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Selected Books

Book on Bioinformatics Database Systems

Book on Pattern Recognition in Computational Molecular Biology

Book on Biological Data Mining and Its Applications in Healthcare

Book on Computational Intelligence and Pattern Analysis in Biological Informatics

Book on Soft Computing Analysis of Biological Data

Book on Data Mining in Bioinformatics

Book on Computational Biology and Genome Informatics

Book on Mining the World Wide Web

Book on Pattern Discovery in Biomolecular Data

Selected Publications

A partial list of publications in DBLP Bibliography Server

A partial list of publications in NASA ADS

A partial list of publications in PubMed

A partial list of publications in Google Scholar

A partial list of publications in Collection of Computer Science Bibliographies

A partial list of citations in Google Scholar Citation

A partial list of publications and citations in ResearchGate

Fast Publication in Computer Science - Elsevier

Top Computer Science Conferences and Journals

Top Publications in Data Mining and Analysis

Top Publications in Databases and Information Systems

Top Publications in Artificial Intelligence

Top Journals and Conferences in Data Mining / Data Science

Top Journals for Machine Learning and Artificial Intelligence

Selected Journal Papers

Hameedullah Farooki, Sung Jun Noh, Jeongwoo Lee, Haimin Wang, Hyomin Kim, Yasser Abduallah, Jason T. L. Wang, Yu Chen, Sergio Servidio, Francesco Pecora, "A Closer Look at Small-scale Magnetic Flux Ropes in the Solar Wind at 1 au: Results from Improved Automated Detection," The Astrophysical Journal Supplement Series, 271:42 (27pp), 2024.

Chunhui Xu, Jason T. L. Wang, Haimin Wang, Haodi Jiang, Qin Li, Yasser Abduallah, Yan Xu, "Super-Resolution of SOHO/MDI Magnetograms of Solar Active Regions Using SDO/HMI Data and an Attention-Aided Convolutional Neural Network," Solar Physics, 299:36 (16pp), 2024.

Yasser Abduallah, Khalid A. Alobaid, Jason T. L. Wang, Haimin Wang, Vania K. Jordanova, Vasyl Yurchyshyn, Huseyin Cavus, Ju Jing, "Prediction of the SYM-H Index Using a Bayesian Deep Learning Method with Uncertainty Quantification," Space Weather, 22, e2023SW003824 (18pp), 2024.

Firas Gerges, Michel C. Boufadel, Elie Bou-Zeid, Hani Nassif, Jason T. L. Wang, "Long-Term Prediction of Daily Solar Irradiance Using Bayesian Deep Learning and Climate Simulation Data," Knowledge and Information Systems, 66(1):613-633, 2024.

H. Farooki, Y. Abduallah, S.-J. Noh, H. Kim, G. Bizos, Y. Shin, J. T. L. Wang, H. Wang, "A Machine Learning Approach to Understanding the Physical Properties of Magnetic Flux Ropes in the Solar Wind at 1 au," The Astrophysical Journal, 961:81 (11pp), 2024.

K. A. Alobaid, Y. Abduallah, J. T. L. Wang, H. Wang, S. Fan, J. Li, H. Cavus and V. Yurchyshyn, "Estimating Coronal Mass Ejection Mass and Kinetic Energy by Fusion of Multiple Deep-learning Models," The Astrophysical Journal Letters, 958:L34 (8pp), 2023.

Y. Abduallah, J. T. L. Wang, H. Wang and Y. Xu, "Operational Prediction of Solar Flares Using a Transformer-Based Framework," Scientific Reports, 13:13665 (11pp), 2023.

R. Anirudh et al., "2022 Review of Data-Driven Plasma Science," IEEE Transactions on Plasma Science, 51(7):1750-1838, 2023.

H. Jiang, Q. Li, N. Liu, Z. Hu, Y. Abduallah, J. Jing, Y. Xu, J. T. L. Wang and H. Wang, "Generating Photospheric Vector Magnetograms of Solar Active Regions for SOHO/MDI Using SDO/HMI and BBSO Data with Deep Learning," Solar Physics, 298:87 (17pp), 2023.

F. Gerges, M. C. Boufadel, E. Bou-Zeid, H. Nassif and J. T. L. Wang, "Deep Learning-Based Downscaling of Temperatures for Monitoring Local Climate Change Using Global Climate Simulation Data," World Scientific Annual Review of Artificial Intelligence, Vol. 1, 2250001 (24 pages), 2023.

H. Zhang, Q. Li, Y. Yang, J. Jing, J. T. L. Wang, H. Wang and Z. Shang, "Solar Flare Index Prediction Using SDO/HMI Vector Magnetic Data Products with Statistical and Machine Learning Methods," The Astrophysical Journal Supplement Series, 263:28 (12pp), 2022.

H. Jiang, Q. Li, Y. Xu, W. Hsu, K. Ahn, W. Cao, J. T. L. Wang and H. Wang, "Inferring Line-of-Sight Velocities and Doppler Widths from Stokes Profiles of GST/NIRIS Using Stacked Deep Neural Networks," The Astrophysical Journal, 939:66 (12pp), 2022.

