scholarly journals Detecting High-Order Epistasis in Nonlinear Genotype-Phenotype Maps

2016 ◽  
Author(s):  
Zachary R Sailer ◽  
Michael J Harms
Keyword(s):  
Total Variation ◽  
Strong Evidence ◽  
Complex Traits ◽  
High Order ◽  
Simple Method ◽  
Epistasis Model ◽  
Nonlinear Scale ◽  
Statistical Artifact

High-order epistasis has been observed in many genotype-phenotype maps. These multi-way interactions between mutations may be useful for dissecting complex traits and could have profound implications for evolution. Alternatively, they could be a statistical artifact. High-order epistasis models assume the effects of mutations should add, when they could in fact multiply or combine in some other nonlinear way. A mismatch in the "scale" of the epistasis model and the scale of the underlying map would lead to spurious epistasis. In this paper, we develop an approach to estimate the nonlinear scales of arbitrary genotype-phenotype maps. We can then linearize these maps and extract high-order epistasis. We investigated seven experimental genotype-phenotype maps for which high-order epistasis had been reported previously. We find that five of the seven maps exhibited nonlinear scales. Interestingly, even after accounting for nonlinearity, we found statistically significant high-order epistasis in all seven maps. The contributions of high-order epistasis to the total variation ranged from 2.2% to 31.0%, with an average across maps of 12.7%. Our results provide strong evidence for extensive high-order epistasis, even after nonlinear scale is taken into account. Further, we describe a simple method to estimate and account for nonlinearity in genotype-phenotype maps.

Total variation and high-order total variation adaptive model for restoring blurred images with Cauchy noise

2019 ◽  
Vol 77 (5) ◽  
pp. 1255-1272 ◽  
Author(s):  
Jing-Hua Yang ◽  
Xi-Le Zhao ◽  
Jin-Jin Mei ◽  
Si Wang ◽  
Tian-Hui Ma ◽  
...  
Keyword(s):  
Total Variation ◽  
High Order ◽  
Adaptive Model ◽  
Blurred Images

High order total variation method for interior tomography

2012 ◽  
Author(s):  
Jiansheng Yang ◽  
Hengyong Yu ◽  
Wenxiang Cong ◽  
Ming Jiang ◽  
Ge Wang
Keyword(s):  
Total Variation ◽  
High Order ◽  
Variation Method

scholarly journals Image Restoration by a Mixed High-Order Total Variation and l1 Regularization Model

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Jianguang Zhu ◽  
Kai Li ◽  
Binbin Hao
Keyword(s):  
Total Variation ◽  
High Order ◽  
Variational Model ◽  
Total Variation Regularization ◽  
Current State ◽  
Model Combining ◽  
Alternating Direction ◽  
Proposed Model ◽  
Sharp Edges ◽  
Thresholding Algorithm

Total variation regularization is well-known for recovering sharp edges; however, it usually produces staircase artifacts. In this paper, in order to overcome the shortcoming of total variation regularization, we propose a new variational model combining high-order total variation regularization and l1 regularization. The new model has separable structure which enables us to solve the involved subproblems more efficiently. We propose a fast alternating method by employing the fast iterative shrinkage-thresholding algorithm (FISTA) and the alternating direction method of multipliers (ADMM). Compared with some current state-of-the-art methods, numerical experiments show that our proposed model can significantly improve the quality of restored images and obtain higher SNR and SSIM values.

Genome-wide association and genomic selection in animal breedingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 876-883 ◽  
Author(s):  
Ben Hayes ◽  
Mike Goddard
Keyword(s):  
Genomic Selection ◽  
Complex Traits ◽  
Association Studies ◽  
Genome Wide Association ◽  
Relationship Matrix ◽  
Genome Wide Association Studies ◽  
Simple Method ◽  
Breeding Values ◽  
Genome Wide ◽  
A Genome

