Manifold Learning in MR spectroscopy using nonlinear dimensionality reduction and unsupervised clustering

Purpose To investigate whether nonlinear dimensionality reduction improves unsupervised classification of 1H MRS brain tumor data compared with a linear method. Methods In vivo single-voxel 1H magnetic resonance spectroscopy (55 patients) and 1H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. Results An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With 1H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. Conclusion Purpose To investigate whether nonlinear dimensionality reduction improves unsupervised classification of 1H MRS brain tumor data compared with a linear method. Methods In vivo single-voxel 1H magnetic resonance spectroscopy (55 patients) and 1H magnetic resonance spectroscopy imaging (MRSI) (29 patients) data were acquired from histopathologically diagnosed gliomas. Data reduction using Laplacian eigenmaps (LE) or independent component analysis (ICA) was followed by k-means clustering or agglomerative hierarchical clustering (AHC) for unsupervised learning to assess tumor grade and for tissue type segmentation of MRSI data. Results An accuracy of 93% in classification of glioma grade II and grade IV, with 100% accuracy in distinguishing tumor and normal spectra, was obtained by LE with unsupervised clustering, but not with the combination of k-means and ICA. With 1H MRSI data, LE provided a more linear distribution of data for cluster analysis and better cluster stability than ICA. LE combined with k-means or AHC provided 91% accuracy for classifying tumor grade and 100% accuracy for identifying normal tissue voxels. Color-coded visualization of normal brain, tumor core, and infiltration regions was achieved with LE combined with AHC. Conclusion The LE method is promising for unsupervised clustering to separate brain and tumor tissue with automated color-coding for visualization of 1H MRSI data after cluster analysis

Sparsity Based Poisson Denoising with Dictionary Learning

The problem of Poisson denoising appears in various imaging applications, such as low-light photography, medical imaging and microscopy. In cases of high SNR, several transformations exist so as to convert the Poisson noise into an additive i.i.d. Gaussian noise, for which many effective algorithms are available. However, in a low SNR regime, these transformations are significantly less accurate, and a strategy that relies directly on the true noise statistics is required. A recent work by Salmon et al. took this route, proposing a patch-based exponential image representation model based on GMM (Gaussian mixture model), leading to state-of-the-art results. In this paper, we propose to harness sparse-representation modeling to the image patches, adopting the same exponential idea. Our scheme uses a greedy pursuit with boot-strapping based stopping condition and dictionary learning within the denoising process. The reconstruction performance of the proposed scheme is competitive with leading methods in high SNR, and achieving state-of-the-art results in cases of low SNR.Comment: 13 pages, 9 figure

Image Deblurring and Super-resolution by Adaptive Sparse Domain Selection and Adaptive Regularization

As a powerful statistical image modeling technique, sparse representation has been successfully used in various image restoration applications. The success of sparse representation owes to the development of l1-norm optimization techniques, and the fact that natural images are intrinsically sparse in some domain. The image restoration quality largely depends on whether the employed sparse domain can represent well the underlying image. Considering that the contents can vary significantly across different images or different patches in a single image, we propose to learn various sets of bases from a pre-collected dataset of example image patches, and then for a given patch to be processed, one set of bases are adaptively selected to characterize the local sparse domain. We further introduce two adaptive regularization terms into the sparse representation framework. First, a set of autoregressive (AR) models are learned from the dataset of example image patches. The best fitted AR models to a given patch are adaptively selected to regularize the image local structures. Second, the image non-local self-similarity is introduced as another regularization term. In addition, the sparsity regularization parameter is adaptively estimated for better image restoration performance. Extensive experiments on image deblurring and super-resolution validate that by using adaptive sparse domain selection and adaptive regularization, the proposed method achieves much better results than many state-of-the-art algorithms in terms of both PSNR and visual perception.Comment: 35 pages. This paper is under review in IEEE TI

Solving Inverse Problems with Piecewise Linear Estimators: From Gaussian Mixture Models to Structured Sparsity

A general framework for solving image inverse problems is introduced in this paper. The approach is based on Gaussian mixture models, estimated via a computationally efficient MAP-EM algorithm. A dual mathematical interpretation of the proposed framework with structured sparse estimation is described, which shows that the resulting piecewise linear estimate stabilizes the estimation when compared to traditional sparse inverse problem techniques. This interpretation also suggests an effective dictionary motivated initialization for the MAP-EM algorithm. We demonstrate that in a number of image inverse problems, including inpainting, zooming, and deblurring, the same algorithm produces either equal, often significantly better, or very small margin worse results than the best published ones, at a lower computational cost.Comment: 30 page

Graph Regularized Tensor Sparse Coding for Image Representation

Sparse coding (SC) is an unsupervised learning scheme that has received an increasing amount of interests in recent years. However, conventional SC vectorizes the input images, which destructs the intrinsic spatial structures of the images. In this paper, we propose a novel graph regularized tensor sparse coding (GTSC) for image representation. GTSC preserves the local proximity of elementary structures in the image by adopting the newly proposed tubal-tensor representation. Simultaneously, it considers the intrinsic geometric properties by imposing graph regularization that has been successfully applied to uncover the geometric distribution for the image data. Moreover, the returned sparse representations by GTSC have better physical explanations as the key operation (i.e., circular convolution) in the tubal-tensor model preserves the shifting invariance property. Experimental results on image clustering demonstrate the effectiveness of the proposed scheme