Publications

• TaeHyun Hwang, Ze Tian, Jean-Pierre Kocher, and Rui Kuang.
  Learning on Weighted Hypergraphs to Integrate Protein Interactions and Gene Expressions for Cancer Outcome Prediction, [Paper]
  Accepted In the Eighth IEEE International Conference on Data Mining (ICDM), Dec. 2008.

• TaeHyun Hwang, Hugues Sicotte, Ze Tian, Baolin Wu, Dennis Wigle, Jean-Pierre Kocher, Vipin Kumar and Rui Kuang.
  Robust and Efficient Identification of Biomarkers by Classifying Features on Graphs, [Paper] [Download]
  Bioinformatics, Vol. 24, No. 18, pages 2023-2029, 2008

• TaeHyun Hwang and Rui Kuang.
  A Comparative Study of Breast Cancer Microarray Gene Expression Profiles using Label Propagation, [Paper]
  Proceedings of the Workshop on Data Mining for Biomedical Informatics, held in conjunction with SIAM International Conference on Data Mining, 2008.

• TaeHyun Hwang, Hugues Sicotte, Dennis Wigle, Jean-Pierre Kocher, Vipin Kumar and Rui Kuang.
  Identifying Clinical and Genetic Markers of Human Disease by Classifying Features on Graphs, [Paper]
  Technical Report UMN-CS-07-021, Sept. 2007

• Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford Noble and Christina Leslie.
  SVM-fold: a tool for discriminative multi-class protein fold and superfamily recognition, [Paper]
  BMC Bioinformatics 2007, 8 (Suppl 4) : S2

• Rui Kuang
  Inferring Protein Structure with Discriminative Learning and Network Diffusion, [Manuscript]
  Ph.D. Thesis (Columbia University), 2006 

• Jason Weston, Rui Kuang, Christina Leslie and William Stafford Noble.
  Protein Ranking by Semi-Supervised Network Propagation, [Paper]
  BMC Bioinformatics 2006, 7 (Suppl 1) : S10

• Rui Kuang , Jason Weston, William Stafford Noble and Christina Leslie.
  Motif-based Protein Ranking by Network Propagation, [Paper] [Download]
  Bioinformatics Vol.21 No.19, pages 3711-3718, 2005

• Rui Kuang ,Eugene Ie, Ke Wang, Kai Wang,Mahira Siddiqi, Yoav Freund and Christina Leslie.
  Profile-based String Kernels for Remote Homology Detection and Motif Extraction,[Paper ][Download]
  Journal of Bioinformatics and Computational Biology Vol. 3, No. 3 527-550, 2005 (Journal version of CSB 2004 paper)

• William Stafford Noble, Rui Kuang, Christina Leslie and Jason Weston.
  Identifying Remote Protein Homologs by Network Propagation, [Paper]
  The FEBS Journal. 272(20):5119-5128, 2005

• Rui Kuang ,Eugene Ie, Ke Wang, Kai Wang,Mahira Siddiqi, Yoav Freund and Christina Leslie.
  Profile-based String Kernels for Remote Homology Detection and Motif Extraction,
  [Paper][Download] [Slides]
  Proc. of the Computational Systems Bioinformatics Conference (IEEE CSB), 2004

• Christina Leslie and Rui Kuang.
  Fast String Kernels Using Inexact Matching for Protein Sequences, [Paper] [Download]
  Journal of Machine Learning Research Vol. 5, pages 1435--1455, 2004 (Journal version of COLT/KW 2003 paper)

• Rui Kuang, Christina Leslie and An-Suei Yang.
  Protein Backbone Angle Prediction with Machine Learning Approaches, [Paper] [Download]
  Bioinformatics Vol.20 No.10, pages 1612-1621, 2004

• Christina Leslie, Rui Kuang and Eleazar Eskin.
  Inexact Matching String Kernels for Protein Classification, [Book]
  Kernel Methods in Computational Biology. B. Schoelkopf, K. Tsuda and J.-P. Vert, ed. MIT Press, 2004

• Christina Leslie and Rui Kuang.
  Fast Kernels for Inexact String Matching, [Paper][Download]
  Proc. of Conference on Learning Theory and Kernel Workshop (COLT/KW), 2003