boost swMATH ID: 35655 Software Authors: Marcel Dettling Description: R package boost: BagBoosting for tumor classification with gene expression data. Motivation: Microarray experiments are expected to contribute significantly to the progress in cancer treatment by enabling a precise and early diagnosis. They create a need for class prediction tools, which can deal with a large number of highly correlated input variables, perform feature selection and provide class probability estimates that serve as a quantification of the predictive uncertainty. A very promising solution is to combine the two ensemble schemes bagging and boosting to a novel algorithm called BagBoosting. Results: When bagging is used as a module in boosting, the resulting classifier consistently improves the predictive performance and the probability estimates of both bagging and boosting on real and simulated gene expression data. This quasi-guaranteed improvement can be obtained by simply making a bigger computing effort. The advantageous predictive potential is also confirmed by comparing BagBoosting to several established class prediction tools for microarray data. Availability: Software for the modified boosting algorithms, for benchmark studies and for the simulation of microarray data are available as an R package under GNU public license at http://stat.ethz.ch/ dettling/bagboost.html Homepage: https://academic.oup.com/bioinformatics/article/20/18/3583/202535 Dependencies: R Related Software: ElemStatLearn; R; glmnet; rda; glasso; UCI-ml; penalizedLDA; mclust; impute; L1-MAGIC; AdaBoost.MH; sparcl; PDCO; GeneSrF; mboost; Bioconductor; Scikit; clusteval; MBCbook; AS 136 Cited in: 41 Publications all top 5 Cited by 86 Authors 4 Bühlmann, Peter 3 Yang, Aijun 3 Zhu, Lixing 2 Ahn, Jeongyoun 2 Chen, Huangyue 2 Hothorn, Torsten 2 Jin, Jiashun 2 Kabán, Ata 2 Kong, Lingchen 2 Leng, Chenlei 2 Li, Yunxian 2 Lin, Jinguan 2 Wang, Tao 1 Anderlucci, Laura 1 Arias-Castro, Ery 1 Askari, Armin 1 Bertsimas, Dimitris John 1 Bozdogan, Hamparsum 1 Cai, Jia 1 Cai, Tony Tony 1 Çalik, Sinan 1 Cheng, Lulu 1 Cho, Sung-Bae 1 d’Aspremont, Alexandre 1 Donoho, David Leigh 1 Durrant, Robert J. 1 Fan, Yan 1 Fang, Yixin 1 Fortunato, Francesca 1 Gai, Yujie 1 Green, Paul E. 1 Hall, Peter Gavin 1 Hong, Jin-Hyuk 1 Huang, Song 1 Huo, Junyi 1 Huo, Yanhao 1 Hwang, Changha 1 Jeon, Yongho 1 Jiang, Binyan 1 Jiang, Xuejun 1 Kang, Chuanze 1 Kim, Inyoung 1 Kim, Kyung In 1 Kim, Sujong 1 King, Angela 1 Kuhn, Daniel 1 Lange, Kenneth L. 1 Lee, Jaewon 1 Li, Yan 1 Liu, Pengfei 1 Ma, Qin 1 Mandozzi, Jacopo 1 Mazumder, Rahul 1 Miller, Hugh III 1 Mohajerin Esfahani, Peyman 1 Montanari, Angela 1 Müller, Patric 1 Nürnberg, Gerd 1 Pamukçu, Esra 1 Pan, Shanshan 1 Pang, Herbert 1 Pu, Xiao 1 Repsilber, Dirk 1 Safo, Sandra E. 1 Shang, Pan 1 Shim, Jooyong 1 Shu, Lianjie 1 Simon, Richard M. 1 Sohn, Insuk 1 Sun, Wei 1 Tang, Niansheng 1 Telaar, Anna 1 Tian, Yuzhu 1 Tong, Tiejun 1 Van de Geer, Sara Anna 1 Wang, Guanwei 1 Wang, Junhui 1 Wang, Minghui 1 Wang, Xiangyu 1 Wu, Tongtong 1 Xin, Lihui 1 Yin, Zanhua 1 Zhang, Chunxia 1 Zhang, Jiangshe 1 Zhang, Linjun 1 Zhao, Hongyu all top 5 Cited in 28 Serials 6 Computational Statistics and Data Analysis 4 Computational Statistics 3 Statistical Science 2 The Annals of Statistics 2 Pattern Recognition 2 Bernoulli 1 Metrika 1 Scandinavian Journal of Statistics 1 Applied Mathematics and Computation 1 Biometrical Journal 1 Biometrics 1 Operations Research 1 Journal of Classification 1 Journal of Complexity 1 Communications in Statistics. Theory and Methods 1 Mathematical Problems in Engineering 1 Journal of Applied Statistics 1 Journal of Systems Science and Complexity 1 Journal of Machine Learning Research (JMLR) 1 Communications on Pure and Applied Analysis 1 Computational Biology and Chemistry 1 Computational & Mathematical Methods in Medicine 1 Electronic Journal of Statistics 1 The Annals of Applied Statistics 1 Science China. Mathematics 1 Journal of Agricultural, Biological, and Environmental Statistics 1 Journal of Theoretical Biology 1 SIAM Journal on Mathematics of Data Science all top 5 Cited in 6 Fields 39 Statistics (62-XX) 6 Computer science (68-XX) 5 Numerical analysis (65-XX) 3 Operations research, mathematical programming (90-XX) 3 Biology and other natural sciences (92-XX) 1 Convex and discrete geometry (52-XX) Citations by Year