arXiv subjects

Bin Dong

Publications and source records attributed to Bin Dong.

144 records · Page 8Linked to original sources

arXiv2017

A New Reduced-Rank Linear Discriminant Analysis Method and Its Applications

We consider multi-class classification problems for high dimensional data. Following the idea of reduced-rank linear discriminant analysis (LDA), we introduce a new dimension reduction tool with a flavor of supervised principal component analysis (PCA). The proposed method is computationally efficient and can incorporate the correlation structure among the features. Besides the theoretical insights, we show that our method is a competitive classification tool by simulated and real data examples.

stat.ME↗

arXiv2017

An Edge Driven Wavelet Frame Model for Image Restoration

Wavelet frame systems are known to be effective in capturing singularities from noisy and degraded images. In this paper, we introduce a new edge driven wavelet frame model for image restoration by approximating images as piecewise smooth functions. With an implicit representation of image singularities sets, the proposed model inflicts different strength of regularization on smooth and singular image regions and edges. The proposed edge driven model is robust to both image approximation and singularity estimation. The implicit formulation also enables an asymptotic analysis of the proposed models and a rigorous connection between the discrete model and a general continuous variational model. Finally, numerical results on image inpainting and deblurring show that the proposed model is compared favorably against several popular image restoration models.

math.NA↗

arXiv2016

Building a comprehensive syntactic and semantic corpus of Chinese clinical texts

Objective: To build a comprehensive corpus covering syntactic and semantic annotations of Chinese clinical texts with corresponding annotation guidelines and methods as well as to develop tools trained on the annotated corpus, which supplies baselines for research on Chinese texts in the clinical domain. Materials and methods: An iterative annotation method was proposed to train annotators and to develop annotation guidelines. Then, by using annotation quality assurance measures, a comprehensive corpus was built, containing annotations of part-of-speech (POS) tags, syntactic tags, entities, assertions, and relations. Inter-annotator agreement (IAA) was calculated to evaluate the annotation quality and a Chinese clinical text processing and information extraction system (CCTPIES) was developed based on our annotated corpus. Results: The syntactic corpus consists of 138 Chinese clinical documents with 47,424 tokens and 2553 full parsing trees, while the semantic corpus includes 992 documents that annotated 39,511 entities with their assertions and 7695 relations. IAA evaluation shows that this comprehensive corpus is of good quality, and the system modules are effective. Discussion: The annotated corpus makes a considerable contribution to natural language processing (NLP) research into Chinese texts in the clinical domain. However, this corpus has a number of limitations. Some additional types of clinical text should be introduced to improve corpus coverage and active learning methods should be utilized to promote annotation efficiency. Conclusions: In this study, several annotation guidelines and an annotation method for Chinese clinical texts were proposed, and a comprehensive corpus with its NLP modules were constructed, providing a foundation for further study of applying NLP techniques to Chinese texts in the clinical domain.

cs.CL↗

arXiv2016

Limited Tomography Reconstruction via Tight Frame and Sinogram Extrapolation

X-ray computed tomography (CT) is one of widely used diagnostic tools for medical and dental tomographic imaging of the human body. However, the standard filtered backprojection reconstruction method requires the complete knowledge of the projection data. In the case of limited data, the inverse problem of CT becomes more ill-posed, which makes the reconstructed image deteriorated by the artifacts. In this paper, we consider two dimensional CT reconstruction using the horizontally truncated projections. Over the decades, the numerous results including the sparsity model based approach has enabled the reconstruction of the image inside the region of interest (ROI) from the limited knowledge of the data. However, unlike these existing methods, we try to reconstruct the entire CT image from the limited knowledge of the sinogram via the tight frame regularization and the simultaneous sinogram extrapolation. Our proposed model shows more promising numerical simulation results compared with the existing sparsity model based approach.

math.NA↗

arXiv2016

Image Restoration: A General Wavelet Frame Based Model and Its Asymptotic Analysis

