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Bioinformatics


Protein Structure: Prediction, Alignment, Docking
  1. Saeed Salem, Mohammed J. Zaki and Chris Bystroff, Iterative Non-Sequential Protein Structural Alignment. Journal of Bioinformatics and Computational Biology, 7(3):571-596. June 2009. (PDF) (BibTeX)
  2. Saeed Salem, Mohammed J. Zaki and Chris Bystroff, FlexSnap: Flexible Non-Sequential Protein Structure Alignment. In 9th Workshop on Algorithms in Bioinformatics. September 2009. (PDF) (BibTeX)
  3. Saeed Salem, Mohammed J. Zaki and Chris Bystroff, FlexSnap: Flexible Non-Sequential Protein Structure Alignment. Algorithms in Molecular Biology, to appear. 2009. (BibTeX)
  4. Zujun Shentu, Mohammad Al Hasan, Chris Bystroff and Mohammad J. Zaki, Context Shapes: Efficient Complementary Shape Matching for Protein-Protein Docking. Proteins: Structure, Function and Bioinformatics, 70(3):1056-1073. February 2008. (PDF) (BibTeX)
  5. Feng Gao and Mohammed J. Zaki, Indexing Protein Structures Using Suffix Trees. In Protein Structure Prediction, pages 147-169. Springer/Humana Press 2008. (PDF) (BibTeX)
  6. Mohammed J. Zaki and Chris Bystroff, Protein Structure Prediction. (Mohammed J. Zaki and Chris Bystroff, Eds.) Humana Press/Springer (http://www.springer.com/978-1-58829-752-5) 2008. ((URL)) (BibTeX)
  7. Feng Gao and Mohammed J. Zaki, PSIST: A Scalable Approach to Indexing Protein Structures using Suffix Trees. Journal of Parallel and Distributed Computing, 68(1):55-63. January 2008. (PDF) (BibTeX)
  8. Saeed Salem and Mohammed J. Zaki, Iterative Non-Sequential Protein Structural Alignment. In 7th Annual International Conference on Computational Systems Bioinformatics. August 2008. (PDF) (BibTeX)
  9. Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan and Chris Bystroff, Predicting Protein Folding Pathways. In Data Mining in Bioinformatics, pages 127-141. Springer-Verlag London Ltd. 2005. (PDF) (BibTeX)
  10. Feng Gao and Mohammed J. Zaki, PSIST: Indexing Protein Structures using Suffix Trees. In IEEE Computational Systems Bioinformatics Conference. August 2005. (PDF) (BibTeX)
  11. Mohammed J. Zaki, Jingjing Hu and Chris Bystroff, Methods for Mining Protein Contact Maps. In Data Mining: Next Generation Challenges and Future Directions, pages 291-314. AAAI/MIT Press 2004. (PDF) (BibTeX)
  12. Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan and Chris Bystroff, Predicting protein folding pathways. Bioinformatics, 20(1):i386-i393. August 2004. (PDF) (BibTeX)
  13. Mohammed J. Zaki, Shan Jin and Chris Bystroff, Mining Residue Contacts in Proteins Using Local Structure Predictions. IEEE Transactions on Systems, Man and Cybernetics -- B, 33(5):789-801. October 2003. (PDF) (BibTeX)
  14. Jingjing Hu, Xiaolan Shen, Yu Shao, Chris Bystroff and Mohammed J. Zaki, Mining Protein Contact Maps. In 2nd BIOKDD Workshop on Data Mining in Bioinformatics (with SIGKDD). July 2002. (PDF) (BibTeX)
  15. Yu Shao, Malik Magdon-Ismail, Daniel Freedman , Srinivas Akella, Mohammed J. Zaki and Chris Bystroff, Compression of Protein Conformational Space. In 6th Annual International Conference on Research in Computational Molecular Biology (Poster). April 2002. (PDF) (BibTeX)
  16. Mohammed J. Zaki and Chris Bystroff, Mining Residue Contacts in Proteins. In Data Mining for Scientific and Engineering Applications, pages 141-164. Kluwer Academic Publishers 2001. (PDF) (BibTeX)
  17. Mohammed J. Zaki, Shan Jin and Chris Bystroff, Mining Residue Contacts in Proteins Using Local Structure Predictions. In IEEE International Symposium on Bioinformatics and Biomedical Engineering. November 2000. (PDF) (BibTeX)

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Gene Expression and Microarray Analysis
  1. Naren Ramakrishnan and Mohammed J. Zaki, Redescription Mining and Applications in Bioinformatics. In Biological Data Mining. CRC Press 2009. ((URL)) (PDF) (BibTeX)
  2. Igor B. Kuznetsov and Mohammed J. Zaki, Integration of multiple types of genome-wide datasets and analysis of functional relationships among genes in the human genome. Technical report 09-03, Rensselaer Polytechnic Institute August 2009. (PDF) (BibTeX)
  3. Renata B. Araujo, Guilherme H. T. Ferreira, Gustavo H. Orair, Wagner Meira Jr., Renato A. C. Ferreira, Dorgival O. G. Neto and Mohammed J. Zaki, The ParTriCluster Algorithm for Gene Expression Analysis. International Journal of Parallel Programming, 36(2):226-249. April 2008. (PDF) (BibTeX)
  4. Lizhuang Zhao, Mohammed J. Zaki and Naren Ramakrishnan, BLOSOM: A Framework for Mining Arbitrary Boolean Expressions. In 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2006. (PDF) (BibTeX)
  5. Lizhuang Zhao and Mohammed J. Zaki, MicroCluster: An Efficient Deterministic Biclustering Algorithm for Microarray Data. IEEE Intelligent Systems, 20(6):40-49. November/December 2005. (PDF) (BibTeX)
  6. Lizhuang Zhao and Mohammed J. Zaki, TriCluster: An Effective Algorithm for Mining Coherent Clusters in 3D Microarray Data. In ACM SIGMOD Conference on Management of Data. June 2005. (PDF) (BibTeX)
  7. Feng Pan, Gao Cong, Anthony K. H. Tung, Jiong Yang and Mohammed J. Zaki, CARPENTER: Finding Closed Patterns in Long Biological Datasets. In 9th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2003. (PDF) (BibTeX)
  8. Vinay Nadimpally and Mohammed J. Zaki, A Novel Approach to Determine Normal Variation in Gene Expression Data. SIGKDD Explorations, 5(2):4-13. December 2003. (PDF) (BibTeX)

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Genome Indexing and Sequence Analysis
  1. Mohammed J. Zaki, Christopher D. Carothers and Boleslaw K. Szymanski, VOGUE: A Variable Order Hidden Markov Model with Duration based on Frequent Sequence Mining. ACM Transactions on Knowledge Discovery in Data, to Appear. 2009. (PDF) (BibTeX)
  2. Benjarath Phoophakdee and Mohammed J. Zaki, TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences using Suffix Trees. In 13th Pacific Symposium on Biocomputing. January 2008. (PDF) (BibTeX)
  3. Benjarath Phoophakdee and Mohammed J. Zaki, Genome-scale Disk-based Suffix Tree Indexing. In ACM SIGMOD International Conference on Management of Data. June 2007. (PDF) (BibTeX)
  4. Yongqiang Zhang and Mohammed J. Zaki, EXMOTIF: efficient structured motif extraction. Algorithms for molecular biology, 1(21). November 2006. ((URL)) (PDF) (BibTeX)
  5. Bouchra Bouqata, Christopher D. Carothers, Boleslaw K. Szymanski and Mohammed J. Zaki, VOGUE: A Novel Variable Order-Gap State Machine for Modeling Sequences. In 10th European Conference on Principles and Practice of Knowledge Discovery. September 2006. (PDF) (BibTeX)
  6. Yongqiang Zhang and Mohammed J. Zaki, SMOTIF: efficient structured pattern and profile motif search. Algorithms for molecular biology, 1(22). November 2006. ((URL)) (PDF) (BibTeX)
  7. Yongqiang Zhang and Mohammed J. Zaki, ExMotif: Efficient structured motif extraction. In 6th SIGKDD Workshop on Data Mining in Bioinformatics. August 2006. (PDF) (BibTeX)

