Publications

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You can also find the code and data along with the full text below.

We gratefully acknowledge the funding from the following agencies and companies that made the research possible:

  • NSF

  • DOE Office of Science

  • NIH

  • DARPA

  • IBM (AI Horizon Network and AIRC)

  • HP (Innovation Research Award)

  • Google (Faculty Research Award)

  • NVIDIA (Academic Partnership Award)

You can also find my publications on googlescholar and dblp.

Books

dmmlbook dmabook psp dmb lspdm

Datasets

Publications

2020

  • Yu Chen, Lingfei Wu, and Mohammed J. Zaki. Deep iterative and adaptive learning for graph neural networks. In The First International Workshop on Deep Learning on Graphs: Methodologies and Applications (with AAAI). February 2020. *Best Student Paper Award*. URL: https://dlg2019.bitbucket.io/aaai20.
    [abstract▼] [full text] [Arxiv] [BibTeX▼]
  • Muhammad Abulaish, Ashraf Kamal, and Mohammed J. Zaki. A survey of figurative language and its computational detection in online social networks. ACM Transactions on the Web, January 2020. doi:10.1145/3375547.
    [abstract▼] [full text] [Kudos] [BibTeX▼]
  • Yu Chen, Lingfei Wu, and Mohammed J. Zaki. Reinforcement learning based graph-to-sequence model for natural question generation. In International Conference on Learning Representations (ICLR). April 2020. URL: https://arxiv.org/abs/1908.04942.
    [abstract▼] [full text] [githubcode] [BibTeX▼]
  • Jonathan J. Harris, Ching-Hua Chen, and Mohammed J. Zaki. A framework for generating explanations from temporal personal health data. CoRR, 2020. URL: https://arxiv.org/abs/2003.09530.
    [abstract▼] [githubcode] [BibTeX▼]
  • Nidhi Rastogi and Mohammed J. Zaki. Personal health knowledge graphs for patients. In Workshop on the Personal Health Knowledge Graph (with the Knowledge Graph Conference). May 2020.
    [full text] [BibTeX▼]
  • Yu Chen, Lingfei Wu, and Mohammed J. Zaki. GraphFlow: exploiting conversation flow with graph neural networks for conversational machine comprehension. In International Joint Conference on Artificial Intelligence (IJCAI). July 2020. URL: https://arxiv.org/abs/1908.00059.
    [abstract▼] [full text] [githubcode] [BibTeX▼]
  • Vipula Rawte, Aparna Gupta, and Mohammed J. Zaki. A comparative analysis of temporal long text similarity: application to financial documents. In Proceedings of The Fifth Workshop on MIning DAta for financial applicationS (with ECML-PKDD), MIDAS'20. September 2020.
    [full text] [BibTeX▼]
  • Vipula Rawte, Aparna Gupta, and Mohammed J. Zaki. Hierarchical contextual document embeddings forlong financial text regression. In Proceedings of the 3rd Workshop KDD Workshop on Machine Learning in Finance (with SIGKDD). August 2020.
    [full text] [BibTeX▼]
  • Yu Chen, Ching-Hua Chen, and Mohammed J. Zaki. Combining user preferences and health needs in personalized food recommendation. In Proceedings of the American Medical Informatics Association (AMIA) Virtual Annual Symposium, AMIA'20. November 2020.
    [full text] [BibTeX▼]
  • Nidhi Rastogi, Sharmishtha Dutta, Mohammed J. Zaki, Alex Gittens, and Charu Aggarwal. MALOnt: an ontology for malware threat intelligence. In Proceedings of MLHat: The First International Workshop on Deployable Machine Learning for Security Defense (with SIGKDD). August 2020.
    [full text] [BibTeX▼]
  • Diya Li and Mohammed J. Zaki. RECIPTOR: an effective pretrained model for recipe representation learning. In ACM SIGKDD International Conference on Data Mining and Knowledge Discovery. Aug 2020. doi:10.1145/3394486.3403223.
    [abstract▼] [full text] [githubcode] [BibTeX▼]

2019

  • Rodrigo L. Cardoso, Wagner Meira Jr, Virgilio Almeida, and Mohammed J. Zaki. A framework for benchmarking discrimination-aware models in machine learning. In AAAI/ACM Conference on AI, Ethics, and Society. January 2019.
    [full text] [BibTeX▼]
  • Yu Chen, Lingfei Wu, and Mohammed J. Zaki. Bidirectional attentive memory networks for question answering over knowledge bases. In Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL). June 2019.
    [full text] [githubcode] [BibTeX▼]
  • Yu Chen, Lingfei Wu, and Mohammed J. Zaki. Graphflow: exploiting conversation flow with graph neural networks for conversational machine comprehension. In ICML Workshop on Learning and Reasoning with Graph-Structured Representations. June 2019. URL: https://graphreason.github.io/papers.
    [full text] [BibTeX▼]
  • Steven Haussmann, Oshani Seneviratne, Yu Chen, Yarden Ne'eman, James Codella, Ching-Hua Chen, Deborah L. McGuinness, and Mohammed J. Zaki. Foodkg: a semantics-driven knowledge graph for food recommendation. In International Semantic Web Conference (Resources Track Full Paper). October 2019.
    [full text] [githubcode] [BibTeX▼]
  • Steven Haussmann, Yu Chen, Oshani Seneviratne, Nidhi Rastogi, James Codella, Ching-Hua Chen, Deborah L. McGuinness, and Mohammed J. Zaki. Foodkg enabled Q&A application. In International Semantic Web Conference (Demo Track). October 2019.
    [full text] [githubcode] [BibTeX▼]
  • Yu Chen, Lingfei Wu, and Mohammed J. Zaki. Reinforcement learning based graph-to-sequence model for natural question generation. In NeurIPS 2019 Workshop on Graph Representation Learning. December 2019. URL: https://grlearning.github.io/papers/.
    [full text] [BibTeX▼]

2018

  • Mohamed Elshrif, Stefano G. Rizzo, Franz D. Betz, Dragos D. Margineantu, Mohammed J. Zaki, and Sanjay Chawla. Embeddings for the identification of aircraft faults (merit). In IEEE International Conference on Prognostics and Health Management. Jun 2018.
    [full text] [BibTeX▼]
  • Vipula Rawte, Aparna Gupta, and Mohammed J. Zaki. Analysis of year-over-year changes in risk factors disclosure in 10-k filings. In Proceedings of the Fourth International Workshop on Data Science for Macro-Modeling with Financial and Economic Datasets, DSMM'18, 8:1–8:4. New York, NY, USA, 2018. ACM. doi:10.1145/3220547.3220555.
    [full text] [BibTeX▼]
  • Vipula Rawte, Aparna Gupta, and Mohammed J. Zaki. Using supervised learning techniques for entity relationships. In Proceedings of the Fourth International Workshop on Data Science for Macro-Modeling with Financial and Economic Datasets, DSMM'18, 13:1–13:2. New York, NY, USA, 2018. ACM. doi:10.1145/3220547.3226044.
    [full text] [BibTeX▼]
  • Xin Gao, Jake Y. Chen, and Mohammed J. Zaki. Multiscale and multimodal analysis for computational biology. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(6):1951–1952, 2018. doi:10.1109/TCBB.2018.2838658.
    [BibTeX▼]

