Decoding the Encoding of Functional Brain Networks: an fMRI Classification Comparison of Non-negative Matrix Factorization (NMF), Independent Component Analysis (ICA), and Sparse Coding Algorithms

Brain networks in fMRI are typically identified using spatial independent component analysis (ICA), yet mathematical constraints such as sparse coding and positivity both provide alternate biologically-plausible frameworks for generating brain networks. Non-negative Matrix Factorization (NMF) would suppress negative BOLD signal by enforcing positivity. Spatial sparse coding algorithms ($L1$ Regularized Learning and K-SVD) would impose local specialization and a discouragement of multitasking, where the total observed activity in a single voxel originates from a restricted number of possible brain networks. The assumptions of independence, positivity, and sparsity to encode task-related brain networks are compared; the resulting brain networks for different constraints are used as basis functions to encode the observed functional activity at a given time point. These encodings are decoded using machine learning to compare both the algorithms and their assumptions, using the time series weights to predict whether a subject is viewing a video, listening to an audio cue, or at rest, in 304 fMRI scans from 51 subjects. For classifying cognitive activity, the sparse coding algorithm of $L1$ Regularized Learning consistently outperformed 4 variations of ICA across different numbers of networks and noise levels (p$<$0.001). The NMF algorithms, which suppressed negative BOLD signal, had the poorest accuracy. Within each algorithm, encodings using sparser spatial networks (containing more zero-valued voxels) had higher classification accuracy (p$<$0.001). The success of sparse coding algorithms may suggest that algorithms which enforce sparse coding, discourage multitasking, and promote local specialization may capture better the underlying source processes than those which allow inexhaustible local processes such as ICA

Supervised Dictionary Learning and Sparse Representation-A Review

Dictionary learning and sparse representation (DLSR) is a recent and successful mathematical model for data representation that achieves state-of-the-art performance in various fields such as pattern recognition, machine learning, computer vision, and medical imaging. The original formulation for DLSR is based on the minimization of the reconstruction error between the original signal and its sparse representation in the space of the learned dictionary. Although this formulation is optimal for solving problems such as denoising, inpainting, and coding, it may not lead to optimal solution in classification tasks, where the ultimate goal is to make the learned dictionary and corresponding sparse representation as discriminative as possible. This motivated the emergence of a new category of techniques, which is appropriately called supervised dictionary learning and sparse representation (S-DLSR), leading to more optimal dictionary and sparse representation in classification tasks. Despite many research efforts for S-DLSR, the literature lacks a comprehensive view of these techniques, their connections, advantages and shortcomings. In this paper, we address this gap and provide a review of the recently proposed algorithms for S-DLSR. We first present a taxonomy of these algorithms into six categories based on the approach taken to include label information into the learning of the dictionary and/or sparse representation. For each category, we draw connections between the algorithms in this category and present a unified framework for them. We then provide guidelines for applied researchers on how to represent and learn the building blocks of an S-DLSR solution based on the problem at hand. This review provides a broad, yet deep, view of the state-of-the-art methods for S-DLSR and allows for the advancement of research and development in this emerging area of research

Faster Matrix Completion Using Randomized SVD

Matrix completion is a widely used technique for image inpainting and personalized recommender system, etc. In this work, we focus on accelerating the matrix completion using faster randomized singular value decomposition (rSVD). Firstly, two fast randomized algorithms (rSVD-PI and rSVD- BKI) are proposed for handling sparse matrix. They make use of an eigSVD procedure and several accelerating skills. Then, with the rSVD-BKI algorithm and a new subspace recycling technique, we accelerate the singular value thresholding (SVT) method in [1] to realize faster matrix completion. Experiments show that the proposed rSVD algorithms can be 6X faster than the basic rSVD algorithm [2] while keeping same accuracy. For image inpainting and movie-rating estimation problems, the proposed accelerated SVT algorithm consumes 15X and 8X less CPU time than the methods using svds and lansvd respectively, without loss of accuracy.Comment: 8 pages, 5 figures, ICTAI 2018 Accepte

Low-Rank Modeling and Its Applications in Image Analysis

Low-rank modeling generally refers to a class of methods that solve problems by representing variables of interest as low-rank matrices. It has achieved great success in various fields including computer vision, data mining, signal processing and bioinformatics. Recently, much progress has been made in theories, algorithms and applications of low-rank modeling, such as exact low-rank matrix recovery via convex programming and matrix completion applied to collaborative filtering. These advances have brought more and more attentions to this topic. In this paper, we review the recent advance of low-rank modeling, the state-of-the-art algorithms, and related applications in image analysis. We first give an overview to the concept of low-rank modeling and challenging problems in this area. Then, we summarize the models and algorithms for low-rank matrix recovery and illustrate their advantages and limitations with numerical experiments. Next, we introduce a few applications of low-rank modeling in the context of image analysis. Finally, we conclude this paper with some discussions.Comment: To appear in ACM Computing Survey

Two Algorithms for Orthogonal Nonnegative Matrix Factorization with Application to Clustering

