Efficient Set-Correlation Operator Inside Databases

2016 ◽  
Vol 31 (4) ◽  
pp. 683-701 ◽  
Author(s):  
Fei Gao ◽  
Shao-Xu Song ◽  
Lei Chen ◽  
Jian-Min Wang
2020 ◽  
Vol 15 ◽  
Author(s):  
Chen-An Tsai ◽  
James J. Chen

Background: Gene set enrichment analyses (GSEA) provide a useful and powerful approach to identify differentially expressed gene sets with prior biological knowledge. Several GSEA algorithms have been proposed to perform enrichment analyses on groups of genes. However, many of these algorithms have focused on identification of differentially expressed gene sets in a given phenotype. Objective: In this paper, we propose a gene set analytic framework, Gene Set Correlation Analysis (GSCoA), that simultaneously measures within and between gene sets variation to identify sets of genes enriched for differential expression and highly co-related pathways. Methods: We apply co-inertia analysis to the comparisons of cross-gene sets in gene expression data to measure the costructure of expression profiles in pairs of gene sets. Co-inertia analysis (CIA) is one multivariate method to identify trends or co-relationships in multiple datasets, which contain the same samples. The objective of CIA is to seek ordinations (dimension reduction diagrams) of two gene sets such that the square covariance between the projections of the gene sets on successive axes is maximized. Simulation studies illustrate that CIA offers superior performance in identifying corelationships between gene sets in all simulation settings when compared to correlation-based gene set methods. Result and Conclusion: We also combine between-gene set CIA and GSEA to discover the relationships between gene sets significantly associated with phenotypes. In addition, we provide a graphical technique for visualizing and simultaneously exploring the associations of between and within gene sets and their interaction and network. We then demonstrate integration of within and between gene sets variation using CIA and GSEA, applied to the p53 gene expression data using the c2 curated gene sets. Ultimately, the GSCoA approach provides an attractive tool for identification and visualization of novel associations between pairs of gene sets by integrating co-relationships between gene sets into gene set analysis.


2020 ◽  
Vol 61 (10) ◽  
Author(s):  
M. Edwards ◽  
R. Theunissen ◽  
C. B. Allen ◽  
D. J. Poole

Abstract This paper presents a method which allows for a reduced portion of a particle image velocimetry (PIV) image to be analysed, without introducing numerical artefacts near the edges of the reduced region. Based on confidence intervals of statistics of interest, such a region can be determined automatically depending on user-imposed confidence requirements, allowing for already satisfactorily converged regions of the field of view to be neglected in further analysis, offering significant computational benefits. Temporal fluctuations of the flow are unavoidable even for very steady flows, and the magnitude of such fluctuations will naturally vary over the domain. Moreover, the non-linear modulation effects of the cross-correlation operator exacerbate the perceived temporal fluctuations in regions of strong spatial displacement gradients. It follows, therefore, that steady, uniform, flow regions will require fewer contributing images than their less steady, spatially fluctuating, counterparts within the same field of view, and hence the further analysis of image pairs may be solely driven by small, isolated, non-converged regions. In this paper, a methodology is presented which allows these non-converged regions to be identified and subsequently analysed in isolation from the rest of the image, while ensuring that such localised analysis is not adversely affected by the reduced analysis region, i.e. does not introduce boundary effects, thus accelerating the analysis procedure considerably. Via experimental analysis, it is shown that under typical conditions a 44% reduction in the required number of correlations for an ensemble solution is achieved, compared to conventional image processing routines while maintaining a specified level of confidence over the domain. Graphic abstract


2021 ◽  
pp. 94-110
Author(s):  
Thorsten Götte ◽  
Christina Kolb ◽  
Christian Scheideler ◽  
Julian Werthmann

2009 ◽  
Vol 131 (20) ◽  
pp. 204102 ◽  
Author(s):  
Vitaly A. Rassolov

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