2017

  • Eslam Hussain, Abdurrahman Ghanem, Vinicius Vitor dos Santos Dias, Carlos H.C. Teixeira, Ghadeer AbuOda, Marco Serafini, Georgos Siganos, Gianmarco De Francisci Morales, Ashraf Aboulnaga, and Mohammed J. Zaki. Graph data mining with arabesque. In Proceedings of the ACM SIGMOD International Conference on Management of Data (Demo Track). May 2017. doi:10.1145/3035918.3058742.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Closed itemset mining and non-redundant association rule mining. In Ling Liu and M. Tamer Ozsu, editors, Encyclopedia of Database Systems. Springer-Verlag, 2017. doi:10.1007/978-1-4899-7993-3_66-2.
    [full text] [BibTeX▼]
  • Yu Chen and Mohammed J. Zaki. Kate: k-competitive autoencoder for text. In ACM SIGKDD International Conference on Data Mining and Knowledge Discovery. Aug 2017. doi:10.1145/3097983.3098017.
    [full text] [githubcode] [BibTeX▼]
  • Yu Chen, Rhaad M. Rabbani, Aparna Gupta, and Mohammed J. Zaki. Comparative text analytics via topic modeling in banking. In IEEE Symposium on Computational Intelligence for Financial Engineering and Economics. 2017.
    [full text] [BibTeX▼]

2016

  • Geng Li and Mohammed J. Zaki. Sampling frequent and minimal boolean patterns: theory and application in classification. Data Mining and Knowledge Discovery, 30(1):181–225, January 2016. doi:10.1007/s10618-015-0409-y.
    [full text] [githubcode] [BibTeX▼]
  • Luam C. Totti, Prasenjit Mitra, Mourad Ouzzani, and Mohammed J. Zaki. A query-oriented approach for relevance in citation networks. In Proceedings of the 25th International Conference Companion on World Wide Web: 3rd WWW Workshop on Big Scholarly Data: Towards the Web of Scholars, 401–406. WWW, 2016. doi:10.1145/2872518.2890518.
    [full text] [data] [BibTeX▼]
  • Mirka Saarela, Bulent Yener, Mohammed J. Zaki, and Tommi Karkkainen. Predicting math performance from raw large-scale educational assessments data: a machine learning approach. In ICML Workshop on Machine Learning for Digital Education and Assessment Systems. 2016.
    [full text] [BibTeX▼]
  • Divyakant Agrawal, Sanjay Chawla, Ahmed Elmagarmid, Zoi Kaoudi, Mourad Ouzzani, Paolo Papotti, Jorge Quiane, Nan Tang, and Mohammed J. Zaki. Road to freedom in big data analytics. In Proceedings of the 19th International Conference on Extending Database Technology (EDBT). 2016.
    [full text] [BibTeX▼]
  • Aparna Gupta, Majeed Simaan, and Mohammed J. Zaki. When positive sentiment is not so positive: textual analytics and bank failures. Available at SSRN: Social Science Research Network, 2773939, 2016. doi:10.2139/ssrn.2773939.
    [full text] [BibTeX▼]
  • Aparna Gupta, Majeed Simaan, and Mohammed J. Zaki. Investigating bank failures using text mining. In IEEE Symposium Series on Computational Intelligence. 2016. doi:10.1109/SSCI.2016.7850006.
    [full text] [BibTeX▼]
  • Nilothpal Talukder and Mohammed J. Zaki. A distributed approach for graph mining in massive networks. Data Mining and Knowledge Discovery: Special Issue on ECML/PKDD 2016 Journal Track Papers, 30(5):1024–1052, 2016. doi:10.1007/s10618-016-0466-x.
    [full text] [githubcode] [data] [BibTeX▼]
  • Divy Agrawal, Mouhamadou Lamine Ba, Laure Berti-Equille, Sanjay Chawla, Ahmed K. Elmagarmid, Hossam Hammady, Yasser Idris, Zoi Kaoudi, Zuhair Khayyat, Sebastian Kruse, Mourad Ouzzani, Paolo Papotti, Jorge-Arnulfo Quiane-Ruiz, Nan Tang, and Mohammed J. Zaki. Rheem: enabling multi-platform task execution. In Proceedings of the ACM SIGMOD International Conference on Management of Data (Demo Track), 2069–2072. 2016. doi:10.1145/2882903.2899414.
    [full text] [BibTeX▼]
  • Nilothpal Talukder and Mohammed J. Zaki. Parallel graph mining with dynamic load balancing. In 3rd International Workshop on High Performance Big Graph Data Management, Analysis, and Mining (with IEEE Big Data Conference). Dec 2016.
    [full text] [BibTeX▼]

2015

  • Gesse Dafe, Adriano Veloso, Mohammed J. Zaki, and Wagner Meira Jr. Learning sequential classifiers from long and noisy discrete-event sequences efficiently. Data Mining and Knowledge Discovery, 29(6):1685–1708, November 2015. doi:10.1007/s10618-014-0391-9.
    [full text] [BibTeX▼]
  • Sarath Chandra Janga, Dongxiao Zhu, Jake Y. Chen, and Mohammed J. Zaki. Knowledge discovery using big data in biomedical systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(4):726–728, 2015. doi:10.1109/TCBB.2015.2454551.
    [BibTeX▼]
  • Carlos H. C. Teixeira, Alexandre J. Fonseca, Marco Serafini, Georgios Siganos, Mohammed J. Zaki, and Ashraf Aboulnaga. Arabesque: a system for distributed graph pattern mining. In Proceedings of the 25th ACM Symposium on Operating Systems Principles (SOSP). October 2015.
    [full text] [githubcode] [BibTeX▼]

2014

  • Rene Rodrigues Veloso, Loic Cerf, Wagner Meira Junior, and Mohammed J. Zaki. Reachability queries in very large graphs: a fast refined online search approach. In Proceedings of the 17th International Conference on Extending Database Technology (EDBT), 511–522. March 2014. doi:10.5441/002/edbt.2014.46.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Zoran Obradovic, Pang-Ning Tan, Arindam Banerjee, Chandrika Kamath, and Srinivasan Parthasarathy, editors. Proceedings of the 2014 SIAM International Conference on Data Mining, Philadelphia, Pennsylvania, USA, April 24-26, 2014, SIAM, 2014. doi:10.1137/1.9781611973440.
    [BibTeX▼]
  • Mohammed J. Zaki and Jr. Wagner Meira. Data Mining and Analysis: Fundamental Concepts and Algorithms. Cambridge University Press, 2014. ISBN 9780521766333. URL: http://www.dataminingbook.info.
    [BibTeX▼]
  • Robert Kessl, Nilothpal Talukder, Pranay Anchuri, and Mohammed J. Zaki. Parallel graph mining with GPUs. Proceedings of the 3rd International Workshop on Big Data, Streams and Heterogeneous Source Mining: Algorithms, Systems, Programming Models and Applications (with SIGKDD'14), Journal of Machine Learning Research: Conference and Workshop Proceedings, 36:1–36, 2014. URL: http://jmlr.org/proceedings/papers/v36/.
    [full text] [githubcode] [BibTeX▼]
  • Benjarath Pupacdi, Asif Javed, Mohammed J. Zaki, and Mathuros Ruchirawat. NSIT: novel sequence identification tool. PLoS ONE, 9(9):e108011, 2014. doi:10.1371/journal.pone.0108011.
    [full text] [BibTeX▼]

