Bayesian Robust Tensor Factorization for Incomplete Multiway Data

We propose a generative model for robust tensor factorization in the presence of both missing data and outliers. The objective is to explicitly infer the underlying low-CP-rank tensor capturing the global information and a sparse tensor capturing the local information (also considered as outliers), thus providing the robust predictive distribution over missing entries. The low-CP-rank tensor is modeled by multilinear interactions between multiple latent factors on which the column sparsity is enforced by a hierarchical prior, while the sparse tensor is modeled by a hierarchical view of Student-$t$ distribution that associates an individual hyperparameter with each element independently. For model learning, we develop an efficient closed-form variational inference under a fully Bayesian treatment, which can effectively prevent the overfitting problem and scales linearly with data size. In contrast to existing related works, our method can perform model selection automatically and implicitly without need of tuning parameters. More specifically, it can discover the groundtruth of CP rank and automatically adapt the sparsity inducing priors to various types of outliers. In addition, the tradeoff between the low-rank approximation and the sparse representation can be optimized in the sense of maximum model evidence. The extensive experiments and comparisons with many state-of-the-art algorithms on both synthetic and real-world datasets demonstrate the superiorities of our method from several perspectives.Comment: in IEEE Transactions on Neural Networks and Learning Systems, 201

Non-Convex Rank Minimization via an Empirical Bayesian Approach

In many applications that require matrix solutions of minimal rank, the underlying cost function is non-convex leading to an intractable, NP-hard optimization problem. Consequently, the convex nuclear norm is frequently used as a surrogate penalty term for matrix rank. The problem is that in many practical scenarios there is no longer any guarantee that we can correctly estimate generative low-rank matrices of interest, theoretical special cases notwithstanding. Consequently, this paper proposes an alternative empirical Bayesian procedure build upon a variational approximation that, unlike the nuclear norm, retains the same globally minimizing point estimate as the rank function under many useful constraints. However, locally minimizing solutions are largely smoothed away via marginalization, allowing the algorithm to succeed when standard convex relaxations completely fail. While the proposed methodology is generally applicable to a wide range of low-rank applications, we focus our attention on the robust principal component analysis problem (RPCA), which involves estimating an unknown low-rank matrix with unknown sparse corruptions. Theoretical and empirical evidence are presented to show that our method is potentially superior to related MAP-based approaches, for which the convex principle component pursuit (PCP) algorithm (Candes et al., 2011) can be viewed as a special case.Comment: 10 pages, 6 figures, UAI 2012 pape

Rectified Gaussian Scale Mixtures and the Sparse Non-Negative Least Squares Problem

In this paper, we develop a Bayesian evidence maximization framework to solve the sparse non-negative least squares (S-NNLS) problem. We introduce a family of probability densities referred to as the Rectified Gaussian Scale Mixture (R- GSM) to model the sparsity enforcing prior distribution for the solution. The R-GSM prior encompasses a variety of heavy-tailed densities such as the rectified Laplacian and rectified Student- t distributions with a proper choice of the mixing density. We utilize the hierarchical representation induced by the R-GSM prior and develop an evidence maximization framework based on the Expectation-Maximization (EM) algorithm. Using the EM based method, we estimate the hyper-parameters and obtain a point estimate for the solution. We refer to the proposed method as rectified sparse Bayesian learning (R-SBL). We provide four R- SBL variants that offer a range of options for computational complexity and the quality of the E-step computation. These methods include the Markov chain Monte Carlo EM, linear minimum mean-square-error estimation, approximate message passing and a diagonal approximation. Using numerical experiments, we show that the proposed R-SBL method outperforms existing S-NNLS solvers in terms of both signal and support recovery performance, and is also very robust against the structure of the design matrix.Comment: Under Review by IEEE Transactions on Signal Processin

Robust Bayesian Tensor Factorization with Zero-Inflated Poisson Model and Consensus Aggregation

Tensor factorizations (TF) are powerful tools for the efficient representation and analysis of multidimensional data. However, classic TF methods based on maximum likelihood estimation underperform when applied to zero-inflated count data, such as single-cell RNA sequencing (scRNA-seq) data. Additionally, the stochasticity inherent in TFs results in factors that vary across repeated runs, making interpretation and reproducibility of the results challenging. In this paper, we introduce Zero Inflated Poisson Tensor Factorization (ZIPTF), a novel approach for the factorization of high-dimensional count data with excess zeros. To address the challenge of stochasticity, we introduce Consensus Zero Inflated Poisson Tensor Factorization (C-ZIPTF), which combines ZIPTF with a consensus-based meta-analysis. We evaluate our proposed ZIPTF and C-ZIPTF on synthetic zero-inflated count data and synthetic and real scRNA-seq data. ZIPTF consistently outperforms baseline matrix and tensor factorization methods in terms of reconstruction accuracy for zero-inflated data. When the probability of excess zeros is high, ZIPTF achieves up to $2.4\times$ better accuracy. Additionally, C-ZIPTF significantly improves the consistency and accuracy of the factorization. When tested on both synthetic and real scRNA-seq data, ZIPTF and C-ZIPTF consistently recover known and biologically meaningful gene expression programs

Inference via low-dimensional couplings

We investigate the low-dimensional structure of deterministic transformations between random variables, i.e., transport maps between probability measures. In the context of statistics and machine learning, these transformations can be used to couple a tractable "reference" measure (e.g., a standard Gaussian) with a target measure of interest. Direct simulation from the desired measure can then be achieved by pushing forward reference samples through the map. Yet characterizing such a map---e.g., representing and evaluating it---grows challenging in high dimensions. The central contribution of this paper is to establish a link between the Markov properties of the target measure and the existence of low-dimensional couplings, induced by transport maps that are sparse and/or decomposable. Our analysis not only facilitates the construction of transformations in high-dimensional settings, but also suggests new inference methodologies for continuous non-Gaussian graphical models. For instance, in the context of nonlinear state-space models, we describe new variational algorithms for filtering, smoothing, and sequential parameter inference. These algorithms can be understood as the natural generalization---to the non-Gaussian case---of the square-root Rauch-Tung-Striebel Gaussian smoother.Comment: 78 pages, 25 figure