All Stories

  1. 25th International Workshop on Data Mining in Bioinformatics (BIOKDD 2026)

    Article • August 2026, ACM (Association for Computing Machinery)

    Prof. Truong Son Hy, Prof. Mohammed J Zaki, Da Yan

  2. Semantic Graph Based Learning for Trend Prediction from Long Financial Documents

    Article • ACM Transactions on Management Information Systems, June 2026, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  3. 24 th International Workshop on Data Mining in Bioinformatics (BIOKDD 2025)

    Article • August 2025, ACM (Association for Computing Machinery)

    Da Yan, Prof. Mohammed J Zaki, Prof. Truong Son Hy

  4. LLaVA-Chef: A Multi-modal Generative Model for Food Recipes

    Article • October 2024, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  5. 23 rd International Workshop on Data Mining in Bioinformatics (BIOKDD 2024)

    Article • August 2024, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  6. FETILDA: An Evaluation Framework for Effective Representations of Long Financial Documents

    Article • ACM Transactions on Knowledge Discovery from Data, April 2024, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  7. Toward Subgraph-Guided Knowledge Graph Question Generation With Graph Neural Networks

    Article • IEEE Transactions on Neural Networks and Learning Systems, January 2024, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  8. 22nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023)

    Article • August 2023, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  9. The Information Pathways Hypothesis: Transformers are Dynamic Self-Ensembles

    Article • August 2023, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki, Md Shamim Hussain

  10. Health-guided recipe recommendation over knowledge graphs

    Article • Journal of Web Semantics, January 2023, Elsevier

    Prof. Mohammed J Zaki

  11. Domain-Specific Keyword Extraction Using Joint Modeling of Local and Global Contextual Semantics

    Article • ACM Transactions on Knowledge Discovery from Data, August 2022, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  12. 21th International Workshop on Data Mining in Bioinformatics (BIOKDD 2022)

    Article • August 2022, ACM (Association for Computing Machinery)

    Da Yan, Prof. Mohammed J Zaki

  13. Global Self-Attention as a Replacement for Graph Convolution

    Article • August 2022, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki, Md Shamim Hussain

  14. 20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021)

    Article • August 2021, ACM (Association for Computing Machinery)

    Da Yan, Dr Zhaohui S. Qin, Prof. Mohammed J Zaki

  15. A Framework for Generating Summaries from Temporal Personal Health Data

    Article • ACM Transactions on Computing for Healthcare, July 2021, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki, Jonathan Harris

  16. Personalized Food Recommendation as Constrained Question Answering over a Large-scale Food Knowledge Graph

    Article • March 2021, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  17. A Comparative Analysis of Temporal Long Text Similarity: Application to Financial Documents

    Article • January 2021, Springer Science + Business Media

    Prof. Mohammed J Zaki

  18. An Efficient Heartbeats Classifier Based on Optimizing Convolutional Neural Network Model

    Article • IEEE Access, January 2021, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  19. RECIPTOR: An Effective Pretrained Model for Recipe Representation Learning

    Article • August 2020, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  20. Figurative language in social media

    Article • ACM Transactions on the Web, February 2020, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  21. MALOnt: An Ontology for Malware Threat Intelligence

    Article • January 2020, Springer Science + Business Media

    Prof. Mohammed J Zaki

  22. FoodKG: A Semantics-Driven Knowledge Graph for Food Recommendation

    Article • January 2019, Springer Science + Business Media

    Prof. Mohammed J Zaki

  23. KATE

    Article • August 2017, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  24. Graph Data Mining with Arabesque

    Article • May 2017, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  25. Rheem

    Article • June 2016, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  26. A distributed approach for graph mining in massive networks

    Article • Data Mining and Knowledge Discovery, June 2016, Springer Science + Business Media

    Prof. Mohammed J Zaki

  27. Sampling frequent and minimal boolean patterns: theory and application in classification

    Article • Data Mining and Knowledge Discovery, March 2015, Springer Science + Business Media

