Wenyuan LI

Molecular and Computational Biology

University of Southern California, Los Angeles, CA 90089, USA

 

Phone:

(213) 821-3983

Email:

WEL@USC.EDU

WWW:

http://www-rcf.usc.edu/~wel

Research Interests and CV

Publications

Presentations

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Practice English

I work on theories of data mining, machine learning, matrix computation and their applications to data analysis. My work is more focused on theoretical aspects of data analysis.

 

Research Interests:

Data mining, Machine Learning, Graph Theory and Algorithms, Spectral Techniques, and Matrix Computation, Statistical Mechanism of Complex Network, Bioinformatics and Biomedical Informatics.

Curriculum Vitae [PDF]

Publications

Book:

  1. Wenyuan Li, Kok-Leong Ong, and Wee-Keong Ng. Spectral Analysis of Complex Data: Data Mining Enhancements Using the Spectral Characteristics of Data. (ISBN: 978-3639175431), VDM Verlag, 2009.

Book Chapters:

  1. Wenyuan Li, Haiyan Hu, Yu Huang, Haifeng Li, Michael R. Mehan, Juan Nunez-Iglesias, Min Xu, Xifeng Yan, and Xianghong Jasmine Zhou. Pattern Mining Across Many Massive Networks.  Functional Coherence of Biological Networks. (M. Koyuturk, S. Subramaniam, and A. Grama Eds.), Springer, in press.
  2. Wenyuan Li, Wee-Keong Ng and Kok-Leong Ong. Graph-based Data Mining. Research and Trends in Data Mining Technologies and Applications: Advances in Data Warehousing and Mining, volume 1 (David Taniar, eds.), Idea Group Publishing, 2007.
  1. Wenyuan Li, Wee-Keong Ng and Kok-Leong Ong. Information Navigation and Knowledge Discovery in Virtual Communities. Encyclopedia of Virtual Communities and Technologies (Subhasish Dasgupta, eds., ISBN: 1-59140-563-7),  Idea Group Publishing, 2005. [PDF]
  1. Wenyuan Li and Wee-Keong Ng. Spectral Methods for Data Clustering. Encyclopedia of Data Warehousing and Mining (John Wang eds., ISBN: 1-59140-557-2), Idea Group Publishing, 2005.

Journals (* indicates joint first authors):