K. A. Alobaid, Y. Abduallah, J. T. L. Wang, H. Wang, H. Jiang, Y. Xu, V. Yurchyshyn, H. Zhang, H. Cavus and J. Jing, "Predicting CME Arrival Time through Data Integration and Ensemble Learning," Frontiers in Astronomy and Space Sciences, 9:1013345 (13pp), 2022.

Y. Abduallah, V. K. Jordanova, H. Liu, Q. Li, J. T. L. Wang and H. Wang, "Predicting Solar Energetic Particles Using SDO/HMI Vector Magnetic Data Products and a Bidirectional LSTM Network," The Astrophysical Journal Supplement Series, 260:16 (18pp), 2022.

H. Jiang, J. Jing, J. Wang, C. Liu, Q. Li, Y. Xu, J. T. L. Wang and H. Wang, "Tracing H-alpha Fibrils through Bayesian Deep Learning," The Astrophysical Journal Supplement Series, 256:20 (16pp), 2021.

A. Raheem, H. Cavus, G. C. Coban, A. C. Kinaci, H. Wang and J. T. L. Wang, "An Investigation of the Causal Relationship between Sunspot Groups and Coronal Mass Ejections by Determining Source Active Regions," Monthly Notices of the Royal Astronomical Society, 506(2):1916-1926, 2021.

Y. Abduallah, J. T. L. Wang, Y. Nie, C. Liu and H. Wang, "DeepSun: Machine-Learning-as-a-Service for Solar Flare Prediction," Research in Astronomy and Astrophysics, 21:160 (11pp), 2021.

H. Jiang, J. Wang, C. Liu, J. Jing, H. Liu, J. T. L. Wang and H. Wang, "Identifying and Tracking Solar Magnetic Flux Elements with Deep Learning," The Astrophysical Journal Supplement Series, 250:5 (13pp), 2020.

H. Liu, Y. Xu, J. Wang, J. Jing, C. Liu, J. T. L. Wang and H. Wang, "Inferring Vector Magnetic Fields from Stokes Profiles of GST/NIRIS Using a Convolutional Neural Network," The Astrophysical Journal, 894:70 (19pp), 2020.

Z. Hu, T. Turki and J. T. L. Wang, "Generative Adversarial Networks for Stochastic Video Prediction with Action Control," IEEE Access, Vol. 8, 2020, pp. 63336-63348.

H. Liu, C. Liu, J. T. L. Wang and H. Wang, "Predicting Coronal Mass Ejections Using SDO/HMI Vector Magnetic Data Products and Recurrent Neural Networks," The Astrophysical Journal, 890:12 (9pp), 2020.

Y. Abduallah and J. T. L. Wang, "New Algorithms for Inferring Gene Regulatory Networks from Time-Series Expression Data on Apache Spark," International Journal of Big Data Intelligence, Vol. 6, No. 3/4, 2019, pp. 153-162.

H. Liu, C. Liu, J. T. L. Wang and H. Wang, "Predicting Solar Flares Using a Long Short-term Memory Network," The Astrophysical Journal, 877:121 (14pp), 2019.

T. Turki and J. T. L. Wang, "Clinical Intelligence: New Machine Learning Techniques for Predicting Clinical Drug Response," Computers in Biology and Medicine, Vol. 107, 2019, pp. 302-322.

S. Zhang, Z. Du, J. T. L. Wang and H. Jiang, "Discovering Frequent Induced Subgraphs from Directed Networks," Intelligent Data Analysis, Vol. 22, No. 6, 2018, pp. 1279-1296.

Kevin Byron and Jason T. L. Wang, "A Comparative Review of Recent Bioinformatics Tools for Inferring Gene Regulatory Networks Using Time-Series Expression Data," International Journal of Data Mining and Bioinformatics, Vol. 20, No. 4, 2018, pp. 320-340.

Zhihang Hu, Turki Turki, NhatHai Phan and Jason T. L. Wang, "A 3D Atrous Convolutional Long Short-Term Memory Network for Background Subtraction," IEEE Access, Vol. 6, 2018, pp. 43450-43459.

Turki Turki, Zhi Wei and Jason T. L. Wang, "A Transfer Learning Approach via Procrustes Analysis and Mean Shift for Cancer Drug Sensitivity Prediction," Journal of Bioinformatics and Computational Biology, Vol. 16, No. 3, 1840014 (31pp), 2018.