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Data Mining in Bioinformatics
  1. Amanda W. Lund, Cagatay C. Bilgin, Mohammed Al Hasan, Lindsey M. McKeen, Jan P. Stegeman and Bulent Yener, Mohammed J. Zaki and George E. Plopper, Quantification of Spatial Parameters in 3D Cellular Constructs Using Graph Theory. Journal of Biomedicine and Biotechnology, 2009(928286):16. 2009. ((URL)) (PDF) (BibTeX)
  2. Amir H. Qureshi, Vineet Chaoji, Dony Maiguel and Hafeez Faridi, Constantinos Barth, Erliang Zheng, Jeremy Besson, Saeed M. Salem, Mudita Singhal, David Sarracino, Bryan Krastins and Mitsunori Ogihara, Mohammed J. Zaki and Vineet Gupta, Proteomic and Phospho-proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling. PLoS ONE, to appear. 2009. (BibTeX)
  3. Mohammed J. Zaki, Naren Ramakrishnan and Srinivasan Parthasarathy, Editorial: Biological data mining. Scientific Programming, 16(1):3. 2008. (PDF) (BibTeX)
  4. Stefano Lonardi, Jake Y. Chen and Mohammed J Zaki, Proceedings of BIOKDD08: ACM SIGKDD International Workshop on Data Mining in Bioinformatics. (Stefano Lonardi and Jake Y. Chen and Mohammed J Zaki, Eds.) 2008. ((URL)) (PDF) (BibTeX)
  5. Jake Y. Chen, Mohammed J. Zaki and Stefano Lonardi, BIOKDD08: A Workshop report on Data Mining in Bioinformatics. SIGKDD Explorations, 10(2):54-56. December 2008. (PDF) (BibTeX)
  6. Mohammed J. Zaki, George Karypis, Jiong Yang and Wei Wang, Introduction to special issue on bioinformatics. ACM Transactions on Knowledge Discovery from Data, 2(1). March 2008. (PDF) (BibTeX)
  7. Jake Y. Chen, Stefano Lonardi and Mohammed J. Zaki, Proceedings of BIOKDD07: ACM SIGKDD International Workshop on Data Mining in Bioinformatics. (Jake Y. Chen and Stefano Lonardi and Mohammed J. Zaki, Eds.) 2007. ((URL)) (PDF) (BibTeX)
  8. Mohammed J. Zaki, George Karypis and Jiong Yang, Editorial: Data Mining in Bioinformatics. Algorithms for molecular biology, 2(4). 2007. ((URL)) (PDF) (BibTeX)
  9. Mohammed J. Zaki, Akifumi Makinouchi and Shunsuke Uemura, Editorial: special issue on Biomedical Data Engineering. International Journal of Bioinformatics Research and Applications, 3(1):1-3. 2007. (PDF) (BibTeX)
  10. Mohammed J. Zaki, George Karypis and Jiong Yang, Proceedings of BIOKDD06: ACM SIGKDD Workshop on Data Mining in Bioinformatics. (Mohammed J. Zaki and George Karypis and Jiong Yang, Eds.) 2006. ((URL)) (PDF) (BibTeX)
  11. Yongqiang Zhang and Mohammed J. Zaki, ExMotif: Efficient structured motif extraction. In 6th SIGKDD Workshop on Data Mining in Bioinformatics. August 2006. (PDF) (BibTeX)
  12. Mohammed J. Zaki, George Karypis and Jiong Yang, BIOKDD06: Data Mining in Bioinformatics. SIGKDD Explorations, 8(2):78. December 2006. (PDF) (BibTeX)
  13. Mohammed J. Zaki and Karlton Sequeira, Data Mining in Computational Biology. In Handbook of Computational Molecular Biology, pages 38/1-38/26. Chapman \& Hall/CRC Press 2006. (PDF) (BibTeX)
  14. Srinivasan Parthasarathy, Wei Wang and Mohammed J. Zaki, Proceedings of BIOKDD05: ACM SIGKDD International Workshop on Data Mining in Bioinformatics. (Srinivasan Parthasarathy and Wei Wang and Mohammed J. Zaki, Eds.), ACM Digital Library (http://portal.acm.org/toc.cfm?id=1134030) 2005. ((URL)) (PDF) (BibTeX)
  15. Shunsuke Uemura, Akifumi Makinouchi and Mohammed J. Zaki, Proceedings of the IEEE International Workshop on Biomedical Data Engineering (BDME:with ICDE). (Shunsuke Uemura and Akifumi Makinouchi and Mohammed J. Zaki, Eds.), IEEE Xplore Digital Library April 2005. ((URL)) (BibTeX)
  16. Jason T. L. Wang, Mohammed J. Zaki, Hannu T. T. Toivonen and Dennis Shasha, Data Mining in Bioinformatics. (Jason T. L. Wang, Mohammed J. Zaki, Hannu T. T. Toivonen and Dennis Shasha, Eds.) Springer-Verlag London, UK (http://www.springer.com/978-1-85233-671-4) 2005. ((URL)) (BibTeX)
  17. Srinivasan Parthasarathy, Wei Wang and Mohammed J Zaki, BIOKDD 2005 Workshop Report. SIGKDD Explorations, 7(2):129-131. December 2005. (PDF) (BibTeX)
  18. Mohammed J. Zaki, Jingjing Hu and Chris Bystroff, Methods for Mining Protein Contact Maps. In Data Mining: Next Generation Challenges and Future Directions, pages 291-314. AAAI/MIT Press 2004. (PDF) (BibTeX)
  19. Mohammed J. Zaki, Shinichi Morishita and Isidore Rigoutsos, Proceedings of BIOKDD04: ACM SIGKDD International Workshop on Data Mining in Bioinformatics. (Mohammed J. Zaki and Shinichi Morishita and Isidore Rigoutsos, Eds.) 2004. ((URL)) (PDF) (BibTeX)
  20. Mohammed J. Zaki, Shinichi Morishita and Isidore Rigoutsos, Report on BIOKDD04: Workshop on Data Mining in Bioinformatics. SIGKDD Explorations, 6(2):153-154. December 2004. (PDF) (BibTeX)
  21. Mohammed J. Zaki and Limsoon Wong, Data Mining Techniques. In Selected Topics in Post-Genome Knowledge Discovery, pages 125-163. World Scientific Publishers 2004. (PDF) (BibTeX)
  22. Mohammed J. Zaki, Hannu Toivonen and Jason Wang, Proceedings of BIOKDD03: ACM SIGKDD International Workshop on Data Mining in Bioinformatics. (Mohammed J. Zaki and Hannu Toivonen and Jason Wang, Eds.) 2003. ((URL)) (BibTeX)
  23. Mohammed J. Zaki, Hannu Toivonen and Jason Wang, Data Mining in Bioinformatics: Report on BIOKDD'03. SIGKDD Explorations, 5(2):119-120. December 2003. (PDF) (BibTeX)
  24. Mohammed J. Zaki, Mining Data in Bioinformatics. In Handbook of Data Mining, pages 573-596. Lawrence Earlbaum Associates 2003. (PDF) (BibTeX)
  25. Mohammed J. Zaki and Jason T.L. Wang, Editorial: Data Management in Bioinformatics. Information Systems: An International Journal, 28(4):241-242. June 2003. (PDF) (BibTeX)
  26. Jingjing Hu, Xiaolan Shen, Yu Shao, Chris Bystroff and Mohammed J. Zaki, Mining Protein Contact Maps. In 2nd BIOKDD Workshop on Data Mining in Bioinformatics (with SIGKDD). July 2002. (PDF) (BibTeX)
  27. Mohammed J. Zaki, Hannu Toivonen and Jason Wang, Proceedings of BIOKDD02: ACM SIGKDD International Workshop on Data Mining in Bioinformatics. (Mohammed J. Zaki and Hannu Toivonen and Jason Wang, Eds.) 2002. ((URL)) (BibTeX)
  28. Mohammed J. Zaki, Hannu Toivonen and Jason Wang, Recent Advances in Data Mining in Bioinformatics. SIGKDD Explorations, 4(2):112-114. December 2002. (PDF) (BibTeX)
  29. Mohammed J. Zaki, Hannu Toivonen and Jason Wang, Proceedings of BIOKDD01: ACM SIGKDD International Workshop on Data Mining in Bioinformatics. (Mohammed J. Zaki and Hannu Toivonen and Jason Wang, Eds.) 2001. ((URL)) (BibTeX)
  30. Mohammed J. Zaki and Chris Bystroff, Mining Residue Contacts in Proteins. In Data Mining for Scientific and Engineering Applications, pages 141-164. Kluwer Academic Publishers 2001. (PDF) (BibTeX)
  31. Mohammed J. Zaki, Hannu Toivonen and Jason Wang, BIOKDD01: Workshop on Data Mining in Bioinformatics. SIGKDD Explorations, 3(2):71-73. February 2001. (PDF) (BibTeX)
  32. Mohammed J. Zaki, Shan Jin and Chris Bystroff, Mining Residue Contacts in Proteins Using Local Structure Predictions. In IEEE International Symposium on Bioinformatics and Biomedical Engineering. November 2000. (PDF) (BibTeX)

