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Recent publications |
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| Antonia Kolokythas, Mitchell J Bosman, Kristen B Pytynia, Suchismita Panda,Herve Y Sroussi, Yang Dai, Joel L Schwartz, Guy R Adami."A prototype tobacco-associated oral squamous cell carcinoma classifier using RNA from brush cytology.". J Oral Pathol Med. (2013). doi: 10.1111/jop.12068. PubMed
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| Yang Dai, Lei Huang. "Integrative Bioinformatics Approaches toward Systems-level Understanding of Breast Cancers, in Breast Cancer Metastasis and Drug Resistance". Progress and Prospects, (ed. A. Ahmad), Springer-Verlag New York Inc. (2013), pp.249-259. doi:10:100/7/978-1-4614-5647-6_14.
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| Wenbo Mu, Damian Roqueiro, Yang Dai. "A Local Genetic Algorithm for the Identification of Condition-Specific MicroRNA-Gene Modules.". Scientific World Journal (2013). doi:10.1155/2013/197406. PubMed
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| Damian Roqueiro, Lei Huang, Yang Dai. "Identifying Transcription Factors and microRNAs as Key Regulators of Pathways Using Bayesian Inference on Known Pathway Structures". Proteome Science (2012). doi:10.1186/1477-5956-10-S1-S15. PubMed
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| Ping Yin, Damian Roqueiro, Lei Huang, Jonas K. Owen, Anna Xie, Antonia Navarro, Diana Monsivais, John S. Coon V, J. Julie Kim, Yang Dai, Serdar E. Bulun. "Genome-Wide Progesterone Receptor Binding: Cell Type-Specific and Shared Mechanisms in T47D Breast Cancer Cells and Primary Leiomyoma Cells". PLoS ONE, 7(1) (2012): e29021. doi:10.1371/journal.pone.0029021. PLoS ONE
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Cheng Wang, Xiqiang Liu, Zujian Chen, Hongzhang Huang, Yi Jin, Antonia Kolokythas, Anxun Wang, Yang Dai, David T.W. Wong, Xiaofeng Zhou. "Polycomb group protein EZH2-mediated E-cadherin repression promotes metastasis of oral tongue squamous cell carcinoma". Molecular Carcinogenesis (2011). doi: 10.1002/mc.21848. PubMed
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| Yi Jin, Cheng Wang, Xiqiang Liu, Wenbo Mu, Zujian Chen, Dongsheng Yu, Anxun Wang, Yang Dai, and Xiaofeng Zhou. "Molecular Characterization of the MicroRNA-138-Fos-like Antigen 1 (FOSL1) Regulatory Module in Squamous Cell Carcinoma". Journal of Biological Chemistry, 286 (46) (2011) 40104-40109. PubMed
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| Damian Roqueiro, Lei Huang, Yang Dai. "Identifying Transcription Factors and microRNAs as Key Regulators of Pathways Using Bayesian Inference on Known Pathway Structures". Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference, pp.228-233 (2011) doi: 10.1109/BIBM.2011.120 IEEE Digital Library
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| Lei Huang, Shuangping Zhao, Jonna Frasor and Yang Dai. "An integrated bioinformatics approach identifies elevated cyclin E2 expression and E2F actvity as distinguishing characteristics of tamoxifen resistant breast tumors". PLoS ONE 6(7), 2011. e22274. doi:10.1371/journal.pone.0022274. PubMed
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| Xiqiang Liu, Cheng Wang, Zujian Chen, Yi Jin, Yun Wang, Antonia Kolokythas, Yang Dai and Xiaofeng Zhou. "MicroRNA-138 suppresses epithelial-mesenchymal transition in squamous cell carcinoma cell lines". Biochemical Journal (2011). doi:10.1042/BJ20111006. PubMed
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| Joel Fontanarosa and Yang Dai. "Using lasso regression to detect predictive aggregate effects in genetic studies". BMC Proceedings, (2011) 5(Suppl 9):S69. doi:10.1186/1753-6561-5-S9-S69 BioMed Central
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| Cheng Wang, Xiqiang Liu, Hongzhang Huang, Huibin Ma, Weixin Cai, Jingsong Hou, Lei Huang, Yang Dai, Tianwei Yu, Xiaofeng Zhou. "Deregulation of Snai2 is associated with metastasis and poor prognosis in tongue squamous cell carcinoma". International Journal of Cancer, 2011 Jun 6. doi: 10.1002/ijc.26226. PubMed
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| Hong Hu, Damian Roqueiro, Yang Dai. "Prioritizing predicted cis-regulatory elements for
co-expressed gene sets based on Lasso regression models". Engineering in Medicine and Biology Society,EMBC, 2011 Annual International Conference of the IEEE , pp.6853-6856 (2011) doi: 10.1109/IEMBS.2011.6091690 IEEE Digital Library.