Chang Liu, Na Deng, Jason T. L. Wang and Haimin Wang, "Predicting Solar Flares Using SDO/HMI Vector Magnetic Data Products and the Random Forest Algorithm," The Astrophysical Journal, 843:104 (14pp), 2017. [pdf]

Turki Turki, Zhi Wei and Jason T. L. Wang, "Transfer Learning Approaches to Improve Drug Sensitivity Prediction in Multiple Myeloma Patients," IEEE Access, Vol. 5, 2017, pp. 7381-7393. [pdf]

Yasser Abduallah, Turki Turki, Kevin Byron, Zongxuan Du, Miguel Cervantes-Cervantes and Jason T. L. Wang, "MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach," BioMed Research International, 2017:6261802 (8pp), 2017. [pdf]

Lei Hua, Yang Song, Namhee Kim, Christian Laing, Jason T. L. Wang and Tamar Schlick, "CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking," PLoS ONE, 11(1): e0147097 (22pp), 2016. [pdf] [PubMed]

Nihir Patel and Jason T. L. Wang, "Semi-Supervised Prediction of Gene Regulatory Networks Using Machine Learning Algorithms," Journal of Biosciences, Vol. 40, No. 4, 2015, pp. 731-740. [pdf] [PubMed]

Sen Zhang, Z. Du and Jason T. L. Wang, "New Techniques for Mining Frequent Patterns in Unordered Trees," IEEE Transactions on Cybernetics, Vol. 45, No. 6, 2015, pp. 1113-1125. [PubMed]

Yang Song, Lei Hua, Bruce A. Shapiro and Jason T. L. Wang, "Effective Alignment of RNA Pseudoknot Structures Using Partition Function Posterior Log-Odds Scores," BMC Bioinformatics, 16:39 (15pp), 2015. [pdf] [PubMed]

Kevin Byron, Jason T. L. Wang and Dongrong Wen, "Genome-Wide Prediction of Coaxial Helical Stacking Using Random Forests and Covariance Models," International Journal on Artificial Intelligence Tools, Vol. 23, No. 3, 2014, 1460008 (15 pages).

Palak Sheth, Miguel Cervantes-Cervantes, Akhila Nagula, Christian Laing and Jason T. L. Wang, "Novel Features for Identifying A-Minors in Three-Dimensional RNA Molecules," Computational Biology and Chemistry, Vol. 47, 2013, pp. 240-245. [pdf] [PubMed]

Ling Zhong, Jason T. L. Wang, Dongrong Wen, Virginie Aris, Patricia Soteropoulos and Bruce A. Shapiro, "Effective Classification of MicroRNA Precursors Using Feature Mining and AdaBoost Algorithms," OMICS: A Journal of Integrative Biology, Vol. 17, 2013, pp. 486-493. [pdf] [PubMed]

Kevin Byron, Christian Laing, Dongrong Wen and Jason T. L. Wang, "A Computational Approach to Finding RNA Tertiary Motifs in Genomic Sequences: A Case Study," Recent Patents on DNA & Gene Sequences, Vol. 7, No. 2, 2013, pp. 115-122. [PubMed]

Lei Hua, Jason T. L. Wang, Xiang Ji, Ankur Malhotra, Mugdha Khaladkar, Bruce A. Shapiro and Kaizhong Zhang, "A Method for Discovering Common Patterns from Two RNA Secondary Structures and Its Application to Structural Repeat Detection," Journal of Bioinformatics and Computational Biology, Vol. 10, No. 4, 2012, 1250001 (15 pages). [pdf] [PubMed]

Michael Bao, Miguel Cervantes-Cervantes, Ling Zhong and Jason T. L. Wang, "Searching for Non-coding RNAs in Genomic Sequences Using ncRNAscout," Genomics Proteomics & Bioinformatics, Vol. 10, No. 2, 2012, pp. 114-121. [PubMed]

Xin Zhang, Dennis Shasha, Yang Song and Jason T. L. Wang, "Fast Elastic Peak Detection for Mass Spectrometry Data Mining," IEEE Transactions on Knowledge and Data Engineering, Vol. 24, No. 4, 2012, pp. 634-648. [pdf]

Christian Laing, Dongrong Wen, Jason T. L. Wang and Tamar Schlick, "Predicting Coaxial Helical Stacking in RNA Junctions," Nucleic Acids Research, Vol. 40, No. 2, 2012, pp. 487-498. [pdf] [Supplementary Data] [PubMed]

Stephen J. Griesmer, Miguel Cervantes-Cervantes, Yang Song and Jason T. L. Wang, "In Silico Prediction of Noncoding RNAs Using Supervised Learning and Feature Ranking Methods," International Journal of Bioinformatics Research and Applications, Vol. 7, No. 4, 2011, pp. 355-375. [pdf] [PubMed]

Vandanaben Patel, Jason T. L. Wang, Shefali Setia, Anurag Verma, Charles D. Warden and Kaizhong Zhang, "On Comparing Two Structured RNA Multiple Alignments," Journal of Bioinformatics and Computational Biology, Vol. 8, No. 6, 2010, pp. 967-980.

Richipal Singh Bindra, Jason T. L. Wang and Paramjeet Singh Bagga, "Bioinformatics Methods for Studying MicroRNA and ARE-Mediated Regulation of Post-Transcriptional Gene Expression," International Journal of Knowledge Discovery in Bioinformatics, Vol. 1, No. 3, 2010, pp. 97-112. [pdf]

Kevin Byron, M. Cervantes-Cervantes, Jason T. L. Wang, W.C. Lin and Y. Park, "Mining roX1 RNA in Drosophila Genomes Using Covariance Models," International Journal of Computational Bioscience, Vol. 1, No. 1, 2010, pp. 22-32.

