Classification is an important tool with many useful applications. Among the many classification methods, Fisher's Linear Discriminant Analysis (LDA) is a traditional model-based approach which makes use of the covariance information. However, in the high-dimensional, low-sample size setting, LDA cannot be directly deployed because the sample covariance is not invertible. While there are modern methods designed to deal with high-dimensional data, they may not fully use the covariance information as LDA does. Hence in some situations, it is still desirable to use a model-based method such as LDA for classification. This article exploits the potential of LDA in more complicated data settings. In many real applications, it is costly to manually place labels on observations; hence it is often that only a small portion of labeled data is available while a large number of observations are left without a label. It is a great challenge to obtain good classification performance through the labeled data alone, especially when the dimension is greater than the size of the labeled data. In order to overcome this issue, we propose a semi-supervised sparse LDA classifier to take advantage of the seemingly useless unlabeled data. They provide additional information which helps to boost the classification performance in some situations. A direct estimation method is used to reconstruct LDA and achieve the sparsity; meanwhile we employ the difference-convex algorithm to handle the non-convex loss function associated with the unlabeled data. Theoretical properties of the proposed classifier are studied. Our simulated examples help to understand when and how the information extracted from the unlabeled data can be useful. A real data example further illustrates the usefulness of the proposed method.

Nonnegative Tucker decomposition (NTD) is a powerful tool for the extraction of nonnegative parts-based and physically meaningful latent components from high-dimensional tensor data while preserving the natural multilinear structure of data. However, as the data tensor often has multiple modes and is large-scale, existing NTD algorithms suffer from a very high computational complexity in terms of both storage and computation time, which has been one major obstacle for practical applications of NTD. To overcome these disadvantages, we show how low (multilinear) rank approximation (LRA) of tensors is able to significantly simplify the computation of the gradients of the cost function, upon which a family of efficient first-order NTD algorithms are developed. Besides dramatically reducing the storage complexity and running time, the new algorithms are quite flexible and robust to noise because any well-established LRA approaches can be applied. We also show how nonnegativity incorporating sparsity substantially improves the uniqueness property and partially alleviates the curse of dimensionality of the Tucker decompositions. Simulation results on synthetic and real-world data justify the validity and high efficiency of the proposed NTD algorithms.

Gathering the most information by picking the least amount of data is a common task in experimental design or when exploring an unknown environment in reinforcement learning and robotics. A widely used measure for quantifying the information contained in some distribution of interest is its entropy. Greedily minimizing the expected entropy is therefore a standard method for choosing samples in order to gain strong beliefs about the underlying random variables. We show that this approach is prone to temporally getting stuck in local optima corresponding to wrongly biased beliefs. We suggest instead maximizing the expected cross entropy between old and new belief, which aims at challenging refutable beliefs and thereby avoids these local optima. We show that both criteria are closely related and that their difference can be traced back to the asymmetry of the Kullback-Leibler divergence. In illustrative examples as well as simulated and real-world experiments we demonstrate the advantage of cross entropy over simple entropy for practical applications.

Consider a classification problem where we do not have access to labels for individual training examples, but only have average labels over subpopulations. We give practical examples of this setup and show how such a classification task can usefully be analyzed as a weakly supervised clustering problem. We propose three approaches to solving the weakly supervised clustering problem, including a latent variables model that performs well in our experiments. We illustrate our methods on an analysis of aggregated elections data and an industry data set that was the original motivation for this research.

The group membership prediction (GMP) problem involves predicting whether or not a collection of instances share a certain semantic property. For instance, in kinship verification given a collection of images, the goal is to predict whether or not they share a {\it familial} relationship. In this context we propose a novel probability model and introduce latent {\em view-specific} and {\em view-shared} random variables to jointly account for the view-specific appearance and cross-view similarities among data instances. Our model posits that data from each view is independent conditioned on the shared variables. This postulate leads to a parametric probability model that decomposes group membership likelihood into a tensor product of data-independent parameters and data-dependent factors. We propose learning the data-independent parameters in a discriminative way with bilinear classifiers, and test our prediction algorithm on challenging visual recognition tasks such as multi-camera person re-identification and kinship verification. On most benchmark datasets, our method can significantly outperform the current state-of-the-art.

Tree structures are ubiquitous in data across many domains, and many datasets are naturally modelled by unobserved tree structures. In this paper, first we review the theory of random fragmentation processes [Bertoin, 2006], and a number of existing methods for modelling trees, including the popular nested Chinese restaurant process (nCRP). Then we define a general class of probability distributions over trees: the Dirichlet fragmentation process (DFP) through a novel combination of the theory of Dirichlet processes and random fragmentation processes. This DFP presents a stick-breaking construction, and relates to the nCRP in the same way the Dirichlet process relates to the Chinese restaurant process. Furthermore, we develop a novel hierarchical mixture model with the DFP, and empirically compare the new model to similar models in machine learning. Experiments show the DFP mixture model to be convincingly better than existing state-of-the-art approaches for hierarchical clustering and density modelling.

