The scalability of statistical estimators is of increasing importance in modern applications. One approach to implementing scalable algorithms is to compress data into a low dimensional latent space using dimension reduction methods. In this paper we develop an approach for dimension reduction that exploits the assumption of low rank structure in high dimensional data to gain both computational and statistical advantages. We adapt recent randomized low-rank approximation algorithms to provide an efficient solution to principal component analysis (PCA), and we use this efficient solver to improve parameter estimation in large-scale linear mixed models (LMM) for association mapping in statistical and quantitative genomics. A key observation in this paper is that randomization serves a dual role, improving both computational and statistical performance by implicitly regularizing the covariance matrix estimate of the random effect in a LMM. These statistical and computational advantages are highlighted in our experiments on simulated data and large-scale genomic studies.

We consider the problem of Bayesian learning on sensitive datasets and present two simple but somewhat surprising results that connect Bayesian learning to "differential privacy:, a cryptographic approach to protect individual-level privacy while permiting database-level utility. Specifically, we show that that under standard assumptions, getting one single sample from a posterior distribution is differentially private "for free". We will see that estimator is statistically consistent, near optimal and computationally tractable whenever the Bayesian model of interest is consistent, optimal and tractable. Similarly but separately, we show that a recent line of works that use stochastic gradient for Hybrid Monte Carlo (HMC) sampling also preserve differentially privacy with minor or no modifications of the algorithmic procedure at all, these observations lead to an "anytime" algorithm for Bayesian learning under privacy constraint. We demonstrate that it performs much better than the state-of-the-art differential private methods on synthetic and real datasets.

We introduce a novel sensitivity analysis framework for large scale classification problems that can be used when a small number of instances are incrementally added or removed. For quickly updating the classifier in such a situation, incremental learning algorithms have been intensively studied in the literature. Although they are much more efficient than solving the optimization problem from scratch, their computational complexity yet depends on the entire training set size. It means that, if the original training set is large, completely solving an incremental learning problem might be still rather expensive. To circumvent this computational issue, we propose a novel framework that allows us to make an inference about the updated classifier without actually re-optimizing it. Specifically, the proposed framework can quickly provide a lower and an upper bounds of a quantity on the unknown updated classifier. The main advantage of the proposed framework is that the computational cost of computing these bounds depends only on the number of updated instances. This property is quite advantageous in a typical sensitivity analysis task where only a small number of instances are updated. In this paper we demonstrate that the proposed framework is applicable to various practical sensitivity analysis tasks, and the bounds provided by the framework are often sufficiently tight for making desired inferences.

As a robust nonlinear similarity measure in kernel space, correntropy has received increasing attention in domains of machine learning and signal processing. In particular, the maximum correntropy criterion (MCC) has recently been successfully applied in robust regression and filtering. The default kernel function in correntropy is the Gaussian kernel, which is, of course, not always the best choice. In this work, we propose a generalized correntropy that adopts the generalized Gaussian density (GGD) function as the kernel (not necessarily a Mercer kernel), and present some important properties. We further propose the generalized maximum correntropy criterion (GMCC), and apply it to adaptive filtering. An adaptive algorithm, called the GMCC algorithm, is derived, and the mean square convergence performance is studied. We show that the proposed algorithm is very stable and can achieve zero probability of divergence (POD). Simulation results confirm the theoretical expectations and demonstrate the desirable performance of the new algorithm.

AdaBoost is one of the most popular machine-learning algorithms. It is simple to implement and often found very effective by practitioners, while still being mathematically elegant and theoretically sound. AdaBoost's behavior in practice, and in particular the test-error behavior, has puzzled many eminent researchers for over a decade: It seems to defy our general intuition in machine learning regarding the fundamental trade-off between model complexity and generalization performance. In this paper, we establish the convergence of "Optimal AdaBoost," a term coined by Rudin, Daubechies, and Schapire in 2004. We prove the convergence, with the number of rounds, of the classifier itself, its generalization error, and its resulting margins for fixed data sets, under certain reasonable conditions. More generally, we prove that the time/per-round average of almost any function of the example weights converges. Our approach is to frame AdaBoost as a dynamical system, to provide sufficient conditions for the existence of an invariant measure, and to employ tools from ergodic theory. Unlike previous work, we do not assume AdaBoost cycles; actually, we present empirical evidence against it on real-world datasets. Our main theoretical results hold under a weaker condition. We show sufficient empirical evidence that Optimal AdaBoost always met the condition on every real-world dataset we tried. Our results formally ground future convergence-rate analyses, and may even provide opportunities for slight algorithmic modifications to optimize the generalization ability of AdaBoost classifiers, thus reducing a practitioner's burden of deciding how long to run the algorithm.