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| Joel Fontanarosa and Yang Dai. "An evolutionary optimization strategy using
graphics processing units to efficiently investigate gene-gene interactions in genetic association studies". Engineering in Medicine and Biology Society,EMBC, 2011 Annual International Conference of the IEEE , pp.5547-5550 (2011) doi: 10.1109/IEMBS.2011.6091415 IEEE Digital Library. |
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| Lei Huang, Damian Roqueiro, Yang Dai. "Analyzing mRNA and microRNA co-expression
profiles to identify pathways and their potential regulators in ER+ and ER- breast tumors". Engineering in Medicine and Biology Society,EMBC, 2011 Annual International Conference of the IEEE , pp.932-935 (2011) doi: 10.1109/IEMBS.2011.6090210 IEEE Digital Library. |
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| Lu Jiang, Yang Dai, Xiqiang Liu, Cheng Wang, Anxun Wang, Zujian Chen, Caroline E. Heidbreder, Antonia Kolokythas and Xiaofeng Zhou. "Identification and functional validation of G protein alpha inhibiting activity polypeptide 2 (GNAI2) as a microRNA-138 target in tongue squamous cell carcinoma". Human Genetics, 129(2) (2011) 189-97. PDF |
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| Joel Fontanarosa and Yang Dai. "A block-based evolutionary optimization strategy to investigate gene-gene interactions in genetic association studies". Proceedings of 2010 IEEE International conference on Bioinformatics and Biomedicine Workshop, (2010) 330-335. IEEE Digital Library |
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| Oleksiy Karpenko and Yang Dai. "Relational Database Index Choices for Genome Annotation Data". Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference, pp.264-268 (2010) doi: 10.1109/BIBMW.2010.5703810 IEEE Digital Library |
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| Damian Roqueiro, Jonna Frasor and Yang Dai. "bindSDb: A Binding-information Spatial Database". Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference, pp.573-578 (2010) doi: 10.1109/BIBMW.2010.5703864 IEEE Digital Library |
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| Peter Larsen, Frank Collart and Yang Dai, "Incorporating network topology improves prediction of protein interaction networks from transcriptomic data".
International Journal of Knowledge discovery and Bioinformatics, 1(3), pp.1-19. 2010. Abstract |
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X. Liu, A. Wang, CE. Heidbreder, L. Jiang, J. Yu, A. Kolokythas, L. Huang, Y. Dai, X. Zhou. "MicroRNA-24 targeting RNA-binding protein DND1 in tongue squamous cell carcinoma." FEBS letters, 58(18), pp.4114-4120. 2010. PubMed |
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L. Jiang, X. Liu, Z. Chen, Y. Jin, C. E. Heidbreder, A. Kolokythas, A.
