Never look back - A modified EnKF method and its application to the training of neural networks without back propagation

In this work, we present a new derivative-free optimization method and investigate its use for training neural networks. Our method is motivated by the Ensemble Kalman Filter (EnKF), which has been used successfully for solving optimization problems that involve large-scale, highly nonlinear dynamical systems. A key benefit of the EnKF method is that it requires only the evaluation of the forward propagation but not its derivatives. Hence, in the context of neural networks, it alleviates the need for back propagation and reduces the memory consumption dramatically. However, the method is not a pure "black-box" global optimization heuristic as it efficiently utilizes the structure of typical learning problems. Promising first results of the EnKF for training deep neural networks have been presented recently by Kovachki and Stuart. We propose an important modification of the EnKF that enables us to prove convergence of our method to the minimizer of a strongly convex function. Our method also bears similarity with implicit filtering and we demonstrate its potential for minimizing highly oscillatory functions using a simple example. Further, we provide numerical examples that demonstrate the potential of our method for training deep neural networks

Determinants of participation in colonoscopic screening by siblings of colorectal cancer patients in France

International audienceBACKGROUND: Targeted colonosocopic screening is recommended for first-degree relatives of colorectal cancer patients diagnosed before the age of 60 and offers the possibility of reducing morbidity and mortality, but participation remains too low. The objective of this study was to determine in a French population the factors that affect siblings' participation in screening, notably those relating to the individuals, their medical care, their family and their social network. METHODS: A cross sectional survey was conducted in siblings of index patients having undergone surgery for colorectal cancer between 1999 and 2002 in two French counties. Siblings were contacted during 2007 and 2008 through the index patient. The factors affecting participation in colonoscopic screening were studied by logistic regression taking into account family cluster effect. RESULTS: 172 siblings of 74 index cases were included. The declared rate of undergoing at least one colonoscopy among siblings was 66%; 95%CI 59-73%. Five variables were independently associated with colonoscopic screening: perceiving fewer barriers to screening (OR = 3.2; 95%CI 1.2-8.5), having received the recommendation to undergo screening from a physician (OR = 4.9; 1.7-13.7), perceiving centres practising colonoscopy as more accessible (OR = 3.2, 1.3-7.8), having discussed screening with all siblings (OR = 3.9; 1.6-9.6) and being a member of an association (OR = 2.6; 1.0-6.6). CONCLUSIONS: The factors independently associated with participation in CRC screening by an individual at increased risk belonged to each of four dimensions relating to his individual psychosocial characteristics, to his relationship with a physician, within the family and social environment. The relevance of these results to clinical practice may help to improve compliance to recommendations in a global preventive strategy including all stages of the information pathway from the physician to the index patient and his relatives

A stabilized multigrid solver for hyperelastic image registration

Image registration is a central problem in a variety of areas involving imaging techniques and is known to be challenging and ill-posed. Regularization functionals based on hyperelasticity provide a powerful mechanism for limiting the ill-posedness. A key feature of hyperelastic image registration approaches is their ability to model large deformations while guaranteeing their invertibility, which is crucial in many applications. To ensure that numerical solutions satisfy this requirement, we discretize the variational problem using piecewise linear finite elements, and then solve the discrete optimization problem using the Gauss-Newton method. In this work, we focus on computational challenges arising in approximately solving the Hessian system. We show that the Hessian is a discretization of a strongly coupled system of partial differential equations whose coefficients can be severely inhomogeneous. Motivated by a local Fourier analysis, we stabilize the system by thresholding the coefficients. We propose a Galerkin-multigrid scheme with a collective pointwise smoother. We demonstrate the accuracy and effectiveness of the proposed scheme, first on a two-dimensional problem of a moderate size and then on a large-scale real-world application with almost 9million degrees of freedom

A new method for joint susceptibility artefact correction and super-resolution for dMRI