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Hidden Markov Models
  1. Mohammed J. Zaki, Christopher D. Carothers and Boleslaw K. Szymanski, VOGUE: A Variable Order Hidden Markov Model with Duration based on Frequent Sequence Mining. ACM Transactions on Knowledge Discovery in Data, to Appear. 2009. (PDF) (BibTeX)
  2. Bouchra Bouqata, Christopher D. Carothers, Boleslaw K. Szymanski and Mohammed J. Zaki, VOGUE: A Novel Variable Order-Gap State Machine for Modeling Sequences. In 10th European Conference on Principles and Practice of Knowledge Discovery. September 2006. (PDF) (BibTeX)

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Suffix Trees
  1. Feng Gao and Mohammed J. Zaki, PSIST: A Scalable Approach to Indexing Protein Structures using Suffix Trees. Journal of Parallel and Distributed Computing, 68(1):55-63. January 2008. (PDF) (BibTeX)
  2. Feng Gao and Mohammed J. Zaki, Indexing Protein Structures Using Suffix Trees. In Protein Structure Prediction, pages 147-169. Springer/Humana Press 2008. (PDF) (BibTeX)
  3. Benjarath Phoophakdee and Mohammed J. Zaki, TRELLIS+: An Effective Approach for Indexing Genome-Scale Sequences using Suffix Trees. In 13th Pacific Symposium on Biocomputing. January 2008. (PDF) (BibTeX)
  4. Benjarath Phoophakdee and Mohammed J. Zaki, Genome-scale Disk-based Suffix Tree Indexing. In ACM SIGMOD International Conference on Management of Data. June 2007. (PDF) (BibTeX)
  5. Feng Gao and Mohammed J. Zaki, PSIST: Indexing Protein Structures using Suffix Trees. In IEEE Computational Systems Bioinformatics Conference. August 2005. (PDF) (BibTeX)

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DNA Computing
  1. Vineet Gupta, Srinivasan Parthasarathy and Mohammed J. Zaki, Arithmetic and Logic Operations with DNA. In 3rd DIMACS Workshop on DNA Based Computers. June 1997. (PDF) (BibTeX)

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Pattern Mining


Graph Mining and Social Networks
  1. Mohammad Al Hasan and Mohammed J. Zaki, Output Space Sampling for Graph Patterns. In 35th International Conference on Very Large Data Bases. August 2009. (PDF) (BibTeX)
  2. Stephen Kelley, Mark Goldberg, Malik Magdon-Ismail, Konstantin Mertsalov, William Wallace and Mohammed J. Zaki, graphOnt: An Ontology Based Library for Conversion from Semantic Graphs to JUNG. In 7th IEEE International Conference on Intelligence and Security Informatics. June 2009. (PDF) (BibTeX)
  3. Mohammad Al Hasan and Mohammed J. Zaki, MUSK: Uniform Sampling of k Maximal Patterns. In 9th SIAM International Conference on Data Mining. April 2009. (PDF) (BibTeX)
  4. Mohammad Al Hasan, Saeed Salem, Benjarath Pupacdi and Mohammed J. Zaki, Clustering with Lower Bound on Similarity. In 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining. April 2009. (PDF) (BibTeX)
  5. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem and Mohammed J. Zaki, An integrated, generic approach to pattern mining: data mining template library. Data Mining and Knowledge Discovery, 17(3):457-495. December 2008. (PDF) (BibTeX)
  6. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem , Jeremy Besson and Mohammed J. Zaki, ORIGAMI: A Novel and Effective Approach for Mining Representative Orthogonal Graph Patterns. Statistical Analysis and Data Mining, 1(2):67-84. June 2008. (PDF) (BibTeX)
  7. Mohammad Hasan, Vineet Chaoji, Saeed Salem, Jeremy Besson and Mohammed J. Zaki, ORIGAMI: Mining Representative Orthogonal Graph Patterns. In 7th IEEE International Conference on Data Mining. October 2007. (PDF) (BibTeX)
  8. Karlton Sequeira and Mohammed J. Zaki, Exploring Similarities across High-dimensional Datasets. In Research and Trends in Data Mining Technologies and Applications, pages 53-85. Idea Group, Inc. 2007. (PDF) (BibTeX)
  9. Jeffery Baumes, Mark Goldberg, Mykola Hayvanovych, Malik Magdon-Ismail, William Wallace and Mohammed J. Zaki, Finding Hidden Group Structure in a Stream of Communications. In IEEE International Conference on Intelligence and Security Informatics. May 2006. (PDF) (BibTeX)
  10. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem and Mohammed J. Zaki, Link Prediction using Supervised Learning. In Workshop on Link Analysis, Counter-terrorism and Security (with SDM). April 2006. (PDF) (BibTeX)
  11. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem , Nagender Parimi and Mohammed J. Zaki, DMTL: A Generic Data Mining Template Library. In Workshop on Library-Centric Software Design (with OOPSLA). October 2005. (PDF) (BibTeX)
  12. Mohammed J. Zaki, Nilanjana De, Feng Gao, Paolo Palmerini, Nagender Parimi, Jeevan Pathuri, Benjarath Phoophakdee and Joe Urban, Generic Pattern Mining via Data Mining Template Library. In Constraint-Based Mining, pages 362-279. Springer-Verlag 2005. (PDF) (BibTeX)

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Tree Mining
  1. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem and Mohammed J. Zaki, An integrated, generic approach to pattern mining: data mining template library. Data Mining and Knowledge Discovery, 17(3):457-495. December 2008. (PDF) (BibTeX)
  2. Mohammed J. Zaki, A Unified Approach to Rooted Tree Mining: Algorithms and Applications. In Mining Graph Data, pages 381-410. John Wiley and Sons, Inc. 2007. (PDF) (BibTeX)
  3. Mohammed J. Zaki and Charu C. Aggarwal, Xrules: An effective structural classifier for XML data. Machine Learning Journal, 62(1-2):137-170. February 2006. (PDF) (BibTeX)
  4. Mohammed J. Zaki, Efficiently Mining Frequent Embedded Unordered Trees. Fundamenta Informaticae, 66(1-2):33-52. March/April 2005. (PDF) (BibTeX)
  5. Mohammed J. Zaki, Efficiently Mining Frequent Trees in a Forest: Algorithms and Applications. IEEE Transactions on Knowledge and Data Engineering, 17(8):1021-1035. August 2005. (PDF) (BibTeX)
  6. Mohammed J. Zaki and Charu C. Aggarwal, Xrules: An effective structural classifier for XML data. In 9th ACM SIGKDD International Conference Knowledge Discovery and Data Mining. August 2003. (PDF) (BibTeX)
  7. Mohammed J. Zaki, Efficiently Mining Frequent Trees in a Forest. In 8th ACM SIGKDD International Conference Knowledge Discovery and Data Mining. July 2002. (PDF) (BibTeX)

