledge Discovery and Data Mining, Washington, DC, August 2003.

  32. Ganesh Ramesh, William A. Maniatty, Mohammed J. Zaki, Feasible Itemset Distributions in Data Mining: Theory and Application, 22nd ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems, San Diego, CA, June 2003.

  33. Adriano Veloso, Wagner Meira, Jr., Marcio Carvalho, Srini Parthasarathy, Mohammed J. Zaki, Parallel, Incremental and Interactive Mining for Frequent Itemsets in Evolving Databases, 6th International Workshop on High Performance Data Mining: Pervasive and Data Stream Mining (with SIAM International Conference on Data Mining), San Francisco, May 2003.

  34. B. Bouqata, C. Carothers, B. Syzmanski, and M. Zaki, Understanding Filesystem Performance for Data Mining Applications, 6th International Workshop on High Performance Data Mining: Pervasive and Data Stream Mining (with SIAM International Conference on Data Mining), San Francisco, May 2003.

  35. Mohammed J. Zaki, Mining Protein Contact Maps, Workshop on Information Technology, Rabat, Morocco, March 2003.

  36. Adriano Veloso, Bruno Gusmao, Wagner Meira, Marcio Carvalho, S. Parthasarathy, Mohammed J. Zaki, Efficiently Mining Approximate Models of Associations in Evolving Databases, 6th European Conference on Principles of Knowledge Discovery in Databases, August 2002.

  37. Mohammed J. Zaki, Efficiently Mining Frequent Trees in a Forest, 8th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, July 2002.

  38. Karlton Sequeira, Mohammed J. Zaki, ADMIT: Anomaly-base Data Mining for Intrusions, 8th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, July 2002.

  39. Jingjing Hu, Xioalan Shen, Yu Shao, Chris Bystroff, Mohammed J. Zaki, Mining Protein Contact Maps, 2nd BIOKDD Workshop on Data Mining in Bioinformatics, July 2002.

  40. Ganesh Ramesh, William Maniatty, Mohammed J. Zaki, Indexing and Data Access Methods for Database Mining, ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery, May 2002.

  41. Yu Shao, Malik Magdon-Ismail, Danial Freedman, Srinivas Akella, Mohammed Zaki, Chris Bystroff, Compression of Protein Conformational Space (Poster), in 6th Annual International Conference on Research in Computational Molecular Biology (RECOMB02), Washington, DC, April 2002.

  42. Mohammed J. Zaki, Ching-Jui Hsiao, CHARM: An Efficient Algorithm for Closed Itemset Mining, 2nd SIAM International Conference on Data Mining, Arlington, April 2002.

  43. Adriano Veloso, Wagner Meira, Jr., Marcio Carvalho, Bruno Possas, Srini Parthasarathy, Mohammed J. Zaki, Mining Frequent Itemsets in Evolving Databases, 2nd SIAM International Conference on Data Mining, Arlington, April 2002.

  44. Scott Epter, Mukkai Krishnamoorthy, Mohammed J. Zaki, Clusterability Detection and Cluster Initialization, SIAM Workshop on Clustering High Dimensional Data and its Applications, Arlington, April 2002 (with SIAM data mining conference).

  45. Chris Carothers, Bolek Szymanski, Mohammed J. Zaki, Performance Mining of Large-Scale Data-Intensive Applications, IPDPS Workshop on Next Generation Systems, Ft. Lauderdale, FL, April 2002.

  46. Karam Gouda, Mohammed J. Zaki, Efficiently Mining Maximal Frequent Itemsets in 1st IEEE International Conference on Data Mining , San Jose, November 2001.

  47. John Punin, Mukkai Krishnamoorthy, Mohammed J. Zaki, LOGML -- Log Markup Language for Web Usage Mining , in WEBKDD Workshop 2001: Mining Log Data Across All Customer TouchPoints (with SIGKDD01), San Francisco, August 2001.

