Clutter suppression in ultrasound: performance evaluation and review of low-rank and sparse matrix decomposition methods

Vessel diseases are often accompanied by abnormalities related to vascular shape and size. Therefore, a clear visualization of vasculature is of high clinical significance. Ultrasound color flow imaging (CFI) is one of the prominent techniques for flow visualization. However, clutter signals originating from slow-moving tissue are one of the main obstacles to obtain a clear view of the vascular network. Enhancement of the vasculature by suppressing the clutters is a significant and irreplaceable step for many applications of ultrasound CFI. Currently, this task is often performed by singular value decomposition (SVD) of the data matrix. This approach exhibits two well-known limitations. First, the performance of SVD is sensitive to the proper manual selection of the ranks corresponding to clutter and blood subspaces. Second, SVD is prone to failure in the presence of large random noise in the dataset. A potential solution to these issues is using decomposition into low-rank and sparse matrices (DLSM) framework. SVD is one of the algorithms for solving the minimization problem under the DLSM framework. Many other algorithms under DLSM avoid full SVD and use approximated SVD or SVD-free ideas which may have better performance with higher robustness and less computing time. In practice, these models separate blood from clutter based on the assumption that steady clutter represents a low-rank structure and that the moving blood component is sparse. In this paper, we present a comprehensive review of ultrasound clutter suppression techniques and exploit the feasibility of low-rank and sparse decomposition schemes in ultrasound clutter suppression. We conduct this review study by adapting 106 DLSM algorithms and validating them against simulation, phantom, and in vivo rat datasets. Two conventional quality metrics, signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), are used for performance evaluation. In addition, computation times required by different algorithms for generating clutter suppressed images are reported. Our extensive analysis shows that the DLSM framework can be successfully applied to ultrasound clutter suppression

Rigorous optimization recipes for sparse and low rank inverse problems with applications in data sciences

Many natural and man-made signals can be described as having a few degrees of freedom relative to their size due to natural parameterizations or constraints; examples include bandlimited signals, collections of signals observed from multiple viewpoints in a network-of-sensors, and per-flow traffic measurements of the Internet. Low-dimensional models (LDMs) mathematically capture the inherent structure of such signals via combinatorial and geometric data models, such as sparsity, unions-of-subspaces, low-rankness, manifolds, and mixtures of factor analyzers, and are emerging to revolutionize the way we treat inverse problems (e.g., signal recovery, parameter estimation, or structure learning) from dimensionality-reduced or incomplete data. Assuming our problem resides in a LDM space, in this thesis we investigate how to integrate such models in convex and non-convex optimization algorithms for significant gains in computational complexity. We mostly focus on two LDMs: $(i)$ sparsity and $(ii)$ low-rankness. We study trade-offs and their implications to develop efficient and provable optimization algorithms, and--more importantly--to exploit convex and combinatorial optimization that can enable cross-pollination of decades of research in both

Frank-Wolfe Methods for Optimization and Machine Learning

In Chapter 2, we present the Frank-Wolfe algorithm (FW) and all necessary background material. We explain the projection-free and sparsity properties of the algorithm, provide motivation for real-world problems, and analyze the convergence rates and a lower bound on the complexity. In Chapter 3, we review the complexity bounds of linear minimizations and projections on several sets commonly used in optimization, providing a rigorous support to the use of FW. We also propose two methods for projecting onto the lp-ball and the Birkhoff polytope respectively, and we analyze their complexity. Computational experiments for the l1-ball and the nuclear norm-ball are presented. In Chapter 4, we identify the well-known drawback in FW, a naive zig-zagging phenomenon that slows down the algorithm. In response to this issue, we propose a boosting procedure generating descent directions better aligned with the negative gradients and preserving the projection-free property. Although the method is relatively simple and intuitive, it provides significant computational speedups over the state of the art on a variety of experiments. In Chapter 5, we address the large-scale finite-sum optimization setting arising in many tasks of machine learning. Based on a sliding technique, we propose a generic template to integrate adaptive gradients into stochastic Frank-Wolfe algorithms in a practical way. Computational experiments on standard convex optimization problems and on the nonconvex training of neural networks demonstrate that the blend of the two methods is successful. Both developments in Chapters 4 and 5 are motivated by the projection-free property of FW. In Chapter 6, we leverage the natural sparsity of the iterates generated by FW and study an application to the approximate Carathéodory problem. We show that FW generates a simple solution to the problem and that with no modification of the algorithm, better cardinality bounds can be established using existing convergence analysis of FW in different scenarios. We also consider a nonsmooth variant of FW. In Chapter 7, we carry on with the sparsity property and we consider an extension of the Frank-Wolfe algorithm to the unconstrained setting. It addresses smooth convex optimization problems over the linear span of a given set and resembles the matching pursuit algorithm. We propose a blending method that combines fast convergence and high sparsity of the iterates. Computational experiments validate the purpose of our method.Ph.D

