Mathematical and Statistical Sciences

Dr Haixuan Yang

MSc, PhD

Biography

I enjoyed my research on Pure Mathematics, mainly guided by my PhD advisor Prof. Yuqi Guo.

However, in 2004, driven by my interest to solve practical problems, I decided to move to Computer Science. I joined the PhD programme in Computer Science & Engineering of CUHK where I obtained my second PhD (and later conducted months of postdoc research) under the supervision of Prof. Irwin King and Prof. Michael R. Lyu. In my thesis, I established three machine learning modelling frameworks: (i) Heat Diffusion Models on Random Graphs, (ii) Predictive Random Graph Ranking, and (iii) Random Graph Dependency. These belong to Statistical Modelling and Inference for Networks. For my postdoctoral training I decided to work in Bioinformatics -- an area with many interesting practical problems which are both challenging and significant. During a period of more than three years with Prof. Alberto Paccanaro at Royal Holloway University of London, I have been developing novel graph-based statistical approaches (random walks, heat diffusion, semi-supervised machine learning, establishment of significance tests, etc.) for some significant biological problems such as inferring protein-protein interactions, calculating semantic similarity measures, predicting protein functions, and comparing different graphs. All these work belong to Bioinformatics using Statistical Methodology.

Now comes an ideal convergence point of my previous experiences: I am continuing my academic efforts on designing/applying statistical methods to tackle some Biological problems -- to which, I feel that, I am fully exploiting my abilities in Mathematics, Machine Learning, and Computer Science, and -- for which, my curiosity about living beings is substantially satisfied. A short phrase describing my current research is Bioinformatics & Statistical Modelling, especially of network data such as PPI, co-expression, and functional similarity.