Approximate matrix factorization techniques with both nonnegativity and orthogonality constraints, referred to as orthogonal nonnegative matrix factorization (ONMF), have been recently introduced and shown to work remarkably well for clustering tasks such as document classification. In this paper, we introduce two new methods to solve ONMF. First, we show athematical equivalence between ONMF and a weighted variant of spherical k-means, from which we derive our first method, a simple EM-like algorithm. This also allows us to determine when ONMF should be preferred to k-means and spherical k-means. Our second method is based on an augmented Lagrangian approach. Standard ONMF algorithms typically enforce nonnegativity for their iterates while trying to achieve orthogonality at the limit (e.g., using a proper penalization term or a suitably chosen search direction). Our method works the opposite way: orthogonality is strictly imposed at each step while nonnegativity is asymptotically obtained, using a quadratic penalty. Finally, we show that the two proposed approaches compare favorably with standard ONMF algorithms on synthetic, text and image data sets.Comment: 17 pages, 8 figures. New numerical experiments (document and synthetic data sets

Robust Matrix Completion via Maximum Correntropy Criterion and Half Quadratic Optimization

Robust matrix completion aims to recover a low-rank matrix from a subset of noisy entries perturbed by complex noises, where traditional methods for matrix completion may perform poorly due to utilizing $l_2$ error norm in optimization. In this paper, we propose a novel and fast robust matrix completion method based on maximum correntropy criterion (MCC). The correntropy based error measure is utilized instead of using $l_2$-based error norm to improve the robustness to noises. Using the half-quadratic optimization technique, the correntropy based optimization can be transformed to a weighted matrix factorization problem. Then, two efficient algorithms are derived, including alternating minimization based algorithm and alternating gradient descend based algorithm. The proposed algorithms do not need to calculate singular value decomposition (SVD) at each iteration. Further, the adaptive kernel selection strategy is proposed to accelerate the convergence speed as well as improve the performance. Comparison with existing robust matrix completion algorithms is provided by simulations, showing that the new methods can achieve better performance than existing state-of-the-art algorithms

Linked Component Analysis from Matrices to High Order Tensors: Applications to Biomedical Data

With the increasing availability of various sensor technologies, we now have access to large amounts of multi-block (also called multi-set, multi-relational, or multi-view) data that need to be jointly analyzed to explore their latent connections. Various component analysis methods have played an increasingly important role for the analysis of such coupled data. In this paper, we first provide a brief review of existing matrix-based (two-way) component analysis methods for the joint analysis of such data with a focus on biomedical applications. Then, we discuss their important extensions and generalization to multi-block multiway (tensor) data. We show how constrained multi-block tensor decomposition methods are able to extract similar or statistically dependent common features that are shared by all blocks, by incorporating the multiway nature of data. Special emphasis is given to the flexible common and individual feature analysis of multi-block data with the aim to simultaneously extract common and individual latent components with desired properties and types of diversity. Illustrative examples are given to demonstrate their effectiveness for biomedical data analysis.Comment: 20 pages, 11 figures, Proceedings of the IEEE, 201

Longitudinal data analysis using matrix completion

In clinical practice and biomedical research, measurements are often collected sparsely and irregularly in time while the data acquisition is expensive and inconvenient. Examples include measurements of spine bone mineral density, cancer growth through mammography or biopsy, a progression of defect of vision, or assessment of gait in patients with neurological disorders. Since the data collection is often costly and inconvenient, estimation of progression from sparse observations is of great interest for practitioners. From the statistical standpoint, such data is often analyzed in the context of a mixed-effect model where time is treated as both random and fixed effect. Alternatively, researchers analyze Gaussian processes or functional data where observations are assumed to be drawn from a certain distribution of processes. These models are flexible but rely on probabilistic assumptions and require very careful implementation. In this study, we propose an alternative elementary framework for analyzing longitudinal data, relying on matrix completion. Our method yields point estimates of progression curves by iterative application of the SVD. Our framework covers multivariate longitudinal data, regression and can be easily extended to other settings. We apply our methods to understand trends of progression of motor impairment in children with Cerebral Palsy. Our model approximates individual progression curves and explains 30% of the variability. Low-rank representation of progression trends enables discovering that subtypes of Cerebral Palsy exhibit different progression trends

A survey of dimensionality reduction techniques

Experimental life sciences like biology or chemistry have seen in the recent decades an explosion of the data available from experiments. Laboratory instruments become more and more complex and report hundreds or thousands measurements for a single experiment and therefore the statistical methods face challenging tasks when dealing with such high dimensional data. However, much of the data is highly redundant and can be efficiently brought down to a much smaller number of variables without a significant loss of information. The mathematical procedures making possible this reduction are called dimensionality reduction techniques; they have widely been developed by fields like Statistics or Machine Learning, and are currently a hot research topic. In this review we categorize the plethora of dimension reduction techniques available and give the mathematical insight behind them

Cascaded Channel Estimation for Large Intelligent Metasurface Assisted Massive MIMO

In this letter, we consider the problem of channel estimation for large intelligent metasurface (LIM) assisted massive multiple-input multiple-output (MIMO) systems. The main challenge of this problem is that the LIM integrated with a large number of low-cost metamaterial antennas can only passively reflect the incident signal by a certain phase shift, and does not have any signal processing capability. To deal with this, we introduce a general framework for the estimation of the transmitter-LIM and LIM-receiver cascaded channel, and propose a two-stage algorithm that includes a sparse matrix factorization stage and a matrix completion stage. Simulation results illustrate that the proposed method can achieve accurate channel estimation for LIM-assisted massive MIMO systems.Comment: 3 figures, 5 page