arXiv subjects

Yin Xian

Publications and source records attributed to Yin Xian.

9 recordsLinked to original sources

arXiv2022

Generative Adversarial Networks for Robust Cryo-EM Image Denoising

The cryo-electron microscopy (Cryo-EM) becomes popular for macromolecular structure determination. However, the 2D images which Cryo-EM detects are of high noise and often mixed with multiple heterogeneous conformations or contamination, imposing a challenge for denoising. Traditional image denoising methods can not remove Cryo-EM image noise well when the signal-noise-ratio (SNR) of images is meager. Thus it is desired to develop new effective denoising techniques to facilitate further research such as 3D reconstruction, 2D conformation classification, and so on. In this paper, we approach the robust image denoising problem in Cryo-EM by a joint Autoencoder and Generative Adversarial Networks (GAN) method. Equipped with robust $\ell_1$ Autoencoder and some designs of robust $β$-GANs, one can stabilize the training of GANs and achieve the state-of-the-art performance of robust denoising with low SNR data and against possible information contamination. The method is evaluated by both a heterogeneous conformational dataset on the Thermus aquaticus RNA Polymerase (RNAP) and a homogenous dataset on the Plasmodium falciparum 80S ribosome dataset (EMPIRE-10028), in terms of Mean Square Error (MSE), Peak Signal to Noise Ratio (PSNR), Structural Similarity Index Measure (SSIM), as well as heterogeneous conformation clustering. These results suggest that our proposed methodology provides an effective tool for Cryo-EM 2D image denoising. Our code is available in "https://github.com/ghl1995/denoise-gan-in-cryo-em".

eess.IV↗

arXiv2021

Provable Near-Optimal Low-Multilinear-Rank Tensor Recovery

We consider the problem of recovering a low-multilinear-rank tensor from a small amount of linear measurements. We show that the Riemannian gradient algorithm initialized by one step of iterative hard thresholding can reconstruct an order-$d$ tensor of size $n\times\ldots\times n$ and multilinear rank $(r,\ldots,r)$ with high probability from only $O(nr^2 + r^{d+1})$ measurements, assuming $d$ is a constant. This sampling complexity is optimal in $n$, compared to existing results whose sampling complexities are all unnecessarily large in $n$. The analysis relies on the tensor restricted isometry property (TRIP) and the geometry of the manifold of all tensors with a fixed multilinear rank. High computational efficiency of our algorithm is also achieved by doing higher order singular value decomposition on intermediate small tensors of size only $2r\times \ldots\times 2r$ rather than on tensors of size $n\times \ldots\times n$ as usual.

math.NA↗

arXiv2019

Optimal low rank tensor recovery

We investigate the sample size requirement for exact recovery of a high order tensor of low rank from a subset of its entries. In the Tucker decomposition framework, we show that the Riemannian optimization algorithm with initial value obtained from a spectral method can reconstruct a tensor of size $n\times n \times\cdots \times n$ tensor of ranks $(r,\cdots,r)$ with high probability from as few as $O((r^d+dnr)\log(d))$ entries. In the case of order 3 tensor, the entries can be asymptotically as few as $O(nr)$ for a low rank large tensor. We show the theoretical guarantee condition for the recovery. The analysis relies on the tensor restricted isometry property (tensor RIP) and the curvature of the low rank tensor manifold. Our algorithm is computationally efficient and easy to implement. Numerical results verify that the algorithms are able to recover a low rank tensor from minimum number of measurements. The experiments on hyperspectral images recovery also show that our algorithm is capable of real world signal processing problems.

stat.ML↗

arXiv2019

Kam method for Cryo-EM particle reconstruction

The Cryo-EM 3D particle reconstruction is essential for identifying protein and uncover the biological mechanism of the macro-molecules. In this paper, we use Kam method for reconstruction. Kam method is \textit{ab-initio}, and it assumes that the projection angles of the particle are uniformly distributed. Based on the data covariance matrix, we compute the radial frequency component of the matrix. The particle density function can be obtained by the radial frequency component and the angular frequency basis function. In order to uniquely and accurately identify the radial frequency component, an initial guess of the structure is applied. Experiment shows that Kam method works for low resolution particle reconstruction. Further improvement can be made by including projection angle distribution in covariance matrix, and applying the fast algorithm to enhance computation speed.

