Publications

Refereed Journal Papers

  1. H. Xiong, Y. Zhang, and X Chen, Data-dependent Kernel Machines for Microarray Data Classification, IEEE/ACM Transaction on Computational Biology and Bioinformatics (TCBB), 2007 (in press).

  2. Y. Zhang, H. Zha, C. Chu, and X. Ji, Towards Inferring Protein Interactions: Challenges and Solutions, EURASIP Journal on Applied Signal Processing (Special issue on Advanced Signal/Image Processing Techniques for Bioinformatics), 2006.

  3. J. Z. Wang, K. Grieb, Y. Zhang, C. Chen, Y. Chen, and J. Li, Machine Annotation and Retrieval for Digital Imagery of Historical Materials, International Journal on Digital Libraries (special Issue on Multimedia Contents and Management in Digital Libraries), 6(1), pp.18-29, Springer-Verlag, 2006.

  4. Y. Zhang, C. H. Chu, Y. Chen, H. Zha, and X. Ji, Splice Site Prediction Using Support Vector Machines with a Bayes Kernel, Expert Systems with Applications: An International Journal, (special issue on Intelligent Bioinformatics Systems), 30(1):73-81, 2006

  5. Y. Zhang, J.-M. Chandonia, C. Ding and S. R. Holbrook, Comparative Mapping of Sequence-based and Structure-based Protein Domains, BMC Bioinformatics 2005, 6:77.

  6. Y. Zhang, X. Ji, C. H. Chu, and H. Zha, Correlating Summarization of Multisource News with K-Way Graph Biclustering, SIGKDD explorations (special issue on Web Content Mining), 6(2):34-42, 2004.

Refereed Conference Papers

  1. K. Chen, Y. Zhang, Z. Zheng, H. Zha, and G. Sun, Adapting Ranking Functions to User Preference, in Proc. of ICDE Workshop on Ranking in Databases (DBRank 2008), accepted.

  2. A. Chen, Y. Zhang, and G. Sun, A Two-Stage Approach to Chinese Part-of-Speech Tagging, in Proc. of the Sixth SIGHAN Workshop on Chinese Language Processing (the Fourth International Chinese Language Processing Bakeoff ), January 2008.

  3. H. Xiong, Y. Zhang, and X. Chen. Normalized Linear Transform for Cross-Platform Microarray Data Integration, in Proc. of the Sixth International Conference on Machine Learning and Applications (ICMLA), 2007, pp. 612-617.

  4. C. Ding, Y. Zhang, T. Li, and S. Holbrook, Biclustering Protein Complex Interactions with a Biclique Finding Algorithm, in Proc. of the 6th IEEE International Conference on Data Mining (ICDM), 2006.

  5. Y. Zhang, Y. Chen, and X. Ji, Motif Discovery as a Multiple-Instance Problem, in Proc. of the 18th IEEE International Conference on Tools with Artificial Intelligence (ICTAI), 2006, to appear.

  6. A. Senf, X.-W. Chen, and Y. Zhang, Comparison of One-Class SVM and Two-Class SVM for Fold Recognition, in Proc. of the 13th International Conference on Neural Information Processing, Hong Kong, Lecture Notes in Computer Science (LNCS), Springer-Verlag, pp. 140-149, October 2006.

  7. Y. Chen, Y. Zhang, and X. Ji, Size Regularized Cut for Data Clustering, Advances in Neural Information Processing Systems (NIPS) 18, MIT Press, Cambridge, MA, pp. 211-218, 2006.

  8. Y. Zhang, H. Zha, C. H. Chu, and X. Ji, Protein Interaction Inference as a MAX-SAT Problem, in Proc. of the IEEE CVPR 2005 Workshop on Computer Vision Methods for Bioinformatics, San Diego, CA,, U.S.A., 2005. [Winner of the Best Paper Award]

  9. D. Zhou, Y. Song, Y. Zhang, H. Zha, Towards Discovering Organizational Structure from Email Corpus, in Proc. of the 4th IEEE International Conference on Machine Learning and Applications (ICMLA 2005), Los Angeles , CA, U.S.A. 2005.

  10. A. Chen, Y. Zhou, Y. Zhang, and G. Sun. Unigram Language Model for Chinese Word Segmentation, Fourth SIGHAN Workshop on Chinese Language Processing (Second International Chinese Segmentation Bakeoff), 2005.

  11. Y. Zhang, C. H. Chu, H. Zha, Y. Chen, and X. Ji, A Probabilistic Kernel for Splice Site Prediction, in Proc. of the 8th Joint Conference on Information Sciences, Salt Lake City, UT, July 21-26, 2005, pp. 1278-1281.

  12. Y. Zhang, H. Zha, and C. H. Chu, A Time-Series Biclustering Algorithm for Revealing Co-regulated Genes, in Proc. of IEEE International Conference on Information and Technology: Coding and Computing, (ITCC 2005), pp. 32-37.

  13. H. Xiong, X. He, C. Ding, Y. Zhang, V. Kumar, S. R. Holbrook, Identification of Functional Modules in Protein Complexes via Hyperclique Pattern Discovery, in Proc. of the Pacific Symposium on Biocomputing, (PSB), 2005.

  14. Y. Zhang and J. Z. Wang, Progressive Display of Very High Resolution Images using Wavelets, Journal of American Medical Informatics Association, Symposium Supplement, vol. 2002 suppl., pp. 944-948, November 2002. [Nominated for the Best Paper Award] [Online Demo]

Thesis and Other Publications

  1. Ya Zhang, Towards Inferring Biologically Informative Protein-protein Interactions, Ph.D Dissertation, School of Information Sciences and Technology, The Pennsylvania State University, August 2005.

  2. Y. Zhang, H. Zha, J. Z. Wang and C. H. Chu, Gene Co-regulation vs. Co-expression, the eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), San Diego, CA (March 27-31, 2004)., Currents in Computational Molecular Biology, A. Gramada & P. Bourne (eds.) ACM Press, March 2004., pp 232-233. (Poster)

  3. Y. Zhang, H. Zha, J. Z. Wang and C. H. Chu, Clustering of Time-course Gene Expression Data, the eighth Annual International Conference on Research in Computational Molecular Biology (RECOMB), San Diego, CA (March 27-31, 2004)., Currents in Computational Molecular Biology, A. Gramada & P. Bourne (eds.) ACM Press, March 2004., pp.240-241. (Poster)

  4. H. Wang and Y. Zhang, Book review: Shaping Web Usability: Interaction Design in Context, Information Processing and Management, 39(4), 665-666, 2003.