Parametric Level-sets Enhanced To Improve Reconstruction (PaLEnTIR)

In this paper, we consider the restoration and reconstruction of piecewise constant objects in two and three dimensions using PaLEnTIR, a significantly enhanced Parametric level set (PaLS) model relative to the current state-of-the-art. The primary contribution of this paper is a new PaLS formulation which requires only a single level set function to recover a scene with piecewise constant objects possessing multiple unknown contrasts. Our model offers distinct advantages over current approaches to the multi-contrast, multi-object problem, all of which require multiple level sets and explicit estimation of the contrast magnitudes. Given upper and lower bounds on the contrast, our approach is able to recover objects with any distribution of contrasts and eliminates the need to know either the number of contrasts in a given scene or their values. We provide an iterative process for finding these space-varying contrast limits. Relative to most PaLS methods which employ radial basis functions (RBFs), our model makes use of non-isotropic basis functions, thereby expanding the class of shapes that a PaLS model of a given complexity can approximate. Finally, PaLEnTIR improves the conditioning of the Jacobian matrix required as part of the parameter identification process and consequently accelerates the optimization methods by controlling the magnitude of the PaLS expansion coefficients, fixing the centers of the basis functions, and the uniqueness of parametric to image mappings provided by the new parameterization. We demonstrate the performance of the new approach using both 2D and 3D variants of X-ray computed tomography, diffuse optical tomography (DOT), denoising, deconvolution problems. Application to experimental sparse CT data and simulated data with different types of noise are performed to further validate the proposed method.Comment: 31 pages, 56 figure

A regularizing iterative ensemble Kalman method for PDE-constrained inverse problems

We introduce a derivative-free computational framework for approximating solutions to nonlinear PDE-constrained inverse problems. The aim is to merge ideas from iterative regularization with ensemble Kalman methods from Bayesian inference to develop a derivative-free stable method easy to implement in applications where the PDE (forward) model is only accessible as a black box. The method can be derived as an approximation of the regularizing Levenberg-Marquardt (LM) scheme [14] in which the derivative of the forward operator and its adjoint are replaced with empirical covariances from an ensemble of elements from the admissible space of solutions. The resulting ensemble method consists of an update formula that is applied to each ensemble member and that has a regularization parameter selected in a similar fashion to the one in the LM scheme. Moreover, an early termination of the scheme is proposed according to a discrepancy principle-type of criterion. The proposed method can be also viewed as a regularizing version of standard Kalman approaches which are often unstable unless ad-hoc fixes, such as covariance localization, are implemented. We provide a numerical investigation of the conditions under which the proposed method inherits the regularizing properties of the LM scheme of [14]. More concretely, we study the effect of ensemble size, number of measurements, selection of initial ensemble and tunable parameters on the performance of the method. The numerical investigation is carried out with synthetic experiments on two model inverse problems: (i) identification of conductivity on a Darcy flow model and (ii) electrical impedance tomography with the complete electrode model. We further demonstrate the potential application of the method in solving shape identification problems by means of a level-set approach for the parameterization of unknown geometries

Parameter identification problems in the modelling of cell motility

We present a novel parameter identification algorithm for the estimation of parameters in models of cell motility using imaging data of migrating cells. Two alternative formulations of the objective functional that measures the difference between the computed and observed data are proposed and the parameter identification problem is formulated as a minimisation problem of nonlinear least squares type. A Levenberg–Marquardt based optimisation method is applied to the solution of the minimisation problem and the details of the implementation are discussed. A number of numerical experiments are presented which illustrate the robustness of the algorithm to parameter identification in the presence of large deformations and noisy data and parameter identification in three dimensional models of cell motility. An application to experimental data is also presented in which we seek to identify parameters in a model for the monopolar growth of fission yeast cells using experimental imaging data. Our numerical tests allow us to compare the method with the two different formulations of the objective functional and we conclude that the results with both objective functionals seem to agree

On a continuation approach in Tikhonov regularization and its application in piecewise-constant parameter identification

We present a new approach to convexification of the Tikhonov regularization using a continuation method strategy. We embed the original minimization problem into a one-parameter family of minimization problems. Both the penalty term and the minimizer of the Tikhonov functional become dependent on a continuation parameter. In this way we can independently treat two main roles of the regularization term, which are stabilization of the ill-posed problem and introduction of the a priori knowledge. For zero continuation parameter we solve a relaxed regularization problem, which stabilizes the ill-posed problem in a weaker sense. The problem is recast to the original minimization by the continuation method and so the a priori knowledge is enforced. We apply this approach in the context of topology-to-shape geometry identification, where it allows to avoid the convergence of gradient-based methods to a local minima. We present illustrative results for magnetic induction tomography which is an example of PDE constrained inverse problem

A nested mixture model for protein identification using mass spectrometry

Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected to mass spectrometry, which generates thousands of spectra, each characteristic of its generating peptide. Here we consider the problem of inferring, from these spectra, which proteins and peptides are present in the sample. We develop a statistical approach to the problem, based on a nested mixture model. In contrast to commonly used two-stage approaches, this model provides a one-stage solution that simultaneously identifies which proteins are present, and which peptides are correctly identified. In this way our model incorporates the evidence feedback between proteins and their constituent peptides. Using simulated data and a yeast data set, we compare and contrast our method with existing widely used approaches (PeptideProphet/ProteinProphet) and with a recently published new approach, HSM. For peptide identification, our single-stage approach yields consistently more accurate results. For protein identification the methods have similar accuracy in most settings, although we exhibit some scenarios in which the existing methods perform poorly.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS316 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org