  1. Wenyuan Li, Chun-Chi Liu, Tong Zhang, Haifeng Li, Michael S. Waterman, Xianghong Jasmine Zhou. Integrative Analysis of Many Weighted Co-expression Networks Using Tensor Computation. PLoS Computational Biology. In press.
  2. Wenyuan Li, Min Xu and Xianghong Jasmine Zhou. Unraveling Complex Temporal Associations in Cellular Systems across Multiple Time-Series Microarray Datasets. Journal of Biomedical Informatics. 43(4):550--559, August 2010.
  1. Min Xu*, Wenyuan Li*, Gareth M. James, Michael R. Mehan and Xianghong Jasmine Zhou. Automated Multidimensional Phenotypic Profiling Using Large Public Microarray Repositories. Proceedings of the National Academy of Sciences (PNAS). 106(30): 12323-12328, July 2009. PMID: 19590007. (Highlighted in Nature Methods 6, 632; Selected by 2010 International Medical Informatics Association Yearbook of Medical Informatics) [Online]
  1. Ying Liu and Wenyuan Li. Visualizing Microarray Data for Biomarker Discovery by Matrix Reordering and Replicator Dynamics. Journal of Bioinformatics and Computational Biology (JBCB). 6(6): 1089-1113, December 2008. PMID: 19090019. [Online]
  1. Xiaotu Ma, Aaron M. Tarone, and Wenyuan Li. Mapping Genetically Compensatory Pathways from Synthetic Lethal Interaction in Yeast. PLoS ONE. 3(4): e1922, 2008. PMID: 18398455 (doi:10.1371/journal.pone.0001922)
  1. Yongjing Lin, Wenyuan Li, Keke Chen, and Ying Liu. A Document Clustering and Ranking System for Exploring MEDLINE Citations. Journal of the American Medical Informatics Association (JAMIA). 14(5): 651-661, September/October 2007. PMID: 17600104. (Selected by 2008 International Medical Informatics Association Yearbook of Medical Informatics)
  1. Xiuwen Zheng, Hung-Chung Huang, Wenyuan Li, Peng Liu, Quan-Zhen Li, and Ying Liu. Modeling Nonlinearity in Dilution Design Microarray Data. Bioinformatics. 23(11): 1339-1347, June 2007. PMID: 17237040. [Online]
  1. Wenyuan Li, Yanxiong Peng, Hung-Chung Huang and Ying Liu. Biomarker Discovery And Visualization in Gene Expression Data with Efficient Generalized Matrix Approximations. Journal of Bioinformatics and Computational Biology (JBCB). 5(02A): 251-279, April 2007. PMID: 17589961. [Online]
  1. Wenyuan Li, Wee-Keong Ng,Ying Liu and Kok-Leong Ong. Enhancing the Effectiveness of Clustering with Spectra Analysis. IEEE Transactions on Knowledge and Data Engineering (TKDE). 19(7): 887-902, July 2007.
  1. Wenyuan Li, Ying Liu, Hung-Chung Huang, Yanxiong Peng, Yongjing Lin, Wee-Keong Ng and Kok-Leong Ong. Dynamical Systems for Discovering Protein Complexes and Functional Modules from Biological Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). 4(2): 233-250, April-June 2007. PMID: 17473317.
  1. Wenyuan Li*, Yongjing Lin*, and Ying Liu. The Structure of Weighted Small-World Network. Physica A: Statistical Mechanics and its Applications, 376: 708-718, 15 March 2007. (doi:10.1016/j.physa.2006.10.015) [Online]
  1. Yanxiong Peng, Wenyuan Li and Ying Liu. A Hybrid Approach for Biomarker Discovery from Microarray Gene Expression Data. Cancer Informatics. 2: 301-311, 2006. [Online]
  1. Wenyuan Li, Yinliang Zhao, Jinfang Yang. Intermittent Performance Analysis Approach of Parallel Programs. Journal of Xi'an Jiao Tong University. 67(3), 2003. (In Chinese)
  1. Zhijun Zheng, Wenyuan Li, Shouqi, Zheng. Solving Complicated Problems of Pattern Recognition Using Multi-model of Artificial Neural Networks with Serial-parallel Structure, Journal of Computer Engineering, 27(6) 2001. (In Chinese)

Conferences and Workshops:

