Numerical encoding plays an important role in DNA sequence analysis via computational methods, in which numerical values are associated with corresponding symbolic characters. After numerical representation, digital signal processing methods can be exploited to analyze DNA sequences. To reflect the biological properties of the original sequence, it is vital that the representation is one-to-one. Chaos Game Representation (CGR) is an iterative mapping technique that assigns each nucleotide in a DNA sequence to a respective position on the plane that allows the depiction of the DNA sequence in the form of image. Using CGR, a biological sequence can be transformed one-to-one to a numerical sequence that preserves the main features of the original sequence. In this research, we propose to encode DNA sequences by considering 2D CGR coordinates as complex numbers, and apply digital signal processing methods to analyze their evolutionary relationship. Computational experiments indicate that this approach gives comparable results to the state-of-the-art multiple sequence alignment method, Clustal Omega, and is significantly faster. The MATLAB code for our method can be accessed from: www.mathworks.com/matlabcentral/fileexchange/57152

Let $$\mathcal{H}^{1,1} (T^1 )$$ denote the Hardy space of real-valued functions on the unit circle with weak derivatives in the usual real Hardy space $$\mathcal{H}^1 (T^1 )$$ . It is shown that when the weak derivative of a locally Lipschitz continuous function$f$has bounded variation on compact sets the Nemytskii operator$F$, defined by$F(u)=f·u$, maps $$\mathcal{H}^{1,1} (T^1 )$$ continuously into itself. A further condition sufficient for the continuous Fréchet differentiability of$F$is then added.

It has been an open question whether the family of merit functions $\psi _p\(p> 1) $, the generalized Fischer-Burmeister (FB) merit function, associated to the second-order cone is smooth or not. In this paper we answer it partly, and show that \psi _p is smooth for \psi _p , and we provide the condition for its coerciveness. Numerical results are reported to illustrate the influence of \psi _p on the performance of the merit function method based on \psi _p .

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The alternating direction method of multipliers (ADMM) is a popular approach for solving optimization problems that are potentially non-smooth and with hard constraints. It has been applied to various computer graphics applications, including physical simulation, geometry processing, and image processing. However, ADMM can take a long time to converge to a solution of high accuracy. Moreover, many computer graphics tasks involve non-convex optimization, and there is often no convergence guarantee for ADMM on such problems since it was originally designed for convex optimization. In this paper, we propose a method to speed up ADMM using Anderson acceleration, an established technique for accelerating fixed-point iterations. We show that in the general case, ADMM is a fixed-point iteration of the second primal variable and the dual variable, and Anderson acceleration can be directly applied. Additionally, when the problem has a separable target function and satisfies certain conditions, ADMM becomes a fixed-point iteration of only one variable, which further reduces the computational overhead of Anderson acceleration. Moreover, we analyze a particular non-convex problem structure that is common in computer graphics, and prove the convergence of ADMM on such problems under mild assumptions. We apply our acceleration technique on a variety of optimization problems in computer graphics, with notable improvement on their convergence speed.