Junilda Spirollari, Jason T. L. Wang, Kaizhong Zhang, Vivian Bellofatto, Yongkyu Park and Bruce A. Shapiro, "Predicting Consensus Structures for RNA Alignments Via Pseudo-Energy Minimization," Bioinformatics and Biology Insights, Vol. 3, June 2009, pp. 51-69.

Dongrong Wen and Jason T. L. Wang, "Design of an RNA Structural Motif Database," International Journal of Computational Intelligence in Bioinformatics and Systems Biology, Vol. 1, No. 1, 2009, pp. 32-41.

Mugdha Khaladkar, Vandanaben Patel, Vivian Bellofatto, Jeffrey Wilusz and Jason T. L. Wang, "Detecting Conserved Secondary Structures in RNA Molecules Using Constrained Structural Alignment," Computational Biology and Chemistry, Vol. 32, No. 4, August 2008, pp. 264-272. [pdf] [PubMed]

Mugdha Khaladkar, Jianghui Liu, Dongrong Wen, Jason T. L. Wang and Bin Tian, "Mining Small RNA Structure Elements in Untranslated Regions of Human and Mouse mRNAs Using Structure-Based Alignment," BMC Genomics, 9:189 (12pp), 2008. [pdf] [PubMed]

Sen Zhang and Jason T. L. Wang, "Discovering Frequent Agreement Subtrees from Phylogenetic Data," IEEE Transactions on Knowledge and Data Engineering, Vol. 20, No. 1, January 2008, pp. 68-82. [pdf]

Mugdha Khaladkar, Vivian Bellofatto, Jason T. L. Wang, Bin Tian and Bruce A. Shapiro, "RADAR: A Web Server for RNA Data Analysis and Research," Nucleic Acids Research, Vol. 35, Web Server Issue, 2007, pp. W300-W304. [pdf] [PubMed]

Katherine G. Herbert and Jason T. L. Wang, "Biological Data Cleaning: A Case Study," International Journal of Information Quality, Vol. 1, No. 1, 2007, pp. 60-82.

Jason T. L. Wang and Xiaoming Wu, "Kernel Design for RNA Classification Using Support Vector Machines," International Journal of Data Mining and Bioinformatics, Vol. 1, 2006, pp. 57-76. [pdf] [PubMed]

Jason T. L. Wang, Huiyuan Shan, Dennis Shasha and William H. Piel, "Fast Structural Search in Phylogenetic Databases," Evolutionary Bioinformatics, Vol. 1, October 2005, pp. 37-46. [pdf] [PubMed]

Jason T. L. Wang, Xiong Wang, Dennis Shasha and Kaizhong Zhang, "MetricMap: An Embedding Technique for Processing Distance-Based Queries in Metric Spaces," IEEE Transactions on Systems, Man and Cybernetics, Part B, Cybernetics, Vol. 35, No. 5, October 2005, pp. 973-987. [pdf] [PubMed]

Jason T. L. Wang, Jianghui Liu and Junhan Wang, "XML Clustering and Retrieval through Principal Component Analysis," International Journal on Artificial Intelligence Tools, Vol. 14, No. 4, August 2005, pp. 683-699. [pdf]

Jianghui Liu, Jason T. L. Wang, Jun Hu and Bin Tian, "A Method for Aligning RNA Secondary Structures and Its Application to RNA Motif Detection," BMC Bioinformatics, 6:89 (20pp), 2005. [pdf] [PubMed]

Katherine G. Herbert, Narain H. Gehani, William H. Piel, Jason T. L. Wang and Cathy H. Wu, "BIO-AJAX: An Extensible Framework for Biological Data Cleaning," ACM SIGMOD Record, Special Section on Data Engineering for Life Sciences, Vol. 33, No. 2, June 2004, pp. 51-57. [pdf]

Michael M. Yin and Jason T. L. Wang, "GeneScout: A Data Mining System for Predicting Vertebrate Genes in Genomic DNA Sequences," Information Sciences, Special Issue on Soft Computing Data Mining, Vol. 163, Issues 1-3, June 2004, pp. 201-218. [pdf]

Sen Zhang, Jason T. L. Wang and Katherine G. Herbert, "XML Query by Example," International Journal of Computational Intelligence and Applications, Special Issue on Internet-Based Intelligent Systems, Vol. 2, No. 3, 2002, pp. 329-337. [html]

Xiong Wang, Jason T. L. Wang, Dennis Shasha, Bruce A. Shapiro, Isidore Rigoutsos and Kaizhong Zhang, "Finding Patterns in Three Dimensional Graphs: Algorithms and Applications to Scientific Data Mining," IEEE Transactions on Knowledge and Data Engineering, Vol. 14, No. 4, July/August 2002, pp. 731-749. [pdf]