  1.  Ying Liu, Wenyuan Li, Yongjing Lin, Liping Jing. Spectral Geometry For Simultaneously Clustering and Ranking Query Search Results. 31st Annual International ACM SIGIR Conference, Singapore, July 2008.
  1. Wenyuan Li, Xiuwen Zheng, and Ying Liu. Gene Selection by Matrix Reordering and Replicator Dynamics.  7th International Workshop on Data Mining in Bioinformatics (BIOKDD '07) in ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Jose, CA, USA, August 2007.
  1. Wenyuan Li and Ying Liu. Modeling Species-Genes Data for Efficient Phylogenetic Inference.  Life Science Society Computational Systems Bioinformatics Conference (CSB), University of California San Diego, USA, August 2007. PMID: 17951845.
  1. Wenyuan Li and Ying Liu. Generalized Replicator Dynamics for Efficient Phylogenetic Inference. 7th SIAM International Conference on Data Mining (SDM) Workshop on Data Mining for Biomedical Informatics, Minneapolis, USA, April 2007.
  1. Wenyuan Li, Yanxiong Peng, Hung-Chung Huang and Ying Liu. Efficient Generalized Matrix Approximations for Biomarker Discovery and Visualization in Gene Expression Data. Life Science Society Computational Systems Bioinformatics Conference (CSB), Stanford University, USA, August 2006. PMID: 17369632.
  1. Wenyuan Li, Kok-Leong Ong and Wee-Keong Ng. Text Mining: A Discrete Dynamical System Approach Using the Resonance Model. Proc. 4th Australasian Data Mining Conf., Sydney, Australia, December 2005.
  1. Wenyuan Li, Kok-Leong Ong and Wee-Keong Ng. Visual Terrain Analysis of High-dimensional Datasets. Proc. of the 9th European Conf. on Principles of Data Mining and Knowledge Discovery (PKDD), Porto, Portugal, October 2005.
  1. Wenyuan Li, Kok-Leong Ong, Wee-Keong Ng and Aixin Sun. Spectral Kernels for Classification. Proc. of the 7th Int. Conf. on Data Warehousing and Knowledge Discovery (DaWaK), Copenhagen, Denmark, August 2005. [PDF]
  1. Hai Wang, Wenyuan Li, Zengzhi Li and Lin Fan. Finding Closed Itemsets in Data Streams. Special Session on Knowledge Discovery in Data Streams in Conjunction with the 9th Int. Conf. on Knowledge-based Intelligent Information & Engineering Systems, Melbourne, Australia, September, 2005.
  1. Wenyuan Li, Wee-Keong Ng, and Ee-Peng Lim. Spectral Analysis of Text Collection for Similarity-based Clustering Proc. of the 20th International Conference on Data Engineering (ICDE), Boston, USA, March 2004. [CiteSeer Impact Factor: 167/1221, top 13.67%]
  1. Wenyuan Li, Wee-Keong Ng, Kok-Leong Ong and Ee-Peng Lim. A Spectroscopy of Texts for Effective Clustering. Proc. of the 8th European Conf. on Principles of Data Mining and Knowledge Discovery (PKDD), Pisa, Italy, September 2004. [PDF]
  1. Kok-Leong Ong, Wenyuan Li, Wee-Keong Ng and Ee-Peng Lim. SCLOPE: An Algorithm for Clustering Data Streams of Categorical Attributes. Proc. of the 6th Int. Conf. on Data Warehousing and Knowledge Discovery (DaWaK), Zaragoza, Spain, September 2004. [PDF]

Technical Reports:

  1. Wenyuan Li, Yongjing Lin and Ying Liu. Spectral Analysis of Complex Networks. Technical Report (UTDCS-17-07), March 2007.
  1. Wenyuan Li and Ying Liu. Generalized Replicator Dynamics for Efficiently Building Phylogenetic Tree. Technical Report (UTDCS-25-06), June 2006.
  1. Wenyuan Li, Kok-Leong Ong and Wee-Keong Ng. Visual Terrain Analysis of High-dimensional Datasets. Technical Report (TRC04/06), May 2005. [PDF]
  1. Wenyuan Li, Kok-Leong Ong, Wee-Keong Ng and Aixin Sun. Spectral Kernels for Classification. Technical Report (TRC05/05), March 2005. [PDF]
  1. Kok-Leong Ong, Wenyuan Li, Wee-Keong Ng and Ee-Peng Lim. SCLOPE: An Algorithm for Clustering Data Streams of Categorical Attributes. Technical Report (TRC04/05), May 2004. [PDF]
  1. Wenyuan Li, Kok-Leong Ong and Wee-Keong Ng. Enhancing the Effectiveness of Clustering with Spectra Analysis. Technical Report (TRC04/03), March 2004. [PDF]

Presentations in Conferences and Workshops:

Life Science Society Computational Systems Bioinformatics Conference (http://www.lifesciencessociety.org/CSB2006/program.html), Stanford university, August 2006.

Dallas Area Bioinformatics and Computational Biology Workshop (http://webpath.swmed.edu/dab/DABsched.html), Dallas, August 2006.

The 8th European Conference on Principles of Data Mining and Knowledge Discovery (http://ecmlpkdd.isti.cnr.it/programDetail.html), Pisa Italy, September 2004.

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