A Systems Biology Approach for Unsupervised Clustering of High-Dimensional Data

2016 ◽  
pp. 193-203 ◽  
Author(s):  
Diana Diaz ◽  
Tin Nguyen ◽  
Sorin Draghici
Keyword(s):  
Systems Biology ◽  
High Dimensional Data ◽  
Unsupervised Clustering ◽  
High Dimensional

Exploratory Analysis of Multiple Omics Datasets Using the Adjusted RV Coefficient

2011 ◽  
Vol 10 (1) ◽  
Author(s):  
Claus-Dieter Mayer ◽  
Julie Lorent ◽  
Graham W Horgan
Keyword(s):  
Systems Biology ◽  
High Dimensional Data ◽  
High Dimensional ◽  
Data Sets ◽  
Multivariate Statistical ◽  
Data Set ◽  
Analysis Of Similarity ◽  
Matrix Correlation ◽  
Substantial Bias ◽  
Rv Coefficient

The integration of multiple high-dimensional data sets (omics data) has been a very active but challenging area of bioinformatics research in recent years. Various adaptations of non-standard multivariate statistical tools have been suggested that allow to analyze and visualize such data sets simultaneously. However, these methods typically can deal with two data sets only, whereas systems biology experiments often generate larger numbers of high-dimensional data sets. For this reason, we suggest an explorative analysis of similarity between data sets as an initial analysis steps. This analysis is based on the RV coefficient, a matrix correlation, that can be interpreted as a generalization of the squared correlation from two single variables to two sets of variables. It has been shown before however that the high-dimensionality of the data introduces substantial bias to the RV.We therefore introduce an alternative version, the adjusted RV, which is unbiased in the case of independent data sets. We can also show that in many situations, particularly for very high-dimensional data sets, the adjusted RV is a better estimator than previously RV versions in terms of the mean square error and the power of the independence test based on it.We demonstrate the usefulness of the adjusted RV by applying it to data set of 19 different multivariate data sets from a systems biology experiment. The pairwise RV values between the data sets define a similarity matrix that we can use as an input to a hierarchical clustering or a multi-dimensional scaling. We show that this reveals biological meaningful subgroups of data sets in our study.

A Fast Clustering Algorithm for Large-scale and High Dimensional Data

2009 ◽  
Vol 35 (7) ◽  
pp. 859-866
Author(s):  
Ming LIU ◽  
Xiao-Long WANG ◽  
Yuan-Chao LIU
Keyword(s):  
Large Scale ◽  
Clustering Algorithm ◽  
High Dimensional Data ◽  
High Dimensional

Approximate Cluster Heat Maps of Large High-Dimensional Data

2018 ◽  
Author(s):  
Punit Rathore ◽  
James C. Bezdek ◽  
Dheeraj Kumar ◽  
Sutharshan Rajasegarar ◽  
Marimuthu Palaniswami
Keyword(s):  
High Dimensional Data ◽  
High Dimensional ◽  
Heat Maps

scholarly journals The Generalized Bayes Method for High-Dimensional Data Recognition with Applications to Audio Signal Recognition

Symmetry ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 19
Author(s):  
Hsiuying Wang
Keyword(s):  
Gaussian Mixture Model ◽  
Mixture Model ◽  
Conventional Method ◽  
High Dimensional Data ◽  
Audio Signal ◽  
Gaussian Mixture ◽  
High Dimensional ◽  
Signal Recognition ◽  
Bayes Method ◽  
Generalized Bayes

High-dimensional data recognition problem based on the Gaussian Mixture model has useful applications in many area, such as audio signal recognition, image analysis, and biological evolution. The expectation-maximization algorithm is a popular approach to the derivation of the maximum likelihood estimators of the Gaussian mixture model (GMM). An alternative solution is to adopt a generalized Bayes estimator for parameter estimation. In this study, an estimator based on the generalized Bayes approach is established. A simulation study shows that the proposed approach has a performance competitive to that of the conventional method in high-dimensional Gaussian mixture model recognition. We use a musical data example to illustrate this recognition problem. Suppose that we have audio data of a piece of music and know that the music is from one of four compositions, but we do not know exactly which composition it comes from. The generalized Bayes method shows a higher average recognition rate than the conventional method. This result shows that the generalized Bayes method is a competitor to the conventional method in this real application.

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