SearcharxivSearch

arXiv subjects

Daniela Calvetti

Publications and source records attributed to Daniela Calvetti.

26 records · Page 2Linked to original sources

Sparsity promoting hybrid solvers for hierarchical Bayesian inverse problems

The recovery of sparse generative models from few noisy measurements is an important and challenging problem. Many deterministic algorithms rely on some form of $\ell_1$-$\ell_2$ minimization to combine the computational convenience of the $\ell_2$ penalty and the sparsity promotion of the $\ell_1$. It was recently shown within the Bayesian framework that sparsity promotion and computational efficiency can be attained with hierarchical models with conditionally Gaussian priors and gamma hyperpriors. The related Gibbs energy function is a convex functional and its minimizer, which is the MAP estimate of the posterior, can be computed efficiently with the globally convergent Iterated Alternating Sequential (IAS) algorithm \cite{CSS}. Generalization of the hyperpriors for these sparsity promoting hierarchical models to generalized gamma family yield either globally convex Gibbs energy functionals, or can exhibit local convexity for some choices for the hyperparameters. \cite{CPrSS}. The main problem in computing the MAP solution for greedy hyperpriors that strongly promote sparsity is the presence of local minima. To overcome the premature stopping at a spurious local minimizer, we propose two hybrid algorithms that first exploit the global convergence associated with gamma hyperpriors to arrive in a neighborhood of the unique minimizer, then adopt a generalized gamma hyperprior that promote sparsity more strongly. The performance of the two algorithms is illustrated with computed examples.

math.NA

Brain activity mapping from MEG data via a hierarchical Bayesian algorithm with automatic depth weighting: sensitivity and specificity analysis

A recently proposed IAS MEG inverse solver algorithm, based on the coupling of a hierarchical Bayesian model with computationally efficient Krylov subspace linear solver, has been shown to perform well for both superficial and deep brain sources. However, a systematic study of its sensitivity and specificity as a function of the activity location is still missing. We propose novel statistical protocols to quantify the performance of MEG inverse solvers, focusing in particular on their sensitivity and specificity in identifying active brain regions. We use these protocols for a systematic study of the sensitivity and specificity of the IAS MEG inverse solver, comparing the performance with three standard inversion methods, wMNE, dSPM, and sLORETA. To avoid the bias of anecdotal tests towards a particular algorithm, the proposed protocols are Monte Carlo sampling based, generating an ensemble of activity patches in each brain region identified in a given atlas. The sensitivity is measured by how much, on average, the reconstructed activity is concentrated in the brain region of the simulated active patch. The specificity analysis is based on Bayes factors, interpreting the estimated current activity as data for testing the hypothesis that the active brain region is correctly identified, vs. the hypothesis of any erroneous attribution. The methodology allows the presence of a single or several simultaneous activity regions, without assuming the knowledge of the number of active regions. The testing protocols suggest that the IAS solver performs well in terms of sensitivity and specificity both with cortical and subcortical activity estimation.

q-bio.NC

Iterative Updating of Model Error for Bayesian Inversion

In computational inverse problems, it is common that a detailed and accurate forward model is approximated by a computationally less challenging substitute. The model reduction may be necessary to meet constraints in computing time when optimization algorithms are used to find a single estimate, or to speed up Markov chain Monte Carlo (MCMC) calculations in the Bayesian framework. The use of an approximate model introduces a discrepancy, or modeling error, that may have a detrimental effect on the solution of the ill-posed inverse problem, or it may severely distort the estimate of the posterior distribution. In the Bayesian paradigm, the modeling error can be considered as a random variable, and by using an estimate of the probability distribution of the unknown, one may estimate the probability distribution of the modeling error and incorporate it into the inversion. We introduce an algorithm which iterates this idea to update the distribution of the model error, leading to a sequence of posterior distributions that are demonstrated empirically to capture the underlying truth with increasing accuracy. Since the algorithm is not based on rejections, it requires only limited full model evaluations. We show analytically that, in the linear Gaussian case, the algorithm converges geometrically fast with respect to the number of iterations. For more general models, we introduce particle approximations of the iteratively generated sequence of distributions; we also prove that each element of the sequence converges in the large particle limit. We show numerically that, as in the linear case, rapid convergence occurs with respect to the number of iterations. Additionally, we show through computed examples that point estimates obtained from this iterative algorithm are superior to those obtained by neglecting the model error.

stat.ME

Computational issues and numerical experiments for Linear Multistep Method Particle Filtering