2013

  • Gaurav Pandey, Huzefa Rangwala, George Karypis, Jake Yue Chen, and Mohammed J. Zaki, editors. Proceedings of the 12th International Workshop on Data Mining in Bioinformatics, BIOKDD 2013, Chicago, IL, USA, August 11, 2013, ACM, 2013. URL: http://dl.acm.org/citation.cfm?id=2500863.
    [BibTeX▼]
  • Hilmi Yildirim, Vineet Chaoji, and Mohammed J. Zaki. Dagger: a scalable index for reachability queries in large dynamic graphs. arXiv Computing Research Repository, 2013. URL: http://arxiv.org/abs/1301.0977.
    [full text] [githubcode] [data] [BibTeX▼]
  • Geng Li, Stephan Gunnemann, and Mohammed J. Zaki. Stochastic subspace search for top-k multi-view clustering. In 4th MultiClust Workshop on Multiple Clusterings, Multi-view Data, and Multi-source Knowledge-driven Clustering (with SIGKDD'13). August 2013.
    [full text] [BibTeX▼]
  • Arlei Silva, Sara Guimaraes, Wagner Meira Jr., and Mohammed J. Zaki. Profilerank: finding relevant content and influential users based on information diffusion. In The 7th SNAKDD Workshop on Social Network Mining and Analysis (with SIGKDD'13). August 2013.
    [full text] [BibTeX▼]
  • Pranay Anchuri, Mohammed J. Zaki, Omer Barkol, Shahar Golan, and Moshe Shamy. Approximate graph mining with label costs. In 19th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2013. URL: http://dl.acm.org/citation.cfm?doid=2487575.2487602.
    [full text] [BibTeX▼]
  • Chandan K. Reddy, Mohammad Al Hasan, and Mohammed J. Zaki. Clustering biological data. In Charu C. Aggarwal and Chandan K. Reddy, editors, Data Clustering: Algorithms and Applications, pages 381–414. CRC Press, 2013.
    [BibTeX▼]
  • Apirak Hoonlor, Boleslaw K. Szymanski, and Mohammed J. Zaki. Trends in computer science research. Communications of the ACM, 56(10):74–83, October 2013. doi:10.1145/2500892.
    [full text] [BibTeX▼]

2012

  • Tamer Kahveci, Saeed Salem, Mehmet Koyuturk, Jake Yue Chen, and Mohammed J. Zaki, editors. Proceedings of the 11th International Workshop on Data Mining in Bioinformatics, BIOKDD 2012, Beijing, China, August 12, 2012, ACM, 2012. URL: http://dl.acm.org/citation.cfm?id=2350176.
    [BibTeX▼]
  • Vibin Ramakrishnan, Sai Praveen Srinivasan, Saeed Salem, Suzanne Matthews, Wilfredo Colon, Mohammed J. Zaki, and Chris Bystroff. GeoFold: topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability. Proteins: Structure, Function, and Bioinformatics, 80(3):920–934, March 2012. doi:10.1002/prot.23249/full.
    [full text] [BibTeX▼]
  • Arlei Silva, Mohammed J. Zaki, and Wagner Meira Jr. Mining attribute-structure correlated patterns in large attributed graphs. PVLDB, 5(5):466–477, 2012.
    [full text] [githubcode] [data] [BibTeX▼]
  • Glivia A.R. Barbosa, Wagner Meira, Ismail A. Silva, Raquel O. Prates, Mohammed J. Zaki, and Adriano Veloso. Characterizing the effectiveness of twitter hashtags to detect and track online population sentiment. In ACM SIGCHI Conference on Human Factors in Computing Systems – Juried Works-in-Progress. May 2012.
    [full text] [BibTeX▼]
  • Medha Atre, Vineet Chaoji, and Mohammed J. Zaki. Bitpath – label order constrained reachability queries over large graphs. arXiv Computing Research Repository, 2012. URL: http://arxiv.org/abs/1203.2886.
    [full text] [BibTeX▼]
  • Mohammad Al Hasan, Jun Huan, Jake Y. Chen, and Mohammed J. Zaki. Biological knowledge discovery and data mining. Scientific Programming, 20(1):1–2, 2012.
    [full text] [BibTeX▼]
  • Geng Li, Murat Semerci, Bulent Yener, and Mohammed J. Zaki. Effective graph classification based on topological and label attributes. Statistical Analysis and Data Mining, 5(4):265–283, August 2012. doi:10.1002/sam.11153.
    [full text] [BibTeX▼]
  • Hilmi Yildirim, Vineet Chaoji, and Mohammed J. Zaki. Grail: a scalable index for reachability queryies in very large graphs. The VLDB Journal, 21(4):509–534, August 2012. doi:10.1007/s00778-011-0256-4.
    [full text] [githubcode] [data] [BibTeX▼]
  • Geng Li and Mohammed J. Zaki. Sampling minimal frequent boolean (dnf) patterns. In 18th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2012.
    [full text] [githubcode] [BibTeX▼]
  • Pranay Anchuri, Mohammed J. Zaki, Omer Barkol, Ruth Bergman, Yifat Felder, Shahar Golan, and Arik Sityon. Graph mining for discovering infrastructure patterns in configuration management databases. Knowledge and Information Systems, 33(3):491–522, December 2012. doi:10.1007/s10115-012-0528-3.
    [full text] [BibTeX▼]
  • Helio Almeida, Dorgival Olavo Guedes Neto, Wagner Meira Jr., and Mohammed J. Zaki. Towards a better quality metric for graph cluster evaluation. Journal of Information and Data Management, 3(3):378–393, October 2012.
    [full text] [BibTeX▼]
  • Apirak Hoonlor, Boleslaw K. Szymanski, Mohammed J. Zaki, and Vineet Chaoji. Document clustering with bursty information. Computing and Informatics, 31(6+):1533–1555, 2012.
    [full text] [BibTeX▼]
  • Xue-wen Chen, Guy Lebanon, Haixun Wang, and Mohammed J. Zaki, editors. 21st ACM International Conference on Information and Knowledge Management, CIKM'12, Maui, HI, USA, October 29 - November 02, 2012, ACM, 2012. URL: http://dl.acm.org/citation.cfm?id=2396761.
    [BibTeX▼]
  • Mohammed J. Zaki, Arno Siebes, Jeffrey Xu Yu, Bart Goethals, Geoffrey I. Webb, and Xindong Wu, editors. 12th IEEE International Conference on Data Mining, ICDM 2012, Brussels, Belgium, December 10-13, 2012, IEEE Computer Society, 2012. URL: http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6412852.
    [BibTeX▼]
  • Jilles Vreeken, Charles Ling, Mohammed J. Zaki, Arno Siebes, Jeffrey Xu Yu, Bart Goethals, Geoffrey I. Webb, and Xindong Wu, editors. 12th IEEE International Conference on Data Mining Workshops, ICDM Workshops, Brussels, Belgium, December 10, 2012, IEEE Computer Society, 2012. URL: http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6403636.
    [BibTeX▼]