Wang, Y. Dai and X. Zhou. "MicroRNA-7 targets insulin-like growth factor 1 receptor (IGF1R) in tongue squamous cell carcinoma cells." Biochemical Journal, 432, pp.199–205. 2010. PubMed |
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| Yang Dai and Xiaofeng Zhou, "Computational methods for the identification of microRNA targets",
Open Access Bioinformatics, 2:29-39, 2010. PDF |
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| Szilard Asztalos, Peter Gann, Meghan Hayes, Larisa Nonn, Craig Beam, Yang Dai, Elizabeth Wiley, and Debra Tonetti, "Gene expression patterns in the human breast after pregnancy ", Cancer Prevention Research,3(3):301-311,2010. Abstract |
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| Cavallari H. Larisa, Vicki L. Groo, Marlos A. Viana, Yang Dai,
Shitalben R. Patel, and Thomas D. Stamos, "Circulating aldosterone and mineralocorticoid receptor genotype are predictive of potassium response to spironolactone in heart failure", Pharmacotherapy, 30(1):1-9, 2010. PDF |
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| Jonna Frasor, Aisha Weaver, Madhumita Pradhan, Yang Dai, Lance D. Miller, Chin-Yo Lin, and Adina Stanculescu, "Positive Crosstalk between Estrogen Receptor and NFKB in Breast Cancer", Cancer Research, 69(23):8918-8925, 2009. Abstract |
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| Peter Larsen and Yang Dai, "Using Gene Expression Modeling to Determine Biological Relevance of Putative Regulatory Networks",
Proceedings of the 5th International Symposium on Bioinformatics Research and Applications (eds. I. Mandoiu, G. Narasimhan, and Y. Zhang),
Lecture Notes in Computer Science, Springer Verlag, Vol. 5542 (2009) pp. 40-51. PDF |
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| Shantanu Dutt, Yang Dai, Huan Ren, and Joel Fontanarosa, "Selection of Multiple SNPs in Case-Control Association Study Based on a Discretized Network Flow Approach",
Proceedings of the First Conference of Bioinformatics and Computational Biology (BICoB 2009),
Lecture Notes in Computer Science, Springer Verlag, Vol. 5462, pp.1611-3349, 2009. PDF |
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| Yang Dai, Eyad Almasri, Peter Larsen,Guanrao Chen, "Structure Learning of Genetic Regulatory Networks Based on Knowledge Derived from Literature and Microarray Gene Expression Measurements", Book Chapter, Computational Methodologies in Gene Regulatory Networks (S. Das, D. Caragea, W. H. Hsu, S. M. Welch eds.), IGI Global, pp. 289-309, 2009. PDF |
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| Peter Larsen, Eyad Almasri, Guanrao Chen and Yang Dai, "Incorporating Knowledge of Topology Improves Reconstruction of Interaction Networks from Microarray Data ", Proceedings of the 4th International Symposium on Bioinformatics Research and Applications, Lecture Notes in Computer Science, (eds.by I.I. Mandoiu, Raj Sunderraman, and A. Zelikovsky), Springer Verlag, Vol. 4983, pp. 434-443, 2008. PDF |
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| Eyad Almasri, Peter Larsen, Guanrao Chen and Yang Dai, "Incorprating Literature Knowledge in Baysian Network for Inferring Gene Networks with Gene Expression Data", Proceedings of the 4th International Symposium on Bioinformatics Research and Applications, Lecture Notes in Computer Science (eds. by I.I. Mandoiu, Raj Sunderraman, and A. Zelikovsky), Springer Verlag, Vol. 4983, pp.184-195, 2008. PDF |
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| Guanrao Chen, Peter Larsen, Eyad Almasri,and Yang Dai, "Rank-based edge reconstruction for scale-free genetic
regulatory networks", BMC Bioinformatics, 9:75, 2008. PDF |
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| Oleksiy Karpenko, Lei Huang and Yang Dai, "A probabilistic meta-predictor for the MHC class II binding peptides ", Immunogenetics, 60:1, pp.25-36, 2008. PDF |
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Peter Larsen, Eyad Almasri, Guanrao Chen and Yang Dai, "A statistical method to incorporate biological knowledge for generating testable novel gene regulatory interactions from microarray experiments", BMC Bioinformatics, 8:317, 2007. PDF  |
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| Lei Huang, Oleksiy Karpenko, Naveen Murugan and Yang Dai, "Building a Meta-predictor for MHC Class II-Binding Peptides", Book Chapter, Immunoinformatics: Predicting Immunogenicity In Silico (Flower, D.R. ed.), Humana Press Inc., Totowa, NJ. pp. 355-364, 2007. PDF |
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| Zhengdeng Lei and Yang Dai, "Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction",
BMC Bioinformatics, 7:491, 2006. PDF |