    Prof. Mohammed J Zaki

  28. Learning sequential classifiers from long and noisy discrete-event sequences efficiently

    Article • Data Mining and Knowledge Discovery, November 2014, Springer Science + Business Media

    Prof. Mohammed J Zaki

  29. NSIT: Novel Sequence Identification Tool

    Article • PLOS One, September 2014, PLOS

    Prof. Mohammed J Zaki

  30. Trends in computer science research

    Article • Communications of the ACM, October 2013, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  31. Approximate graph mining with label costs

    Article • August 2013, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  32. ProfileRank

    Article • August 2013, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  33. Stochastic subspace search for top-k multi-view clustering

    Article • August 2013, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  34. Message from Program Co-chairs

    Article • December 2012, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  35. Sampling minimal frequent boolean (DNF) patterns

    Article • August 2012, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  36. Graph mining for discovering infrastructure patterns in configuration management databases

    Article • Knowledge and Information Systems, August 2012, Springer Science + Business Media

    Prof. Mohammed J Zaki

  37. Effective graph classification based on topological and label attributes

    Article • Statistical Analysis and Data Mining The ASA Data Science Journal, June 2012, Wiley

    Prof. Mohammed J Zaki

  38. Characterizing the effectiveness of twitter hashtags to detect and track online population sentiment

    Article • May 2012, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  39. A Journey in Pattern Mining

    Article • January 2012, Springer Science + Business Media

    Prof. Mohammed J Zaki

  40. Geofold: Topology-based protein unfolding pathways capture the effects of engineered disulfides on kinetic stability

    Article • Proteins Structure Function and Bioinformatics, December 2011, Wiley

    Suzanne Matthews, Prof. Mohammed J Zaki

  41. Infrastructure Pattern Discovery in Configuration Management Databases via Large Sparse Graph Mining

    Article • December 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  42. Preface

    Article • November 2011, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  43. GRAIL: a scalable index for reachability queries in very large graphs

    Article • The VLDB Journal, September 2011, Springer Science + Business Media

    Prof. Mohammed J Zaki

  44. Calibrated lazy associative classification

    Article • Information Sciences, July 2011, Elsevier

    Prof. Mohammed J Zaki

  45. Is There a Best Quality Metric for Graph Clusters?

    Article • January 2011, Springer Science + Business Media

    Prof. Mohammed J Zaki

  46. Mining Complex Boolean Expressions for Sequential Equivalence Checking

    Article • December 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  47. SimClus: an effective algorithm for clustering with a lower bound on similarity

    Article • Knowledge and Information Systems, November 2010, Springer Science + Business Media

    Prof. Mohammed J Zaki

  48. Structural correlation pattern mining for large graphs

    Article • July 2010, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  49. Matrix "Bit" loaded

    Article • April 2010, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  50. Prism: An effective approach for frequent sequence mining via prime-block encoding

    Article • Journal of Computer and System Sciences, February 2010, Elsevier

    Prof. Mohammed J Zaki

  51. FlexSnap: Flexible Non-sequential Protein Structure Alignment

    Article • Algorithms for Molecular Biology, January 2010, Springer Science + Business Media

    Prof. Mohammed J Zaki

  52. Graph indexing for reachability queries

    Article • January 2010, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  53. VOGUE

    Article • ACM Transactions on Knowledge Discovery from Data, January 2010, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  54. Competence‐conscious associative classification

    Article • Statistical Analysis and Data Mining The ASA Data Science Journal, November 2009, Wiley

    Prof. Mohammed J Zaki

  55. Proteomic and Phospho-Proteomic Profile of Human Platelets in Basal, Resting State: Insights into Integrin Signaling

    Article • PLOS One, October 2009, PLOS

    Prof. Mohammed J Zaki

  56. Robust partitional clustering by outlier and density insensitive seeding

    Article • Pattern Recognition Letters, August 2009, Elsevier

    Prof. Mohammed J Zaki

  57. SPARCL: an effective and efficient algorithm for mining arbitrary shape-based clusters

    Article • Knowledge and Information Systems, June 2009, Springer Science + Business Media

