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Haixuan Yang 

Ph.D. in Computer Science & Engineering
(The Chinese Univ. of Hong Kong, 2007)

Ph.D. in Mathematics
(Lanzhou University, 1996)

Email: haixuan@cs.rhul.ac.uk


[Short Bio] [Current Research Projects] [Publications] [Professional Activities]


I am currently a postdoctoral research assistant in Centre for Systems and Synthetic Biology & Department of Computer Science at Royal Holloway University of London with Prof. Alberto Paccanaro. From Feburary 2008 to July 2008, I was a postdoctoral fellow in the Department of Computer Science and Engineering at CUHK with Prof. Irwin King and Prof. Michael R. Lyu. I am interested in Machine Learning, Bioinformatics, Information Retrieval, and Information Systems.

Current Research Projects

A cell can be viewed as a complex network of inter-relating proteins, nucleic acids and other bio-molecules. A bio-molecular network can be viewed as a collection of nodes, representing the bio-molecules, connected by links, representing relations between the bio-molecules. I am working on learning/mining valuable information from bio-molecular networks.

·         Support Node Partition

·         Graph Dependency

·         Development of a graph-theoretic approach to predict protein function by integrating large scale heterogeneous data

·         Methods for Semantic similarity

Selected Publications (Full list)


1.      Hao Ma, Haixuan Yang, Irwin King, & Michael R. Lyu. Semi-nonnegative matrix factorization with global statistical consistency for collaborative filtering. CIKM09.

2.      Haixuan Yang, Irwin King, & Michael R. Lyu. Learning with consistency between Inductive functions and kernels. NIPS08.

3.      Hao Ma, Haixuan Yang, Michael R. Lyu, & Irwin King. SoRec: social recommendation using probabilistic matrix factorization. CIKM08.

4.      Hao Ma, Haixuan Yang, Irwin King, & Michael R. Lyu. Learning latent semantic relations from query logs for query suggestion. CIKM08.

5.      Hao Ma, Haixuan Yang, Michael R. Lyu, & Irwin King. Mining social networks using heat diffusion processes for marketing candidates selection. CIKM08.

6.      Haixuan Yang, Irwin King, & Michael R. Lyu. DiffusionRank: a possible penicillin for Web spamming. SIGIR07.

7.      Haixuan Yang, Irwin King, & Michael R. Lyu. Predictive random graph ranking on the Web. WCCI06.

8.      Yangfan Zhou, Haixuan Yang, Michael R. Lyu, & Edith C.-H. Ngai. A point-distribution index and its application to sensor grouping in wireless sensor networks. IWCMC06.

9.      Haixuan Yang, Irwin King, & Michael R. Lyu. Predictive ranking: a novel rage ranking approach by estimating the Web structure. WWW05 (Special interest tracks and posters).

10.  Haixuan Yang, Irwin King, & Michael R. Lyu. NHDC and PHDC: non-propagating and propagating heat diffusion classifiers. ICONIP05.


1.     Pierre C. Havugimana, G. Traver Hart, Tamás Nepusz, Haixuan Yang, Andrei L. Turinsky, Zhihua Li, Peggy I. Wang, Daniel R. Boutz, Vincent Fong, Sadhna Phanse, Mohan Babu, Stephanie A. Craig, Pingzhao Hu, Cuihong Wan, James Vlasblom, Vaqaar-un-Nisa Dar, Alexandr Bezginov, Gregory W. Clark, Gabriel C. Wu, Shoshana J. Wodak, Elisabeth R.M. Tillier, Alberto Paccanaro, Edward M. Marcotte, Andrew Emili. A Census of Human Soluble Protein Complexes. Cell, Vol. 150, No. 5, 2012.