Diffusion magnetic resonance imaging (dMRI) has become increasingly relevant in clinical research and neuroscience. It is commonly carried out using the ultra-fast MRI acquisition technique Echo-Planar Imaging (EPI). While offering crucial reduction of acquisition times, two limitations of EPI are distortions due to varying magnetic susceptibilities of the object being imaged and its limited spatial resolution. In the recent years progress has been made both for susceptibility artefact correction and increasing of spatial resolution using image processing and reconstruction methods. However, so far, the interplay between both problems has not been studied and super-resolution techniques could only be applied along one axis, the slice-select direction, limiting the potential gain in spatial resolution. In this work we describe a new method for joint susceptibility artefact correction and super-resolution in EPI-MRI that can be used to increase resolution in all three spatial dimensions and in particular increase in-plane resolutions. The key idea is to reconstruct a distortion-free, high-resolution image from a number of low-resolution EPI data that are deformed in different directions. Numerical results on dMRI data of a human brain indicate that this technique has the potential to provide for the first time in-vivo dMRI at mesoscopic spatial resolution (i.e. 500μm); a spatial resolution that could bridge the gap between white-matter information from ex-vivo histology (≈1μm) and in-vivo dMRI (≈2000μm)

A new method for joint susceptibility artefact correction and super-resolution for dMRI

Diffusion magnetic resonance imaging (dMRI) has become increasingly relevant in clinical research and neuroscience. It is commonly carried out using the ultra-fast MRI acquisition technique Echo-Planar Imaging (EPI). While offering crucial reduction of acquisition times, two limitations of EPI are distortions due to varying magnetic susceptibilities of the object being imaged and its limited spatial resolution. In the recent years progress has been made both for susceptibility artefact correction and increasing of spatial resolution using image processing and reconstruction methods. However, so far, the interplay between both problems has not been studied and super-resolution techniques could only be applied along one axis, the slice-select direction, limiting the potential gain in spatial resolution. In this work we describe a new method for joint susceptibility artefact correction and super-resolution in EPI-MRI that can be used to increase resolution in all three spatial dimensions and in particular increase in-plane resolutions. The key idea is to reconstruct a distortion-free, high-resolution image from a number of low-resolution EPI data that are deformed in different directions. Numerical results on dMRI data of a human brain indicate that this technique has the potential to provide for the first time in-vivo dMRI at mesoscopic spatial resolution (i.e. 500μm); a spatial resolution that could bridge the gap between white-matter information from ex-vivo histology (1μm) and in-vivo dMRI (2000μm). © 2014 SPIE

Hyperelastic susceptibility artifact correction of DTI in SPM

Echo Planar Imaging (EPI) is a MRI acquisition technique that is the backbone of widely used investigation techniques in neuroscience like, e.g., Diffusion Tensor Imaging (DTI). While EPI offers considerable reduction of the acquisition time one major drawback is its high sensitivity to susceptibility artifacts. Susceptibility differences between soft tissue, bone and air cause geometrical distortions and intensity modulations of the EPI data. These susceptibility artifacts severely complicate the fusion of micro-structural information acquired with EPI and conventionally acquired structural information. In this paper, we introduce a new tool for hyperelastic susceptibility correction of DTI data (HySCO) that is integrated into the Statistical Parametric Mapping (SPM) software as a toolbox. Our new correction pipeline is based on two datasets acquired with reversed phase encoding gradients. For the correction, we integrated the variational image registration approach by Ruthotto et al. 2007 into the SPM batch mode. We briefly review the model, discuss involved parameter settings and exemplarily demonstrate the effectiveness of HySCO on a human brain DTI dataset

Motion correction in dual gated cardiac PET using mass-preserving image registration

Respiratory and cardiac motion leads to image degradation in positron emission tomography (PET) studies of the human heart. In this paper we present a novel approach to motion correction based on dual gating and mass-preserving hyperelastic image registration. Thereby, we account for intensity modulations caused by the highly nonrigid cardiac motion. This leads to accurate and realistic motion estimates which are quantitatively validated on software phantom data and carried over to clinically relevant data using a hardware phantom. For patient data, the proposed method is first evaluated in a high statistic (20 min scans) dual gating study of 21 patients. It is shown that the proposed approach properly corrects PET images for dual-cardiac as well as respiratory-motion. In a second study the list mode data of the same patients is cropped to a scan time reasonable for clinical practice (3 min). This low statistic study not only shows the clinical applicability of our method but also demonstrates its robustness against noise obtained by hyperelastic regularization