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| Peter Larsen, Eyad Almasri, Guanrao Chen and Yang Dai, "Correlated discretized expression score: a method for identifying gene interaction networks from time course microarray expression data", Proceedings of the 28th International Conference of IEEE Engineering in Medicine and Biology Society (EMBS) (2006). pp.5842-5845. PDF |
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| Guanrao Chen, Peter Larsen, Eyad Almasri and Yang Dai, "Sample scale-free gene regulatory network using gene ontology", Proceedings of the 28th International Conference of IEEE Engineering in Medicine and Biology Society (EMBS) (2006). pp.5523-5526. PDF |
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| Robert E. Langlois, Alice Diec, Ognjen Perisic, Yang Dai and Hui Lu, "Improved protein fold assignment using support vector machines", International Journal of Bioinformatics Research and Applications, 1(3):319-334, 2006. PDF |
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| Lei Huang and Yang Dai, "Direct prediction of T cell epitopes using SVM with novel sequence encoding schemes", Journal of Bioinformatics and Computational Biology, 4(1):93-107, 2006. PDF |
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| Naveen Murugan and Yang Dai, "Prediction of MHC Class II binding peptides based on an iterative learning model", Immunome Research, 1:6, 2005. PDF |
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| Zhengdeng Lei and Yang Dai, "An SVM-based system for predicting protein subnuclear localizations", BMC Bioinformatics, 6:291, 2005. PDF |
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| J. Balcazar, Y. Dai and O.Watanabe, "Provably fast training algorithms for support vector machines", Theory of Computing Systems, 2005, in press. |
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| S. Kuroda, A.S. Virdi, Y. Dai, S, Shott and D. R. Sumner, "Patterns and localization of gene expression during intramembranous bone regeneration in the rat femoral marrow ablation model", Calcified Tissue International, 77(4):212-25, 2005. |
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| Zhengdeng Lei and Yang Dai, "A class of new kernels based on a matrix of high-scored pairs of k-peptides and its applications in prediction of protein sub-cellular localization", LNCS Transactions on Computational Systems Biology II, Springer-Verlag, pp.48-58, 2005. PDF |
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| Oleksiy Karpenko, Jianming Shi and Yang Dai, "Prediction of MHC class II binders using the ant colony search strategy", Artificial Intelligence in Medicine, Vol. 35, pp.147-156, 2005. PDF |
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| Aladino De Ranieri, Amarjit S. Virdi, Shinji Kuroda, S. Shott, Yang Dai and Dale R. Sumner, "Local application of rhTGF-beta2 modulates dynamic gene expression in a rat implant model", Bone, 36(5) pp.931-940, 2005. PDF |
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| Zhengdeng Lei and Yang Dai, "A new kernel based on a matrix of high-scored pairs of tri-peptides and its applications in prediction of protein sub-cellular localization", Proc. of International Workshop on Bioinformatics Research and Applications, Lecture Notes in Computer Science (LNCS), Springer-Verlag, Berlin, No.3515, pp.903-910, 2005. PDF |
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Y. Dai, J. M. Shi and W.S. Yang, "Conical partition algorithm for maximizing the sum of several dc ratios", Journal of Global Optimization, Vol.31, pp.253-270, 2005. PDF
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| L. Huang and Y. Dai, "A support vector machine approach for prediction of T cell epitopes", Proc. of the Third Asia-Pacific Bioinformatics Conference (APBC2005), Singapore, Jan. 17-21, 2005. pp.312-328, Imperial College Press. PDF |
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| D. Z. Chen, O. Daescu, Y. Dai, N. Katoh, J. Xu and X. Wu, "Efficient algorithms and implementations for optimizing the sum of linear fractional functions, with applications", Journal of Combinatorial Optimization, Vol.9, pp.69-90, 2005. PDF |
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| A.S. Virdi, A.D. Ranieri, S. Kuroda, Y. Dai and D.R. Sumner, "Anabolic agents and gene expression around the bone implant interface", Journal of Musculoskeletal & Neuronal Interactions, 4(4), pp.388-389, 2004. |
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| R.E. Langlois, A. Diec, Y. Dai and H. Lu, "Kernel based approach for protein fold prediction from Sequence", Proc. of the 26th International Conference of IEEE Engineering in Medicine and Biology Society (EMBS2004) (CD-ROM), 2004. |
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G. Chen and Y. Dai, "A new distance measurement for clustering time-course gene expression data", Proc. of the 26th International Conference of IEEE Engineering in Medicine and Biology Society (EMBS2004) (CD-ROM), 2004.
