Dynamic Contrast-enhanced MR Imaging of Carotid Atherosclerotic Plaque: Model Selection, Reproducibility, and Validation.

Purpose: compare four known pharmacokinetic models for their ability to describe dynamic contrast material-enhanced magnetic resonance (MR) imaging of carotid atherosclerotic plaques, to determine reproducibility, and to validate the results with histologic findings. Materials and Methods: The study was approved by the institutional medical ethics committee. Written informed consent was obtained from all patients. Forty-five patients with 30%-99% carotid stenosis underwent dynamic contrast-enhanced MR imaging. Plaque enhancement was measured at 16 time points at approximately 25-second image intervals by using a gadolinium-based contrast material. Pharmacokinetic parameters (volume transfer constant, Ktrans; extracellular extravascular volume fraction, v e; and blood plasma fraction, v p) were determined by fitting a two-compartment model to plaque and blood gadolinium concentration curves. The relative fit errors and parameter uncertainties were determined to find the most suitable model. Sixteen patients underwent imaging twice to determine reproducibility. Carotid endarterectomy specimens from 16 patients who were scheduled for surgery were collected for histologic validation. Parameter uncertainties were compared with the Wilcoxon signed rank test. Reproducibility was assessed by using the coefficient of variation. Correlation with histologic findings was evaluated with the Pearson correlation coefficient. Results: The mean relative fit uncertainty (+/- standard error) for Ktrans was 10% +/- 1 with the Patlak model, which was significantly lower than that with the Tofts (20% +/- 1), extended Tofts (33% +/- 3), and extended graphical (29% +/- 3) models (P <.001). The relative uncertainty for v p was 20% 6 2 with the Patlak model and was significantly higher with the extended Tofts (46% +/- 9) and extended graphical (35% +/- 5) models (P <.001). The reproducibility (coefficient of variation) for the Patlak model was 16% for Ktrans and 26% for v p. Significant positive correlations were found between Ktrans and the endothelial microvessel content determined on histologic slices (Pearson r = 0.72, P = .005). Conclusion: The Patlak model is most suited for describing carotid plaque enhancement. Correlation with histologic findings validated Ktrans as an indicator of plaque microvasculature, and the reproducibility of Ktrans was good. (C)RSNA, 201

Sparse Median Graphs Estimation in a High Dimensional Semiparametric Model

In this manuscript a unified framework for conducting inference on complex aggregated data in high dimensional settings is proposed. The data are assumed to be a collection of multiple non-Gaussian realizations with underlying undirected graphical structures. Utilizing the concept of median graphs in summarizing the commonality across these graphical structures, a novel semiparametric approach to modeling such complex aggregated data is provided along with robust estimation of the median graph, which is assumed to be sparse. The estimator is proved to be consistent in graph recovery and an upper bound on the rate of convergence is given. Experiments on both synthetic and real datasets are conducted to illustrate the empirical usefulness of the proposed models and methods

Neural Connectivity with Hidden Gaussian Graphical State-Model

The noninvasive procedures for neural connectivity are under questioning. Theoretical models sustain that the electromagnetic field registered at external sensors is elicited by currents at neural space. Nevertheless, what we observe at the sensor space is a superposition of projected fields, from the whole gray-matter. This is the reason for a major pitfall of noninvasive Electrophysiology methods: distorted reconstruction of neural activity and its connectivity or leakage. It has been proven that current methods produce incorrect connectomes. Somewhat related to the incorrect connectivity modelling, they disregard either Systems Theory and Bayesian Information Theory. We introduce a new formalism that attains for it, Hidden Gaussian Graphical State-Model (HIGGS). A neural Gaussian Graphical Model (GGM) hidden by the observation equation of Magneto-encephalographic (MEEG) signals. HIGGS is equivalent to a frequency domain Linear State Space Model (LSSM) but with sparse connectivity prior. The mathematical contribution here is the theory for high-dimensional and frequency-domain HIGGS solvers. We demonstrate that HIGGS can attenuate the leakage effect in the most critical case: the distortion EEG signal due to head volume conduction heterogeneities. Its application in EEG is illustrated with retrieved connectivity patterns from human Steady State Visual Evoked Potentials (SSVEP). We provide for the first time confirmatory evidence for noninvasive procedures of neural connectivity: concurrent EEG and Electrocorticography (ECoG) recordings on monkey. Open source packages are freely available online, to reproduce the results presented in this paper and to analyze external MEEG databases

A Survey on Deep Learning-based Architectures for Semantic Segmentation on 2D images