Image restoration is one of the most important areas in imaging science. Mathematical tools have been widely used in image restoration, where wavelet frame based approach is one of the successful examples. In this paper, we introduce a generic wavelet frame based image restoration model, called the "general model", which includes most of the existing wavelet frame based models as special cases. Moreover, the general model also includes examples that are new to the literature. Motivated by our earlier studies [1-3], We provide an asymptotic analysis of the general model as image resolution goes to infinity, which establishes a connection between the general model in discrete setting and a new variatonal model in continuum setting. The variational model also includes some of the existing variational models as special cases, such as the total generalized variational model proposed by [4]. In the end, we introduce an algorithm solving the general model and present one numerical simulation as an example.

math.FA↗

arXiv2016

CT Image Reconstruction by Spatial-Radon Domain Data-Driven Tight Frame Regularization

This paper proposes a spatial-Radon domain CT image reconstruction model based on data-driven tight frames (SRD-DDTF). The proposed SRD-DDTF model combines the idea of joint image and Radon domain inpainting model of \cite{Dong2013X} and that of the data-driven tight frames for image denoising \cite{cai2014data}. It is different from existing models in that both CT image and its corresponding high quality projection image are reconstructed simultaneously using sparsity priors by tight frames that are adaptively learned from the data to provide optimal sparse approximations. An alternative minimization algorithm is designed to solve the proposed model which is nonsmooth and nonconvex. Convergence analysis of the algorithm is provided. Numerical experiments showed that the SRD-DDTF model is superior to the model by \cite{Dong2013X} especially in recovering some subtle structures in the images.

physics.med-ph↗

arXiv2016

Jiamusi Pulsar Observations: I. Abnormal emission events of PSR B0919+06

PSR B0919+06 generally radiates radio pulses in a normal phase range. It has been known for its occasional perplexing abnormal emission events wherein individual pulses come to an earlier phase range for a few tens of periods and then returns to its usual phase. Heretofore, only a few such events have been available for study. We observed PSR B0919+06 for about 30 hours using the Jiamusi 66-m telescope at Jiamusi Deep Space Station at S-band, and detected 92 abnormal emission events. We identify four types of events based on the abrupted or gradual phase-shifting of individual pulses. The abnormal emission events are seen to occur randomly some every 1000 to 3000 periods, and they affect the leading edge of the mean profile by up to 2\% in amplitude. The abnormal emission events are probably related to gradual changes of emission processing in the pulsar magnetosphere.

astro-ph.HE↗

arXiv2016

Randomized Algorithms For High Quality Treatment Planning in Volumetric Modulated Arc Therapy

In recent years, volumetric modulated arc therapy (VMAT) has been becoming a more and more important radiation technique widely used in clinical application for cancer treatment. One of the key problems in VMAT is treatment plan optimization, which is complicated due to the constraints imposed by the involved equipments. In this paper, we consider a model with four major constraints: the bound on the beam intensity, an upper bound on the rate of the change of the beam intensity, the moving speed of leaves of the multi-leaf collimator (MLC) and its directional-convexity. We solve the model by a two-stage algorithm: performing minimization with respect to the shapes of the aperture and the beam intensities alternatively. Specifically, the shapes of the aperture are obtained by a greedy algorithm whose performance is enhanced by random sampling in the leaf pairs with a decremental rate. The beam intensity is optimized using a gradient projection method with non-monotonic line search. We further improve the proposed algorithm by an incremental random importance sampling of the voxels to reduce the computational cost of the energy functional. Numerical simulations on two clinical cancer date sets demonstrate that our method is highly competitive to the state-of-the-art algorithms in terms of both computational time and quality of treatment planning.