q-bio.QM↗

arXiv2019

Uncertainty quantification of modified Cahn-Hilliard equation for image inpainting

In this paper, we review modified Cahn-Hilliard equation for image inpainting and explore the effect when the initial condition is uncertain. We study the statistical properties of the solution when the noise is present. The generalized polynomial chaos and the perturbation expansion are used to analyze the equation. Experimental results are attached for comparison of solution behavior.

math.NA↗

arXiv2018

Data-Driven Tight Frame for Cryo-EM Image Denoising and Conformational Classification

The cryo-electron microscope (cryo-EM) is increasingly popular these years. It helps to uncover the biological structures and functions of macromolecules. In this paper, we address image denoising problem in cryo-EM. Denoising the cryo-EM images can help to distinguish different molecular conformations and improve three dimensional reconstruction resolution. We introduce the use of data-driven tight frame (DDTF) algorithm for cryo-EM image denoising. The DDTF algorithm is closely related to the dictionary learning. The advantage of DDTF algorithm is that it is computationally efficient, and can well identify the texture and shape of images without using large data samples. Experimental results on cryo-EM image denoising and conformational classification demonstrate the power of DDTF algorithm for cryo-EM image denoising and classification.

stat.CO↗

arXiv2017

Adaptive DCTNet for Audio Signal Classification

In this paper, we investigate DCTNet for audio signal classification. Its output feature is related to Cohen's class of time-frequency distributions. We introduce the use of adaptive DCTNet (A-DCTNet) for audio signals feature extraction. The A-DCTNet applies the idea of constant-Q transform, with its center frequencies of filterbanks geometrically spaced. The A-DCTNet is adaptive to different acoustic scales, and it can better capture low frequency acoustic information that is sensitive to human audio perception than features such as Mel-frequency spectral coefficients (MFSC). We use features extracted by the A-DCTNet as input for classifiers. Experimental results show that the A-DCTNet and Recurrent Neural Networks (RNN) achieve state-of-the-art performance in bird song classification rate, and improve artist identification accuracy in music data. They demonstrate A-DCTNet's applicability to signal processing problems.

cs.SD↗

arXiv2016

DCTNet and PCANet for acoustic signal feature extraction

We introduce the use of DCTNet, an efficient approximation and alternative to PCANet, for acoustic signal classification. In PCANet, the eigenfunctions of the local sample covariance matrix (PCA) are used as filterbanks for convolution and feature extraction. When the eigenfunctions are well approximated by the Discrete Cosine Transform (DCT) functions, each layer of of PCANet and DCTNet is essentially a time-frequency representation. We relate DCTNet to spectral feature representation methods, such as the the short time Fourier transform (STFT), spectrogram and linear frequency spectral coefficients (LFSC). Experimental results on whale vocalization data show that DCTNet improves classification rate, demonstrating DCTNet's applicability to signal processing problems such as underwater acoustics.

cs.SD↗

arXiv2015

On Marine Mammal Acoustic Detection Performance Bounds

Since the spectrogram does not preserve phase information contained in the original data, any algorithm based on the spectrogram is not likely to be optimum for detection. In this paper, we present the Short Time Fourier Transform detector to detect marine mammals in the time-frequency plane. The detector uses phase information for detection. We evaluate this detector by comparing it to the existing spectrogram based detectors for different SNRs and various environments including a known ocean, uncertain ocean, and mean ocean. The results show that this detector outperforms the spectrogram based detector. Simulations are presented using the polynomial phase signal model of the North Atlantic Right Whale (NARW), along with the bellhop ray tracing model.

physics.ins-det↗