Jason T. L. Wang, Kaizhong Zhang, George Chang and Dennis Shasha, "Finding Approximate Patterns in Undirected Acyclic Graphs," Pattern Recognition, Vol. 35, 2002, pp. 473-483. [pdf]

Qicheng Ma, Jason T. L. Wang, Dennis Shasha and Cathy H. Wu, "DNA Sequence Classification via an Expectation Maximization Algorithm and Neural Networks: A Case Study," IEEE Transactions on Systems, Man, and Cybernetics, Part C: Applications and Reviews, Special Issue on Knowledge Management, Vol. 31, No. 4, November 2001, pp. 468-475. [pdf]

Michael M. Yin and Jason T. L. Wang, "Effective Hidden Markov Models for Detecting Splicing Junction Sites in DNA Sequences," Information Sciences, Special Issue on Bioinformatics, Vol. 139, 2001, pp. 139-163. [pdf]

Jason T. L. Wang, Qicheng Ma, Dennis Shasha and Cathy H. Wu, "New Techniques for Extracting Features from Protein Sequences," IBM Systems Journal, Special Issue on Deep Computing for the Life Sciences, Vol. 40, No. 2, 2001, pp. 426-441. [pdf]

Jason T. L. Wang and Kaizhong Zhang, "Finding Similar Consensus between Trees: An Algorithm and a Distance Hierarchy," Pattern Recognition, Vol. 34, No. 1, January 2001, pp. 127-137 (Honorable Mention Winner of the 28th Annual Pattern Recognition Society Award).

Jason T. L. Wang and Kaizhong Zhang, "Identifying Consensus of Trees through Alignment," Information Sciences, Vol. 126, No. 1-4, 2000, pp. 165-189.

Xiong Wang, Jason T. L. Wang, King-Ip Lin, Dennis Shasha, Bruce A. Shapiro and Kaizhong Zhang, "An Index Structure for Data Mining and Clustering," Knowledge and Information Systems, Vol. 2, No. 2, May 2000, pp. 161-184. [pdf]

Xiong Wang and Jason T. L. Wang, "Fast Similarity Search in Three-Dimensional Structure Databases," Journal of Chemical Information and Computer Sciences (now Journal of Chemical Information and Modeling), Vol. 40, No. 2, 2000, pp. 442-451. [html] [PubMed]

Qicheng Ma and Jason T. L. Wang, "Biological Data Mining Using Bayesian Neural Networks: A Case Study," International Journal on Artificial Intelligence Tools, Special Issue on Biocomputing, Vol. 8, No. 4, 1999, pp. 433-451.

Jason T. L. Wang, Kaizhong Zhang and Chia-Yo Chang, "Identifying Approximately Common Substructures in Trees Based on a Restricted Edit Distance," Information Sciences, Vol. 121, No. 3-4, 1999, pp. 367-386.

Marcus J. Healey, Jason T. L. Wang, George Chang, Amit Revankar and Gunjan Samtani, "Precise Environmental Searches: EnviroDaemon with Hierarchical Information Search," Environmental Quality Management, Vol. 9, No. 1, 1999, pp. 51-62.

Jason T. L. Wang, Steve Rozen, Bruce A. Shapiro, Dennis Shasha, Zhiyuan Wang and Maisheng Yin, "New Techniques for DNA Sequence Classification," Journal of Computational Biology, Vol. 6, No. 2, 1999, pp. 209-218. [pdf] [PubMed]

Jason T. L. Wang, Bruce A. Shapiro, Dennis Shasha, Kaizhong Zhang and Kathleen M. Currey, "An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees," IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 20, No. 8, August 1998, pp. 889-895. [pdf]

Chia-Yo Chang, Jason T. L. Wang and Roger K. Chang, "Scientific Data Mining: A Case Study," International Journal of Software Engineering and Knowledge Engineering, Vol. 8, No. 1, 1998, pp. 77-96.

C.-S. Wei, Q. Liu, Jason T. L. Wang and Peter A. Ng, "Knowledge Discovering for Document Classification Using Tree Matching in TEXPROS," Information Sciences, Vol. 100, Nos. 1-4, August 1997, pp. 255-310.

Jason T. L. Wang and Chia-Yo Chang, "Fast Retrieval of Electronic Messages That Contain Mistyped Words or Spelling Errors," IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics, Vol. 27, No. 3, June 1997, pp. 441-451. [pdf] [PubMed]

Gang Zhou, Jason T. L. Wang and Peter A. Ng, "Curriculum Knowledge Representation and Manipulation in Knowledge-Based Tutoring Systems," IEEE Transactions on Knowledge and Data Engineering, Vol. 8, No. 5, October 1996, pp. 679-689. [pdf]

Xiaolong Hao, Jason T. L. Wang and Peter A. Ng, "Information Extraction from the Structured Part of Office Documents," Information Sciences, Vol. 91, Nos. 3&4, June 1996, pp. 245-274.