Peer Reviewed Journals

	Year	Publication
	(2016)	'Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization' Yang, HX;Seoighe, C (2016) 'Impact of the Choice of Normalization Method on Molecular Cancer Class Discovery Using Nonnegative Matrix Factorization'. Plos One, 11 [DOI] [Details]
	(2016)	'An expanded evaluation of protein function prediction methods shows an improvement in accuracy' Jiang, YX;Oron, TR;Clark, WT;Bankapur, AR;D'Andrea, D;Lepore, R;Funk, CS;Kahanda, I;Verspoor, KM;Ben-Hur, A;Koo, DCE;Penfold-Brown, D;Shasha, D;Youngs, N;Bonneau, R;Lin, A;Sahraeian, SME;Martelli, PL;Profiti, G;Casadio, R;Cao, RZ;Zhong, Z;Cheng, JL;Altenhoff, A;Skunca, N;Dessimoz, C;Dogan, T;Hakala, K;Kaewphan, S;Mehryary, F;Salakoski, T;Ginter, F;Fang, H;Smithers, B;Oates, M;Gough, J;Toronen, P;Koskinen, P;Holm, L;Chen, CT;Hsu, WL;Bryson, K;Cozzetto, D;Minneci, F;Jones, DT;Chapman, S;Dukka, BKC;Khan, IK;Kihara, D;Ofer, D;Rappoport, N;Stern, A;Cibrian-Uhalte, E;Denny, P;Foulger, RE;Hieta, R;Legge, D;Lovering, RC;Magrane, M;Melidoni, AN;Mutowo-Meullenet, P;Pichler, K;Shypitsyna, A;Li, B;Zakeri, P;ElShal, S;Tranchevent, LC;Das, S;Dawson, NL;Lee, D;Lees, JG;Sillitoe, I;Bhat, P;Nepusz, T;Romero, AE;Sasidharan, R;Yang, HX;Paccanaro, A;Gillis, J;Sedeno-Cortes, AE;Pavlidis, P;Feng, S;Cejuela, JM;Goldberg, T;Hamp, T;Richter, L;Salamov, A;Gabaldon, T;Marcet-Houben, M;Supek, F;Gong, QT;Ning, W;Zhou, YP;Tian, WD;Falda, M;Fontana, P;Lavezzo, E;Toppo, S;Ferrari, C;Giollo, M;Piovesan, D;Tosatto, SCE;del Pozo, A;Fernandez, JM;Maietta, P;Valencia, A;Tress, ML;Benso, A;Di Carlo, S;Politano, G;Savino, A;Rehman, HU;Re, M;Mesiti, M;Valentini, G;Bargsten, JW;van Dijk, ADJ;Gemovic, B;Glisic, S;Perovic, V;Veljkovic, V;Veljkovic, N;Almeida-e-Silva, DC;Vencio, RZN;Sharan, M;Vogel, J;Kansakar, L;Zhang, S;Vucetic, S;Wang, Z;Sternberg, MJE;Wass, MN;Huntley, RP;Martin, MJ;O'Donovan, C;Robinson, PN;Moreau, Y;Tramontano, A;Babbitt, PC;Brenner, SE;Linial, M;Orengo, CA;Rost, B;Greene, CS;Mooney, SD;Friedberg, I;Radivojac, P (2016) 'An expanded evaluation of protein function prediction methods shows an improvement in accuracy'. Genome Biology, 17 [DOI] [Details]
	(2014)	'GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology' Horacio Caniza, Alfonso E Romero, Samuel Heron, Haixuan Yang, Alessandra Devoto, Marco Frasca, Marco Mesiti, Giorgio Valentini, Alberto Paccanaro (2014) 'GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology'. Bioinformatics, 30 (15):2235-2236 [Details]
	(2014)	'Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules' Sandra P Smieszek, Haixuan Yang, Alberto Paccanaro, Paul F Devlin (2014) 'Progressive promoter element combinations classify conserved orthogonal plant circadian gene expression modules'. Journal Of The Royal Society Interface, 11 (99) [Details]
	(2013)	'A large-scale evaluation of computational protein function prediction' Radivojac, Predrag and Clark, Wyatt T and Oron, Tal Ronnen and Schnoes, Alexandra M and Wittkop, Tobias and Sokolov, Artem and Graim, Kiley and Funk, Christopher and Verspoor, Karin and Ben-Hur, Asa and others (2013) 'A large-scale evaluation of computational protein function prediction'. Nature Methods, :221-227 [Details]
	(2012)	'Computational Selection of Transcriptomics Experiments Improves Guilt-by-Association Analyses' Bhat, Prajwal and Yang, Haixuan and B\"ogre, L\'aszl\'o and Devoto, Alessandra and Paccanaro, Alberto (2012) 'Computational Selection of Transcriptomics Experiments Improves Guilt-by-Association Analyses'. PloS one, 7 (8) [ARAN Link] [Details]
	(2012)	'Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty' Yang, Haixuan and Nepusz, Tam\'as and Paccanaro, Alberto (2012) 'Improving GO semantic similarity measures by exploring the ontology beneath the terms and modelling uncertainty'. Bioinformatics, 28 (10):1383-1389 [Details]
	(2012)	'A census of human soluble protein complexes' Havugimana, Pierre C and Hart, G Traver and Nepusz, Tam\'as and Yang, Haixuan and Turinsky, Andrei L and Li, Zhihua and Wang, Peggy I and Boutz, Daniel R and Fong, Vincent and Phanse, Sadhna and others (2012) 'A census of human soluble protein complexes'. Cell, 150 (5):1068-1081 [ARAN Link] [Details]
	(2009)	'A volume-based heat-diffusion classifier' Yang, Haixuan and Lyu, Michael R and King, Irwin (2009) 'A volume-based heat-diffusion classifier'. Systems, Man, and Cybernetics, Part B: Cybernetics, IEEE Transactions on, 39 (2):417-430 [Details]