  48. John Punin, Mukkai Krishnamoorthy, Mohammed J. Zaki, LOGML -- XML Language for Web Usage Mining (Poster), in 10th International World Wide Web Conference , Hong Kong, May 2001.

  49. Mohammed J. Zaki, Shan Jin, Chris Bystroff, Mining Residue Contacts in Proteins Using Local Structure Predictions , in IEEE International Symposium on Bioinformatics and Biomedical Engineering , pp 168-175, Washington, DC, November 2000 (also as RPI Technical Report 00-5).

  50. Mohammed J. Zaki, Sequence Mining in Categorical Domains: Incorporating Constraints, in 9th International Conference on Information and Knowledge Management , pp 422-429, Washington, DC, November 2000.

  51. Krishna Rajan and Mohammed J. Zaki, Data Mining through Information Association: A Knowledge Discovery Tool for Materials Science, in 17th International CODATA Conference , Baveno, Italy, Ocotber 2000.

  52. Mohammed J. Zaki, Generating Non-Redundant Association Rules, 6th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp 34-43, Boston, MA, August 2000 (also as RPI Technical Report 99-12).

  53. W. A. Maniatty, Mohammed J. Zaki, A Requirement Analysis for Parallel KDD Systems , 3rd IPDPS Workshop on High Performance Data Mining , Cancun, Mexico, May 2000. Appears in Jose Rolim et al. (including Mohammed J. Zaki, Vipin Kumar and David B. Skillicorn) (editors), Parallel and Distributed Processing, LNCS, Vol. 1800, pp 358-265, Springer-Verlag, 2000.

  54. Srinivasan Parthasarathy, Mohammed J. Zaki, Mitsunori Ogihara, Sandhya Dwarkadas, Incremental and Interactive Sequence Mining, 8th International Conference on Information and Knowledge Management , pp 251-258, Kansas City, MO, November 1999.

  55. Mohammed J. Zaki, Parallel Sequence Mining on SMP Machines, Workshop on Large-Scale Parallel KDD Systems (in conjunction 5th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining), pp 57-65, San Diego, CA, August 1999.

  56. Neal Lesh, Mohammed J. Zaki, Mitsunori Ogihara, Mining features for Sequence Classification, 5th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD), pp 342-246, San Diego, CA, August 1999.

  57. Mohammed J. Zaki, Ching-Tien Ho, Rakesh Agrawal, Scalable Parallel Classification for Data Mining on Shared-Memory Multiprocessors, IEEE International Conference on Data Engineering, pp 198-205, Sydney, Australia, March 1999.

  58. Rakesh Agrawal, Ching-Tien Ho, Leon Pauser, Mohammed J. Zaki, Parallel Data Mining on Shared-Memory Multiprocessors, 9th SIAM Conference on Parallel Processing for Scientific Computing, Minisymposium on High-Performance Data Mining , San Antonio, TX, March 1999.

  59. Mohammed J. Zaki, Efficient Enumeration of Frequent Sequences, 7th International Conference on Information and Knowledge Management, pp 68-75, Washington DC, November 1998.

  60. Mohammed J. Zaki, Neal Lesh, Mitsunori Ogihara, PLANMINE: Sequence Mining for Plan Failures, 4th International Conference on Knowledge Discovery and Data Mining (KDD), pp 369-373, New York, August 1998.

  61. Srinivasan Parthasarathy, Mohammed J. Zaki, Wei Li, Memory Placement Techniques for Parallel Association Mining, 4th International Conference on Knowledge Discovery and Data Mining (KDD), pp 304-308, New York, August 1998.

  62. Mohammed J. Zaki, Mitsunori Ogihara, Theoretical Foundations of Association Rules, 3rd SIGMOD'98 Workshop on Research Issues in Data Mining and Knowledge Discovery (DMKD), pp 7:1-7:8, Seattle, WA, June 1998.

  63. Mohammed J. Zaki, Ching-Tien Ho, Rakesh Agrawal, Parallel Classification on SMP Systems, 1st Workshop on High Performance Data Mining (HPDM -- in conjunction with IPPS), Orlando, Florida, March 1998.