2011

  • Vineet Chaoji, Geng Li, Hilmi Yildirim, and Mohammed J. Zaki. ABACUS: mining arbitrary shaped clusters from large datasets based on backbone identification. In 11th SIAM International Conference on Data Mining. April 2011.
    [full text] [BibTeX▼]
  • Elisa B. de Lima, Raquel C. Minardi, Jr. Wagner Meira, and Mohammed J. Zaki. Data integration via constrained clustering: an application to enzyme clustering. In 11th SIAM International Conference on Data Mining. April 2011.
    [full text] [BibTeX▼]
  • Adriano Veloso, Jr. Wagner Meira, Macros Goncalves, Humberto Almeida, and Mohammed J. Zaki. Calibrated lazy associative classification. Information Sciences, 181(13):2656–2670, July 2011.
    [full text] [BibTeX▼]
  • Mohammad Al Hasan and Mohammed J. Zaki. A survey of link prediction in social networks. In Charu Aggarwal, editor, Social Network Data Analytics, chapter 9, pages 243–275. Springer, 2011.
    [full text] [BibTeX▼]
  • Geng Li, Murat Semerci, Bulent Yener, and Mohammed J. Zaki. Graph classification via topological and label attributes. In 9th Workshop on Mining and Learning with Graphs (with SIGKDD). August 2011.
    [full text] [BibTeX▼]
  • Helio Almeida, Dorgival Olavo Guedes Neto, Wagner Meira Jr., and Mohammed J. Zaki. Is there a best quality metric for graph clusters? In 15th European Conference on Principles and Practice of Knowledge Discovery in Databases. September 2011.
    [full text] [BibTeX▼]
  • Pranay Anchuri, Mohammed J. Zaki, Omer Barkol, Ruth Bergman, Yifat Felder, Shahar Golan, and Arik Sityon. Infrastructure pattern discovery in configuration management databases via large sparse graph mining. In 11th IEEE International Conference on Data Mining. December 2011. *Best Papers Selection*.
    [full text] [BibTeX▼]
  • Mohammad Al Hasan, Saeed Salem, and Mohammed J. Zaki. Simclus: an effective algorithm for clustering with a lower bound on similarity. Knowledge and Information Systems, 28(3):665–685, 2011.
    [full text] [BibTeX▼]
  • Mohammad Al Hasan, Jun Huan, Jake Y. Chen, and Mohammed J. Zaki, editors. Proceedings of BIOKDD11: 10th ACM SIGKDD International Workshop on Data Mining in Bioinformatics, 2011. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD11/.
    [full text] [BibTeX▼]
  • Fang-Xiang Wu, Mohammed J. Zaki, Shinichi Morishita, Yi Pan, Stephen Wong, Anastasia Christianson, and Xiaohua Hu, editors. IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, Atlanta, GA, USA, 12-15 November, 2011, IEEE, 2011. URL: http://ieeexplore.ieee.org/xpl/mostRecentIssue.jsp?punumber=6120121.
    [BibTeX▼]

2010

  • 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, 4(1):Article 5, January 2010.
    [full text] [githubcode] [BibTeX▼]
  • Saeed Salem, Mohammed J. Zaki, and Chris Bystroff. FlexSnap: flexible non-sequential protein structure alignment. Algorithms in Molecular Biology, January 2010. Special issue on best papers from WABI'09. URL: http://www.almob.org/content/5/1/12.
    [full text] [BibTeX▼]
  • 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, February 2010. Special issue on Intelligent Data Analysis. doi:10.1016/j.jcss.2009.05.008.
    [full text] [githubcode] [BibTeX▼]
  • Medha Atre, Vineet Chaoji, Mohammed J. Zaki, and James A. Hendler. Matrix bit loaded: a scalable lightweight join query processor for rdf data. In 19th International World Wide Web Conference. April 2010.
    [full text] [BibTeX▼]
  • Jierui Xie, Boleslaw Szymanski, and Mohammed J. Zaki. Learning dissimilarities for categorical symbols. In Workshop on Feature Selection in Data Mining (with PAKDD). June 2010. URL: http://jmlr.csail.mit.edu/proceedings/papers/v10/.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Jeffrey X. Yu, B. Ravindran, and Vikram Pudi. Advances in Knowledge Discovery and Data Mining, Part I, Proceedings of the 14th Pacific-Asia Conference (PAKDD 2010). Volume 6118 of LNAI. Springer, 2010. ISBN: 978-3-642-13656-6. URL: http://www.springerlink.com/content/978-3-642-13656-6/.
    [BibTeX▼]
  • Mohammed J. Zaki, Jeffrey X. Yu, B. Ravindran, and Vikram Pudi. Advances in Knowledge Discovery and Data Mining, Part II, Proceedings of the 14th Pacific-Asia Conference (PAKDD 2010). Volume 6119 of LNAI. Springer, 2010. ISBN: 978-3-642-13671-9. URL: http://www.springerlink.com/content/978-3-642-13671-9/.
    [BibTeX▼]
  • Mohammed J. Zaki. Practical graph mining. In 18th International Conference on Conceptual Structures, 13. 2010. doi:10.1007/978-3-642-14197-3_5.
    [BibTeX▼]
  • Arlei Silva, Jr. Wagner Meira, and Mohammed J. Zaki. Structural correlation pattern mining for large graphs. In 8th Workshop on Mining and Learning with Graphs (with SIGKDD). July 2010.
    [full text] [githubcode] [data] [BibTeX▼]
  • Saeed Salem, Khedidja Seridi, Loqmane Seridi, Jianfei Wu, and Mohammed J. Zaki. Voknn: voting-based nearest neighbor approach for scalable svm training. In 2nd Workshop on Large-scale Data Mining: Theory and Applications (with SIGKDD). July 2010.
    [full text] [BibTeX▼]
  • Jun Huan, Jake Y. Chen, and Mohammed J. Zaki, editors. Proceedings of BIOKDD10: ACM SIGKDD International Workshop on Data Mining in Bioinformatics. Selected papers available as special issue of BMC Bioinformatics (http://www.biomedcentral.com/bmcbioinformatics/supplements/12/S12), 2010. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD10/.
    [full text] [BibTeX▼]
  • Hilmi Yildirim, Vineet Chaoji, and Mohammed J. Zaki. Grail: scalable reachability index for large graphs. Proceedings of the VLDB Endowment (36th International Conference on Very Large Data Bases), 3(1):276–284, 2010.
    [full text] [githubcode] [data] [BibTeX▼]
  • Neha Goel, Michael S. Hsiao, Naren Ramakrishnan, and Mohammed J. Zaki. Mining complex boolean expressions for sequential equivalence checking. In Proceedings of the 19th Asian Test Symposium, Shanghai, China. December 2010.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Naren Ramakrishnan, and Lizhuang Zhao. Mining frequent boolean expressions: application to gene expression and regulatory modeling. International Journal of Knowledge Discovery in Bioinformatics, 1(3):68–96, September 2010. Special issue on Mining Complex Structures in Biology.
    [full text] [githubcode] [BibTeX▼]