Jason T. L. Wang, Thomas G. Marr, Dennis Shasha, Bruce A. Shapiro, Gung-Wei Chirn and T. Y. Lee, "Complementary Classification Approaches for Protein Sequences," Protein Engineering, Vol. 9, No. 5, May 1996, pp. 381-386. [PubMed]

Kaizhong Zhang, Jason T. L. Wang and Dennis Shasha, "On the Editing Distance between Undirected Acyclic Graphs," International Journal of Foundations of Computer Science, Special Issue on Computational Biology, Vol. 7, No. 1, March 1996, pp. 43-57. [pdf]

Fortune Mhlanga, Zhijian Zhu, Jason T. L. Wang and Peter A. Ng, "A New Approach to Modeling Personal Office Documents," Data and Knowledge Engineering, Vol. 17, 1995, pp. 127-158.

Jason T. L. Wang, Kaizhong Zhang and Gung-Wei Chirn, "Algorithms for Approximate Graph Matching," Information Sciences, Vol. 82, 1995, pp. 45-74.

Jason T. L. Wang, Thomas G. Marr, Dennis Shasha, Bruce A. Shapiro and Gung-Wei Chirn, "Discovering Active Motifs in Sets of Related Protein Sequences and Using Them for Classification," Nucleic Acids Research, Vol. 22, No. 14, Aug. 1994, pp. 2769-2775. [pdf] [PubMed]

Jason T. L. Wang, Kaizhong Zhang, Karpjoo Jeong and Dennis Shasha, "A System for Approximate Tree Matching," IEEE Transactions on Knowledge and Data Engineering, Vol. 6, No. 4, August 1994, pp. 559-571. [pdf]

Xiaolong Hao, Jason T. L. Wang, Michael Bieber and Peter A. Ng, "Heuristic Classification of Office Documents," International Journal on Artificial Intelligence Tools, Vol. 3, No. 2, 1994, pp. 233-265.

Dennis Shasha, Jason T. L. Wang, Kaizhong Zhang and Frank Y. Shih, "Exact and Approximate Algorithms for Unordered Tree Matching," IEEE Transactions on Systems, Man and Cybernetics, Vol. 24, No. 4, April 1994, pp. 668-678. [pdf]

Kaizhong Zhang, Dennis Shasha and Jason T. L. Wang, "Approximate Tree Matching in the Presence of Variable Length Don't Cares," Journal of Algorithms, Vol. 16, No. 1, January 1994, pp. 33-66. [pdf]

Jason T. L. Wang and Peter A. Ng, "TEXPROS: An Intelligent Document Processing System," International Journal of Software Engineering and Knowledge Engineering, Vol. 2, No. 2, June 1992, pp. 171-196.

Dennis Shasha and Tsong-Li Wang, "Optimizing Equi-Join Queries in Distributed Databases where Relations are Hash Partitioned," ACM Transactions on Database Systems, Vol. 16, No. 2, June 1991, pp. 279-308. [pdf]

Dennis Shasha and Tsong-Li Wang, "New Techniques for Best-Match Retrieval," ACM Transactions on Information Systems, Vol. 8, No. 2, April 1990, pp. 140-158; also appeared in ACM Computing Reviews, Vol. 32, June 1991, pp. 9106-0454. [pdf]

Selected Conference Papers and Book Chapters

F. Gerges, M. C. Boufadel, E. Bou-Zeid, A. Darekar, H. Nassif and J. T. L. Wang, "Bayesian Multi-Head Convolutional Neural Networks with Bahdanau Attention for Forecasting Daily Precipitation in Climate Change Monitoring," Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD 2022), Part V, Grenoble, France, September 2022, pp. 565-580.

F. Gerges, M. C. Boufadel, E. Bou-Zeid, H. Nassif and J. T. L. Wang, "A Novel Bayesian Deep Learning Approach to the Downscaling of Wind Speed with Uncertainty Quantification," Proceedings of the 26th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2022), Chengdu, China, May 2022, pp. 55-66.

Y. Abduallah, J. T. L. Wang, Y. Shen, K. A. Alobaid, S. Criscuoli and H. Wang, "Reconstruction of Total Solar Irradiance by Deep Learning," Proceedings of the 34th International Florida Artificial Intelligence Research Society Conference (FLAIRS-34), North Miami Beach, Florida, USA, May 2021. [pdf]

H. Jiang, T. Turki and J. T. L. Wang, "DLGraph: Malware Detection Using Deep Learning and Graph Embedding," Proceedings of the 17th IEEE International Conference on Machine Learning and Applications, Orlando, Florida, USA, December 2018, pp. 1029-1033. [pdf]

Haodi Jiang, Turki Turki, Sen Zhang and Jason T. L. Wang, "Reverse Engineering Gene Regulatory Networks Using Graph Mining," Proceedings of the 14th International Conference on Machine Learning and Data Mining in Pattern Recognition, Part I, New York, USA, July 2018, pp. 335-349.

