Deep Learning Methods for Parallel Magnetic Resonance Image Reconstruction

Following the success of deep learning in a wide range of applications, neural network-based machine learning techniques have received interest as a means of accelerating magnetic resonance imaging (MRI). A number of ideas inspired by deep learning techniques from computer vision and image processing have been successfully applied to non-linear image reconstruction in the spirit of compressed sensing for both low dose computed tomography and accelerated MRI. The additional integration of multi-coil information to recover missing k-space lines in the MRI reconstruction process, is still studied less frequently, even though it is the de-facto standard for currently used accelerated MR acquisitions. This manuscript provides an overview of the recent machine learning approaches that have been proposed specifically for improving parallel imaging. A general background introduction to parallel MRI is given that is structured around the classical view of image space and k-space based methods. Both linear and non-linear methods are covered, followed by a discussion of recent efforts to further improve parallel imaging using machine learning, and specifically using artificial neural networks. Image-domain based techniques that introduce improved regularizers are covered as well as k-space based methods, where the focus is on better interpolation strategies using neural networks. Issues and open problems are discussed as well as recent efforts for producing open datasets and benchmarks for the community.Comment: 14 pages, 7 figure

Understanding Machine-learned Density Functionals

Kernel ridge regression is used to approximate the kinetic energy of non-interacting fermions in a one-dimensional box as a functional of their density. The properties of different kernels and methods of cross-validation are explored, and highly accurate energies are achieved. Accurate {\em constrained optimal densities} are found via a modified Euler-Lagrange constrained minimization of the total energy. A projected gradient descent algorithm is derived using local principal component analysis. Additionally, a sparse grid representation of the density can be used without degrading the performance of the methods. The implications for machine-learned density functional approximations are discussed

Sampling of Planar Curves: Theory and Fast Algorithms

We introduce a continuous domain framework for the recovery of a planar curve from a few samples. We model the curve as the zero level set of a trigonometric polynomial. We show that the exponential feature maps of the points on the curve lie on a low-dimensional subspace. We show that the null-space vector of the feature matrix can be used to uniquely identify the curve, given a sufficient number of samples. The worst-case theoretical guarantees show that the number of samples required for unique recovery depends on the bandwidth of the underlying trigonometric polynomial, which is a measure of the complexity of the curve. We introduce an iterative algorithm that relies on the low-rank property of the feature maps to recover the curves when the samples are noisy or when the true bandwidth of the curve is unknown. We also demonstrate the preliminary utility of the proposed curve representation in the context of image segmentation

Image Reconstruction with Predictive Filter Flow

We propose a simple, interpretable framework for solving a wide range of image reconstruction problems such as denoising and deconvolution. Given a corrupted input image, the model synthesizes a spatially varying linear filter which, when applied to the input image, reconstructs the desired output. The model parameters are learned using supervised or self-supervised training. We test this model on three tasks: non-uniform motion blur removal, lossy-compression artifact reduction and single image super resolution. We demonstrate that our model substantially outperforms state-of-the-art methods on all these tasks and is significantly faster than optimization-based approaches to deconvolution. Unlike models that directly predict output pixel values, the predicted filter flow is controllable and interpretable, which we demonstrate by visualizing the space of predicted filters for different tasks.Comment: https://www.ics.uci.edu/~skong2/pff.htm

Dual optimization for convex constrained objectives without the gradient-Lipschitz assumption

The minimization of convex objectives coming from linear supervised learning problems, such as penalized generalized linear models, can be formulated as finite sums of convex functions. For such problems, a large set of stochastic first-order solvers based on the idea of variance reduction are available and combine both computational efficiency and sound theoretical guarantees (linear convergence rates). Such rates are obtained under both gradient-Lipschitz and strong convexity assumptions. Motivated by learning problems that do not meet the gradient-Lipschitz assumption, such as linear Poisson regression, we work under another smoothness assumption, and obtain a linear convergence rate for a shifted version of Stochastic Dual Coordinate Ascent (SDCA) that improves the current state-of-the-art. Our motivation for considering a solver working on the Fenchel-dual problem comes from the fact that such objectives include many linear constraints, that are easier to deal with in the dual. Our approach and theoretical findings are validated on several datasets, for Poisson regression and another objective coming from the negative log-likelihood of the Hawkes process, which is a family of models which proves extremely useful for the modeling of information propagation in social networks and causality inference

Estimation of low-rank tensors via convex optimization

In this paper, we propose three approaches for the estimation of the Tucker decomposition of multi-way arrays (tensors) from partial observations. All approaches are formulated as convex minimization problems. Therefore, the minimum is guaranteed to be unique. The proposed approaches can automatically estimate the number of factors (rank) through the optimization. Thus, there is no need to specify the rank beforehand. The key technique we employ is the trace norm regularization, which is a popular approach for the estimation of low-rank matrices. In addition, we propose a simple heuristic to improve the interpretability of the obtained factorization. The advantages and disadvantages of three proposed approaches are demonstrated through numerical experiments on both synthetic and real world datasets. We show that the proposed convex optimization based approaches are more accurate in predictive performance, faster, and more reliable in recovering a known multilinear structure than conventional approaches.Comment: 19 pages, 7 figure