	(2007)	'The generalized dependency degree between attributes' Yang, Haixuan and King, Irwin and Lyu, Michael R (2007) 'The generalized dependency degree between attributes'. Journal of the American Society for Information Science and Technology, 58 (14):2280-2294 [Details]
	(2002)	'Two Operators on the Lattice of Completely Regular Semigroup Varieties' Yang, Haixuan (2002) 'Two Operators on the Lattice of Completely Regular Semigroup Varieties'. Semigroup Forum, 64 (3):397-424 [Details]
	(2002)	'Identity of semigroup semiring (in Chinese)' Haixuan Yang and Chang-ming Zheng (2002) 'Identity of semigroup semiring (in Chinese)'. Journal of Tianjin University of Commerce volume=22, 22 (3):17-18 [Details]
	(2001)	'The identity of completely $\Pi$ regular semigroup rings (in Chinese)' Haixuan Yang (2001) 'The identity of completely $\Pi$ regular semigroup rings (in Chinese)'. Journal of Lanzhou University, 37 (2):34-37 [Details]
	(1998)	'Identities of Regular Semigroup Rings' Yang, Haixuan (1998) 'Identities of Regular Semigroup Rings'. Semigroup Forum, 57 (2):293-295 [Details]
	(1998)	'Properties of a Class of Lattice of Subvarieties of Variety of Completely Regular Semigroups' Yang, H (1998) 'Properties of a Class of Lattice of Subvarieties of Variety of Completely Regular Semigroups'. ACTA MATHEMATICA SINICA-CHINESE EDITION-, 41 :727-730 [Details]
	(1998)	'Semigroups whose idempotents are primitive' Yang, Hai Xuan and Zhao, Xi Ying (1998) 'Semigroups whose idempotents are primitive'. J. Lanzhou Univ. Nat. Sci, 34 (3):6-9 [Details]
	(1997)	'A note on $\scr H$ relation on an inverse semigroup' Sen, M. K. and Yang, H. X. and Guo, Y. Q. (1997) 'A note on $\scr H$ relation on an inverse semigroup'. J. Pure Math, 14 :1-3 [Details]
	(1997)	'The existence of identity of periodic semigroup rings' Yang, Haixuan and Luo, Yanfeng (1997) 'The existence of identity of periodic semigroup rings'. Chinese science bulletin, 42 (7):614-615 [Details]
	(1997)	'The identity of periodic semigroup rings (in Chinese)' Haixuan Yang and Cong Cao and Bingshen Yang (1997) 'The identity of periodic semigroup rings (in Chinese)'. Journal of Lanzhou University, 33 (2):11-13 [Details]
	(1997)	'Orthogroups of which every subgroup is abelian (in Chinese)' Haixuan Yang (1997) 'Orthogroups of which every subgroup is abelian (in Chinese)'. Journal of Lanzhou University, 33 (004):25-28 [Details]
	(1996)	'The descriptions of semigropups whose H realtion is a left congruence (in Chinese)' Haixuan Yang and Zhenji Tian (1996) 'The descriptions of semigropups whose H realtion is a left congruence (in Chinese)'. Journal of Lanzhou Railway University, 15 (002):88-90 [Details]
	(1996)	'The join of the varieties of completely regular semigroups (in Chinese)' Haixuan Yang (1996) 'The join of the varieties of completely regular semigroups (in Chinese)'. Journal of Yunnan University, 18 (004):373-376 [Details]
	(1996)	'The join of the varieties OLBG and ORBG' Yang, HAIXUAN (1996) 'The join of the varieties OLBG and ORBG'. Soochow Journal of Mathematics, 22 (3):405-410 [Details]
	(1996)	'Excellent extensions and Smach products (in Chinese)' Liu Zhongkui and Haixuan Yang (1996) 'Excellent extensions and Smach products (in Chinese)'. Journal of Northwest Normal Univeristy, 32 (1):3-7 [Details]
	(1996)	'The existence of identity of periodic semigroup rings (In Chinese)' Haixuan Yang and Yanfeng Luo (1996) 'The existence of identity of periodic semigroup rings (In Chinese)'. Chinese Science Bulletin, 21 :023-023 [Details]
	(1996)	'Characterizations of some kinds of regular semigroups by inverses of elements' Sen, M. K. and Yang, H. X. and Guo, Y. Q. (1996) 'Characterizations of some kinds of regular semigroups by inverses of elements'. Filomat, (10):99-105 [Details]
	(1995)	'Congruences and homomorphic image of left c-semigroup (in Chinese)' Yanfeng Luo and Haixuan Yang (1995) 'Congruences and homomorphic image of left c-semigroup (in Chinese)'. Journal of Lanzhou University, 31 (004):22-27 [Details]
	(1992)	'An application of a cyclic matrix (in Chinese)' Haixuan Yang (1992) 'An application of a cyclic matrix (in Chinese)'. Journal of Shandong Normal University, 7 (004):157-157 [Details]

