Multidimensional persistence in biomolecular data

Persistent homology has emerged as a popular technique for the topological simplification of big data, including biomolecular data. Multidimensional persistence bears considerable promise to bridge the gap between geometry and topology. However, its practical and robust construction has been a challenge. We introduce two families of multidimensional persistence, namely pseudomultidimensional persistence and multiscale multidimensional persistence. The former is generated via the repeated applications of persistent homology filtration to high‐dimensional data, such as results from molecular dynamics or partial differential equations. The latter is constructed via isotropic and anisotropic scales that create new simiplicial complexes and associated topological spaces. The utility, robustness, and efficiency of the proposed topological methods are demonstrated via protein folding, protein flexibility analysis, the topological denoising of cryoelectron microscopy data, and the scale dependence of nanoparticles. Topological transition between partial folded and unfolded proteins has been observed in multidimensional persistence. The separation between noise topological signatures and molecular topological fingerprints is achieved by the Laplace–Beltrami flow. The multiscale multidimensional persistent homology reveals relative local features in Betti‐0 invariants and the relatively global characteristics of Betti‐1 and Betti‐2 invariants. © 2015 Wiley Periodicals, Inc.     

基于Demons算法改进的图像去噪模型研究

在Demons算法的基础上, 将扩散过程看作图像配准, 建立一种新的基于图像配准的Demons 去噪模型. 实验表明, 该模型去噪效果优于经典的Perona-Malik模型, 排除了模型的病态性. 考虑到新模型在图像去噪过程中仅靠梯度信息表示图像的局部特征还不完善, 故将水平集曲率作为控制图像结构的驱动力因素引入到此模型中, 提出了一种新的梯度和曲率双重驱动力的图像去噪模型. 分析和仿真结果表明, 两种新模型都可有效抑制噪声, 清晰度也有明显的提高, 其中双重驱动力的图像去噪模型去噪效果更具优越性.     

A class of fractional-order multi-scale variational models and alternating projection algorithm for image denoising

The total variation model proposed by Rudin, Osher and Fatemi performs very well for removing noise while preserving edges. However, it favors a piecewise constant solution in BV space which often leads to the staircase effect, and small details such as textures are often filtered out with noise in the process of denoising. To preserve the textures and eliminate the staircase effect, we improve the total variation model in this paper. This is accomplished by the following steps: (1) we define a new space of functions of fractional-order bounded variation called the BV_α space by using the Grünwald–Letnikov definition of fractional-order derivative; (2) we model the structure of the image as a function belonging to the BV_α space, and the textures in different scales as functions belonging to different negative Sobolev spaces. Thus, we propose a class of fractional-order multi-scale variational models for image denoising. (3) We analyze some properties of the fraction-order total variation operator and its conjugate operator. By using these properties, we develop an alternation projection algorithm for the new model and propose an efficient condition of the convergence of the algorithm. The numerical results show that the fractional-order multi-scale variational model can improve the peak signal to noise ratio of image, preserve textures and eliminate the staircase effect efficiently in the process of denoising.     

基于小波变换的图像去噪方法的研究

小波变换能有效的去除高斯噪声,中值滤波能有效的去除脉冲噪声,两者结合可以更有效的去除高斯噪声和脉冲噪声的混合噪声.当医学图像去除混合噪声时,先进行中值滤波再进行小波去噪的方法优于先进行小波去噪后再进行中值滤波的方法,且去噪后图像视觉效果较好,而且图像均方误差(M SE)也较小.在图像去噪处理中这种方法具有实际应用价值.     

A Dynamic Programming Algorithm for the Fused Lasso and L 0-Segmentation

We propose a dynamic programming algorithm for the one-dimensional Fused Lasso Signal Approximator (FLSA). The proposed algorithm has a linear running time in the worst case. A similar approach is developed for the task of least squares segmentation, and simulations indicate substantial performance improvement over existing algorithms. Examples of R and C implementations are provided in the online Supplementary materials, posted on the journal web site.     

Generalized total variation-based MRI Rician denoising model with spatially adaptive regularization parameters

Magnetic resonance imaging (MRI) is an outstanding medical imaging modality but the quality often suffers from noise pollution during image acquisition and transmission. The purpose of this study is to enhance image quality using feature-preserving denoising method. In current literature, most existing MRI denoising methods did not simultaneously take the global image prior and local image features into account. The denoising method proposed in this paper is implemented based on an assumption of spatially varying Rician noise map. A two-step wavelet-domain estimation method is developed to extract the noise map. Following a Bayesian modeling approach, a generalized total variation-based MRI denoising model is proposed based on global hyper-Laplacian prior and Rician noise assumption. The proposed model has the properties of backward diffusion in local normal directions and forward diffusion in local tangent directions. To further improve the denoising performance, a local variance estimator-based method is introduced to calculate the spatially adaptive regularization parameters related to local image features and spatially varying noise map. The main benefit of the proposed method is that it takes full advantage of the global MR image prior and local image features. Numerous experiments have been conducted on both synthetic and real MR data sets to compare our proposed model with some state-of-the-art denoising methods. The experimental results have demonstrated the superior performance of our proposed model in terms of quantitative and qualitative image quality evaluations.     

一种快速稀疏分解图像去噪新方法*

提出了一种基于分层树型结构正交匹配追踪算法的快速图像去噪方法.通过选择高斯函数和墨西哥草帽小波母函数构建混合冗余字典,采用分层树状结构表示字典,结合构正交匹配追踪算法,实现图像稀疏表示,提高了图像表示的稀疏性,降低了算法的复杂度.依据噪音能量阈值,通过多次迭代达到图像去噪的目的.实验结果表明,在相同的噪音水平下,该迭代去噪算法取得了较高的较好的PSNR,获得更好的视觉效果.