Minimax Optimal Sparse Signal Recovery with Poisson Statistics

We are motivated by problems that arise in a number of applications such as Online Marketing and Explosives detection, where the observations are usually modeled using Poisson statistics. We model each observation as a Poisson random variable whose mean is a sparse linear superposition of known patterns. Unlike many conventional problems observations here are not identically distributed since they are associated with different sensing modalities. We analyze the performance of a Maximum Likelihood (ML) decoder, which for our Poisson setting involves a non-linear optimization but yet is computationally tractable. We derive fundamental sample complexity bounds for sparse recovery when the measurements are contaminated with Poisson noise. In contrast to the least-squares linear regression setting with Gaussian noise, we observe that in addition to sparsity, the scale of the parameters also fundamentally impacts $\ell_2$ error in the Poisson setting. We show tightness of our upper bounds both theoretically and experimentally. In particular, we derive a minimax matching lower bound on the mean-squared error and show that our constrained ML decoder is minimax optimal for this regime.Comment: Submitted to IEEE Trans. on Signal Processing. arXiv admin note: substantial text overlap with arXiv:1307.466

Minimax Lower Bounds for Noisy Matrix Completion Under Sparse Factor Models

This paper examines fundamental error characteristics for a general class of matrix completion problems, where the matrix of interest is a product of two a priori unknown matrices, one of which is sparse, and the observations are noisy. Our main contributions come in the form of minimax lower bounds for the expected per-element squared error for this problem under under several common noise models. Specifically, we analyze scenarios where the corruptions are characterized by additive Gaussian noise or additive heavier-tailed (Laplace) noise, Poisson-distributed observations, and highly-quantized (e.g., one-bit) observations, as instances of our general result. Our results establish that the error bounds derived in (Soni et al., 2016) for complexity-regularized maximum likelihood estimators achieve, up to multiplicative constants and logarithmic factors, the minimax error rates in each of these noise scenarios, provided that the nominal number of observations is large enough, and the sparse factor has (on an average) at least one non-zero per column.Comment: 21 page

Minimax Optimal Rates for Poisson Inverse Problems with Physical Constraints

This paper considers fundamental limits for solving sparse inverse problems in the presence of Poisson noise with physical constraints. Such problems arise in a variety of applications, including photon-limited imaging systems based on compressed sensing. Most prior theoretical results in compressed sensing and related inverse problems apply to idealized settings where the noise is i.i.d., and do not account for signal-dependent noise and physical sensing constraints. Prior results on Poisson compressed sensing with signal-dependent noise and physical constraints provided upper bounds on mean squared error performance for a specific class of estimators. However, it was unknown whether those bounds were tight or if other estimators could achieve significantly better performance. This work provides minimax lower bounds on mean-squared error for sparse Poisson inverse problems under physical constraints. Our lower bounds are complemented by minimax upper bounds. Our upper and lower bounds reveal that due to the interplay between the Poisson noise model, the sparsity constraint and the physical constraints: (i) the mean-squared error does not depend on the sample size $n$ other than to ensure the sensing matrix satisfies RIP-like conditions and the intensity $T$ of the input signal plays a critical role; and (ii) the mean-squared error has two distinct regimes, a low-intensity and a high-intensity regime and the transition point from the low-intensity to high-intensity regime depends on the input signal $f^*$. In the low-intensity regime the mean-squared error is independent of $T$ while in the high-intensity regime, the mean-squared error scales as $\frac{s \log p}{T}$, where $s$ is the sparsity level, $p$ is the number of pixels or parameters and $T$ is the signal intensity.Comment: 30 pages, 5 figure