physics.med-ph↗

arXiv2015

Sparse Representation on Graphs by Tight Wavelet Frames and Applications

In this paper, we introduce a new (constructive) characterization of tight wavelet frames on non-flat domains in both continuum setting, i.e. on manifolds, and discrete setting, i.e. on graphs; discuss how fast tight wavelet frame transforms can be computed and how they can be effectively used to process graph data. We start with defining the quasi-affine systems on a given manifold $\cM$ that is formed by generalized dilations and shifts of a finite collection of wavelet functions $Ψ:=\{ψ_j: 1\le j\le r\}\subset L_2(\R)$. We further require that $ψ_j$ is generated by some refinable function $ϕ$ with mask $a_j$. We present the condition needed for the masks $\{a_j: 0\le j\le r\}$ so that the associated quasi-affine system generated by $Ψ$ is a tight frame for $L_2(\cM)$. Then, we discuss how the transition from the continuum (manifolds) to the discrete setting (graphs) can be naturally done. In order for the proposed discrete tight wavelet frame transforms to be useful in applications, we show how the transforms can be computed efficiently and accurately by proposing the fast tight wavelet frame transforms for graph data (WFTG). Finally, we consider two specific applications of the proposed WFTG: graph data denoising and semi-supervised clustering. Utilizing the sparse representation provided by the WFTG, we propose $\ell_1$-norm based optimization models on graphs for denoising and semi-supervised clustering. On one hand, our numerical results show significant advantage of the WFTG over the spectral graph wavelet transform (SGWT) by [1] for both applications. On the other hand, numerical experiments on two real data sets show that the proposed semi-supervised clustering model using the WFTG is overall competitive with the state-of-the-art methods developed in the literature of high-dimensional data classification, and is superior to some of these methods.

math.FA↗

arXiv2014

Sparsifying the Fisher Linear Discriminant by Rotation

Many high dimensional classification techniques have been proposed in the literature based on sparse linear discriminant analysis (LDA). To efficiently use them, sparsity of linear classifiers is a prerequisite. However, this might not be readily available in many applications, and rotations of data are required to create the needed sparsity. In this paper, we propose a family of rotations to create the required sparsity. The basic idea is to use the principal components of the sample covariance matrix of the pooled samples and its variants to rotate the data first and to then apply an existing high dimensional classifier. This rotate-and-solve procedure can be combined with any existing classifiers, and is robust against the sparsity level of the true model. We show that these rotations do create the sparsity needed for high dimensional classifications and provide theoretical understanding why such a rotation works empirically. The effectiveness of the proposed method is demonstrated by a number of simulated and real data examples, and the improvements of our method over some popular high dimensional classification rules are clearly shown.

stat.ME↗

arXiv2013

A Contour-Guided Deformable Image Registration Algorithm for Adaptive Radiotherapy

In adaptive radiotherapy, deformable image registration is often conducted between the planning CT and treatment CT (or cone beam CT) to generate a deformation vector field (DVF) for dose accumulation and contour propagation. The auto propagated contours on the treatment CT may contain relatively large errors, especially in low contrast regions. A clinician inspection and editing of the propagated contours are frequently needed. The edited contours are able to meet the clinical requirement for adaptive therapy; however, the DVF is still inaccurate and inconsistent with the edited contours. The purpose of this work is to develop a contour-guided deformable image registration (CG-DIR) algorithm to improve the accuracy and consistency of the DVF for adaptive radiotherapy. Incorporation of the edited contours into the registration algorithm is realized by regularizing the objective function of the original demons algorithm with a term of intensity matching between the delineated structures set pairs. The CG-DIR algorithm is implemented on computer graphics processing units (GPUs) by following the original GPU-based demons algorithm computation framework [Gu et al, Phys Med Biol. 55(1): 207-219, 2010]. The performance of CG-DIR is evaluated on five clinical head-and-neck and one pelvic cancer patient data. It is found that compared with the original demons, CG-DIR improves the accuracy and consistency of the DVF, while retaining similar high computational efficiency.

physics.med-ph↗

arXiv2012

Optimal Surface Marker Locations for Tumor Motion Estimation in Lung Cancer Radiotherapy