Density-Aware Linear Algebra in a Column-Oriented In-Memory Database System

Linear algebra operations appear in nearly every application in advanced analytics, machine learning, and of various science domains. Until today, many data analysts and scientists tend to use statistics software packages or hand-crafted solutions for their analysis. In the era of data deluge, however, the external statistics packages and custom analysis programs that often run on single-workstations are incapable to keep up with the vast increase in data volume and size. In particular, there is an increasing demand of scientists for large scale data manipulation, orchestration, and advanced data management capabilities. These are among the key features of a mature relational database management system (DBMS). With the rise of main memory database systems, it now has become feasible to also consider applications that built up on linear algebra. This thesis presents a deep integration of linear algebra functionality into an in-memory column-oriented database system. In particular, this work shows that it has become feasible to execute linear algebra queries on large data sets directly in a DBMS-integrated engine (LAPEG), without the need of transferring data and being restricted by hard disc latencies. From various application examples that are cited in this work, we deduce a number of requirements that are relevant for a database system that includes linear algebra functionality. Beside the deep integration of matrices and numerical algorithms, these include optimization of expressions, transparent matrix handling, scalability and data-parallelism, and data manipulation capabilities. These requirements are addressed by our linear algebra engine. In particular, the core contributions of this thesis are: firstly, we show that the columnar storage layer of an in-memory DBMS yields an easy adoption of efficient sparse matrix data types and algorithms. Furthermore, we show that the execution of linear algebra expressions significantly benefits from different techniques that are inspired from database technology. In a novel way, we implemented several of these optimization strategies in LAPEG’s optimizer (SpMachO), which uses an advanced density estimation method (SpProdest) to predict the matrix density of intermediate results. Moreover, we present an adaptive matrix data type AT Matrix to obviate the need of scientists for selecting appropriate matrix representations. The tiled substructure of AT Matrix is exploited by our matrix multiplication to saturate the different sockets of a multicore main-memory platform, reaching up to a speed-up of 6x compared to alternative approaches. Finally, a major part of this thesis is devoted to the topic of data manipulation; where we propose a matrix manipulation API and present different mutable matrix types to enable fast insertions and deletes. We finally conclude that our linear algebra engine is well-suited to process dynamic, large matrix workloads in an optimized way. In particular, the DBMS-integrated LAPEG is filling the linear algebra gap, and makes columnar in-memory DBMS attractive as efficient, scalable ad-hoc analysis platform for scientists

Conditional Gradient Methods

The purpose of this survey is to serve both as a gentle introduction and a coherent overview of state-of-the-art Frank--Wolfe algorithms, also called conditional gradient algorithms, for function minimization. These algorithms are especially useful in convex optimization when linear optimization is cheaper than projections. The selection of the material has been guided by the principle of highlighting crucial ideas as well as presenting new approaches that we believe might become important in the future, with ample citations even of old works imperative in the development of newer methods. Yet, our selection is sometimes biased, and need not reflect consensus of the research community, and we have certainly missed recent important contributions. After all the research area of Frank--Wolfe is very active, making it a moving target. We apologize sincerely in advance for any such distortions and we fully acknowledge: We stand on the shoulder of giants.Comment: 238 pages with many figures. The FrankWolfe.jl Julia package (https://github.com/ZIB-IOL/FrankWolfe.jl) providces state-of-the-art implementations of many Frank--Wolfe method