A data-dependent weighted LASSO under Poisson noise

Sparse linear inverse problems appear in a variety of settings, but often the noise contaminating observations cannot accurately be described as bounded by or arising from a Gaussian distribution. Poisson observations in particular are a feature of several real-world applications. Previous work on sparse Poisson inverse problems encountered several limiting technical hurdles. This paper describes a novel alternative analysis approach for sparse Poisson inverse problems that (a) sidesteps the technical challenges in previous work, (b) admits estimators that can readily be computed using off-the-shelf LASSO algorithms, and (c) hints at a general framework for broad classes of noise in sparse linear inverse problems. At the heart of this new approach lies a weighted LASSO estimator for which data-dependent weights are based on Poisson concentration inequalities. Unlike previous analyses of the weighted LASSO, the proposed analysis depends on conditions which can be checked or shown to hold in general settings with high probability.Comment: 25 pages (48 pages with appendix), 3 figure

Reconstruction Error Bounds for Compressed Sensing under Poisson Noise using the Square Root of the Jensen-Shannon Divergence

Reconstruction error bounds in compressed sensing under Gaussian or uniform bounded noise do not translate easily to the case of Poisson noise. Reasons for this include the signal dependent nature of Poisson noise, and also the fact that the negative log likelihood (NLL) in case of a Poisson distribution (which is related to the generalized Kullback-Leibler divergence (GKLD)) is not a metric and does not obey the triangle inequality. There exist prior theoretical results in the form of provable error bounds for computationally tractable estimators for compressed sensing problems under Poisson noise. However, these results do not apply to realistic compressive systems, which must obey some crucial constraints such as non-negativity and flux preservation. On the other hand, there exist provable error bounds for such realistic systems in the published literature, but they are for estimators that are computationally intractable. In this paper, we develop error bounds for a computationally tractable estimator which also applies to realistic compressive systems obeying the required constraints. Our technique replaces the GKLD, with an information theoretic metric - namely the square root of the Jensen-Shannon divergence (JSD), which is related to an approximate, symmetrized version of the Poisson NLL. We show that this allows for simple proofs of the error bounds. We propose and prove interesting statistical properties of the square root of JSD and exploit other known ones. Numerical experiments are performed showing the use of the technique in signal and image reconstruction from compressed measurements under Poisson noise. Our technique applies to sparse/ compressible signals in any orthonormal basis, works with high probability for any randomly generated non-negative and flux-preserving sensing matrix and is proposes an estimator whose parameters are purely statistically motivated.Comment: We are submitting a newer version of the article, with statistical and experimental analysis of the statistical properties (distribution) of the quantity $\sqrt{J(y,\Phi x)}$, i.e. the square root of the Jensen Shannon divergence between the Poisson-noisy measurement vector $y$ and the unknown measurement vector $\Phi x

Statistical and Computational Limits for Sparse Matrix Detection

This paper investigates the fundamental limits for detecting a high-dimensional sparse matrix contaminated by white Gaussian noise from both the statistical and computational perspectives. We consider $p\times p$ matrices whose rows and columns are individually $k$-sparse. We provide a tight characterization of the statistical and computational limits for sparse matrix detection, which precisely describe when achieving optimal detection is easy, hard, or impossible, respectively. Although the sparse matrices considered in this paper have no apparent submatrix structure and the corresponding estimation problem has no computational issue at all, the detection problem has a surprising computational barrier when the sparsity level $k$ exceeds the cubic root of the matrix size $p$: attaining the optimal detection boundary is computationally at least as hard as solving the planted clique problem. The same statistical and computational limits also hold in the sparse covariance matrix model, where each variable is correlated with at most $k$ others. A key step in the construction of the statistically optimal test is a structural property for sparse matrices, which can be of independent interest

High-dimensional Log-Error-in-Variable Regression with Applications to Microbial Compositional Data Analysis

In microbiome and genomic study, the regression of compositional data has been a crucial tool for identifying microbial taxa or genes that are associated with clinical phenotypes. To account for the variation in sequencing depth, the classic log-contrast model is often used where read counts are normalized into compositions. However, zero read counts and the randomness in covariates remain critical issues. In this article, we introduce a surprisingly simple, interpretable, and efficient method for the estimation of compositional data regression through the lens of a novel high-dimensional log-error-in-variable regression model. The proposed method provides both corrections on sequencing data with possible overdispersion and simultaneously avoids any subjective imputation of zero read counts. We provide theoretical justifications with matching upper and lower bounds for the estimation error. We also consider a general log-error-in-variable regression model with corresponding estimation method to accommodate broader situations. The merit of the procedure is illustrated through real data analysis and simulation studies