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Sequence Mining
  1. Karam Gouda, Mosab Hassaan and Mohammed J. Zaki, PRISM: An Effective Approach for Frequent Sequence Mining via Prime-Block Encoding. Journal of Computer and Systems Sciences, 76(1):88-102. January 2010. (PDF) (BibTeX)
  2. Mohammed J. Zaki, Christopher D. Carothers and Boleslaw K. Szymanski, VOGUE: A Variable Order Hidden Markov Model with Duration based on Frequent Sequence Mining. ACM Transactions on Knowledge Discovery in Data, to Appear. 2009. (PDF) (BibTeX)
  3. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem and Mohammed J. Zaki, An integrated, generic approach to pattern mining: data mining template library. Data Mining and Knowledge Discovery, 17(3):457-495. December 2008. (PDF) (BibTeX)
  4. Karam Gouda, Mosab Hassaan and Mohammed J. Zaki, PRISM: A Prime-Encoding Approach for Frequent Sequence Mining. In 7th IEEE International Conference on Data Mining. October 2007. (PDF) (BibTeX)
  5. Yongqiang Zhang and Mohammed J. Zaki, EXMOTIF: efficient structured motif extraction. Algorithms for molecular biology, 1(21). November 2006. ((URL)) (PDF) (BibTeX)
  6. Bouchra Bouqata, Christopher D. Carothers, Boleslaw K. Szymanski and Mohammed J. Zaki, VOGUE: A Novel Variable Order-Gap State Machine for Modeling Sequences. In 10th European Conference on Principles and Practice of Knowledge Discovery. September 2006. (PDF) (BibTeX)
  7. Mohammed J. Zaki, Nilanjana De, Feng Gao, Paolo Palmerini, Nagender Parimi, Jeevan Pathuri, Benjarath Phoophakdee and Joe Urban, Generic Pattern Mining via Data Mining Template Library. In Constraint-Based Mining, pages 362-279. Springer-Verlag 2005. (PDF) (BibTeX)
  8. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem , Nagender Parimi and Mohammed J. Zaki, DMTL: A Generic Data Mining Template Library. In Workshop on Library-Centric Software Design (with OOPSLA). October 2005. (PDF) (BibTeX)
  9. Mohammed J. Zaki, Parallel Sequence Mining on Shared-Memory Machines. March 2001. (PDF) (BibTeX)
  10. Mohammed J. Zaki, Neal Lesh and Mitsunori Ogihara, Predicting Failures in Event Sequences. 2001. (PDF) (BibTeX)
  11. Mohammed J. Zaki, SPADE: An Efficient Algorithm for Mining Frequent Sequences. Machine Learning Journal, 42(1/2):31-60. January/February 2001. (PDF) (BibTeX)
  12. Mohammed J. Zaki, Sequence Mining in Categorical Domains: Algorithms and Applications. In Sequence Learning: Paradigms, Algorithms, and Applications, pages 162-187. Springer-Verlag, Heidelberg, Germany 2000. (PDF) (BibTeX)
  13. Mohammed J. Zaki, Sequences Mining in Categorical Domains: Incorporating Constraints. In 9th ACM International Conference on Information and Knowledge Management. November 2000. (PDF) (BibTeX)
  14. Neal Lesh, Mohammed J. Zaki and Mitsunori Ogihara, Scalable Feature Mining for Sequential Data. IEEE Intelligent Systems and their Applications, 15(2):48-56. March/April 2000. (PDF) (BibTeX)
  15. Srinivasan Parthasarathy, Mohammed J. Zaki, Mitsunori Ogihara and Sandhya Dwarkadas, Sequence Mining in Dynamic and Interactive Environments. In Knowledge Discovery for Business Information Systems, pages 377-395. Kluwer Academic Publishers, Boston, MA 2000. (PDF) (BibTeX)
  16. Mohammed J. Zaki, Parallel sequence mining on SMP machines. In Large-Scale Parallel Data Mining. Springer-Verlag, Heidelberg, Germany 2000. (PDF) (BibTeX)
  17. Mohammed J. Zaki, Neal Lesh and Mitsunori Ogihara, PLANMINE: Predicting Plan Failures using Sequence mining. Artificial Intelligence Review, 14(6):421-446. December 2000. (PDF) (BibTeX)
  18. Mohammed J. Zaki, Parallel Sequence Mining on Shared-Memory Machines. In Workshop on Large-Scale Parallel Data Mining Systems (with KDD). August 1999. (PDF) (BibTeX)
  19. Neal Lesh, Mohammed J. Zaki and Mitsunori Ogihara, Mining features for Sequence Classification. In 5th International Conference on Knowledge Discovery and Data Mining (KDD). August 1999. (PDF) (BibTeX)
  20. Srinivasan Parthasarathy, Mohammed J. Zaki, Mitsunori Ogihara and Sandhya Dwarkadas, Incremental and Interactive Sequence Mining. In 8th ACM International Conference Information and Knowledge Management. November 1999. (PDF) (BibTeX)
  21. Mohammed J. Zaki, Efficient Enumeration of Frequent Sequences. In 7th ACM International Conference on Information and Knowledge Management. November 1998. (PDF) (BibTeX)
  22. Mohammed J. Zaki, Scalable data mining for rules. Technical report URCS-TR-702 (Ph.D. Thesis), University of Rochester July 1998. (PDF) (BibTeX)
  23. Mohammed J. Zaki, Neal Lesh and Mitsunori Ogihara, PLANMINE: Sequence mining for plan failures. In 4th International Conference on Knowledge Discovery and Data Mining (KDD). August 1998. (PDF) (BibTeX)