The Linear Multistep Method Particle Filter (LMM PF) is a method for predicting the evolution in time of a evolutionary system governed by a system of differential equations. If some of the parameters of the governing equations are unknowns, it is possible to organize the calculations so as to estimate them while following the evolution of the system in time. The underlying assumption in the approach that we present is that all unknowns are modelled as random variables, where the randomness is an indication of the uncertainty of their values rather than an intrinsic property of the quantities. Consequently, the states of the system and the parameters are described in probabilistic terms by their density, often in the form of representative samples. This approach is particularly attractive in the context of parameter estimation inverse problems, because the statistical formulation naturally provides a means of assessing the uncertainty in the solution via the spread of the distribution. The computational efficiency of the underlying sampling technique is crucial for the success of the method, because the accuracy of the solution depends on the ability to produce representative samples from the distribution of the unknown parameters. In this paper LMM PF is tested on a skeletal muscle metabolism problem, which was previously treated within the Ensemble Kalman filtering framework. Here numerical evidences are used to highlight the correlation between the main sources of errors and the influence of the linera multistep method adopted. Finally, we analyzed the effect of replacing LMM with Runge-Kutta class integration methods for supporting the PF technique.

math.NA

Bayes meets Krylov: preconditioning CGLS for underdetermined systems

The solution of linear inverse problems when the unknown parameters outnumber data requires addressing the problem of a nontrivial null space. After restating the problem within the Bayesian framework, a priori information about the unknown can be utilized for determining the null space contribution to the solution. More specifically, if the solution of the associated linear system is computed by the Conjugate Gradient for Least Squares (CGLS) method, the additional information can be encoded in the form of a right preconditioner. In this paper we study how the right preconditioned changes the Krylov subspaces where the CGLS iterates live, and draw a tighter connection between Bayesian inference and Krylov subspace methods. The advantages of a Krylov-meet-Bayes approach to the solution of underdetermined linear inverse problems is illustrated with computed examples.

math.NA

Energy Demand and Metabolite Partitioning in Spatially Lumped and Distributed Models of Neuron-Astrocyte Complex

The degrees of freedom of multi-compartment mathematical models for energy metabolism of a neuron-astrocyte complex may offer a key to understand the different ways in which the energetic needs of the brain are met. In this paper we address the problem within a steady state framework and we use the techniques of linear algebra to identify the degrees of freedom first in a lumped model, then in its extension to a spatially distributed case. The interpretation of the degrees of freedom in metabolic terms, more specifically in terms of glucose and oxygen partitioning, is then leveraged to derive constraints on the free parameters needed to guarantee that the model is energetically feasible. We also demonstrate how the model can be used to estimate the stoichiometric energy needs of the cells as well as the household energy based on observed oxidative cerebral metabolic rate (CMR) of glucose, and the glutamate cycling. Moreover, our analysis shows that in the lumped model the direction of lactate dehydrogenase (LDH) in the cells can be deduced from the glucose partitioning between the compartments. The extension of the lumped model into a spatially distributed multi-compartment setting that includes diffusion fluxes from capillary to tissue increases the number of degrees of freedom, requiring the use of statistical sampling techniques. The analysis of distributed model reveals that some of the conclusions, e.g., concerning the LDH activity and glucose partitioning, based on a spatially lumped model may no longer hold.

q-bio.QM

Vectorized and Parallel Particle Filter SMC Parameter Estimation for Stiff ODEs

Particle filter (PF) sequential Monte Carlo (SMC) methods are very attractive for the estimation of parameters of time dependent systems where the data is either not all available at once, or the range of time constants is wide enough to create problems in the numerical time propagation of the states. The need to evolve a large number of particles makes PF-based methods computationally challenging, the main bottlenecks being the time propagation of each particle and the large number of particles. While parallelization is typically advocated to speed up the computing time, vectorization of the algorithm on a single processor may result in even larger speedups for certain problems. In this paper we present a formulation of the PF-SMC class of algorithms proposed in Arnold et al. (2013), which is particularly amenable to a parallel or vectorized computing environment, and we illustrate the performance with a few computed examples in MATLAB.

stat.CO

Conditionally Gaussian Hypermodels for Cerebral Source Localization

Bayesian modeling and analysis of the MEG and EEG modalities provide a flexible framework for introducing prior information complementary to the measured data. This prior information is often qualitative in nature, making the translation of the available information into a computational model a challenging task. We propose a generalized gamma family of hyperpriors which allows the impressed currents to be focal and we advocate a fast and efficient iterative algorithm, the Iterative Alternating Sequential (IAS) algorithm for computing maximum a posteriori (MAP) estimates. Furthermore, we show that for particular choices of the scalar parameters specifying the hyperprior, the algorithm effectively approximates popular regularization strategies such as the Minimum Current Estimate and the Minimum Support Estimate. The connection between priorconditioning and adaptive regularization methods is also pointed out. The posterior densities are explored by means of a Markov Chain Monte Carlo (MCMC) strategy suitable for this family of hypermodels. The computed experiments suggest that the known preference of regularization methods for superficial sources over deep sources is a property of the MAP estimators only, and that estimation of the posterior mean in the hierarchical model is better adapted for localizing deep sources.

math-ph