Traditional Kalman filter (KF) is derived under the well-known minimum mean square error (MMSE) criterion, which is optimal under Gaussian assumption. However, when the signals are non-Gaussian, especially when the system is disturbed by some heavy-tailed impulsive noises, the performance of KF will deteriorate seriously. To improve the robustness of KF against impulsive noises, we propose in this work a new Kalman filter, called the maximum correntropy Kalman filter (MCKF), which adopts the robust maximum correntropy criterion (MCC) as the optimality criterion, instead of using the MMSE. Similar to the traditional KF, the state mean and covariance matrix propagation equations are used to give prior estimations of the state and covariance matrix in MCKF. A novel fixed-point algorithm is then used to update the posterior estimations. A sufficient condition that guarantees the convergence of the fixed-point algorithm is given. Illustration examples are presented to demonstrate the effectiveness and robustness of the new algorithm.

We consider the matrix completion problem of recovering a structured matrix from noisy and partial measurements. Recent works have proposed tractable estimators with strong statistical guarantees for the case where the underlying matrix is low--rank, and the measurements consist of a subset, either of the exact individual entries, or of the entries perturbed by additive Gaussian noise, which is thus implicitly suited for thin--tailed continuous data. Arguably, common applications of matrix completion require estimators for (a) heterogeneous data--types, such as skewed--continuous, count, binary, etc., (b) for heterogeneous noise models (beyond Gaussian), which capture varied uncertainty in the measurements, and (c) heterogeneous structural constraints beyond low--rank, such as block--sparsity, or a superposition structure of low--rank plus elementwise sparseness, among others. In this paper, we provide a vastly unified framework for generalized matrix completion by considering a matrix completion setting wherein the matrix entries are sampled from any member of the rich family of exponential family distributions; and impose general structural constraints on the underlying matrix, as captured by a general regularizer $\mathcal{R}(.)$. We propose a simple convex regularized $M$--estimator for the generalized framework, and provide a unified and novel statistical analysis for this general class of estimators. We finally corroborate our theoretical results on simulated datasets.

High-throughput mRNA sequencing (RNA-Seq) is widely used for transcript quantification of gene isoforms. Since RNA-Seq data alone is often not sufficient to accurately identify the read origins from the isoforms for quantification, we propose to explore protein domain-domain interactions as prior knowledge for integrative analysis with RNA-seq data. We introduce a Network-based method for RNA-Seq-based Transcript Quantification (Net-RSTQ) to integrate protein domain-domain interaction network with short read alignments for transcript abundance estimation. Based on our observation that the abundances of the neighboring isoforms by domain-domain interactions in the network are positively correlated, Net-RSTQ models the expression of the neighboring transcripts as Dirichlet priors on the likelihood of the observed read alignments against the transcripts in one gene. The transcript abundances of all the genes are then jointly estimated with alternating optimization of multiple EM problems. In simulation Net-RSTQ effectively improved isoform transcript quantifications when isoform co-expressions correlate with their interactions. qRT-PCR results on 25 multi-isoform genes in a stem cell line, an ovarian cancer cell line, and a breast cancer cell line also showed that Net-RSTQ estimated more consistent isoform proportions with RNA-Seq data. In the experiments on the RNA-Seq data in The Cancer Genome Atlas (TCGA), the transcript abundances estimated by Net-RSTQ are more informative for patient sample classification of ovarian cancer, breast cancer and lung cancer. All experimental results collectively support that Net-RSTQ is a promising approach for isoform quantification.

Ridge regularized linear models (RRLMs), such as ridge regression and the SVM, are a popular group of methods that are used in conjunction with coefficient hypothesis testing to discover explanatory variables with a significant multivariate association to a response. However, many investigators are reluctant to draw causal interpretations of the selected variables due to the incomplete knowledge of the capabilities of RRLMs in causal inference. Under reasonable assumptions, we show that a modified form of RRLMs can get very close to identifying a subset of the Markov boundary by providing a worst-case bound on the space of possible solutions. The results hold for any convex loss, even when the underlying functional relationship is nonlinear, and the solution is not unique. Our approach combines ideas in Markov boundary and sufficient dimension reduction theory. Experimental results show that the modified RRLMs are competitive against state-of-the-art algorithms in discovering part of the Markov boundary from gene expression data.