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Itemset Mining and Association Rules
  1. Mohammed J. Zaki, Closed Itemset Mining and Non-redundant Association Rule Mining. In Encyclopedia of Database Systems. Springer-Verlag 2009. ((URL)) (PDF) (BibTeX)
  2. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem and Mohammed J. Zaki, An integrated, generic approach to pattern mining: data mining template library. Data Mining and Knowledge Discovery, 17(3):457-495. December 2008. (PDF) (BibTeX)
  3. Adriano Veloso, Wagner Meira, Jr., Marcos Golcalves and Mohammed J. Zaki, Multi-Label Lazy Associative Classification. In 11th European Conference on Principles and Practice of Knowledge Discovery. September 2007. (PDF) (BibTeX)
  4. Adriano Veloso, Wagner Meira, Jr. and Mohammed J. Zaki, Lazy Associative Classification. In 6th IEEE International Conference on Data Mining. December 2006. (PDF) (BibTeX)
  5. Lizhuang Zhao, Mohammed J. Zaki and Naren Ramakrishnan, BLOSOM: A Framework for Mining Arbitrary Boolean Expressions. In 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2006. (PDF) (BibTeX)
  6. Adriano Veloso, Wagner Meira, Jr., Marco Cristo, Marcos Golcalves and Mohammed J. Zaki, Multi-Evidence, Multi-Criteria, Lazy Associative Document Classification. In 15th ACM International Conference on Information and Knowledge Management. November 2006. (PDF) (BibTeX)
  7. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem , Nagender Parimi and Mohammed J. Zaki, DMTL: A Generic Data Mining Template Library. In Workshop on Library-Centric Software Design (with OOPSLA). October 2005. (PDF) (BibTeX)
  8. Mohammed J. Zaki, Nilanjana De, Feng Gao, Paolo Palmerini, Nagender Parimi, Jeevan Pathuri, Benjarath Phoophakdee and Joe Urban, Generic Pattern Mining via Data Mining Template Library. In Constraint-Based Mining, pages 362-279. Springer-Verlag 2005. (PDF) (BibTeX)
  9. Mohammed J. Zaki and Ching-Jui Hsiao, Efficient Algorithms for Mining Closed Itemsets and their Lattice Structure. IEEE Transactions on Knowledge and Data Engineering, 17(4):462-478. April 2005. (PDF) (BibTeX)
  10. Bart Goethals, Siegfried Nijssen and Mohammed J Zaki, Open Source Data Mining: Workshop Report. SIGKDD Explorations, 7(2):143-144. December 2005. (PDF) (BibTeX)
  11. Karam Gouda and Mohammed J. Zaki, GenMax: An Efficient Algorithm for Mining Maximal Frequent Itemsets. Data Mining and Knowledge Discovery: An International Journal, 11(3):223-242. November 2005. (PDF) (BibTeX)
  12. Mohammed J. Zaki and Naren Ramakrishnan, Reasoning about Sets using Redescription Mining. In 11th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2005. (PDF) (BibTeX)
  13. Bart Goethals, Siegfried Nijssen and Mohammed J Zaki, Proceedings of the 1st ACM SIGKDD International workshop on open source data mining: frequent pattern mining implementations. (Bart Goethals and Siegfried Nijssen and Mohammed J Zaki, Eds.), ACM Digital Library (http://portal.acm.org/toc.cfm?id=1133905) 2005. ((URL)) (PDF) (BibTeX)
  14. Mohammed J. Zaki, Mining Maximal and Closed Frequent Itemsets. In New Generation of Data Mining Applications, pages 571-598. IEEE/Wiley Press 2005. (PDF) (BibTeX)
  15. Ganesh Ramesh, Mohammed J. Zaki and William A. Maniatty, Distribution-Based Synthetic Database Generation Techniques for Itemset Mining. In 9th International Database Engineering and Applications Symposium. July 2005. (PDF) (BibTeX)
  16. Bart Goethals and Mohammed J. Zaki, Advances in Frequent Itemset Mining Implementations: report on FIMI'03. SIGKDD Explorations, 6(1):109-117. June 2004. (PDF) (BibTeX)
  17. Mohammed J. Zaki, Mining Non-Redundant Association Rules. Data Mining and Knowledge Discovery: An International Journal, 9(3):223-248. November 2004. (PDF) (BibTeX)
  18. Roberto Bayardo, Bart Goethals and Mohammed J Zaki, Proceedings of the 2nd IEEE ICDM Workshop on Frequent Itemset Mining Implementations. (Roberto Bayardo and Bart Goethals and Mohammed J Zaki, Eds.), CEUR Workshop Proceedings 2004. ((URL)) (PDF) (BibTeX)
  19. Feng Pan, Gao Cong, Anthony K. H. Tung, Jiong Yang and Mohammed J. Zaki, CARPENTER: Finding Closed Patterns in Long Biological Datasets. In 9th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2003. (PDF) (BibTeX)
  20. Mohammed J. Zaki and Karam Gouda, Fast Vertical Mining Using Diffsets. In 9th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2003. (PDF) (BibTeX)
  21. Bart Goethals and Mohammed J. Zaki, Proceedings of the 1st IEEE ICDM Workshop on Frequent Itemset Mining Implementations. (Bart Goethals and Mohammed J. Zaki, Eds.), CEUR Workshop Proceedings 2003. ((URL)) (PDF) (BibTeX)
  22. Mohammed J. Zaki and Benjarath Phoophakdee, MIRAGE: A Framework for Mining, Exploring and Visualizing Minimal Association Rules. Technical report 03-4, Computer Science Department, Rensselaer Polytechnic Institute July 2003. (PDF) (BibTeX)
  23. Ganesh Ramesh, William A. Maniatty and Mohammed J. Zaki, Feasible Itemset Distributions in Data Mining: Theory and Application. In 22nd {ACM SIGACT-SIGMOD-SIGART} Symposium on Principles of Database Systems. June 2003. (PDF) (BibTeX)
  24. Adriano Veloso, Wagner Meira, Jr., Marcio Carvalho, Srinivasan Parthasarathy and Mohammed J. Zaki, Incremental and Interactive Mining for Frequent Itemsets in Evolving Databases. In 6th International Workshop on High Performance Data Mining: Pervasive and Data Stream Mining. May 2003. (PDF) (BibTeX)
  25. Mohammed J. Zaki and Ching-Jui Hsiao, CHARM: An Efficient Algorithm for Closed Itemset Mining. In 2nd {SIAM} International Conference on Data Mining. April 2002. (PDF) (BibTeX)
  26. Adriano Veloso, Bruno Gusmao, Wagner Meira, Jr., Marcio Carvalho, Srinivasan Parthasarathy and Mohammed J. Zaki, Efficiently Mining Approximate Models of Associations in Evolving Databases. In 6th European Conference on Principles of Knowledge Discovery in Databases. August 2002. (PDF) (BibTeX)
  27. Adriano Veloso, Wagner Meira, Jr., Marcio Carvalho, Bruno Possas, Srinivasan Parthasarathy and Mohammed J. Zaki, Mining Frequent Itemsets in Evolving Databases. In 2nd {SIAM} International Conference on Data Mining. April 2002. (PDF) (BibTeX)
  28. Karam Gouda and Mohammed J. Zaki, Efficiently Mining Maximal Frequent Itemsets. In 1st IEEE International Conference on Data Mining. November 2001. (PDF) (BibTeX)
  29. Srinivasan Parthasarathy, Mohammed J. Zaki, Mitsunori Ogihara and Wei Li, Parallel Data Mining for Association Rules on Shared-memory Systems. Knowledge and Information Systems, 3(1):1-29. February 2001. (PDF) (BibTeX)
  30. Mohammed J. Zaki, Generating Non-Redundant Association Rules. In 6th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2000. (PDF) (BibTeX)
  31. Mohammed J. Zaki, Scalable Algorithms for Association Mining. IEEE Transactions on Knowledge and Data Engineering, 12(3):372-390. May/June 2000. (PDF) (BibTeX)
  32. Mohammed J. Zaki, Hierarchical Parallel Algorithms for Association Mining. In Advances in Distributed and Parallel Knowledge Discovery, pages 339-376. AAAI Press, Menlo Park, CA 2000. (PDF) (BibTeX)
  33. Mohammed J. Zaki, Parallel and Distributed Association Mining: A Survey. IEEE Concurrency, 7(4):14-25. December 1999. (PDF) (BibTeX)
  34. Mohammed J. Zaki and Mitsunori Ogihara, Theoretical Foundations of Association Rules. In 3rd ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery. June 1998. (PDF) (BibTeX)
  35. Srinivasan Parthasarathy, Mohammed J. Zaki and Wei Li, Memory placement techniques for parallel association mining. In 4th International Conference on Knowledge Discovery and Data Mining (KDD). August 1998. (PDF) (BibTeX)
  36. Mohammed J. Zaki, Scalable data mining for rules. Technical report URCS-TR-702 (Ph.D. Thesis), University of Rochester July 1998. (PDF) (BibTeX)
  37. Mohammed J. Zaki, Srinivasan Parthasarathy, Mitsunori Ogihara and Wei Li, New algorithms for fast discovery of association rules. In 3rd International Conference on Knowledge Discovery and Data Mining (KDD). August 1997. (PDF) (BibTeX)
  38. Mohammed J. Zaki, Srinivasan Parthasarathy, Mitsunori Ogihara and Wei Li, New algorithms for fast discovery of association rules. Technical report URCS-TR-651, University of Rochester July 1997. (PDF) (BibTeX)
  39. Mohammed J. Zaki, Srinivasan Parthasarathy and Wei Li, A localized algorithm for parallel association mining. In 9th Annual ACM Symposium on Parallel Algorithms and Architectures. June 1997. (PDF) (BibTeX)
  40. Mohammed J. Zaki, Srinivasan Parthasarathy, Mitsunori Ogihara and Wei Li, Parallel algorithms for discovery of association rules. Data Mining and Knowledge Discovery: An International Journal, 1(4):343-373. December 1997. (PDF) (BibTeX)
  41. Mohammed J. Zaki, Srinivasan Parthasarathy, Wei Li and Mitsunori Ogihara, Evaluation of Sampling for Data Mining of Association Rules. In 7th IEEE International Workshop on Research Issues in Data Engineering (with ICDE). April 1997. (PDF) (BibTeX)
  42. Mohammed J. Zaki, Mitsunori Ogihara, Srinivasan Parthasarathy and Wei Li, Parallel Data Mining for Association Rules on Shared-memory Multi-processors. In Supercomputing'96. November 1996. (PDF) (BibTeX)

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Web Mining

  1. Amir H. Youssefi, David J. Duke and Mohammed J. Zaki, Visual Web Mining. In 13th International World Wide Web Conference (Poster). May 2004. (PDF) (BibTeX)
  2. Amir H. Youssefi, David J. Duke, Ephraim P. Glinert, and Mohammed J. Zaki, Towards Visual Web Mining. In 3rd International Workshop on Visual Data Mining (with ICDM). November 2003. (PDF) (BibTeX)
  3. John Punin, Mukkai Krishnamoorthy and Mohammed J. Zaki, Web Usage Mining: Languages and Algorithms. In Explanatory Data Analysis in Empirical Research, pages 266-281. Springer-Verlag 2002. (PDF) (BibTeX)
  4. John Punin, Mukkai Krishnamoorthy and Mohammed J. Zaki, LOGML: Log markup language for web usage mining. In ACM WEBKDD Workshop on Mining Log Data Across All Customer TouchPoints (with SIGKDD). August 2001. (PDF) (BibTeX)
  5. John Punin, Mukkai Krishnamoorthy and Mohammed J. Zaki, LOGML: XML language for web usage mining. In 10th International World Wide Web Conference (Poster). May 2001. (PDF) (BibTeX)

