Total variation regularization for manifold-valued data

We consider total variation minimization for manifold valued data. We propose a cyclic proximal point algorithm and a parallel proximal point algorithm to minimize TV functionals with $\ell^p$-type data terms in the manifold case. These algorithms are based on iterative geodesic averaging which makes them easily applicable to a large class of data manifolds. As an application, we consider denoising images which take their values in a manifold. We apply our algorithms to diffusion tensor images, interferometric SAR images as well as sphere and cylinder valued images. For the class of Cartan-Hadamard manifolds (which includes the data space in diffusion tensor imaging) we show the convergence of the proposed TV minimizing algorithms to a global minimizer

Jump-sparse and sparse recovery using Potts functionals

We recover jump-sparse and sparse signals from blurred incomplete data corrupted by (possibly non-Gaussian) noise using inverse Potts energy functionals. We obtain analytical results (existence of minimizers, complexity) on inverse Potts functionals and provide relations to sparsity problems. We then propose a new optimization method for these functionals which is based on dynamic programming and the alternating direction method of multipliers (ADMM). A series of experiments shows that the proposed method yields very satisfactory jump-sparse and sparse reconstructions, respectively. We highlight the capability of the method by comparing it with classical and recent approaches such as TV minimization (jump-sparse signals), orthogonal matching pursuit, iterative hard thresholding, and iteratively reweighted $\ell^1$ minimization (sparse signals)

Mumford-Shah and Potts Regularization for Manifold-Valued Data with Applications to DTI and Q-Ball Imaging

Mumford-Shah and Potts functionals are powerful variational models for regularization which are widely used in signal and image processing; typical applications are edge-preserving denoising and segmentation. Being both non-smooth and non-convex, they are computationally challenging even for scalar data. For manifold-valued data, the problem becomes even more involved since typical features of vector spaces are not available. In this paper, we propose algorithms for Mumford-Shah and for Potts regularization of manifold-valued signals and images. For the univariate problems, we derive solvers based on dynamic programming combined with (convex) optimization techniques for manifold-valued data. For the class of Cartan-Hadamard manifolds (which includes the data space in diffusion tensor imaging), we show that our algorithms compute global minimizers for any starting point. For the multivariate Mumford-Shah and Potts problems (for image regularization) we propose a splitting into suitable subproblems which we can solve exactly using the techniques developed for the corresponding univariate problems. Our method does not require any a priori restrictions on the edge set and we do not have to discretize the data space. We apply our method to diffusion tensor imaging (DTI) as well as Q-ball imaging. Using the DTI model, we obtain a segmentation of the corpus callosum

The L1-Potts functional for robust jump-sparse reconstruction

We investigate the non-smooth and non-convex $L^1$-Potts functional in discrete and continuous time. We show $\Gamma$-convergence of discrete $L^1$-Potts functionals towards their continuous counterpart and obtain a convergence statement for the corresponding minimizers as the discretization gets finer. For the discrete $L^1$-Potts problem, we introduce an $O(n^2)$ time and $O(n)$ space algorithm to compute an exact minimizer. We apply $L^1$-Potts minimization to the problem of recovering piecewise constant signals from noisy measurements $f.$ It turns out that the $L^1$-Potts functional has a quite interesting blind deconvolution property. In fact, we show that mildly blurred jump-sparse signals are reconstructed by minimizing the $L^1$-Potts functional. Furthermore, for strongly blurred signals and known blurring operator, we derive an iterative reconstruction algorithm

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and the data analysis remains challenging. In this study, we generated high depth MBD-seq data in MCF-7 cell and developed a bi-asymmetric-Laplace model (BALM) to perform data analysis. We found that optimal efficiency of MBD-seq experiments was achieved by sequencing ∼100 million unique mapped tags from a combination of 500 mM and 1000 mM salt concentration elution in MCF-7 cells. Clonal bisulfite sequencing results showed that the methylation status of each CpG dinucleotides in the tested regions was accurately detected with high resolution using the proposed model. These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution

Thromb Res

The use of direct oral anticoagulants (DOAC) is increasing. Specific concentrations are available and have been proven to be reliable and reproducible in optimising patient care. This retrospective, monocentric study aimed to describe the indications and consequences of monitoring DOAC plasma levels on patient care. We collected data of patients hospitalised at the Bordeaux University Hospital between January 2017 and December 2018. These included demographics, indications, type, dose of DOAC, standard coagulation tests, creatinine clearance and DOAC plasma concentration using specifically calibrated rivaroxaban and apixaban anti-Xa and dabigatran anti-IIa assays. The date of last DOAC intake, the time between intake and plasma level measurement were also collected and analysed. A total of 2197 DOAC assays in 1488 patients were obtained in various clinical situations: urgent or elective procedures, context of acute renal failure, suspicion or occurrence of ischemic strokes, intra-cranial and other bleeding sites. Interpretation of these assays led physicians to maintain, postpone or cancel invasive and high haemorrhagic risk procedures in 757, 261 and 56 cases respectively. The remaining 1123 assays were associated with no significant modification of patient care. DOAC plasma concentration was ≤30 ng ml (sensitivity 85.4%, specificity 73.6%, positive predictive value 71.1%, negative predictive value 86.7%, AUC 0.81) after a last intake of at least 2 days. Our study is, to date, the largest report of real-life measurement of specific DOAC plasma level at a single institution. Patient care was not modified in more than half of the assays