Generalized system identification with stable spline kernels

Regularized least-squares approaches have been successfully applied to linear system identification. Recent approaches use quadratic penalty terms on the unknown impulse response defined by stable spline kernels, which control model space complexity by leveraging regularity and bounded-input bounded-output stability. This paper extends linear system identification to a wide class of nonsmooth stable spline estimators, where regularization functionals and data misfits can be selected from a rich set of piecewise linear-quadratic (PLQ) penalties. This class includes the 1-norm, Huber, and Vapnik, in addition to the least-squares penalty. By representing penalties through their conjugates, the modeler can specify any piecewise linear-quadratic penalty for misfit and regularizer, as well as inequality constraints on the response. The interior-point solver we implement (IPsolve) is locally quadratically convergent, with $O(\min(m,n)^2(m+n))$ arithmetic operations per iteration, where $n$ the number of unknown impulse response coefficients and $m$ the number of observed output measurements. IPsolve is competitive with available alternatives for system identification. This is shown by a comparison with TFOCS, libSVM, and the FISTA algorithm. The code is open source (https://github.com/saravkin/IPsolve). The impact of the approach for system identification is illustrated with numerical experiments featuring robust formulations for contaminated data, relaxation systems, nonnegativity and unimodality constraints on the impulse response, and sparsity promoting regularization. Incorporating constraints yields particularly significant improvements.Comment: 23 pages, 6 figure

The Random Feature Model for Input-Output Maps between Banach Spaces

Well known to the machine learning community, the random feature model, originally introduced by Rahimi and Recht in 2008, is a parametric approximation to kernel interpolation or regression methods. It is typically used to approximate functions mapping a finite-dimensional input space to the real line. In this paper, we instead propose a methodology for use of the random feature model as a data-driven surrogate for operators that map an input Banach space to an output Banach space. Although the methodology is quite general, we consider operators defined by partial differential equations (PDEs); here, the inputs and outputs are themselves functions, with the input parameters being functions required to specify the problem, such as initial data or coefficients, and the outputs being solutions of the problem. Upon discretization, the model inherits several desirable attributes from this infinite-dimensional, function space viewpoint, including mesh-invariant approximation error with respect to the true PDE solution map and the capability to be trained at one mesh resolution and then deployed at different mesh resolutions. We view the random feature model as a non-intrusive data-driven emulator, provide a mathematical framework for its interpretation, and demonstrate its ability to efficiently and accurately approximate the nonlinear parameter-to-solution maps of two prototypical PDEs arising in physical science and engineering applications: viscous Burgers' equation and a variable coefficient elliptic equation

Linearly constrained Gaussian processes

We consider a modification of the covariance function in Gaussian processes to correctly account for known linear constraints. By modelling the target function as a transformation of an underlying function, the constraints are explicitly incorporated in the model such that they are guaranteed to be fulfilled by any sample drawn or prediction made. We also propose a constructive procedure for designing the transformation operator and illustrate the result on both simulated and real-data examples.Comment: A few fixes and added citation inforomatio

Data-driven Seismic Waveform Inversion: A Study on the Robustness and Generalization

Acoustic- and elastic-waveform inversion is an important and widely used method to reconstruct subsurface velocity image. Waveform inversion is a typical non-linear and ill-posed inverse problem. Existing physics-driven computational methods for solving waveform inversion suffer from the cycle skipping and local minima issues, and not to mention solving waveform inversion is computationally expensive. In recent years, data-driven methods become a promising way to solve the waveform inversion problem. However, most deep learning frameworks suffer from generalization and over-fitting issue. In this paper, we developed a real-time data-driven technique and we call it VelocityGAN, to accurately reconstruct subsurface velocities. Our VelocityGAN is built on a generative adversarial network (GAN) and trained end-to-end to learn a mapping function from the raw seismic waveform data to the velocity image. Different from other encoder-decoder based data-driven seismic waveform inversion approaches, our VelocityGAN learns regularization from data and further impose the regularization to the generator so that inversion accuracy is improved. We further develop a transfer learning strategy based on VelocityGAN to alleviate the generalization issue. A series of experiments are conducted on the synthetic seismic reflection data to evaluate the effectiveness, efficiency, and generalization of VelocityGAN. We not only compare it with existing physics-driven approaches and data-driven frameworks but also conduct several transfer learning experiments. The experiment results show that VelocityGAN achieves state-of-the-art performance among the baselines and can improve the generalization results to some extent