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Clustering

  1. Mohammad Al Hasan, Saeed Salem, Benjarath Pupacdi and Mohammed J. Zaki, Clustering with Lower Bound on Similarity. In 13th Pacific-Asia Conference on Knowledge Discovery and Data Mining. April 2009. (PDF) (BibTeX)
  2. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem and Mohammed J. Zaki, Robust Partitional Clustering by Outlier and Density Insensitive Seeding. Pattern Recognition Letters, 30(11):994-1002. August 2009. (PDF) (BibTeX)
  3. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem and Mohammed J. Zaki, SPARCL: An Effective and Efficient Algorithm for Mining Arbitrary Shape-based Clusters. Knowledge and Information Systems, available online. June 2009. (PDF) (BibTeX)
  4. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem and Mohammed J. Zaki, SPARCL: Efficient and Effective Shape-based Clustering. In 8th IEEE International Conference on Data Mining. December 2008. (PDF) (BibTeX)
  5. Mohammed J. Zaki, Markus Peters, Ira Assent and Thomas Seidl, CLICKS: An Effective Algorithm for Mining Subspace Clusters in Categorical Datasets. Data and Knowledge Engineering, 60(1):51-70. January 2007. (PDF) (BibTeX)
  6. Charu A. Aggarwal, Na Ta, Jianyong Wang, Jianhua Feng and Mohammed J. Zaki, XProj: A Framework for Projected Structural Clustering of XML Documents. In 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2007. (PDF) (BibTeX)
  7. Markus Peters and Mohammed Zaki, CLICKS: clustering categorical data using K-partite maximal cliques. In 21st IEEE International Conference on Data Engineering. April 2005. (PDF) (BibTeX)
  8. Mohammed Zaki, Markus Peters, Ira Assent and Thomas Seidl, CLICKS: An Effective Algorithm for Mining Subspace Clusters in Categorical Datasets. In 11th ACM SIGKDD International Conference onKnowledge Discovery and Data Mining. August 2005. (PDF) (BibTeX)
  9. Lizhuang Zhao and Mohammed J. Zaki, TriCluster: An Effective Algorithm for Mining Coherent Clusters in 3D Microarray Data. In ACM SIGMOD Conference on Management of Data. June 2005. (PDF) (BibTeX)
  10. Karlton Sequeira and Mohammed J. Zaki, SCHISM: A New Approach to Interesting Subspace Mining. International Journal of Business Intelligence and Data Mining, 1(2):137-160. 2005. (PDF) (BibTeX)
  11. Karlton Sequeira and Mohammed J. Zaki, SCHISM: A New Approach for Interesting Subspace Mining. In 4th IEEE International Conference on Data Mining. November 2004. (PDF) (BibTeX)
  12. Scott Epter, Mukkai Krishnamoorthy and Mohammed J. Zaki, Clusterability Detection and Cluster Initialization. In {SIAM} Workshop on Clustering High Dimensional Data and its Applications (with SDM). April 2002. (PDF) (BibTeX)
  13. Karlton Sequeira, Mohammed J. Zaki, ADMIT: Anomaly-base Data Mining for Intrusions. In 8th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. July 2002. (PDF) (BibTeX)

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Classification

  1. Adriano Veloso, Mohammed J. Zaki, Wagner Meira, Jr. and Marcos Goncalves, The Metric Dilemma: Competence-Conscious Associative Classification. In 9th SIAM International Conference on Data Mining. April 2009. (PDF) (BibTeX)
  2. Adriano Veloso, Wagner Meira, Jr. and Mohammed J. Zaki, Calibrated Lazy Associative Classification. In Brazilian Symposium on Databases. October 2008. (PDF) (BibTeX)
  3. Adriano Veloso, Wagner Meira, Jr., Marcos Golcalves and Mohammed J. Zaki, Multi-Label Lazy Associative Classification. In 11th European Conference on Principles and Practice of Knowledge Discovery. September 2007. (PDF) (BibTeX)
  4. Adriano Veloso, Wagner Meira, Jr., Marco Cristo, Marcos Golcalves and Mohammed J. Zaki, Multi-Evidence, Multi-Criteria, Lazy Associative Document Classification. In 15th ACM International Conference on Information and Knowledge Management. November 2006. (PDF) (BibTeX)
  5. Mohammed J. Zaki and Charu C. Aggarwal, Xrules: An effective structural classifier for XML data. Machine Learning Journal, 62(1-2):137-170. February 2006. (PDF) (BibTeX)
  6. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem and Mohammed J. Zaki, Link Prediction using Supervised Learning. In Workshop on Link Analysis, Counter-terrorism and Security (with SDM). April 2006. (PDF) (BibTeX)
  7. Adriano Veloso, Wagner Meira, Jr. and Mohammed J. Zaki, Lazy Associative Classification. In 6th IEEE International Conference on Data Mining. December 2006. (PDF) (BibTeX)
  8. Mohammed J. Zaki and Charu C. Aggarwal, Xrules: An effective structural classifier for XML data. In 9th ACM SIGKDD International Conference Knowledge Discovery and Data Mining. August 2003. (PDF) (BibTeX)
  9. Mohammed J. Zaki, Ching-Tien Ho and Rakesh Agrawal, Parallel Classification on Shared-Memory Systems. In Advances in Distributed and Parallel Knowledge Discovery, pages 377-407. AAAI Press, Menlo Park, CA 2000. (PDF) (BibTeX)
  10. Mohammed J. Zaki, Ching-Tien Ho and Rakesh Agrawal, Parallel Classification for Data Mining on Shared-Memory Systems. Technical report RJ10104, IBM 1999. (PDF) (BibTeX)
  11. Neal Lesh, Mohammed J. Zaki and Mitsunori Ogihara, Mining features for Sequence Classification. In 5th International Conference on Knowledge Discovery and Data Mining (KDD). August 1999. (PDF) (BibTeX)
  12. Mohammed J. Zaki, Ching-Tien Ho and Rakesh Agrawal, Parallel Classification for Data Mining on Shared-Memory Multiprocessors. In 15th IEEE International Conference on Data Engineering. March 1999. (PDF) (BibTeX)
  13. Mohammed J. Zaki, Scalable data mining for rules. Technical report URCS-TR-702 (Ph.D. Thesis), University of Rochester July 1998. (PDF) (BibTeX)
  14. Mohammed J. Zaki, Ching-Tien Ho and Rakesh Agrawal, Parallel Classification on SMP Systems. In 1st Workshop on High Performance Data Mining (with IPPS). March 1998. (PDF) (BibTeX)