2009

  • Naren Ramakrishnan and Mohammed J. Zaki. Redescription mining and applications in bioinformatics. In Jake Chen and Stefano Lonardi, editors, Biological Data Mining. CRC Press, 2009. URL: http://www.crcpress.com/product/isbn/9781420086843.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Closed itemset mining and non-redundant association rule mining. In Ling Liu and M. Tamer Ozsu, editors, Encyclopedia of Database Systems. Springer-Verlag, 2009. URL: http://www.springer.com/978-0-387-49616-0.
    [full text] [BibTeX▼]
  • Saeed Salem, Mohammed J. Zaki, and Chris Bystroff. FlexSnap: flexible non-sequential protein structure alignment. In 9th Workshop on Algorithms in Bioinformatics. September 2009. *Best Papers Selection*.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Mohammad Al Hasan and Mohammed J. Zaki. Output space sampling for graph patterns. Proceedings of the VLDB Endowment (35th International Conference on Very Large Data Bases), 2(1):730–741, 2009.
    [full text] [BibTeX▼]
  • Adriano Veloso, Mohammed J. Zaki, Jr. Wagner Meira, and Marcos Goncalves. The metric dilemma: competence-conscious associative classification. In 9th SIAM International Conference on Data Mining. April 2009.
    [full text] [BibTeX▼]
  • Mohammad Al Hasan and Mohammed J. Zaki. Musk: uniform sampling of k maximal patterns. In 9th SIAM International Conference on Data Mining. April 2009. *Best Paper Runner-Up*.
    [full text] [githubcode] [BibTeX▼]
  • 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. doi:10.1016/j.patrec.2009.04.013.
    [full text] [BibTeX▼]
  • John Elder, Francoise Soulie Fogelman, Peter Flach, and Mohammed J. Zaki, editors. Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining, ACM, June 2009. ISBN:978-1-60558-495-9. URL: http://portal.acm.org/toc.cfm?id=1557019.
    [BibTeX▼]
  • 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. *Best Paper Award*.
    [full text] [BibTeX▼]
  • 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. Special issue on the best of CSB'08. doi:10.1142/S0219720009004205.
    [full text] [BibTeX▼]
  • 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, 21(2):201–229, November 2009. Invited: best papers of ICDM'08. doi:10.1007/s10115-009-0216-0.
    [full text] [BibTeX▼]
  • Amanda W. Lund, Cagatay C. Bilgin, Mohammed Al Hasan, Lindsey M. McKeen, Jan P. Stegeman, 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: http://www.hindawi.com/journals/jbb/2009/928286.html, doi:10.1155/2009/928286.
    [full text] [BibTeX▼]
  • Amir H. Qureshi, Vineet Chaoji, Dony Maiguel, Hafeez Faridi, Constantinos Barth, Erliang Zheng, Jeremy Besson, Saeed M. Salem, Mudita Singhal, David Sarracino, Bryan Krastins, 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, 4(10):e7627, 2009. doi:10.1371/journal.pone.0007627.
    [full text] [BibTeX▼]
  • Peter A. Flach, Sebastian Spiegler, Simon Price Bruno Golenia, John Guiver, Ralf Hebrich, Thore Graepel, and Mohammed J. Zaki. Novel tools to streamline the conference review process: experiences from sigkdd'09. SIGKDD Explorations, 11(2):63–67, December 2009. URL: http://www.sigkdd.org/explorations/issue.php?volume=11&issue=2&year=2009&month=12.
    [full text] [BibTeX▼]

2008

  • Mohammed J. Zaki, Naren Ramakrishnan, and Srinivasan Parthasarathy. Editorial: biological data mining. Scientific Programming, 16(1):3, 2008.
    [full text] [BibTeX▼]
  • Stefano Lonardi, Jake Y. Chen, and Mohammed J. Zaki, editors. Proceedings of BIOKDD08: ACM SIGKDD International Workshop on Data Mining in Bioinformatics, 2008. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD08/.
    [full text] [BibTeX▼]
  • Zujun Shentu, Mohammad Al Hasan, Chris Bystroff, and Mohammed J. Zaki. Context Shapes: efficient complementary shape matching for protein-protein docking. Proteins: Structure, Function and Bioinformatics, 70(3):1056–1073, February 2008. doi:10.1002/prot.21600.
    [full text] [githubcode] [BibTeX▼]
  • 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. doi:10.1007/s10618-008-0098-x.
    [full text] [githubcode] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Adriano Veloso, Jr. Wagner Meira, and Mohammed J. Zaki. Calibrated lazy associative classification. In Brazilian Symposium on Databases. October 2008. *Best Paper Runner-Up*.
    [full text] [BibTeX▼]
  • 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. doi:10.1002/sam.10004.
    [full text] [githubcode] [BibTeX▼]
  • 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. Special issue on SBAC-PAD 2006. doi:10.1007/s10766-007-0067-9.
    [full text] [BibTeX▼]
  • Feng Gao and Mohammed J. Zaki. Indexing protein structures using suffix trees. In Mohammed J. Zaki and Chris Bystroff, editors, Protein Structure Prediction, Methods in Molecular Biology 413, chapter 6, pages 147–169. Springer/Humana Press, second edition edition, 2008.
    [full text] [githubcode] [BibTeX▼]
  • 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. Special issue on Parallel Techniques for Information Extraction. doi:10.1016/j.jpdc.2007.07.008.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki and Chris Bystroff. Protein Structure Prediction. Methods in Molecular Biology 413. Humana Press/Springer (http://www.springer.com/978-1-58829-752-5), second edition edition, 2008. URL: http://www.cs.rpi.edu/~zaki/Books/prot-book/.
    [BibTeX▼]
  • Mohammed J. Zaki and Ke Wang. Editorial: special issue on the best papers of sdm'08. Statistical Analysis and Data Mining, 1(3):109–110, November 2008. doi:10.1002/sam.10010.
    [full text] [BibTeX▼]
  • Chid Apte, Haesun Park, Ke Wang, and Mohammed J. Zaki, editors. Proceedings of the 2008 SIAM International Conference on Data Mining, Society for Industrial and Applied Mathematics, Philadelphia, PA, April 2008. ISBN:978-0-89871-654-2. URL: http://www.siam.org/proceedings/datamining/2008/dm08.php.
    [BibTeX▼]
  • Saeed Salem and Mohammed J. Zaki. Iterative non-sequential protein structural alignment. In 7th Annual International Conference on Computational Systems Bioinformatics. August 2008. *Best Papers Selection*.
    [full text] [BibTeX▼]
  • 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. *Best Papers Selection*.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, George Karypis, Jiong Yang, and Wei Wang. Introduction to special issue on bioinformatics. ACM Transactions on Knowledge Discovery from Data, March 2008. doi:10.1145/1342320.1342321.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]

2007

  • Jake Y. Chen, Stefano Lonardi, and Mohammed J. Zaki, editors. Proceedings of BIOKDD07: ACM SIGKDD International Workshop on Data Mining in Bioinformatics, 2007. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD07/.
    [full text] [BibTeX▼]
  • 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. Special issue on Intelligent Data Mining. doi:10.1016/j.datak.2006.01.005.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki, George Karypis, and Jiong Yang. Editorial: data mining in bioinformatics. Algorithms for molecular biology, 2007. URL: http://www.almob.org/content/2/1/4, doi:10.1186/1748-7188-2-4.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Adriano Veloso, Jr. Wagner Meira, Marcos Golcalves, and Mohammed J. Zaki. Multi-label lazy associative classification. In 11th European Conference on Principles and Practice of Knowledge Discovery. September 2007.
    [full text] [BibTeX▼]
  • 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. *Best Papers Selection*.
    [full text] [githubcode] [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]
  • Karlton Sequeira and Mohammed J. Zaki. Exploring similarities across high-dimensional datasets. In David Taniar, editor, Research and Trends in Data Mining Technologies and Applications, chapter 3, pages 53–85. Idea Group, Inc., 2007.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. A unified approach to rooted tree mining: algorithms and applications. In Larry Holder and Diane Cook, editors, Mining Graph Data, chapter 15, pages 381–410. John Wiley and Sons, Inc., 2007.
    [full text] [BibTeX▼]
  • Benjarath Phoophakdee and Mohammed J. Zaki. Genome-scale disk-based suffix tree indexing. In ACM SIGMOD International Conference on Management of Data. June 2007.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]