Haodi Jiang, Turki Turki and Jason T. L. Wang, "Reverse Engineering Regulatory Networks in Cells Using a Dynamic Bayesian Network and Mutual Information Scoring Function," Proceedings of the 16th IEEE International Conference on Machine Learning and Applications, Cancun, Mexico, December 2017, pp. 761-764. [pdf]

Yasser Abduallah and Jason T. L. Wang, "A Time-Delayed Information-Theoretic Approach to the Reverse Engineering of Gene Regulatory Networks Using Apache Spark," Proceedings of the IEEE 2017 International Conference on Big Data Intelligence and Computing, Orlando, Florida, USA, November 2017, pp. 1106-1113.

Turki Turki and Jason T. L. Wang, "Reverse Engineering Gene Regulatory Networks Using Sampling and Boosting Techniques," Proceedings of the 13th International Conference on Machine Learning and Data Mining in Pattern Recognition, New York, NY, USA, July 2017, pp. 63-77. [pdf]

Turki Turki, Jason T. L. Wang and Ibrahim Rajikhan, "Inferring Gene Regulatory Networks by Combining Supervised and Unsupervised Methods," Proceedings of the 15th IEEE International Conference on Machine Learning and Applications, Anaheim, CA, USA, December 2016, pp. 140-145. [pdf]

Turki Turki, William Bassett and Jason T. L. Wang, "A Learning Framework to Improve Unsupervised Gene Network Inference," Proceedings of the 12th International Conference on Machine Learning and Data Mining in Pattern Recognition, New York, NY, USA, July 2016, pp. 28-42. [pdf]

Turki Turki and Jason T. L. Wang, "A New Approach to Link Prediction in Gene Regulatory Networks," Proceedings of the 16th International Conference on Intelligent Data Engineering and Automated Learning (IDEAL 2015), Wroclaw, Poland, October 2015, pp. 404-415. [pdf]

M. Zhu, Y.-F. B. Wu, M. S. Vasavada and J. T. L. Wang, "Learning to Rank Biomedical Documents with only Positive and Unlabeled Examples: A Case Study," in Biological Data Mining and Its Applications in Healthcare, (ed. Xiaoli Li, See-Kiong Ng and Jason T. L. Wang), World Scientific Publishing Co., Inc., 2014, pp. 373-392.

L. Zhong, J. T. L. Wang, D. Wen and B. A. Shapiro, "Pre-miRNA Classification via Combinatorial Feature Mining and Boosting," Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, Pennsylvania, October 2012, pp. 369-372.

Katherine G. Herbert, Junilda Spirollari, Jason T. L. Wang, William H. Piel, John Westbrook, Winona C. Barker, Zhang-Zhi Hu and Cathy H. Wu, "Bioinformatic Databases," in Wiley Encyclopedia of Computer Science and Engineering, (ed. Benjamin Wah), John Wiley & Sons, Inc., 2008, pp. 561:1-561:10.

Jason T. L. Wang, Dongrong Wen, Bruce A. Shapiro, Katherine G. Herbert, Jing Li and Kaushik Ghosh, "Toward an Integrated RNA Motif Database," Proceedings of the 4th International Workshop on Data Integration in the Life Sciences (DILS 2007), Philadelphia, Pennsylvania, June 2007, pp. 27-36.

Mugdha Khaladkar and Jason T. L. Wang, "Detecting Conserved RNA Secondary Structures in Viral Genomes: The RADAR Approach," Proceedings of the 2007 NSF Workshop on Biosurveillance Systems and Case Studies (Biosurveillance 2007), New Brunswick, New Jersey, May 2007, pp. 222-227. [pdf]

Sen Zhang, Katherine G. Herbert, Jason T. L. Wang, William H. Piel and David R. B. Stockwell, "PhyloMiner: A Tool for Evolutionary Data Analysis," Proceedings of the 18th International Conference on Scientific and Statistical Database Management (SSDBM 2006), Vienna, Austria, July 2006, pp. 129-132.

Sen Zhang and Jason T. L. Wang, "Mining Frequent Agreement Subtrees in Phylogenetic Databases," Proceedings of the 6th SIAM International Conference on Data Mining (SDM 2006), Bethesda, Maryland, April 2006, pp. 222-233.

Katherine G. Herbert, Shashikanth Pusapati, Jason T. L. Wang and William H. Piel, "Lineage Path Integration for Phylogenetic Resources," Proceedings of the 17th International Conference on Scientific and Statistical Database Management (SSDBM 2005), Santa Barbara, California, June 2005, pp. 117-120. [pdf]

Katherine G. Herbert, Jason T. L. Wang and Jianghui Liu, "Information Retrieval and Data Mining," in Computer Science Handbook, 2nd edition, (ed. A. B. Tucker), Chapter 75, CRC Press, 2004, pp. 75.1-75.16.