Conference Publications

	Year	Publication
	(2009)	*Advances in Neural Information Processing Systems* Yang, Haixuan and King, Irwin and Lyu, Michael R (2009) Learning with Consistency between Inductive Functions and Kernels Advances in Neural Information Processing Systems , pp.1849-1856 [ARAN Link] [Details]
	(2009)	*Proceeding of the 18th ACM conference on Information and knowledge management* Ma, Hao and Yang, Haixuan and King, Irwin and Lyu, Michael R (2009) Semi-nonnegative matrix factorization with global statistical consistency for collaborative filtering Proceeding of the 18th ACM conference on Information and knowledge management , pp.767-776 [ARAN Link] [Details]
	(2008)	*Learning from Multiple Sources Workshop, NIPS 2008* Yang, Haixuan and Bhat, Prajwal and Shanahan, Hugh and Paccanaro, Alberto (2008) A Maximal Eigenvalue Method for Detecting Process Representative Genes by Integrating Data from Multiple Sources Learning from Multiple Sources Workshop, NIPS 2008 [ARAN Link] [Details]
	(2008)	*Proceeding of the 17th ACM conference on Information and knowledge management* Ma, Hao and Yang, Haixuan and Lyu, Michael R and King, Irwin (2008) Mining social networks using heat diffusion processes for marketing candidates selection Proceeding of the 17th ACM conference on Information and knowledge management , pp.233-242 [ARAN Link] [Details]
	(2008)	*Proceeding of the 17th ACM conference on Information and knowledge management* Ma, Hao and Yang, Haixuan and Lyu, Michael R and King, Irwin (2008) Sorec: social recommendation using probabilistic matrix factorization Proceeding of the 17th ACM conference on Information and knowledge management , pp.931-940 [ARAN Link] [Details]
	(2008)	*Proceeding of the 17th ACM conference on Information and knowledge management* Ma, Hao and Yang, Haixuan and King, Irwin and Lyu, Michael R (2008) Learning latent semantic relations from clickthrough data for query suggestion Proceeding of the 17th ACM conference on Information and knowledge management , pp.709-718 [ARAN Link] [Details]
	(2007)	*Proceedings of the 30th annual international ACM SIGIR conference on Research and development in information retrieval* Yang, Haixuan and King, Irwin and Lyu, Michael R (2007) Diffusionrank: a possible penicillin for web spamming Proceedings of the 30th annual international ACM SIGIR conference on Research and development in information retrieval , pp.431-438 [ARAN Link] [Details]
	(2006)	*Neural Networks, 2006. IJCNN'06. International Joint Conference on* Yang, Haixuan and King, Irwin and Lyu, Michael R (2006) Predictive random graph ranking on the web Neural Networks, 2006. IJCNN'06. International Joint Conference on , pp.1825-1832 [ARAN Link] [Details]
	(2006)	*Proceedings of the 2006 international conference on Wireless communications and mobile computing* Zhou, Yangfan and Yang, Haixuan and Lyu, Michael R and Ngai, Edith C-H (2006) A point-distribution index and its application to sensor-grouping in wireless sensor networks Proceedings of the 2006 international conference on Wireless communications and mobile computing , pp.1171-1176 [ARAN Link] [Details]
	(2005)	*Special interest tracks and posters of the 14th international conference on World Wide Web* Yang, Haixuan and King, Irwin and Lyu, Michael R (2005) Predictive ranking: a novel page ranking approach by estimating the web structure Special interest tracks and posters of the 14th international conference on World Wide Web , pp.944-945 [ARAN Link] [Details]
	(2005)	*Proceedings of 12th International Conference on Neural Information Processing* Yang, Haixuan and King, Irwin and Lyu, Michael R (2005) NHDC and PHDC: Non-propagating and propagating heat diffusion classifiers Proceedings of 12th International Conference on Neural Information Processing , pp.394-399 [ARAN Link] [Details]