Semantic segmentation is the pixel-wise labelling of an image. Since the problem is defined at the pixel level, determining image class labels only is not acceptable, but localising them at the original image pixel resolution is necessary. Boosted by the extraordinary ability of convolutional neural networks (CNN) in creating semantic, high level and hierarchical image features; excessive numbers of deep learning-based 2D semantic segmentation approaches have been proposed within the last decade. In this survey, we mainly focus on the recent scientific developments in semantic segmentation, specifically on deep learning-based methods using 2D images. We started with an analysis of the public image sets and leaderboards for 2D semantic segmantation, with an overview of the techniques employed in performance evaluation. In examining the evolution of the field, we chronologically categorised the approaches into three main periods, namely pre-and early deep learning era, the fully convolutional era, and the post-FCN era. We technically analysed the solutions put forward in terms of solving the fundamental problems of the field, such as fine-grained localisation and scale invariance. Before drawing our conclusions, we present a table of methods from all mentioned eras, with a brief summary of each approach that explains their contribution to the field. We conclude the survey by discussing the current challenges of the field and to what extent they have been solved.Comment: Updated with new studie

Caring, sharing widgets: a toolkit of sensitive widgets

Although most of us communicate using multiple sensory modalities in our lives, and many of our computers are similarly capable of multi-modal interaction, most human-computer interaction is predominantly in the visual mode. This paper describes a toolkit of widgets that are capable of presenting themselves in multiple modalities, but further are capapble of adapting their presentation to suit the contexts and environments in which they are used. This is of increasing importance as the use of mobile devices becomes ubiquitous

The Lazy Flipper: MAP Inference in Higher-Order Graphical Models by Depth-limited Exhaustive Search

This article presents a new search algorithm for the NP-hard problem of optimizing functions of binary variables that decompose according to a graphical model. It can be applied to models of any order and structure. The main novelty is a technique to constrain the search space based on the topology of the model. When pursued to the full search depth, the algorithm is guaranteed to converge to a global optimum, passing through a series of monotonously improving local optima that are guaranteed to be optimal within a given and increasing Hamming distance. For a search depth of 1, it specializes to Iterated Conditional Modes. Between these extremes, a useful tradeoff between approximation quality and runtime is established. Experiments on models derived from both illustrative and real problems show that approximations found with limited search depth match or improve those obtained by state-of-the-art methods based on message passing and linear programming.Comment: C++ Source Code available from http://hci.iwr.uni-heidelberg.de/software.ph

Geometry of rank tests

We study partitions of the symmetric group which have desirable geometric properties. The statistical tests defined by such partitions involve counting all permutations in the equivalence classes. These permutations are the linear extensions of partially ordered sets specified by the data. Our methods refine rank tests of non-parametric statistics, such as the sign test and the runs test, and are useful for the exploratory analysis of ordinal data. Convex rank tests correspond to probabilistic conditional independence structures known as semi-graphoids. Submodular rank tests are classified by the faces of the cone of submodular functions, or by Minkowski summands of the permutohedron. We enumerate all small instances of such rank tests. Graphical tests correspond to both graphical models and to graph associahedra, and they have excellent statistical and algorithmic properties.Comment: 8 pages, 4 figures. See also http://bio.math.berkeley.edu/ranktests/. v2: Expanded proofs, revised after reviewer comment

Factorial graphical lasso for dynamic networks

Dynamic networks models describe a growing number of important scientific processes, from cell biology and epidemiology to sociology and finance. There are many aspects of dynamical networks that require statistical considerations. In this paper we focus on determining network structure. Estimating dynamic networks is a difficult task since the number of components involved in the system is very large. As a result, the number of parameters to be estimated is bigger than the number of observations. However, a characteristic of many networks is that they are sparse. For example, the molecular structure of genes make interactions with other components a highly-structured and therefore sparse process. Penalized Gaussian graphical models have been used to estimate sparse networks. However, the literature has focussed on static networks, which lack specific temporal constraints. We propose a structured Gaussian dynamical graphical model, where structures can consist of specific time dynamics, known presence or absence of links and block equality constraints on the parameters. Thus, the number of parameters to be estimated is reduced and accuracy of the estimates, including the identification of the network, can be tuned up. Here, we show that the constrained optimization problem can be solved by taking advantage of an efficient solver, logdetPPA, developed in convex optimization. Moreover, model selection methods for checking the sensitivity of the inferred networks are described. Finally, synthetic and real data illustrate the proposed methodologies.Comment: 30 pp, 5 figure