Results from genome-wide association studies in livestock, and humans, has lead to the conclusion that the effect of individual quantitative trait loci (QTL) on complex traits, such as yield, are likely to be small; therefore, a large number of QTL are necessary to explain genetic variation in these traits. Given this genetic architecture, gains from marker-assisted selection (MAS) programs using only a small number of DNA markers to trace a limited number of QTL is likely to be small. This has lead to the development of alternative technology for using the available dense single nucleotide polymorphism (SNP) information, called genomic selection. Genomic selection uses a genome-wide panel of dense markers so that all QTL are likely to be in linkage disequilibrium with at least one SNP. The genomic breeding values are predicted to be the sum of the effect of these SNPs across the entire genome. In dairy cattle breeding, the accuracy of genomic estimated breeding values (GEBV) that can be achieved and the fact that these are available early in life have lead to rapid adoption of the technology. Here, we discuss the design of experiments necessary to achieve accurate prediction of GEBV in future generations in terms of the number of markers necessary and the size of the reference population where marker effects are estimated. We also present a simple method for implementing genomic selection using a genomic relationship matrix. Future challenges discussed include using whole genome sequence data to improve the accuracy of genomic selection and management of inbreeding through genomic relationships.

scholarly journals High-order total variation regularization approach for axially symmetric object tomography from a single radiograph

2015 ◽  
Vol 9 (1) ◽  
pp. 55-77 ◽  
Author(s):  
Raymond H. Chan ◽  
◽  
Haixia Liang ◽  
Suhua Wei ◽  
Mila Nikolova ◽  
...  
Keyword(s):  
Total Variation ◽  
High Order ◽  
Total Variation Regularization ◽  
Axially Symmetric

scholarly journals Infrared Image Deblurring via High-Order Total Variation and Lp-Pseudonorm Shrinkage

2020 ◽  
Vol 10 (7) ◽  
pp. 2533 ◽  
Author(s):  
Jingjing Yang ◽  
Yingpin Chen ◽  
Zhifeng Chen
Keyword(s):  
Total Variation ◽  
Infrared Image ◽  
Noise Pollution ◽  
Image Deblurring ◽  
High Order ◽  
L1 Norm ◽  
Alternating Direction ◽  
Image Blurring ◽  
Image Gradients ◽  
Staircase Artifacts

The quality of infrared images is affected by various degradation factors, such as image blurring and noise pollution. Anisotropic total variation (ATV) has been shown to be a good regularization approach for image deblurring. However, there are two main drawbacks in ATV. First, the conventional ATV regularization just considers the sparsity of the first-order image gradients, thus leading to staircase artifacts. Second, it employs the L1-norm to describe the sparsity of image gradients, while the L1-norm has a limited capacity of depicting the sparsity of sparse variables. To address these limitations of ATV, a high-order total variation is introduced in the ATV deblurring model and the Lp-pseudonorm is adopted to depict the sparsity of low- and high-order total variation. In this way, the recovered image can fit the image priors with clear edges and eliminate the staircase artifacts of the ATV model. The alternating direction method of multipliers is used to solve the proposed model. The experimental results demonstrate that the proposed method does not only remove blurs effectively but is also highly competitive against the state-of-the-art methods, both qualitatively and quantitatively.

scholarly journals A Fast High-Order Total Variation Minimization Method for Multiplicative Noise Removal

2013 ◽  
Vol 2013 ◽  
pp. 1-13 ◽  
Author(s):  
Xiao-Guang Lv ◽  
Jiang Le ◽  
Jin Huang ◽  
Liu Jun
Keyword(s):  
Total Variation ◽  
Multiplicative Noise ◽  
Noise Removal ◽  
High Order ◽  
Alternating Minimization ◽  
Minimization Method ◽  
Total Variation Minimization ◽  
Alternating Minimization Algorithm ◽  
Staircase Effect ◽  
Multiplicative Noise Removal

Multiplicative noise removal problem has received considerable attention in recent years. The total variation regularization method for the solution of the noise removal problem can preserve edges well but has the sometimes undesirable staircase effect. In this paper, we propose a fast high-order total variation minimization method to restore multiplicative noisy images. The proposed method is able to preserve edges and at the same time avoid the staircase effect in the smooth regions. An alternating minimization algorithm is employed to solve the proposed high-order total variation minimization problem. We discuss the convergence of the alternating minimization algorithm. Some numerical results show that the proposed method gives restored images of higher quality than some existing multiplicative noise removal methods.

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