2.     Predrag Radivojac, Wyatt T Clark, Tal Ronnen Oron, Alexandra M Schnoes, Tobias Wittkop, Artem Sokolov, Kiley Graim, Christopher Funk, Karin Verspoor, Asa Ben-Hur, Gaurav Pandey, Jeffrey M Yunes, Ameet S Talwalkar, Susanna Repo, Michael L Souza, Damiano Piovesan, Rita Casadio, Zheng Wang, Jianlin Cheng, Hai Fang, Julian Gough, Patrik Koskinen, Petri Törönen, Jussi Nokso-Koivisto, Liisa Holm, Domenico Cozzetto, Daniel W A Buchan, Kevin Bryson, David T Jones, Bhakti Limaye, Harshal Inamdar, Avik Datta, Sunitha K Manjari, Rajendra Joshi, Meghana Chitale, Daisuke Kihara, Andreas M Lisewski, Serkan Erdin, Eric Venner, Olivier Lichtarge, Robert Rentzsch, Haixuan Yang, Alfonso E Romero, Prajwal Bhat, Alberto Paccanaro, Tobias Hamp, Rebecca Kassner, Stefan Seemayer, Esmeralda Vicedo, Christian Schaefer, Dominik Achten, Florian Auer, Ariane Böhm, Tatjana Braun, Maximilian Hecht, Mark Heron, Peter Hönigschmid, Thomas Hopf, Stefanie Kaufmann, Michael Kiening, Denis Krompass, Cedric Landerer, Yannick Mahlich, Manfred Roos, Jari Björne, Tapio Salakoski, Andrew Wong, Hagit Shatkay, Fanny Gatzmann, Ingolf Sommer, Mark N Wass, Michael J E Sternberg, Nives Škunca, Fran Supek, Matko Bošnjak, Panče Panov, Sašo Džeroski, Tomislav Šmuc, Yiannis A I Kourmpetis, Aalt D J van Dijk, Cajo J F ter Braak, Yuanpeng Zhou, Qingtian Gong, Xinran Dong, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Barbara Di Camillo, Stefano Toppo, Liang Lan, Nemanja Djuric, Yuhong Guo, Slobodan Vucetic, Amos Bairoch, Michal Linial, Patricia C Babbitt, Steven E Brenner, Christine Orengo, Burkhard Rost, Sean D Mooney, Iddo Friedberg. A large-scale evaluation of computational protein function prediction. To appear in Nature Methods.

3.      Haixuan Yang, Tamás Nepusz, & Alberto Paccanaro. Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty. Bioinformatics, Vol. 28, No. 10, 2012.

4.      Prajwal Bhat, Haixuan Yang, Laszlo Bögre, Alessandra Devoto, & Alberto Paccanaro. Computational selection of transcriptomics experiments improves Guilt-by-Association analyses. PLoS ONE 7(8), 2012.

5.      Haixuan Yang, Michael R. Lyu, & Irwin King. A volume-based heat diffusion classifier. IEEE Transactions on Systems, Man, and Cybernetics: Part B, Vol. 39, No. 2, 2009.

6.      Haixuan Yang, Irwin King, & Michael R. Lyu. The generalized dependency degree between attributes. Journal of the American Society for Information Science and Technology, Vol.58, No.14, 2007.

7.      Haixuan Yang. Two operators on the lattice of completely regular semigroup varieties. Semigroup Forum, Vol.64, 2002.

8.      Haixuan Yang. Identities of regular semigroup rings. Semigroup Forum, Vol.57, No.2, 1998.

9.      Haixuan Yang. Properties of a class of lattice of subvarieties of varieties of completely regular semigroups. Acta Mathematica Sinica, Vol.41, No.4, 1998.

10.  Haixuan Yang, & Yanfeng Luo, The existence of identity of periodic semigroup rings. Chinese Science Bulletin, Vol.42, No.7, 1997.

Professional Activities

1.      Program Committee. 2011 International Conference on Neural Information Processing (ICONIP 2011).

2.      Program Committee. The 6th Pattern Recognition in Bioinformatics Conference (PRIB 2011).

3.      Program Committee. The 2011 IEEE/WIC/ACM International Conference on Web Intelligence (WI'11).

4.      Program Committee. 2011 International Joint Conference on Neural Networks (IJCNN 2011).

5.      Program Committee. The 17th International Conference on Neural Information Processing (ICONIP 2010).

6.      Program Committee. The 5th Pattern Recognition in Bioinformatics Conference (PRIB 2010).

7.      Program Committee. The 2010 IEEE/WIC/ACM International Conference on Web Intelligence (WI'10).

8.      Technical Program Committee (TPC). The 20th International Conference on Pattern Recognition (ICPR 2010).

9.      Program Committee. The 16th International Conference on Neural Information Processing (ICONIP'09).

10.  Technical Program Committee (TPC). 2008 IEEE World Congress on Computational Intelligence (WCCI 2008).

11.  Program Co-Chair. The Second Beijing-Hong Kong International Doctoral Forum. July 3-6, 2007.

12.  General Secretary. The 13th International Conference on Neural Information Processing (ICONIP'06).