2006

  • 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. doi:10.1007/s10618-006-0041-y.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, George Karypis, and Jiong Yang, editors. Proceedings of BIOKDD06: ACM SIGKDD Workshop on Data Mining in Bioinformatics, 2006. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD06/.
    [full text] [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]
  • Yongqiang Zhang and Mohammed J. Zaki. Exmotif: efficient structured motif extraction. In 6th SIGKDD Workshop on Data Mining in Bioinformatics. August 2006. *Best Papers Selection*.
    [full text] [BibTeX▼]
  • Yongqiang Zhang and Mohammed J. Zaki. Exmotif: efficient structured motif extraction. Algorithms for molecular biology, November 2006. URL: http://www.almob.org/content/1/1/21, doi:10.1186/1748-7188-1-21.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, George Karypis, and Jiong Yang. Biokdd06: data mining in bioinformatics. SIGKDD Explorations, 8(2):78, December 2006.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki and Karlton Sequeira. Data mining in computational biology. In Srinivas Aluru, editor, Handbook of Computational Molecular Biology, Computer and Information Science Series, chapter 38, pages 38/1–38/26. Chapman & Hall/CRC Press, 2006.
    [full text] [BibTeX▼]
  • 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. *Best Paper Honorable Mention*.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Richi Nayak and Mohammed J. Zaki. Knowledge Discovery from XML Documents. Volume 3915 of Lecture Notes in Computer Science. Spring-Verlag, 2006. ISBN: 3-540-33180-8. URL: http://www.springerlink.com/content/l35p30431757/.
    [BibTeX▼]
  • Adriano Veloso, Jr. Wagner Meira, and Mohammed J. Zaki. Lazy Associative Classification. In 6th IEEE International Conference on Data Mining. December 2006.
    [full text] [BibTeX▼]
  • Adriano Veloso, Jr. Wagner Meira, 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Yongqiang Zhang and Mohammed J. Zaki. Smotif: efficient structured pattern and profile motif search. Algorithms for molecular biology, November 2006. URL: http://www.almob.org/content/1/1/22, doi:10.1186/1748-7188-1-22.
    [full text] [BibTeX▼]
  • Lane Hemaspaandra, Mitsunori Ogihara, Mohammed J. Zaki, and Marius Zimand. The complexity of finding top-toda-equivalence-class members. Theory of Computing Systems, 39(5):669–684, September 2006. doi:10.1007/s00224-005-1211-9.
    [full text] [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]
  • 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. Special issue on Statistical Relational Learning and Multi-Relational Data Mining. doi:10.1007/s10994-006-5832-2.
    [full text] [githubcode] [BibTeX▼]

2005

  • Shunsuke Uemura, Akifumi Makinouchi, and Mohammed J. Zaki, editors. Proceedings of the IEEE International Workshop on Biomedical Data Engineering (BDME:with ICDE), IEEE Xplore Digital Library, April 2005. URL: http://ieeexplore.ieee.org/xpl/tocresult.jsp?isnumber=34556&isYear=2005.
    [BibTeX▼]
  • Srinivasan Parthasarathy, Wei Wang, and Mohammed J. Zaki, editors. Proceedings of BIOKDD05: ACM SIGKDD International Workshop on Data Mining in Bioinformatics, ACM Digital Library (http://portal.acm.org/toc.cfm?id=1134030), 2005. ISBN:1-59593-213-5. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD05/.
    [full text] [BibTeX▼]
  • 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. doi:10.1109/69.846291.
    [full text] [CHARMcode] [CHARM-Lcode] [BibTeX▼]
  • Mohammed J. 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 on Knowledge Discovery and Data Mining. August 2005.
    [full text] [githubcode] [BibTeX▼]
  • Markus Peters and Mohammed J. Zaki. CLICKS: clustering categorical data using k-partite maximal cliques. In 21st IEEE International Conference on Data Engineering. April 2005.
    [full text] [githubcode] [BibTeX▼]
  • Jason T. L. Wang, Mohammed J. Zaki, Hannu T. T. Toivonen, and Dennis Shasha. Data Mining in Bioinformatics. Springer-Verlag London, UK (http://www.springer.com/978-1-85233-671-4), 2005. URL: http://www.cs.rpi.edu/~zaki/Books/biokdd-book/.
    [BibTeX▼]
  • 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 Heikki Mannila Jean-Francois Boulicaut, Luc De Raedt, editor, Constraint-Based Mining, volume 3848 of LNAI State-of-the-Art Survey, pages 362–279. Springer-Verlag, 2005.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Srinivasan Parthasarathy, Wei Wang, and Mohammed J. Zaki. Biokdd 2005 workshop report. SIGKDD Explorations, 7(2):129–131, December 2005.
    [full text] [BibTeX▼]
  • Bart Goethals, Siegfried Nijssen, and Mohammed J. Zaki. Open source data mining: workshop report. SIGKDD Explorations, 7(2):143–144, December 2005.
    [full text] [BibTeX▼]
  • 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. doi:10.1007/s10618-005-0002-x.
    [full text] [githubcode] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Mining maximal and closed frequent itemsets. In Mehmet Kantardzic and Jozef Zurada, editors, New Generation of Data Mining Applications, chapter 23, pages 571–598. IEEE/Wiley Press, 2005.
    [full text] [BibTeX▼]
  • Lizhuang Zhao and Mohammed J. Zaki. Microcluster: an efficient deterministic biclustering algorithm for microarray data. IEEE Intelligent Systems, 20(6):40–49, Nov/Dec 2005. Special issue on Data Mining for Bioinformatics.
    [full text] [githubcode] [BibTeX▼]
  • Bart Goethals, Siegfried Nijssen, and Mohammed J. Zaki, editors. Proceedings of the 1st ACM SIGKDD International workshop on open source data mining: frequent pattern mining implementations, ACM Digital Library (http://portal.acm.org/toc.cfm?id=1133905), 2005. ISBN:1-59593-210-0. URL: http://www.cs.rpi.edu/~zaki/Workshops/OSDM05.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, and Chris Bystroff. Predicting protein folding pathways. In Jason Wang, Mohammed Zaki, Hannu Toivonen, and Dennis Shasha, editors, Data Mining in Bioinformatics, pages 127–141. Springer-Verlag London Ltd., 2005.
    [full text] [BibTeX▼]
  • Feng Gao and Mohammed J. Zaki. PSIST: indexing protein structures using suffix trees. In IEEE Computational Systems Bioinformatics Conference. August 2005.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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. doi:10.1504/IJBIDM.2005.008360.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki. Efficiently mining frequent embedded unordered trees. Fundamenta Informaticae, 66(1-2):33–52, Mar/Apr 2005. Special issue on Advances in Mining Graphs, Trees and Sequences.
    [full text] [githubcode] [BibTeX▼]
  • 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. Special issue on Mining Biological Data. doi:10.1109/TKDE.2005.125.
    [full text] [githubcode] [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]