Using fiducial markers on patient's body surface to predict the tumor location is a widely used approach in lung cancer radiotherapy. The purpose of this work is to propose an algorithm that automatically identifies a sparse set of locations on the patient's surface with the optimal prediction power for the tumor motion. The sparse selection of markers on the external surface and the assumed linear relationship between the marker motion and the internal tumor motion are represented by a prediction matrix. Such a matrix is determined by solving an optimization problem, where the objective function contains a sparsity term that penalizes the number of markers chosen on the patient's surface. The performance of our algorithm has been tested on realistic clinical data of four lung cancer patients. Thoracic 4DCT scans with 10 phases are used for the study. On a reference phase, a grid of points are casted on the patient's surface (except for patient's back) and propagated to other phases via deformable image registration of the corresponding CT images. Tumor locations at each phase are also manually delineated. We use 9 out of 10 phases of the 4DCT images to identify a small group of surface markers that are most correlated with the motion of the tumor, and find the prediction matrix at the same time. The 10th phase is then used to test the accuracy of the prediction. It is found that on average 6 to 7 surface markers are necessary to predict tumor locations with a 3D error of about 1mm. In addition, the selected marker locations lie closely in those areas where surface point motion has a high correlation with the tumor motion. Our method can automatically select sparse locations on patient's external surface and estimate a correlation matrix based on 4DCT, so that the selected surface locations can be used to place fiducial markers to optimally predict internal tumor motions.

physics.med-ph↗

arXiv2011

$\ell_0$ Minimization for Wavelet Frame Based Image Restoration

The theory of (tight) wavelet frames has been extensively studied in the past twenty years and they are currently widely used for image restoration and other image processing and analysis problems. The success of wavelet frame based models, including balanced approach and analysis based approach, is due to their capability of sparsely approximating piecewise smooth functions like images. Motivated by the balanced approach and analysis based approach, we shall propose a wavelet frame based $\ell_0$ minimization model, where the $\ell_0$ "norm" of the frame coefficients is penalized. We adapt the penalty decomposition (PD) method to solve the proposed optimization problem. Numerical results showed that the proposed model solved by the PD method can generate images with better quality than those obtained by either analysis based approach or balanced approach in terms of restoring sharp features as well as maintaining smoothness of the recovered images. Some convergence analysis of the PD method will also be provided.

cs.CV↗

arXiv2011

GPU-based Iterative Cone Beam CT Reconstruction Using Tight Frame Regularization

X-ray imaging dose from serial cone-beam CT (CBCT) scans raises a clinical concern in most image guided radiation therapy procedures. It is the goal of this paper to develop a fast GPU-based algorithm to reconstruct high quality CBCT images from undersampled and noisy projection data so as to lower the imaging dose. For this purpose, we have developed an iterative tight frame (TF) based CBCT reconstruction algorithm. A condition that a real CBCT image has a sparse representation under a TF basis is imposed in the iteration process as regularization to the solution. To speed up the computation, a multi-grid method is employed. Our GPU implementation has achieved high computational efficiency and a CBCT image of resolution 512\times512\times70 can be reconstructed in ~5 min. We have tested our algorithm on a digital NCAT phantom and a physical Catphan phantom. It is found that our TF-based algorithm is able to reconstrct CBCT in the context of undersampling and low mAs levels. We have also quantitatively analyzed the reconstructed CBCT image quality in terms of modulation-transfer-function and contrast-to-noise ratio under various scanning conditions. The results confirm the high CBCT image quality obtained from our TF algorithm. Moreover, our algorithm has also been validated in a real clinical context using a head-and-neck patient case. Comparisons of the developed TF algorithm and the current state-of-the-art TV algorithm have also been made in various cases studied in terms of reconstructed image quality and computation efficiency.

