Factor analysis provides linear factors that describe relationships between individual variables of a data set. We extend this classical formulation into linear factors that describe relationships between groups of variables, where each group represents either a set of related variables or a data set. The model also naturally extends canonical correlation analysis to more than two sets, in a way that is more flexible than previous extensions. Our solution is formulated as variational inference of a latent variable model with structural sparsity, and it consists of two hierarchical levels: The higher level models the relationships between the groups, whereas the lower models the observed variables given the higher level. We show that the resulting solution solves the group factor analysis problem accurately, outperforming alternative factor analysis based solutions as well as more straightforward implementations of group factor analysis. The method is demonstrated on two life science data sets, one on brain activation and the other on systems biology, illustrating its applicability to the analysis of different types of high-dimensional data sources.

We propose a new algorithm called PLUTO for building logistic regression trees to binary response data. PLUTO can capture the nonlinear and interaction patterns in messy data by recursively partitioning the sample space. It fits a simple or a multiple linear logistic regression model in each partition. PLUTO employs the cyclical coordinate descent method for estimation of multiple linear logistic regression models with elastic net penalties, which allows it to deal with high-dimensional data efficiently. The tree structure comprises a graphical description of the data. Together with the logistic regression models, it provides an accurate classifier as well as a piecewise smooth estimate of the probability of "success". PLUTO controls selection bias by: (1) separating split variable selection from split point selection; (2) applying an adjusted chi-squared test to find the split variable instead of exhaustive search. A bootstrap calibration technique is employed to further correct selection bias. Comparison on real datasets shows that on average, the multiple linear PLUTO models predict more accurately than other algorithms.

We present a new package in R implementing Bayesian additive regression trees (BART). The package introduces many new features for data analysis using BART such as variable selection, interaction detection, model diagnostic plots, incorporation of missing data and the ability to save trees for future prediction. It is significantly faster than the current R implementation, parallelized, and capable of handling both large sample sizes and high-dimensional data.

Solving logistic regression with L1-regularization in distributed settings is an important problem. This problem arises when training dataset is very large and cannot fit the memory of a single machine. We present d-GLMNET, a new algorithm solving logistic regression with L1-regularization in the distributed settings. We empirically show that it is superior over distributed online learning via truncated gradient.

This paper proposed a new regression model called $l_1$-regularized outlier isolation and regression (LOIRE) and a fast algorithm based on block coordinate descent to solve this model. Besides, assuming outliers are gross errors following a Bernoulli process, this paper also presented a Bernoulli estimate model which, in theory, should be very accurate and robust due to its complete elimination of affections caused by outliers. Though this Bernoulli estimate is hard to solve, it could be approximately achieved through a process which takes LOIRE as an important intermediate step. As a result, the approximate Bernoulli estimate is a good combination of Bernoulli estimate's accuracy and LOIRE regression's efficiency with several simulations conducted to strongly verify this point. Moreover, LOIRE can be further extended to realize robust rank factorization which is powerful in recovering low-rank component from massive corruptions. Extensive experimental results showed that the proposed method outperforms state-of-the-art methods like RPCA and GoDec in the aspect of computation speed with a competitive performance.

We study the problem of variable selection in convex nonparametric regression. Under the assumption that the true regression function is convex and sparse, we develop a screening procedure to select a subset of variables that contains the relevant variables. Our approach is a two-stage quadratic programming method that estimates a sum of one-dimensional convex functions, followed by one-dimensional concave regression fits on the residuals. In contrast to previous methods for sparse additive models, the optimization is finite dimensional and requires no tuning parameters for smoothness. Under appropriate assumptions, we prove that the procedure is faithful in the population setting, yielding no false negatives. We give a finite sample statistical analysis, and introduce algorithms for efficiently carrying out the required quadratic programs. The approach leads to computational and statistical advantages over fitting a full model, and provides an effective, practical approach to variable screening in convex regression.

Labeling data for classification requires significant human effort. To reduce labeling cost, instead of labeling every instance, a group of instances (bag) is labeled by a single bag label. Computer algorithms are then used to infer the label for each instance in a bag, a process referred to as instance annotation. This task is challenging due to the ambiguity regarding the instance labels. We propose a discriminative probabilistic model for the instance annotation problem and introduce an expectation maximization framework for inference, based on the maximum likelihood approach. For many probabilistic approaches, brute-force computation of the instance label posterior probability given its bag label is exponential in the number of instances in the bag. Our key contribution is a dynamic programming method for computing the posterior that is linear in the number of instances. We evaluate our methods using both benchmark and real world data sets, in the domain of bird song, image annotation, and activity recognition. In many cases, the proposed framework outperforms, sometimes significantly, the current state-of-the-art MIML learning methods, both in instance label prediction and bag label prediction.

Modern biotechnologies often result in high-dimensional data sets with much more variables than observations (n $\ll$ p). These data sets pose new challenges to statistical analysis: Variable selection becomes one of the most important tasks in this setting. We assess the recently proposed flexible framework for variable selection called stability selection. By the use of resampling procedures, stability selection adds a finite sample error control to high-dimensional variable selection procedures such as Lasso or boosting. We consider the combination of boosting and stability selection and present results from a detailed simulation study that provides insights into the usefulness of this combination. Limitations are discussed and guidance on the specification and tuning of stability selection is given. The interpretation of the used error bounds is elaborated and insights for practical data analysis are given. The results will be used to detect differentially expressed phenotype measurements in patients with autism spectrum disorders. All methods are implemented in the freely available R package stabs.

Identifying small subsets of features that are relevant for prediction and/or classification tasks is a central problem in machine learning and statistics. The feature selection task is especially important, and computationally difficult, for modern datasets where the number of features can be comparable to, or even exceed, the number of samples. Here, we show that feature selection with Bayesian inference takes a universal form and reduces to calculating the magnetizations of an Ising model, under some mild conditions. Our results exploit the observation that the evidence takes a universal form for strongly-regularizing priors --- priors that have a large effect on the posterior probability even in the infinite data limit. We derive explicit expressions for feature selection for generalized linear models, a large class of statistical techniques that include linear and logistic regression. We illustrate the power of our approach by analyzing feature selection in a logistic regression-based classifier trained to distinguish between the letters B and D in the notMNIST dataset.

In this paper we present a novel agent-based modeling methodology to predict rooftop solar adoptions in the residential energy market. We first applied several linear regression models to estimate missing variables for non-adopters, so that attributes of non-adopters and adopters could be used to train a logistic regression model. Then, we integrated the logistic regression model along with other predictive models into a multi-agent simulation platform and validated our models by comparing the forecast of aggregate adoptions in a typical zip code area with its ground truth. This result shows that the agent-based model can reliably predict future adoptions. Finally, based on the validated agent-based model, we compared the outcome of a hypothesized seeding policy with the original incentive plan, and investigated other alternative seeding policies which could lead to more adopters.