2004

  • Mohammed J. Zaki, Shinichi Morishita, and Isidore Rigoutsos, editors. Proceedings of BIOKDD04: ACM SIGKDD International Workshop on Data Mining in Bioinformatics, 2004. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD04/.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Jingjing Hu, and Chris Bystroff. Methods for mining protein contact maps. In K. Sivakumar H. Kargupta, A. Joshi and Y. Yesha, editors, Data Mining: Next Generation Challenges and Future Directions, chapter 16, pages 291–314. AAAI/MIT Press, 2004.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Bart Goethals and Mohammed J. Zaki. Advances in frequent itemset mining implementations: report on FIMI'03. SIGKDD Explorations, 6(1):109–117, June 2004.
    [full text] [BibTeX▼]
  • Roberto Bayardo, Bart Goethals, and Mohammed J. Zaki, editors. Proceedings of the 2nd IEEE ICDM Workshop on Frequent Itemset Mining Implementations, CEUR Workshop Proceedings, 2004. URL: http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-126/.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Data mining. In William S. Bainbridge, editor, The Encyclopedia of Human-Computer Interaction, pages 149–152. Berkshire Publishing Group, 2004.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Mining non-redundant association rules. Data Mining and Knowledge Discovery: An International Journal, 9(3):223–248, November 2004.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Vinay Nadimpally, Deb Bardhan, and Chris Bystroff. Predicting protein folding pathways. Bioinformatics, 20(1):i386–i393, August 2004. Supplement on the Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki and Limsoon Wong. Data mining techniques. In Limsoon Wong and Louxin Zhang, editors, Selected Topics in Post-Genome Knowledge Discovery, pages 125–163. World Scientific Publishers, 2004.
    [full text] [BibTeX▼]
  • Karlton Sequeira and Mohammed J. Zaki. SCHISM: a new approach for interesting subspace mining. In 4th IEEE International Conference on Data Mining. November 2004.
    [full text] [githubcode] [BibTeX▼]
  • Amir H. Youssefi, David J. Duke, and Mohammed J. Zaki. Visual web mining. In 13th International World Wide Web Conference (Poster). May 2004.
    [full text] [BibTeX▼]

2003

  • Mohammed J. Zaki, Hannu Toivonen, and Jason Wang, editors. Proceedings of BIOKDD03: ACM SIGKDD International Workshop on Data Mining in Bioinformatics, 2003. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD03/.
    [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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. Special issue on Bioengineering and Bioinformatics.
    [full text] [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki and Charu C. Aggarwal, editors. Proceedings of the 8th ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery, June 2003. also as RPI Technical Report 03-05. URL: http://www.cs.rpi.edu/~zaki/Workshops/DMKD03/.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Hannu Toivonen, and Jason Wang. Data mining in bioinformatics: report on biokdd'03. SIGKDD Explorations, 5(2):119–120, December 2003.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Bart Goethals and Mohammed J. Zaki, editors. Proceedings of the 1st IEEE ICDM Workshop on Frequent Itemset Mining Implementations, CEUR Workshop Proceedings, 2003. Also as RPI Technical Report 03-04. URL: http://sunsite.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-90/.
    [full text] [BibTeX▼]
  • 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. Special issue on Microarray Data Analysis.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Mining data in bioinformatics. In Nong Ye, editor, Handbook of Data Mining, pages 573–596. Lawrence Earlbaum Associates, 2003.
    [full text] [BibTeX▼]
  • Adriano Veloso, Jr. Wagner Meira, 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki and Jason T.L. Wang. Editorial: data management in bioinformatics. Information Systems: An International Journal, 28(4):241–242, June 2003.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]

2002

  • Karlton Sequeira and Mohammed J. Zaki. Admit: anomaly-base data mining for intrusions. In 8th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. July 2002.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Hannu Toivonen, and Jason Wang, editors. Proceedings of BIOKDD02: ACM SIGKDD International Workshop on Data Mining in Bioinformatics, 2002. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD02/.
    [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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. doi:10.1023/A:1013918601668.
    [full text] [BibTeX▼]
  • Adriano Veloso, Bruno Gusmao, Jr. Wagner Meira, 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.
    [full text] [BibTeX▼]
  • Adriano Veloso, Jr. Wagner Meira, 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Hannu Toivonen, and Jason Wang. Recent advances in data mining in bioinformatics. SIGKDD Explorations, 4(2):112–114, December 2002.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Editorial: online, interactive and anytime data mining. SIGKDD Explorations, 3(2):i–ii, January 2002. URL: http://www.sigkdd.org/explorations/issue.php?volume=3&issue=2&year=2002&month=01.
    [full text] [BibTeX▼]
  • John Punin, Mukkai Krishnamoorthy, and Mohammed J. Zaki. Web usage mining: languages and algorithms. In M. Schwaiger and O. Opitz, editors, Explanatory Data Analysis in Empirical Research, Studies in Classification, Data Analysis, and Knowledge Organization, pages 266–281. Springer-Verlag, 2002.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Efficiently mining frequent trees in a forest. In 8th ACM SIGKDD International Conference Knowledge Discovery and Data Mining. July 2002.
    [full text] [githubcode] [BibTeX▼]

2001

  • Mohammed J. Zaki, Hannu Toivonen, and Jason Wang, editors. Proceedings of BIOKDD01: ACM SIGKDD International Workshop on Data Mining in Bioinformatics, 2001. URL: http://www.cs.rpi.edu/~zaki/Workshops/BIOKDD01/.
    [BibTeX▼]
  • Mohammed J. Zaki and Chris Bystroff. Mining residue contacts in proteins. In R. Grossman, C. Kamath, P. Kegelmeyer, V. Kumar, and R. Namburu, editors, Data Mining for Scientific and Engineering Applications, pages 141–164. Kluwer Academic Publishers, Boston, MA, 2001.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Hannu Toivonen, and Jason Wang. Biokdd01: workshop on data mining in bioinformatics. SIGKDD Explorations, 3(2):71–73, February 2001.
    [full text] [BibTeX▼]
  • Karam Gouda and Mohammed J. Zaki. Efficiently mining maximal frequent itemsets. In 1st IEEE International Conference on Data Mining. November 2001.
    [full text] [githubcode] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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. doi:10.1007/PL00011656.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Vipin Kumar, and David Skillicorn, editors. Proceedings of Workshop on Parallel and Distributed Data Mining, 2001. URL: http://www.cs.rpi.edu/~zaki/Workshops/PDDM01.
    [full text] [BibTeX▼]
  • 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, editors, Data Mining for Scientific and Engineering Applications, pages 141–164. Kluwer Academic Publishers, Boston, MA, 2001.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Parallel sequence mining on shared-memory machines. Journal of Parallel and Distributed Computing, 61(3):401–426, March 2001. Special issue on High Performance Data Mining.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. SPADE: an efficient algorithm for mining frequent sequences. Machine Learning Journal, 42(1/2):31–60, Jan/Feb 2001. Special issue on Unsupervised Learning. doi:10.1023/A:1007652502315.
    [full text] [githubcode] [BibTeX▼]

