arXiv subjects

Zhizhen Zhao

Publications and source records attributed to Zhizhen Zhao.

58 records · Page 4Linked to original sources

arXiv2015

Fast Steerable Principal Component Analysis

Cryo-electron microscopy nowadays often requires the analysis of hundreds of thousands of 2D images as large as a few hundred pixels in each direction. Here we introduce an algorithm that efficiently and accurately performs principal component analysis (PCA) for a large set of two-dimensional images, and, for each image, the set of its uniform rotations in the plane and their reflections. For a dataset consisting of $n$ images of size $L \times L$ pixels, the computational complexity of our algorithm is $O(nL^3 + L^4)$, while existing algorithms take $O(nL^4)$. The new algorithm computes the expansion coefficients of the images in a Fourier-Bessel basis efficiently using the non-uniform fast Fourier transform. We compare the accuracy and efficiency of the new algorithm with traditional PCA and existing algorithms for steerable PCA.

cs.CV↗

arXiv2015

Data-driven prediction strategies for low-frequency patterns of North Pacific climate variability

The North Pacific exhibits patterns of low-frequency variability on the intra-annual to decadal time scales, which manifest themselves in both model data and the observational record, and prediction of such low-frequency modes of variability is of great interest to the community. While parametric models, such as stationary and non-stationary autoregressive models, possibly including external factors, may perform well in a data-fitting setting, they may perform poorly in a prediction setting. Ensemble analog forecasting, which relies on the historical record to provide estimates of the future based on past trajectories of those states similar to the initial state of interest, provides a promising, nonparametric approach to forecasting that makes no assumptions on the underlying dynamics or its statistics. We apply such forecasting to low-frequency modes of variability for the North Pacific sea surface temperature and sea ice concentration fields extracted through Nonlinear Laplacian Spectral Analysis. We find such methods may outperform parametric methods and simple persistence with increased predictive skill.

math.NA↗

arXiv2014

Rotationally Invariant Image Representation for Viewing Direction Classification in Cryo-EM

We introduce a new rotationally invariant viewing angle classification method for identifying, among a large number of Cryo-EM projection images, similar views without prior knowledge of the molecule. Our rotationally invariant features are based on the bispectrum. Each image is denoised and compressed using steerable principal component analysis (PCA) such that rotating an image is equivalent to phase shifting the expansion coefficients. Thus we are able to extend the theory of bispectrum of 1D periodic signals to 2D images. The randomized PCA algorithm is then used to efficiently reduce the dimensionality of the bispectrum coefficients, enabling fast computation of the similarity between any pair of images. The nearest neighbors provide an initial classification of similar viewing angles. In this way, rotational alignment is only performed for images with their nearest neighbors. The initial nearest neighbor classification and alignment are further improved by a new classification method called vector diffusion maps. Our pipeline for viewing angle classification and alignment is experimentally shown to be faster and more accurate than reference-free alignment with rotationally invariant K-means clustering, MSA/MRA 2D classification, and their modern approximations.

q-bio.BM↗

arXiv2013

Fourier-Bessel rotational invariant eigenimages

We present an efficient and accurate algorithm for principal component analysis (PCA) of a large set of two dimensional images, and, for each image, the set of its uniform rotations in the plane and its reflection. The algorithm starts by expanding each image, originally given on a Cartesian grid, in the Fourier-Bessel basis for the disk. Because the images are bandlimited in the Fourier domain, we use a sampling criterion to truncate the Fourier-Bessel expansion such that the maximum amount of information is preserved without the effect of aliasing. The constructed covariance matrix is invariant to rotation and reflection and has a special block diagonal structure. PCA is efficiently done for each block separately. This Fourier-Bessel based PCA detects more meaningful eigenimages and has improved denoising capability compared to traditional PCA for a finite number of noisy images.

cs.CV↗