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Parallel Data Mining

  1. Renata B. Araujo, Guilherme H. T. Ferreira, Gustavo H. Orair, Wagner Meira Jr., Renato A. C. Ferreira, Dorgival O. G. Neto and Mohammed J. Zaki, The ParTriCluster Algorithm for Gene Expression Analysis. International Journal of Parallel Programming, 36(2):226-249. April 2008. (PDF) (BibTeX)
  2. Mohammed J. Zaki and Yi Pan, Introduction: Recent Developments in Parallel and Distributed Data Mining. Distributed and Parallel Databases: An International Journal, 11(2):123-137. March 2002. (PDF) (BibTeX)
  3. Mohammed J. Zaki, Vipin Kumar and David Skillicorn, Proceedings of Workshop on Parallel and Distributed Data Mining. (Mohammed J. Zaki and Vipin Kumar and David Skillicorn, Eds.) 2001. ((URL)) (PDF) (BibTeX)
  4. Srinivasan Parthasarathy, Mohammed J. Zaki, Mitsunori Ogihara and Wei Li, Parallel Data Mining for Association Rules on Shared-memory Systems. Knowledge and Information Systems, 3(1):1-29. February 2001. (PDF) (BibTeX)
  5. Mohammed J. Zaki, Parallel Sequence Mining on Shared-Memory Machines. March 2001. (PDF) (BibTeX)
  6. Mohammed J. Zaki, Parallel and Distributed Data Mining: An Introduction. In Large-Scale Parallel Data Mining. Springer-Verlag, Heidelberg, Germany 2000. (PDF) (BibTeX)
  7. Mohammed J. Zaki and Gautam Das, Proceedings of HiPC'00: Special Session on Large Scale Data Mining. (Mohammed J. Zaki and Gautam Das, Eds.), Springer LINK (http://www.springerlink.com/content/phpt72qy0ycw) 2000. ((URL)) (BibTeX)
  8. Mohammed J. Zaki and Ching-Tien Ho, Workshop Report: Large-Scale Parallel KDD Systems. SIGKDD Explorations, 1(2):112-114. January 2000. (PDF) (BibTeX)
  9. Mohammed J. Zaki, Parallel sequence mining on SMP machines. In Large-Scale Parallel Data Mining. Springer-Verlag, Heidelberg, Germany 2000. (PDF) (BibTeX)
  10. Mohammed J. Zaki, Vipin Kumar and David Skillicorn, 3rd IPDPS International Workshop on High Performance Data Mining. (Mohammed J. Zaki and Vipin Kumar and David Skillicorn, Eds.), Springer LINK (http://www.springerlink.com/content/101nv8cq9yrw/) 2000. ((URL)) (PDF) (BibTeX)
  11. William A. Maniatty and Mohammed J. Zaki, Systems Support for Scalable Data Mining. SIGKDD Explorations, 2(2):56-65. December 2000. (PDF) (BibTeX)
  12. Mohammed J. Zaki and Ching-Tien Ho, Large-Scale Parallel Data Mining. (Mohammed J. Zaki and Ching-Tien Ho, Eds.) Springer-Verlag, Heidelberg, Germany 2000. ((URL)) (BibTeX)
  13. Mohammed J. Zaki, Hierarchical Parallel Algorithms for Association Mining. In Advances in Distributed and Parallel Knowledge Discovery, pages 339-376. AAAI Press, Menlo Park, CA 2000. (PDF) (BibTeX)
  14. Mohammed J. Zaki, Ching-Tien Ho and Rakesh Agrawal, Parallel Classification on Shared-Memory Systems. In Advances in Distributed and Parallel Knowledge Discovery, pages 377-407. AAAI Press, Menlo Park, CA 2000. (PDF) (BibTeX)
  15. William A. Maniatty and Mohammed J. Zaki, A Requirement Analysis for Parallel KDD Systems. In 3rd IPDPS Workshop on High Performance Data Mining. May 2000. (PDF) (BibTeX)
  16. Mohammed J. Zaki, Ching-Tien Ho and Rakesh Agrawal, Parallel Classification for Data Mining on Shared-Memory Systems. Technical report RJ10104, IBM 1999. (PDF) (BibTeX)
  17. Mohammed J. Zaki and Ching-Tien Ho, Proceedings of the ACM SIGKDD Workshop on Large-Scale Parallel KDD Systems. (Mohammed J. Zaki and Ching-Tien Ho, Eds.) 1999. ((URL)) (PDF) (BibTeX)
  18. Mohammed J. Zaki, Ching-Tien Ho and Rakesh Agrawal, Parallel Classification for Data Mining on Shared-Memory Multiprocessors. In 15th IEEE International Conference on Data Engineering. March 1999. (PDF) (BibTeX)
  19. Mohammed J. Zaki, Parallel Sequence Mining on Shared-Memory Machines. In Workshop on Large-Scale Parallel Data Mining Systems (with KDD). August 1999. (PDF) (BibTeX)
  20. Mohammed J. Zaki, Parallel and Distributed Association Mining: A Survey. IEEE Concurrency, 7(4):14-25. December 1999. (PDF) (BibTeX)
  21. Rakesh Agrawal, Ching-Tien Ho, Leon Pauser and Mohammed J. Zaki, Parallel Data Mining on Shared-Memory Multiprocessors. In 9th SIAM Conference on Parallel Processing for Scientific Computing, Minisymposium on High-Performance Data Mining. March 1999. (PDF) (BibTeX)
  22. Srinivasan Parthasarathy, Mohammed J. Zaki and Wei Li, Memory placement techniques for parallel association mining. In 4th International Conference on Knowledge Discovery and Data Mining (KDD). August 1998. (PDF) (BibTeX)
  23. Mohammed J. Zaki, Ching-Tien Ho and Rakesh Agrawal, Parallel Classification on SMP Systems. In 1st Workshop on High Performance Data Mining (with IPPS). March 1998. (PDF) (BibTeX)
  24. Mohammed J. Zaki, Scalable data mining for rules. Technical report URCS-TR-702 (Ph.D. Thesis), University of Rochester July 1998. (PDF) (BibTeX)
  25. Mohammed J. Zaki, Srinivasan Parthasarathy, Mitsunori Ogihara and Wei Li, Parallel algorithms for discovery of association rules. Data Mining and Knowledge Discovery: An International Journal, 1(4):343-373. December 1997. (PDF) (BibTeX)
  26. Mohammed J. Zaki, Srinivasan Parthasarathy and Wei Li, A localized algorithm for parallel association mining. In 9th Annual ACM Symposium on Parallel Algorithms and Architectures. June 1997. (PDF) (BibTeX)
  27. Mohammed J. Zaki, Mitsunori Ogihara, Srinivasan Parthasarathy and Wei Li, Parallel Data Mining for Association Rules on Shared-memory Multi-processors. In Supercomputing'96. November 1996. (PDF) (BibTeX)

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Online and Incremental Data Mining

  1. Adriano Veloso, Wagner Meira, Jr., Marcio Carvalho, Srinivasan Parthasarathy and Mohammed J. Zaki, Incremental and Interactive Mining for Frequent Itemsets in Evolving Databases. In 6th International Workshop on High Performance Data Mining: Pervasive and Data Stream Mining. May 2003. (PDF) (BibTeX)
  2. Adriano Veloso, Wagner Meira, Jr., Marcio Carvalho, Bruno Possas, Srinivasan Parthasarathy and Mohammed J. Zaki, Mining Frequent Itemsets in Evolving Databases. In 2nd {SIAM} International Conference on Data Mining. April 2002. (PDF) (BibTeX)
  3. Adriano Veloso, Bruno Gusmao, Wagner Meira, Jr., Marcio Carvalho, Srinivasan Parthasarathy and Mohammed J. Zaki, Efficiently Mining Approximate Models of Associations in Evolving Databases. In 6th European Conference on Principles of Knowledge Discovery in Databases. August 2002. (PDF) (BibTeX)
  4. Mohammed J. Zaki, Editorial: Online, Interactive and Anytime Data Mining. SIGKDD Explorations, 3(2):i-ii. January 2002. ((URL)) (PDF) (BibTeX)
  5. Srinivasan Parthasarathy, Mohammed J. Zaki, Mitsunori Ogihara and Sandhya Dwarkadas, Sequence Mining in Dynamic and Interactive Environments. In Knowledge Discovery for Business Information Systems, pages 377-395. Kluwer Academic Publishers, Boston, MA 2000. (PDF) (BibTeX)
  6. Srinivasan Parthasarathy, Mohammed J. Zaki, Mitsunori Ogihara and Sandhya Dwarkadas, Incremental and Interactive Sequence Mining. In 8th ACM International Conference Information and Knowledge Management. November 1999. (PDF) (BibTeX)

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Sampling in Data Mining

  1. Mohammad Al Hasan and Mohammed J. Zaki, Output Space Sampling for Graph Patterns. In 35th International Conference on Very Large Data Bases. August 2009. (PDF) (BibTeX)
  2. Mohammad Al Hasan and Mohammed J. Zaki, MUSK: Uniform Sampling of k Maximal Patterns. In 9th SIAM International Conference on Data Mining. April 2009. (PDF) (BibTeX)
  3. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem , Jeremy Besson and Mohammed J. Zaki, ORIGAMI: A Novel and Effective Approach for Mining Representative Orthogonal Graph Patterns. Statistical Analysis and Data Mining, 1(2):67-84. June 2008. (PDF) (BibTeX)
  4. Mohammad Hasan, Vineet Chaoji, Saeed Salem, Jeremy Besson and Mohammed J. Zaki, ORIGAMI: Mining Representative Orthogonal Graph Patterns. In 7th IEEE International Conference on Data Mining. October 2007. (PDF) (BibTeX)
  5. Mohammed J. Zaki, Srinivasan Parthasarathy, Wei Li and Mitsunori Ogihara, Evaluation of Sampling for Data Mining of Association Rules. In 7th IEEE International Workshop on Research Issues in Data Engineering (with ICDE). April 1997. (PDF) (BibTeX)