    Prof. Mohammed J Zaki

  58. Clustering with Lower Bound on Similarity

    Article • January 2009, Springer Science + Business Media

    Prof. Mohammed J Zaki

  59. FlexSnap: Flexible Non-sequential Protein Structure Alignment

    Article • January 2009, Springer Science + Business Media

    Prof. Mohammed J Zaki

  60. graphOnt: An ontology based library for conversion from semantic graphs to JUNG

    Article • January 2009, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  61. Quantification of Spatial Parameters in 3D Cellular Constructs Using Graph Theory

    Article • BioMed Research International, January 2009, Wiley

    Prof. Mohammed J Zaki

  62. SPARCL: Efficient and Effective Shape-Based Clustering

    Article • December 2008, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  63. An integrated, generic approach to pattern mining: data mining template library

    Article • Data Mining and Knowledge Discovery, May 2008, Springer Science + Business Media

    Prof. Mohammed J Zaki

  64. ORIGAMI: A Novel and Effective Approach for Mining Representative Orthogonal Graph Patterns

    Article • Statistical Analysis and Data Mining The ASA Data Science Journal, April 2008, Wiley

    Prof. Mohammed J Zaki

  65. Introduction to special issue on bioinformatics

    Article • ACM Transactions on Knowledge Discovery from Data, March 2008, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  66. The ParTriCluster Algorithm for Gene Expression Analysis

    Article • International Journal of Parallel Programming, January 2008, Springer Science + Business Media

    Prof. Mohammed J Zaki

  67. Context shapes: Efficient complementary shape matching for protein–protein docking

    Article • Proteins Structure Function and Bioinformatics, January 2008, Wiley

    Prof. Mohammed J Zaki

  68. PSIST: A scalable approach to indexing protein structures using suffix trees

    Article • Journal of Parallel and Distributed Computing, January 2008, Elsevier

    Prof. Mohammed J Zaki

  69. ORIGAMI: Mining Representative Orthogonal Graph Patterns

    Article • October 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  70. Prism: A Primal-Encoding Approach for Frequent Sequence Mining

    Article • October 2007, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  71. Xproj

    Article • August 2007, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  72. Genome-scale disk-based suffix tree indexing

    Article • June 2007, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  73. T ri C luster: Mining Coherent Clusters in Three‐Dimensional Microarray Data

    Article • May 2007, Wiley

    Prof. Mohammed J Zaki

  74. Data Mining in Bioinformatics (BIOKDD)

    Article • Algorithms for Molecular Biology, April 2007, Springer Science + Business Media

    Prof. Mohammed J Zaki

  75. Clicks: An effective algorithm for mining subspace clusters in categorical datasets

    Article • Data & Knowledge Engineering, January 2007, Elsevier

    Prof. Mohammed J Zaki

  76. Exploring Similarities Across High-Dimensional Datasets

    Article • January 2007, IGI Global

    Prof. Mohammed J Zaki

  77. Lazy Associative Classification

    Article • December 2006, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  78. SMOTIF: efficient structured pattern and profile motif search

    Article • Algorithms for Molecular Biology, November 2006, Springer Science + Business Media

    Prof. Mohammed J Zaki

  79. EXMOTIF: efficient structured motif extraction

    Article • Algorithms for Molecular Biology, November 2006, Springer Science + Business Media

    Prof. Mohammed J Zaki

  80. Unified Approach to Rooted Tree Mining: Algorithms and Applications

    Article • April 2006, Wiley

    Prof. Mohammed J Zaki

  81. Mining Multiple Data Sources: Local Pattern Analysis

    Article • Data Mining and Knowledge Discovery, April 2006, Springer Science + Business Media

