The Human and Mouse Enteric Nervous System at Single-Cell Resolution.

Recent research on problem formulations based on decomposition into low-rank plus sparse matrices shows a suitable framework to separate moving objects from the background. The most representative problem formulation is the Robust Principal Component Analysis (RPCA) solved via Principal Component Pursuit (PCP) which decomposes a data matrix in a low-rank matrix and a sparse matrix. However, similar robust implicit or explicit decompositions can be made in the following problem formulations: Robust Non-negative Matrix Factorization (RNMF), Robust Matrix Completion (RMC), Robust Subspace Recovery (RSR), Robust Subspace Tracking (RST) and Robust Low-Rank Minimization (RLRM). The main goal of these similar problem formulations is to obtain explicitly or implicitly a decomposition into low-rank matrix plus additive matrices. In this context, this work aims to initiate a rigorous and comprehensive review of the similar problem formulations in robust subspace learning and tracking based on decomposition into low-rank plus additive matrices for testing and ranking existing algorithms for background/foreground separation. For this, we first provide a preliminary review of the recent developments in the different problem formulations which allows us to define a unified view that we called Decomposition into Low-rank plus Additive Matrices (DLAM). Then, we examine carefully each method in each robust subspace learning/tracking frameworks with their decomposition, their loss functions, their optimization problem and their solvers. Furthermore, we investigate if incremental algorithms and real-time implementations can be achieved for background/foreground separation. Finally, experimental results on a large-scale dataset called Background Models Challenge (BMC 2012) show the comparative performance of 32 different robust subspace learning/tracking methods.

Decomposition into Low-rank plus Additive Matrices for Background/Foreground Separation: A Review for a Comparative Evaluation with a Large-Scale Dataset

Robust principal component analysis (RPCA) via decomposition into low-rank plus sparse matrices offers a powerful framework for a large variety of applications such as image processing, video processing, and 3-D computer vision. Indeed, most of the time these applications require to detect sparse outliers from the observed imagery data that can be approximated by a low-rank matrix. Moreover, most of the time experiments show that RPCA with additional spatial and/or temporal constraints often outperforms the state-of-the-art algorithms in these applications. Thus, the aim of this paper is to survey the applications of RPCA in computer vision. In the first part of this paper, we review representative image processing applications as follows: 1) low-level imaging such as image recovery and denoising, image composition, image colorization, image alignment and rectification, multifocus image, and face recognition; 2) medical imaging such as dynamic magnetic resonance imaging (MRI) for acceleration of data acquisition, background suppression, and learning of interframe motion fields; and 3) imaging for 3-D computer vision with additional depth information such as in structure from motion (SfM) and 3-D motion recovery. In the second part, we present the applications of RPCA in video processing which utilize additional spatial and temporal information compared to image processing. Specifically, we investigate video denoising and restoration, hyperspectral video, and background/foreground separation. Finally, we provide perspectives on possible future research directions and algorithmic frameworks that are suitable for these applications.

/pdf/on-the-applications-of-robust-pca-in-image-and-video-51546ljg1c.pdf

On the Applications of Robust PCA in Image and Video Processing

Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq) data promises further biological insights that cannot be uncovered with individual datasets. Here we present scMerge, an algorithm that integrates multiple single-cell RNA-seq datasets using factor analysis of stably expressed genes and pseudoreplicates across datasets. Using a large collection of public datasets, we benchmark scMerge against published methods and demonstrate that it consistently provides improved cell type separation by removing unwanted factors; scMerge can also enhance biological discovery through robust data integration, which we show through the inference of development trajectory in a liver dataset collection.

https://www.pnas.org/content/pnas/116/20/9775.full.pdf

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

https://hal.archives-ouvertes.fr/hal-01522823/document

Decomposition into low-rank plus additive matrices for background/foreground separation

Matrix decompositions are fundamental tools in the area of applied mathematics, statistical computing, and machine learning. In particular, low-rank matrix decompositions are vital, and widely used for data analysis, dimensionality reduction, and data compression. Massive datasets, however, pose a computational challenge for traditional algorithms, placing significant constraints on both memory and processing power. Recently, the powerful concept of randomness has been introduced as a strategy to ease the computational load. The essential idea of probabilistic algorithms is to employ some amount of randomness in order to derive a smaller matrix from a high-dimensional data matrix. The smaller matrix is then used to compute the desired low-rank approximation. Such algorithms are shown to be computationally efficient for approximating matrices with low-rank structure. We present the \proglang{R} package rsvd, and provide a tutorial introduction to randomized matrix decompositions. Specifically, randomized routines for the singular value decomposition, (robust) principal component analysis, interpolative decomposition, and CUR decomposition are discussed. Several examples demonstrate the routines, and show the computational advantage over other methods implemented in R.

Randomized Matrix Decompositions using R

Matrix decompositions are fundamental tools in the area of applied mathematics, statistical computing, and machine learning. In particular, low-rank matrix decompositions are vital, and widely used for data analysis, dimensionality reduction, and data compression. Massive datasets, however, pose a computational challenge for traditional algorithms, placing significant constraints on both memory and processing power. Recently, the powerful concept of randomness has been introduced as a strategy to ease the computational load. The essential idea of probabilistic algorithms is to employ some amount of randomness in order to derive a smaller matrix from a high-dimensional data matrix. The smaller matrix is then used to compute the desired low-rank approximation. Such algorithms are shown to be computationally efficient for approximating matrices with low-rank structure. We present the R package rsvd, and provide a tutorial introduction to randomized matrix decompositions. Specifically, randomized routines for the singular value decomposition, (robust) principal component analysis, interpolative decomposition, and CUR decomposition are discussed. Several examples demonstrate the routines, and show the computational advantage over other methods implemented in R.

Sergey Voronin

Papers

Randomized Matrix Decompositions using R

Randomized Matrix Decompositions Using R