Reconstruction Error Bounds for Compressed Sensing under Poisson or Poisson-Gaussian Noise Using Variance Stabilization Transforms

Most existing bounds for signal reconstruction from compressive measurements make the assumption of additive signal-independent noise. However in many compressive imaging systems, the noise statistics are more accurately represented by Poisson or Poisson-Gaussian noise models. In this paper, we derive upper bounds for signal reconstruction error from compressive measurements which are corrupted by Poisson or Poisson-Gaussian noise. The features of our bounds are as follows: (1) The bounds are derived for a probabilistically motivated, computationally tractable convex estimator with principled parameter selection. The estimator penalizes signal sparsity subject to a constraint that imposes an upper bound on a term based on variance stabilization transforms to approximate the Poisson or Poisson-Gaussian negative log-likelihoods. (2) They are applicable to signals that are sparse as well as compressible in any orthonormal basis, and are derived for compressive systems obeying realistic constraints such as non-negativity and flux-preservation. We present extensive numerical results for signal reconstruction under varying number of measurements and varying signal intensity levels.Comment: Revised version with more elaborate statistical analysis of the term $R(y,\Phi x)$ in case of Poisson as well as Poisson-Gaussian nois

Multi-sample Estimation of Bacterial Composition Matrix in Metagenomics Data

Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many rare bacterial taxa might not be captured in the final sequencing reads, which results in many zero counts. Naive composition estimation using count normalization leads to many zero proportions, which tend to result in inaccurate estimates of bacterial abundance and diversity. This paper takes a multi-sample approach to the estimation of bacterial abundances in order to borrow information across samples and across species. Empirical results from real data sets suggest that the composition matrix over multiple samples is approximately low rank, which motivates a regularized maximum likelihood estimation with a nuclear norm penalty. An efficient optimization algorithm using the generalized accelerated proximal gradient and Euclidean projection onto simplex space is developed. The theoretical upper bounds and the minimax lower bounds of the estimation errors, measured by the Kullback-Leibler divergence and the Frobenius norm, are established. Simulation studies demonstrate that the proposed estimator outperforms the naive estimators. The method is applied to an analysis of a human gut microbiome dataset

Rare and Weak effects in Large-Scale Inference: methods and phase diagrams

Often when we deal with `Big Data', the true effects we are interested in are Rare and Weak (RW). Researchers measure a large number of features, hoping to find perhaps only a small fraction of them to be relevant to the research in question; the effect sizes of the relevant features are individually small so the true effects are not strong enough to stand out for themselves. Higher Criticism (HC) and Graphlet Screening (GS) are two classes of methods that are specifically designed for the Rare/Weak settings. HC was introduced to determine whether there are any relevant effects in all the measured features. More recently, HC was applied to classification, where it provides a method for selecting useful predictive features for trained classification rules. GS was introduced as a graph-guided multivariate screening procedure, and was used for variable selection. We develop a theoretic framework where we use an Asymptotic Rare and Weak (ARW) model simultaneously controlling the size and prevalence of useful/significant features among the useless/null bulk. At the heart of the ARW model is the so-called phase diagram, which is a way to visualize clearly the class of ARW settings where the relevant effects are so rare or weak that desired goals (signal detection, variable selection, etc.) are simply impossible to achieve. We show that HC and GS have important advantages over better known procedures and achieve the optimal phase diagrams in a variety of ARW settings. HC and GS are flexible ideas that adapt easily to many interesting situations. We review the basics of these ideas and some of the recent extensions, discuss their connections to existing literature, and suggest some new applications of these ideas.Comment: 31 pages, 4 figure