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Z. Lei and Y. Dai, "A novel approach for prediction of protein subcellular localization from sequence using fourier analysis and support vector machines", Proc. of 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics, Seattle, August 22, 2004, pp. 11-17. PDF
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| B. Liu, Y. Dai, X. Li, W. S. Lee and P. Yu, "Building text classifiers using positive and unlabeled examples", Proc. of the Third IEEE International Conference on Data Mining(ICDM'03), Melbourne, Florida, November 19-22, 2003, pp.179-188. PDF |
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| H-M. Lu, S. Gupta and Y. Dai, "Reduce large diagonals in kernel matrices through semidefinite programming", Proc. of 3rd ACM SIGKDD Workshop on Data Mining in Bioinformatics, 2003, pp.57-62. PDF |
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H-M. Lu, L. Huang and Y. Dai, "Application of support vector regression to Quantitative Structure-Activity Relationships(QSAR)", Proc. of the 5th International Conference on Computational Biology and Genome Informatics, Carey, North Carolina, USA, September 26-30, 2003.
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| L. Huang, H-M. Lu and Y. Dai, "Feature selection of support vector regression for Quantitative Structure-Activity Relationships(QSAR)", Proc. of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '03), Las Vegas, Nevada, June, 2003. PDF |
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| Y. Dai, S. Kim and M. Kojima, "Computing all nonsingular solutions of cyclic-n polynomial using polyhedral homotopy continuation methods", Journal of Computational and Applied Mathematics, Vol.152, No.1-2, 2003, pp.83-97. PDF |
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| Y. Dai and Mike Landis, "Feature selection in tumor classification using microarray gene expression data", Proc. of International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '02), Las Vegas, Nevada, June 2002. PDF |
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| A. Sutou and Y. Dai, "Global optimization approach to unequal sphere packing problems in 3D", Journal of Optimization Theory and Applications, Vol.114, No.3, 2002, pp.671-694. PDF |
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| J. Balcazar, Y. Dai and Osamu Watanabe, "Provably fast support vector regression using random sampling", Proc. of SIAM Workshop in Discrete Mathematics and Data Mining, Arlington, VA, April 2002, pp.19-29. PDF |
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| Y. Dai and J. M. Shi,"Conical partition algorithm for maximizing the sum of several dc ratios", Proc. of the 5th International Conference on Optimization: Techniques and Applications(ICOTA2001), Hong Kong, 2001, pp. 600-608. ( Detailed version of the paper ) |
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| J. Balcazar, Y. Dai, and O. Watanabe, "Provably fast training algorithms for support vector machines", Proc. of the first IEEE International Conference on Data Mining, IEEE Computer Society, 2001, pp.43--50. PDF |
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J. Balcazar, Y. Dai, and O. Watanabe, "An application of a random sampling technique to primal-form maximal-margin classifiers", Proc. of the 12th International Conference on Algorithmic Learning Theory, Lecture Notes in Artificial Intelligence, LNAI 2225, Springer-Verlag, 2001, pp119-134. PS
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Y. Dai and N. Katoh, "Generalized LMT-heuristics for several new classes of optimal triangulations", Computational Geometry: Theory and Application 17, 2000, pp.51-68. PDF
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| D. Z. Chen, O. Daescu, Y. Dai, N. Katoh, J. Xu and X. Wu, "Efficient algorithms and implementations for optimizing the sum of linear fractional functions, with applications", Proc. of the 11th Annual SIAM-ACM Symposium on Discrete Algorithms (SODA), San Francisco, 2000, pp.707-716. PS |
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| A. Takeda, Y. Dai, M. Kojima and M. Fukuda, "Towards implementations of successive convex relaxation methods for nonconvex quadratic optimization problems", in Approximation and Complexity in Numerical Optimization: Continuous and Discrete Problems, (P. M. Pardalos, Eds), 2000, pp. 489-510, Kluwer Academic Publishers. PS |
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