    Prof. Mohammed J Zaki

  82. XRules: An effective algorithm for structural classification of XML data

    Article • Machine Learning, January 2006, Springer Science + Business Media

    Prof. Mohammed J Zaki

  83. Finding Hidden Group Structure in a Stream of Communications

    Article • January 2006, Springer Science + Business Media

    Prof. Mohammed J Zaki

  84. Generic Pattern Mining Via Data Mining Template Library

    Article • January 2006, Springer Science + Business Media

    Prof. Mohammed J Zaki

  85. Multi-evidence, multi-criteria, lazy associative document classification

    Article • January 2006, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  86. CLICKS

    Article • August 2005, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  87. Reasoning about sets using redescription mining

    Article • August 2005, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  88. The Complexity of Finding Top-Toda-Equivalence-Class Members

    Article • Theory of Computing Systems, August 2005, Springer Science + Business Media

    Prof. Mohammed J Zaki

  89. Efficiently mining frequent trees in a forest: algorithms and applications

    Article • IEEE Transactions on Knowledge and Data Engineering, August 2005, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  90. GenMax: An Efficient Algorithm for Mining Maximal Frequent Itemsets

    Article • Data Mining and Knowledge Discovery, July 2005, Springer Science + Business Media

    Prof. Mohammed J Zaki

  91. Efficient algorithms for mining closed itemsets and their lattice structure

    Article • IEEE Transactions on Knowledge and Data Engineering, April 2005, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  92. A facile approach to formation of through-hole porous anodic aluminum oxide film

    Article • Materials Letters, January 2005, Elsevier

    Prof. Mohammed J Zaki

  93. PSIST: indexing protein structures using suffix trees

    Article • January 2005, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  94. SCHISM: a new approach to interesting subspace mining

    Article • International Journal of Business Intelligence and Data Mining, January 2005, Inderscience Publishers

    Prof. Mohammed J Zaki

  95. Towards Generic Pattern Mining

    Article • January 2005, Springer Science + Business Media

    Prof. Mohammed J Zaki

  96. Mining Non-Redundant Association Rules

    Article • Data Mining and Knowledge Discovery, November 2004, Springer Science + Business Media

    Prof. Mohammed J Zaki

  97. Predicting protein folding pathways

    Article • Bioinformatics, August 2004, Oxford University Press (OUP)

    Prof. Mohammed J Zaki

  98. Mining residue contacts in proteins using local structure predictions

    Article • IEEE Transactions on Systems Man and Cybernetics Part B (Cybernetics), October 2003, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  99. Carpenter

    Article • August 2003, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  100. Fast vertical mining using diffsets

    Article • August 2003, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  101. Improving spatial locality of programs via data mining

    Article • August 2003, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  102. XRules

    Article • August 2003, ACM (Association for Computing Machinery)

    Prof. Mohammed J Zaki

  103. Special issue on data management in bioinformatics

    Article • Information Systems, June 2003, Elsevier

    Prof. Mohammed J Zaki

  104. Article • Genetic Resources and Crop Evolution, January 2002, Springer Science + Business Media

    Prof. Mohammed J Zaki

  105. Parallel Sequence Mining on Shared-Memory Machines

    Article • Journal of Parallel and Distributed Computing, March 2001, Elsevier

    Prof. Mohammed J Zaki

  106. Article • Machine Learning, January 2001, Springer Science + Business Media

    Prof. Mohammed J Zaki

  107. Article • Artificial Intelligence Review, January 2000, Springer Science + Business Media

    Prof. Mohammed J Zaki

  108. Scalable algorithms for association mining

    Article • IEEE Transactions on Knowledge and Data Engineering, January 2000, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  109. Parallel and distributed association mining: a survey

    Article • IEEE Concurreny, October 1999, Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  110. Customized Dynamic Load Balancing for a Network of Workstations

    Article • Journal of Parallel and Distributed Computing, June 1997, Elsevier

    Prof. Mohammed J Zaki

  111. CLICKS: Mining Subspace Clusters in Categorical Data via K-Partite Maximal Cliques

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki

  112. SCHISM: A New Approach for Interesting Subspace Mining

    Article • Institute of Electrical & Electronics Engineers (IEEE)

    Prof. Mohammed J Zaki