physics.med-ph↗

arXiv2011

Fast Linearized Bregman Iteration for Compressive Sensing and Sparse Denoising

We propose and analyze an extremely fast, efficient, and simple method for solving the problem:min{parallel to u parallel to(1) : Au = f, u is an element of R-n}.This method was first described in [J. Darbon and S. Osher, preprint, 2007], with more details in [W. Yin, S. Osher, D. Goldfarb and J. Darbon, SIAM J. Imaging Sciences, 1(1), 143-168, 2008] and rigorous theory given in [J. Cai, S. Osher and Z. Shen, Math. Comp., to appear, 2008, see also UCLA CAM Report 08-06] and [J. Cai, S. Osher and Z. Shen, UCLA CAM Report, 08-52, 2008]. The motivation was compressive sensing, which now has a vast and exciting history, which seems to have started with Candes, et. al. [E. Candes, J. Romberg and T. Tao, 52(2), 489-509, 2006] and Donoho, [D. L. Donoho, IEEE Trans. Inform. Theory, 52, 1289-1306, 2006]. See [W. Yin, S. Osher, D. Goldfarb and J. Darbon, SIAM J. Imaging Sciences 1(1), 143-168, 2008] and [J. Cai, S. Osher and Z. Shen, Math. Comp., to appear, 2008, see also UCLA CAM Report, 08-06] and [J. Cai, S. Osher and Z. Shen, UCLA CAM Report, 08-52, 2008] for a large set of references. Our method introduces an improvement called "kicking" of the very efficient method of [J. Darbon and S. Osher, preprint, 2007] and [W. Yin, S. Osher, D. Goldfarb and J. Darbon, SIAM J. Imaging Sciences, 1(1), 143-168, 2008] and also applies it to the problem of denoising of undersampled signals. The use of Bregman iteration for denoising of images began in [S. Osher, M. Burger, D. Goldfarb, J. Xu and W. Yin, Multiscale Model. Simul, 4(2), 460-489, 2005] and led to improved results for total variation based methods. Here we apply it to denoise signals, especially essentially sparse signals, which might even be undersampled.

math.OC↗

arXiv2011

A nonlinear PDE-based method for sparse deconvolution

In this paper, we introduce a new nonlinear evolution partial differential equation for sparse deconvolution problems. The proposed PDE has the form of continuity equation that arises in various research areas, e.g. fluid dynamics and optimal transportation, and thus has some interesting physical and geometric interpretations. The underlying optimization model that we consider is the standard $\ell_1$ minimization with linear equality constraints, i.e. $\min_u\{\|u\|_1 : Au=f\}$ with $A$ being an under-sampled convolution operator. We show that our PDE preserves the $\ell_1$ norm while lowering the residual $\|Au-f\|_2$. More importantly the solution of the PDE becomes sparser asymptotically, which is illustrated numerically. Therefore, it can be treated as a natural and helpful plug-in to some algorithms for $\ell_1$ minimization problems, e.g. Bregman iterative methods introduced for sparse reconstruction problems in [W. Yin, S. Osher, D. Goldfarb, and J. Darbon,SIAM J. Imaging Sci., 1 (2008), pp. 143-168]. Numerical experiments show great improvements in terms of both convergence speed and reconstruction quality.

math.OC↗

arXiv2009

A New Multiscale Representation for Shapes and Its Application to Blood Vessel Recovery

In this paper, we will first introduce a novel multiscale representation (MSR) for shapes. Based on the MSR, we will then design a surface inpainting algorithm to recover 3D geometry of blood vessels. Because of the nature of irregular morphology in vessels and organs, both phantom and real inpainting scenarios were tested using our new algorithm. Successful vessel recoveries are demonstrated with numerical estimation of the degree of arteriosclerosis and vessel occlusion.

math.AP↗

arXiv2005

K-Histograms: An Efficient Clustering Algorithm for Categorical Dataset

Clustering categorical data is an integral part of data mining and has attracted much attention recently. In this paper, we present k-histogram, a new efficient algorithm for clustering categorical data. The k-histogram algorithm extends the k-means algorithm to categorical domain by replacing the means of clusters with histograms, and dynamically updates histograms in the clustering process. Experimental results on real datasets show that k-histogram algorithm can produce better clustering results than k-modes algorithm, the one related with our work most closely.

cs.AI↗