Dennis Shasha, Jason T. L. Wang and Sen Zhang, "Unordered Tree Mining with Applications to Phylogeny," Proceedings of the 20th International Conference on Data Engineering (ICDE 2004), Boston, Massachusetts, April 2004, pp. 708-719. [pdf]

Jason T. L. Wang, Huiyuan Shan, Dennis Shasha and William H. Piel, "TreeRank: A Similarity Measure for Nearest Neighbor Searching in Phylogenetic Databases," Proceedings of the 15th International Conference on Scientific and Statistical Database Management (SSDBM 2003), Cambridge, Massachusetts, July 2003, pp. 171-180. [pdf]

Michael M. Yin and Jason T. L. Wang, "Mining Genes in DNA Using GeneScout," Proceedings of the 2002 IEEE International Conference on Data Mining (ICDM 2002), Maebashi City, Japan, December 2002, pp. 733-736. [pdf]

Huiyuan Shan, Katherine G. Herbert, William H. Piel, Dennis Shasha and Jason T. L. Wang, "A Structure-Based Search Engine for Phylogenetic Databases," Proceedings of the 14th International Conference on Scientific and Statistical Database Management (SSDBM 2002), Edinburgh, Scotland, July 2002, pp. 7-10. [pdf]

Dennis Shasha, Jason T. L. Wang, Huiyuan Shan and Kaizhong Zhang, "ATreeGrep: Approximate Searching in Unordered Trees," Proceedings of the 14th International Conference on Scientific and Statistical Database Management (SSDBM 2002), Edinburgh, Scotland, July 2002, pp. 89-98. [pdf]

Dennis Shasha, Jason T. L. Wang and Rosalba Giugno, "Algorithmics and Applications of Tree and Graph Searching," Proceedings of the 21st ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems (PODS 2002), Madison, Wisconsin, June 2002, pp. 39-52. [pdf] [talk slides in powerpoint]

Qicheng Ma, Jason T. L. Wang and James R. Gattiker, "Mining Biomolecular Data Using Background Knowledge and Artificial Neural Networks," in Handbook of Massive Data Sets, (eds. J. Abello, P. M. Pardalos and M. G. C. Resende), Chapter 30, Kluwer Academic Publishers, 2002, pp. 1141-1168. [pdf]

Jason T. L. Wang, Qicheng Ma and Katherine G. Herbert, "Software Engineering and Knowledge Engineering Issues in Bioinformatics," in Handbook of Software Engineering and Knowledge Engineering, Vol. 1, Fundamentals, (ed. S. K. Chang), Chapter 30, World Scientific Publishing Company, 2001, pp. 719-732. [pdf]

Jason T. L. Wang, Qicheng Ma, Dennis Shasha and Cathy H. Wu, "Application of Neural Networks to Biological Data Mining: A Case Study in Protein Sequence Classification," Proceedings of the 6th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 2000), Boston, Massachusetts, August 2000, pp. 305-309. [pdf]

Jason T. L. Wang, Xiong Wang, Dennis Shasha, Bruce A. Shapiro, Kaizhong Zhang, Qicheng Ma and Zasha Weinberg, "An Approximate Search Engine for Structural Databases," Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 2000), Dallas, Texas, May 2000, pp. 584. [pdf]

Jason T. L. Wang, Xiong Wang, King-Ip Lin, Dennis Shasha, Bruce A. Shapiro and Kaizhong Zhang, "Evaluating a Class of Distance-Mapping Algorithms for Data Mining and Clustering," Proceedings of the 5th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD 1999), San Diego, California, August 1999, pp. 307-311.

Xiong Wang, Jason T. L. Wang, Dennis Shasha, Bruce A. Shapiro, Sitaram Dikshitulu, Isidore Rigoutsos and Kaizhong Zhang, "Automated Discovery of Active Motifs in Three Dimensional Molecules," Proceedings of the 3rd International Conference on Knowledge Discovery and Data Mining (KDD 1997), Newport Beach, California, August 1997, pp. 89-95. [pdf]

Jason T. L. Wang, Dennis Shasha, George J. S. Chang, Liam Relihan, Kaizhong Zhang and Girish Patel, "Structural Matching and Discovery in Document Databases," Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 1997), Tucson, Arizona, May 1997, pp. 560-563.

Jason T. L. Wang, Bruce A. Shapiro, Dennis Shasha, Kaizhong Zhang and Chia-Yo Chang, "Automated Discovery of Active Motifs in Multiple RNA Secondary Structures," Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining (KDD 1996), Portland, Oregon, August 1996, pp. 70-75.

Jason T. L. Wang, Kaizhong Zhang and Dennis Shasha, "Pattern Matching and Pattern Discovery in Scientific, Program and Document Databases," Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 1995), San Jose, CA, May 1995, pp. 487.

Jason T. L. Wang, Gung-Wei Chirn, Thomas G. Marr, Bruce A. Shapiro, Dennis Shasha and Kaizhong Zhang, "Combinatorial Pattern Discovery for Scientific Data: Some Preliminary Results," ACM SIGMOD Record, Vol. 23, No. 2, June 1994, pp. 115-125; also appeared in Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 1994), Minneapolis, Minnesota, May 1994.

Tsong-Li Wang and Dennis Shasha, "Query Processing for Distance Metrics," Proceedings of the 16th International Conference on Very Large Data Bases (VLDB 1990), Brisbane, Australia, Aug. 1990, pp. 602-613.

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