Geometric-Based Algorithm for a Full Row-Rank System Matrix Along Multiple Directions in DT

Discrete tomography (DT) is an image reconstruction procedure that deals with computational synthesis of a cross-sectional image of an object from either transmission or reflection data collected by penetrating an object with X-rays from a small number of different directions, and whose range of the underlying function is discrete. Image reconstruction using algebraic approach is time consuming and the computation cost depends on the size of the system matrix. More scanning directions provide an increase in the reconstructed image quality, however they increase the size of the system matrix dramatically. Deletion of linearly dependent rows of this matrix is necessary to reduce computational cost, and is sometimes a requirement for certain reconstruction software. A geometric-based algorithm is derived in this study that will remove linearly dependent rows of the system matrix generated along an arbitrary number of scanning directions. Numerical experiments indicate that the proposed algorithm reduces the system matrix to a full row-rank

Optimal low-rank approximations of Bayesian linear inverse problems

In the Bayesian approach to inverse problems, data are often informative, relative to the prior, only on a low-dimensional subspace of the parameter space. Significant computational savings can be achieved by using this subspace to characterize and approximate the posterior distribution of the parameters. We first investigate approximation of the posterior covariance matrix as a low-rank update of the prior covariance matrix. We prove optimality of a particular update, based on the leading eigendirections of the matrix pencil defined by the Hessian of the negative log-likelihood and the prior precision, for a broad class of loss functions. This class includes the F\"{o}rstner metric for symmetric positive definite matrices, as well as the Kullback-Leibler divergence and the Hellinger distance between the associated distributions. We also propose two fast approximations of the posterior mean and prove their optimality with respect to a weighted Bayes risk under squared-error loss. These approximations are deployed in an offline-online manner, where a more costly but data-independent offline calculation is followed by fast online evaluations. As a result, these approximations are particularly useful when repeated posterior mean evaluations are required for multiple data sets. We demonstrate our theoretical results with several numerical examples, including high-dimensional X-ray tomography and an inverse heat conduction problem. In both of these examples, the intrinsic low-dimensional structure of the inference problem can be exploited while producing results that are essentially indistinguishable from solutions computed in the full space

Sparse approximations of protein structure from noisy random projections

Single-particle electron microscopy is a modern technique that biophysicists employ to learn the structure of proteins. It yields data that consist of noisy random projections of the protein structure in random directions, with the added complication that the projection angles cannot be observed. In order to reconstruct a three-dimensional model, the projection directions need to be estimated by use of an ad-hoc starting estimate of the unknown particle. In this paper we propose a methodology that does not rely on knowledge of the projection angles, to construct an objective data-dependent low-resolution approximation of the unknown structure that can serve as such a starting estimate. The approach assumes that the protein admits a suitable sparse representation, and employs discrete $L^1$-regularization (LASSO) as well as notions from shape theory to tackle the peculiar challenges involved in the associated inverse problem. We illustrate the approach by application to the reconstruction of an E. coli protein component called the Klenow fragment.Comment: Published in at http://dx.doi.org/10.1214/11-AOAS479 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Quantitative photoacoustic imaging in radiative transport regime

The objective of quantitative photoacoustic tomography (QPAT) is to reconstruct optical and thermodynamic properties of heterogeneous media from data of absorbed energy distribution inside the media. There have been extensive theoretical and computational studies on the inverse problem in QPAT, however, mostly in the diffusive regime. We present in this work some numerical reconstruction algorithms for multi-source QPAT in the radiative transport regime with energy data collected at either single or multiple wavelengths. We show that when the medium to be probed is non-scattering, explicit reconstruction schemes can be derived to reconstruct the absorption and the Gruneisen coefficients. When data at multiple wavelengths are utilized, we can reconstruct simultaneously the absorption, scattering and Gruneisen coefficients. We show by numerical simulations that the reconstructions are stable.Comment: 40 pages, 13 figure

Structural Variability from Noisy Tomographic Projections

In cryo-electron microscopy, the 3D electric potentials of an ensemble of molecules are projected along arbitrary viewing directions to yield noisy 2D images. The volume maps representing these potentials typically exhibit a great deal of structural variability, which is described by their 3D covariance matrix. Typically, this covariance matrix is approximately low-rank and can be used to cluster the volumes or estimate the intrinsic geometry of the conformation space. We formulate the estimation of this covariance matrix as a linear inverse problem, yielding a consistent least-squares estimator. For $n$ images of size $N$-by-$N$ pixels, we propose an algorithm for calculating this covariance estimator with computational complexity $\mathcal{O}(nN^4+\sqrt{\kappa}N^6 \log N)$, where the condition number $\kappa$ is empirically in the range $10$--$200$. Its efficiency relies on the observation that the normal equations are equivalent to a deconvolution problem in 6D. This is then solved by the conjugate gradient method with an appropriate circulant preconditioner. The result is the first computationally efficient algorithm for consistent estimation of 3D covariance from noisy projections. It also compares favorably in runtime with respect to previously proposed non-consistent estimators. Motivated by the recent success of eigenvalue shrinkage procedures for high-dimensional covariance matrices, we introduce a shrinkage procedure that improves accuracy at lower signal-to-noise ratios. We evaluate our methods on simulated datasets and achieve classification results comparable to state-of-the-art methods in shorter running time. We also present results on clustering volumes in an experimental dataset, illustrating the power of the proposed algorithm for practical determination of structural variability.Comment: 52 pages, 11 figure