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Intrusion Detection

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

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General Data Mining

  1. John Elder, Francoise Soulie Fogelman, Peter Flach and Mohammed Zaki, Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining. (John Elder and Francoise Soulie Fogelman and Peter Flach and Mohammed Zaki, Eds.), ACM June 2009. ((URL)) (BibTeX)
  2. Vineet Chaoji, Mohammad Al Hasan, Saeed Salem and Mohammed J. Zaki, An integrated, generic approach to pattern mining: data mining template library. Data Mining and Knowledge Discovery, 17(3):457-495. December 2008. (PDF) (BibTeX)
  3. Mohammed J. Zaki, Ke Wang, Editorial: Special Issue on the Best Papers of SDM'08. Statistical Analysis and Data Mining, 1(3):109-110. November 2008. (PDF) (BibTeX)
  4. Chid Apte, Haesun Park, Ke Wang and Mohammed J. Zaki, Proceedings of the 2008 SIAM International Conference on Data Mining. (Chid Apte and Haesun Park and Ke Wang and Mohammed J. Zaki, Eds.), Society for Industrial and Applied Mathematics, Philadelphia, PA April 2008. ((URL)) (BibTeX)
  5. Shichao Zhang and Mohammed J. Zaki, Editorial: Mining Multiple Data Sources: Local Pattern Analysis. Data Mining and Knowledge Discovery: An International Journal, 12(2-3):121-125. May 2006. (PDF) (BibTeX)
  6. Richi Nayak and Mohammed J. Zaki, Knowledge Discovery from XML Documents. (Richi Nayak and Mohammed J. Zaki, Eds.) Spring-Verlag 2006. ((URL)) (BibTeX)
  7. Gregory Piatetsky-Shapiro, Chabane Djeraba, Lise Getoor, Robert Grossman, Ronen Feldman and Mohammed J. Zaki, What are the grand challenges for data mining?: KDD-2006 panel report. SIGKDD Explorations, 8(2):70-77. December 2006. (PDF) (BibTeX)
  8. Mohammed J. Zaki, Nilanjana De, Feng Gao, Paolo Palmerini, Nagender Parimi, Jeevan Pathuri, Benjarath Phoophakdee and Joe Urban, Generic Pattern Mining via Data Mining Template Library. In Constraint-Based Mining, pages 362-279. Springer-Verlag 2005. (PDF) (BibTeX)
  9. Mohammed J. Zaki, Nagender Parimi, Nilanjana De, Feng Gao, Benjarath Phoophakdee, Joe Urban, Vineet Chaoji, Mohammad Al Hasan and Saeed Salem, Towards Generic Pattern Mining (Invited Paper). In International Conference on Formal Concept Analysis. February 2005. (PDF) (BibTeX)
  10. Mohammad Al Hasan, Vineet Chaoji, Saeed Salem , Nagender Parimi and Mohammed J. Zaki, DMTL: A Generic Data Mining Template Library. In Workshop on Library-Centric Software Design (with OOPSLA). October 2005. (PDF) (BibTeX)
  11. Mohammed J. Zaki, Nilanjana De, Feng Gao, Nagender Parimi, Benjarath Phoophakdee, Joe Urban, Vineet Chaoji, Mohammad Al Hasan and Saeed Salem, Towards Generic Pattern Mining (Extended Abstract). In 1st International Conference on Pattern Recognition and Machine Intelligence. December 2005. (PDF) (BibTeX)
  12. Mohammed J. Zaki, Data Mining. In The Encyclopedia of Human-Computer Interaction, pages 149-152. Berkshire Publishing Group 2004. (PDF) (BibTeX)
  13. Mohammed J. Zaki and Limsoon Wong, Data Mining Techniques. In Selected Topics in Post-Genome Knowledge Discovery, pages 125-163. World Scientific Publishers 2004. (PDF) (BibTeX)
  14. Mohammed J. Zaki and Charu C. Aggarwal, Proceedings of the 8th ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery. (Mohammed J. Zaki and Charu C. Aggarwal, Eds.) June 2003. ((URL)) (PDF) (BibTeX)
  15. Karlton Sequeira, Mohammed J. Zaki and Boleslaw Szymanski, Improving Spatial Locality using Data Mining. In 9th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2003. (PDF) (BibTeX)
  16. Bouchra Bouqata, Chris Carothers, Boleslaw K. Szymanski and Mohammed J. Zaki, Understading Filesystem Performance for Data Mining Applications. In 6th International Workshop on High Performance Data Mining: Pervasive and Data Stream Mining (with SDM). August 2003. (PDF) (BibTeX)
  17. Ganesh Ramesh, William A. Maniatty and Mohammed J. Zaki, Indexing and Data Access Methods for Database Mining. In 7th ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery. May 2002. (PDF) (BibTeX)

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Data Mining for Materials Science

  1. Krishna Rajan and Mohammed J. Zaki, Data Mining through Information Association: A Knowledge Discovery Tool for Materials Science. In 17th International CODATA Conference. October 2000. (PDF) (BibTeX)

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Systems, Load Balancing, Network of Workstations

  1. Karlton Sequeira, Mohammed J. Zaki and Boleslaw Szymanski, Improving Spatial Locality using Data Mining. In 9th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2003. (PDF) (BibTeX)
  2. Mohammed J. Zaki, Srinivasan Parthasarathy and Wei Li, Customized Dynamic Load Balancing for Cluster Computing. In High Performance Cluster Computing: Architectures and Systems, pages 582-607. Prentice Hall, Upper Saddle River, NJ 1999. (PDF) (BibTeX)
  3. Mohammed J. Zaki, Wei Li and Srinivasan Parthasarathy, Customized Dynamic Load Balancing for a Network of Workstations. Journal of Parallel and Distributed Computing, 43(2):156-162. June 1997. (PDF) (BibTeX)
  4. Michal Cierniak, Mohammed J. Zaki and Wei Li, Compile-time scheduling algorithms for a heterogeneous network of workstations. The Computer Journal, 40(6):356-372. December 1997. (PDF) (BibTeX)
  5. Michael Scott, Wei Li, Sandhya Dwarkadas, Leonidas Kontothanassis, Galen Hunt, Maged Michael, Rob Stets, Nikos Hardavellas, Wagner Meira, Alex Poulos, Michal Cierniak, Srinivasan Parthasarathy and Mohammed J. Zaki, Implementation of Cashmere. In 6th International Workshop on Scalable Shared Memory Multiprocessors (with ASPLOS). October 1996. (PDF) (BibTeX)
  6. Srinivasan Parthasarathy, Wei Li, M. Cierniak and Mohammed J. Zaki, Compile-Time Inter-Query Dependence Analysis. In 8th IEEE Symposium on Parallel and Distributed Processing. October 1996. (PDF) (BibTeX)
  7. Mohammed J. Zaki, Wei Li and Srinivasan Parthasarathy, Customized Dynamic Load Balancing for a Network of Workstations. In 5th IEEE International Symposium on High-Performance Distributed Computing. August 1996. (PDF) (BibTeX)
  8. Michal Cierniak, Wei Li and Mohammed J. Zaki, Loop scheduling for heterogeneity. In 4th IEEE International Symposium on High-Performance Distributed Computing. August 1995. (PDF) (BibTeX)
  9. Mohammed J. Zaki, Wei Li and Michal Cierniak, Performance Impact of Processor and Memory Heterogeneity in a Network of Machines. In 4th Heterogeneous Computing Workshop (with IPPS). April 1995. (PDF) (BibTeX)

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Theory

  1. Lane Hemaspaandra, Mitsunori Ogihara, Mohammed J. Zaki and Marius Zimand, The Complexity of Finding Top-Toda-Equivalence-Class Members. September 2006. (PDF) (BibTeX)
  2. Lane Hemaspaandra, Mitsunori Ogihara, Mohammed J. Zaki and Marius Zimand, The Complexity of Finding Top-Toda-Equivalence-Class Members. In Latin American Theoretical Informatics Conference. April 2004. (PDF) (BibTeX)
  3. Lane Hemaspaandra, Mohammed J. Zaki and Marius Zimand, Polynomial-Time Semi-Rankable Sets. Journal of Computing and Information, 2(1):50-67. June 1996. (PDF) (BibTeX)

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Robotics

  1. Olac Fuentes, Jonas Karlsson, Wagner Meira, Rajesh Rao, Terry Riopka, Justinian Rosca, Ramesh Sarukkai, Michael van Wie, Mohammed J. Zaki, Terry Becker, R. Frank, Bradford Miller and Chris M. Brown, Mobile Robotics 1994. Technical report Technical Report 588, University of Rochester May 1995. (PDF) (BibTeX)

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