  64. Mohammed J. Zaki, Srinivasan Parthasarathy, Mitsunori Ogihara, Wei Li, New Algorithms for Fast Discovery of Association Rules", 3rd International Conference on Knowledge Discovery and Data Mining (KDD), pp 283-286, Newport, California, August, 1997.

  65. Mohammed J. Zaki, Srinivasan Parthasarathy, Wei Li, A Localized Algorithm for Parallel Association Mining, 9th Annual ACM Symposium on Parallel Algorithms and Architectures (SPAA), pp 321-330, Newport, Rhode Island, June 22-25, 1997.

  66. Vineet Gupta, Srinivasan Parthasarathy, Mohammed J. Zaki, Arithmetic and Logic Operations with DNA, 3rd DIMACS Workshop on DNA Based Computers, Philadelphia, Pennsylvania, June 1997.

  67. Mohammed J. Zaki, Srinivasan Parthasarathy, Wei Li, and Mitsunori Ogihara, Evaluation of Sampling for Data Mining of Association Rules", 7th International Workshop on Research Issues in Data Engineering (RIDE--in conjunction with ICDE), pp 42-50, Birmingham, UK, April 7-8, 1997.

  68. Mohammed J. Zaki, Mitsunori Ogihara, Srinivasan Parthasarathy, and Wei Li, Parallel Data Mining for Association Rules on Shared-memory Multi-processors, Supercomputing'96, Pittsburg, PA, Nov 17-22, 1996.

  69. Srinivasan Parthasarathy, Wei Li, Michal Cierniak and Mohammed J. Zaki, Compile-Time Inter-Query Dependence Analysis, 8th IEEE Symposium on Parallel and Distributed Processing (SPDP), pp 522-529, New Orleans, Louisiana, October 1996.

  70. Mohammed J. Zaki, Wei Li, and Srinivasan Parthasarathy, Customized Dynamic Load Balancing for a Network of Workstations, 5th IEEE International Symposium on High-Performance Distributed Computing (HPDC) , Syracuse, New York, August 1996.

  71. M. Scott, W. Li, S. Dwarkadas, L. Kontothanassis, G. Hunt, M. Michael, R. Stets, N. Hardavellas, W. Meira, A. Poulos, M. Cierniak, S. Parthasarathy, and M. Zaki, Implementation of Cashmere, 6th International Workshop on Scalable Shared Memory Multiprocessors (SSMM--in conjunction with ASPLOS), Cambridge, MA, October 1996.

  72. Harmit S. Malik, Mohammed J. Zaki and Thomas H. Eickbush, R1 and R2 retrotransposition in silico, Eastern Great Lakes Molecular Evolution Meeting , May 11th, Ithaca, NY, 1996.

  73. Michal Cierniak , Wei Li, and Mohammed J. Zaki, Loop Scheduling for Heterogeneity, 4th IEEE International Symposium on High-Performance Distributed Computing (HPDC) , pp 78-85, Pentagon City, Virginia, August 1995.

  74. Mohammed J. Zaki, Wei Li and Michal Cierniak, Performance Impact of Processor and Memory Heterogeneity in a Network of Machines, 4th Heterogeneous Computing Workshop (HCW--in conjunction with IPPS), pp 101-108, Santa Barbara, California, April 1995.


Technical Reports

  1. Mohammed Zaki and Benjarath Phoophakdee, MIRAGE: A framework for mining, exploring and visualizing minimal association rules. RPI CS Dept Technical Report 03-04, July 2003.

  2. O. Fuentes, J. Karlsson, W. Meira, R. Rao, T. Riopka, J. Rosca, R. Sarukkai, M. van Wie, M. J. Zaki, T. Becker, R. Frank, B. Miller, and Prof. C. M. Brown, Mobile Robotics 1994, Technical Report 588, May 1995.

Thesis

  1. Mohammed J. Zaki, Scalable Data Mining for Rules, Technical Report 702, University of Rochester, July 1998.


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