Brain decoding involves the determination of a subject's cognitive state or an associated stimulus from functional neuroimaging data measuring brain activity. In this setting the cognitive state is typically characterized by an element of a finite set, and the neuroimaging data comprise voluminous amounts of spatiotemporal data measuring some aspect of the neural signal. The associated statistical problem is one of classification from high-dimensional data. We explore the use of functional principal component analysis, mutual information networks, and persistent homology for examining the data through exploratory analysis and for constructing features characterizing the neural signal for brain decoding. We review each approach from this perspective, and we incorporate the features into a classifier based on symmetric multinomial logistic regression with elastic net regularization. The approaches are illustrated in an application where the task is to infer, from brain activity measured with magnetoencephalography (MEG), the type of video stimulus shown to a subject.

Complex biological systems have been successfully modeled by biochemical and genetic interaction networks, typically gathered from high-throughput (HTP) data. These networks can be used to infer functional relationships between genes or proteins. Using the intuition that the topological role of a gene in a network relates to its biological function, local or diffusion based "guilt-by-association" and graph-theoretic methods have had success in inferring gene functions. Here we seek to improve function prediction by integrating diffusion-based methods with a novel dimensionality reduction technique to overcome the incomplete and noisy nature of network data. In this paper, we introduce diffusion component analysis (DCA), a framework that plugs in a diffusion model and learns a low-dimensional vector representation of each node to encode the topological properties of a network. As a proof of concept, we demonstrate DCA's substantial improvement over state-of-the-art diffusion-based approaches in predicting protein function from molecular interaction networks. Moreover, our DCA framework can integrate multiple networks from heterogeneous sources, consisting of genomic information, biochemical experiments and other resources, to even further improve function prediction. Yet another layer of performance gain is achieved by integrating the DCA framework with support vector machines that take our node vector representations as features. Overall, our DCA framework provides a novel representation of nodes in a network that can be used as a plug-in architecture to other machine learning algorithms to decipher topological properties of and obtain novel insights into interactomes.

Active learning has shown to reduce the number of experiments needed to obtain high-confidence drug-target predictions. However, in order to actually save experiments using active learning, it is crucial to have a method to evaluate the quality of the current prediction and decide when to stop the experimentation process. Only by applying reliable stoping criteria to active learning, time and costs in the experimental process can be actually saved. We compute active learning traces on simulated drug-target matrices in order to learn a regression model for the accuracy of the active learner. By analyzing the performance of the regression model on simulated data, we design stopping criteria for previously unseen experimental matrices. We demonstrate on four previously characterized drug effect data sets that applying the stopping criteria can result in upto 40% savings of the total experiments for highly accurate predictions.

Many modern tools in machine learning and signal processing, such as sparse dictionary learning, principal component analysis (PCA), non-negative matrix factorization (NMF), $K$-means clustering, etc., rely on the factorization of a matrix obtained by concatenating high-dimensional vectors from a training collection. While the idealized task would be to optimize the expected quality of the factors over the underlying distribution of training vectors, it is achieved in practice by minimizing an empirical average over the considered collection. The focus of this paper is to provide sample complexity estimates to uniformly control how much the empirical average deviates from the expected cost function. Standard arguments imply that the performance of the empirical predictor also exhibit such guarantees. The level of genericity of the approach encompasses several possible constraints on the factors (tensor product structure, shift-invariance, sparsity \ldots), thus providing a unified perspective on the sample complexity of several widely used matrix factorization schemes. The derived generalization bounds behave proportional to $\sqrt{\log(n)/n}$ w.r.t.\ the number of samples $n$ for the considered matrix factorization techniques.

Matrix completion has attracted significant recent attention in many fields including statistics, applied mathematics and electrical engineering. Current literature on matrix completion focuses primarily on independent sampling models under which the individual observed entries are sampled independently. Motivated by applications in genomic data integration, we propose a new framework of structured matrix completion (SMC) to treat structured missingness by design. Specifically, our proposed method aims at efficient matrix recovery when a subset of the rows and columns of an approximately low-rank matrix are observed. We provide theoretical justification for the proposed SMC method and derive lower bound for the estimation errors, which together establish the optimal rate of recovery over certain classes of approximately low-rank matrices. Simulation studies show that the method performs well in finite sample under a variety of configurations. The method is applied to integrate several ovarian cancer genomic studies with different extent of genomic measurements, which enables us to construct more accurate prediction rules for ovarian cancer survival.