2000

  • 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.
    [full text] [BibTeX▼]
  • 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. *Best Papers Selection*.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Sequences mining in categorical domains: incorporating constraints. In 9th ACM International Conference on Information and Knowledge Management. November 2000.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki. Sequence mining in categorical domains: algorithms and applications. In Ron Sun and Lee Giles, editors, Sequence Learning: Paradigms, Algorithms, and Applications, volume 1828 of LNAI State-of-the-Art-Survey, pages 162–187. Springer-Verlag, Heidelberg, Germany, 2000.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki. Scalable algorithms for association mining. IEEE Transactions on Knowledge and Data Engineering, 12(3):372–390, May/Jun 2000. doi:10.1109/69.846291.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki and Ching-Tien Ho. Workshop report: large-scale parallel kdd systems. SIGKDD Explorations, 1(2):112–114, January 2000.
    [full text] [BibTeX▼]
  • Neal Lesh, Mohammed J. Zaki, and Mitsunori Ogihara. Scalable feature mining for sequential data. IEEE Intelligent Systems and their Applications, 15(2):48–56, Mar/Apr 2000. Special issue on Data Mining.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki, Vipin Kumar, and David Skillicorn, editors. 3rd IPDPS International Workshop on High Performance Data Mining, Springer LINK (http://www.springerlink.com/content/101nv8cq9yrw/), 2000. URL: http://www.cs.rpi.edu/~zaki/Workshops/HPDM00/.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki and Gautam Das, editors. Proceedings of HiPC'00: Special Session on Large Scale Data Mining, Springer LINK (http://www.springerlink.com/content/phpt72qy0ycw), 2000. URL: http://www.cs.rpi.edu/~zaki/SpecialIssues/LSDM/.
    [BibTeX▼]
  • Mohammed J. Zaki. Parallel and distributed data mining: an introduction. In Large-Scale Parallel Data Mining, volume 1759 of LNCS/LNAI State-of-the-Art Survey. Springer-Verlag, Heidelberg, Germany, 2000.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Parallel sequence mining on SMP machines. In Large-Scale Parallel Data Mining, volume 1759 of LNCS/LNAI State-of-the-Art Survey. Springer-Verlag, Heidelberg, Germany, 2000.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki and Ching-Tien Ho. Large-Scale Parallel Data Mining. Volume 1759 of LNCS/LNAI State-of-the-Art Survey (http://www.springerlink.com/content/dhadtlv2w1yh/). Springer-Verlag, Heidelberg, Germany, 2000. ISBN: 978-3-540-67194-7. URL: http://www.cs.rpi.edu/~zaki/Books/lspdmbook.html.
    [BibTeX▼]
  • Mohammed J. Zaki. Generating non-redundant association rules. In 6th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. August 2000.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Ching-Tien Ho, and Rakesh Agrawal. Parallel classification on shared-memory systems. In Hillol Kargupta and Philip Chan, editors, Advances in Distributed and Parallel Knowledge Discovery, chapter 14, pages 377–407. AAAI Press, Menlo Park, CA, 2000.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Hierarchical parallel algorithms for association mining. In Hillol Kargupta and Philip Chan, editors, Advances in Distributed and Parallel Knowledge Discovery, chapter 13, pages 339–376. AAAI Press, Menlo Park, CA, 2000.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Neal Lesh, and Mitsunori Ogihara. PLANMINE: predicting plan failures using sequence mining. Artificial Intelligence Review, 14(6):421–446, December 2000. Special issue on Applications of Data Mining. doi:https://doi.org/10.1023/A:1006612804250.
    [full text] [BibTeX▼]
  • William A. Maniatty and Mohammed J. Zaki. Systems support for scalable data mining. SIGKDD Explorations, 2(2):56–65, December 2000.
    [full text] [BibTeX▼]
  • Srinivasan Parthasarathy, Mohammed J. Zaki, Mitsunori Ogihara, and Sandhya Dwarkadas. Sequence mining in dynamic and interactive environments. In Witold Abramowicz and Josef Zurada, editors, Knowledge Discovery for Business Information Systems, pages 377–395. Kluwer Academic Publishers, Boston, MA, 2000.
    [full text] [BibTeX▼]

1999

  • Mohammed J. Zaki, Srinivasan Parthasarathy, and Wei Li. Customized dynamic load balancing for cluster computing. In Rajkumar Buyya, editor, High Performance Cluster Computing: Architectures and Systems, volume 1, pages 582–607. Prentice Hall, Upper Saddle River, NJ, 1999.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki, Ching-Tien Ho, and Rakesh Agrawal. Parallel classification for data mining on shared-memory systems. Technical Report RJ10104, IBM, 1999.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki and Ching-Tien Ho, editors. Proceedings of the ACM SIGKDD Workshop on Large-Scale Parallel KDD Systems, 1999. URL: http://www.cs.rpi.edu/~zaki/Workshops/WKDD99/.
    [full text] [BibTeX▼]
  • 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. See IBM Technical Report RJ10104 \cite 1999-ibmtr for a more detailed version of this paper.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Parallel sequence mining on shared-memory machines. In Workshop on Large-Scale Parallel Data Mining Systems (with KDD). August 1999.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Parallel and distributed association mining: a survey. IEEE Concurrency, 7(4):14–25, December 1999. Special issue on Parallel Mechanisms for Data Mining.
    [full text] [BibTeX▼]

1998

  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Mohammed J. Zaki. Efficient enumeration of frequent sequences. In 7th ACM International Conference on Information and Knowledge Management. November 1998.
    [full text] [githubcode] [BibTeX▼]
  • Mohammed J. Zaki. Scalable data mining for rules. Technical Report URCS-TR-702 (Ph.D. Thesis), University of Rochester, July 1998.
    [full text] [BibTeX▼]

1997

  • 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. Special issue on Workstation Clusters and Network-based Computing: Performance Evaluation, Scheduling, and Fault-Tolerance.
    [full text] [BibTeX▼]
  • Vineet Gupta, Srinivasan Parthasarathy, and Mohammed J. Zaki. Arithmetic and logic operations with dna. In 3rd DIMACS Workshop on DNA Based Computers. June 1997.
    [full text] [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]
  • 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.
    [full text] [githubcode] [BibTeX▼]
  • 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. Special issue on Automatic Loop Parallelization. doi:10.1093/comjnl/40.6.356.
    [full text] [BibTeX▼]
  • 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. Special issue on Scalable High-Performance Computing for KDD. doi:10.1023/A:1009773317876.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]

1996

  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • Lane Hemaspaandra, Mohammed J. Zaki, and Marius Zimand. Polynomial-time semi-rankable sets. Journal of Computing and Information, 2(1):50–67, June 1996. Special issue on 8th International Conference of Computing and Information.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]

1995

  • 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.
    [full text] [BibTeX▼]
  • Michal Cierniak, Wei Li, and Mohammed J. Zaki. Loop scheduling for heterogeneity. In 4th IEEE International Symposium on High-Performance Distributed Computing. August 1995.
    [full text] [BibTeX▼]
  • 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.
    [full text] [BibTeX▼]