scholarly journals Modified Mahalanobis-Taguchi System based on proper orthogonal decomposition for high-dimensional-small-sample-size data classification

2021 ◽  
Vol 18 (1) ◽  
pp. 426-444
Author(s):  
Ting Mao ◽  
◽  
Lanting Yu ◽  
Yueyi Zhang ◽  
Li Zhou ◽  
...  
2016 ◽  
Vol 143 ◽  
pp. 127-142 ◽  
Author(s):  
Kai Dong ◽  
Herbert Pang ◽  
Tiejun Tong ◽  
Marc G. Genton

2021 ◽  
Author(s):  
Xin Chen ◽  
Qingrun Zhang ◽  
Thierry Chekouo

Abstract Background: DNA methylations in critical regions are highly involved in cancer pathogenesis and drug response. However, to identify causal methylations out of a large number of potential polymorphic DNA methylation sites is challenging. This high-dimensional data brings two obstacles: first, many established statistical models are not scalable to so many features; second, multiple-test and overfitting become serious. To this end, a method to quickly filter candidate sites to narrow down targets for downstream analyses is urgently needed. Methods: BACkPAy is a pre-screening Bayesian approach to detect biological meaningful clusters of potential differential methylation levels with small sample size. BACkPAy prioritizes potentially important biomarkers by the Bayesian false discovery rate (FDR) approach. It filters non-informative sites (i.e. non-differential) with flat methylation pattern levels accross experimental conditions. In this work, we applied BACkPAy to a genome-wide methylation dataset with 3 tissue types and each type contains 3 gastric cancer samples. We also applied LIMMA (Linear Models for Microarray and RNA-Seq Data) to compare its results with what we achieved by BACkPAy. Then, Cox proportional hazards regression models were utilized to visualize prognostics significant markers with The Cancer Genome Atlas (TCGA) data for survival analysis. Results: Using BACkPAy, we identified 8 biological meaningful clusters/groups of differential probes from the DNA methylation dataset. Using TCGA data, we also identified five prognostic genes (i.e. predictive to the progression of gastric cancer) that contain some differential methylation probes, whereas no significant results was identified using the Benjamin-Hochberg FDR in LIMMA. Conclusions: We showed the importance of using BACkPAy for the analysis of DNA methylation data with extremely small sample size in gastric cancer. We revealed that RDH13, CLDN11, TMTC1, UCHL1 and FOXP2 can serve as predictive biomarkers for gastric cancer treatment and the promoter methylation level of these five genes in serum could have prognostic and diagnostic functions in gastric cancer patients.


2005 ◽  
Vol 15 (03) ◽  
pp. 997-1013 ◽  
Author(s):  
C. W. ROWLEY

Many of the tools of dynamical systems and control theory have gone largely unused for fluids, because the governing equations are so dynamically complex, both high-dimensional and nonlinear. Model reduction involves finding low-dimensional models that approximate the full high-dimensional dynamics. This paper compares three different methods of model reduction: proper orthogonal decomposition (POD), balanced truncation, and a method called balanced POD. Balanced truncation produces better reduced-order models than POD, but is not computationally tractable for very large systems. Balanced POD is a tractable method for computing approximate balanced truncations, that has computational cost similar to that of POD. The method presented here is a variation of existing methods using empirical Gramians, and the main contributions of the present paper are a version of the method of snapshots that allows one to compute balancing transformations directly, without separate reduction of the Gramians; and an output projection method, which allows tractable computation even when the number of outputs is large. The output projection method requires minimal additional computation, and has a priori error bounds that can guide the choice of rank of the projection. Connections between POD and balanced truncation are also illuminated: in particular, balanced truncation may be viewed as POD of a particular dataset, using the observability Gramian as an inner product. The three methods are illustrated on a numerical example, the linearized flow in a plane channel.


2012 ◽  
Vol 108 (1) ◽  
pp. 138-150 ◽  
Author(s):  
Martin Macaš ◽  
Lenka Lhotská ◽  
Eduard Bakstein ◽  
Daniel Novák ◽  
Jiří Wild ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document