In discrete undirected graphical models, the conditional independence of node labels Y is specified by the graph structure. We study the case where there is another input random vector X (e.g. The main contribution of this paper is to learn the graph structure and the functions conditioned on X at the same time. We prove that discrete undirected graphical models with feature X are equivalent to mul- tivariate discrete models. The reparameterization of the potential functions in graphical models by conditional log odds ratios of the latter offers advantages in representation of the conditional independence structure.

Many studies in biomedical and health sciences involve small sample sizes due to logistic or financial constraints. Often, identifying weak (but scientifically interesting) associations between a set of predictors and a response necessitates pooling datasets from multiple diverse labs or groups. While there is a rich literature in statistical machine learning to address distributional shifts and inference in multi-site datasets, it is less clear ${\it when}$ such pooling is guaranteed to help (and when it does not) -- independent of the inference algorithms we use. In this paper, we present a hypothesis test to answer this question, both for classical and high dimensional linear regression. We precisely identify regimes where pooling datasets across multiple sites is sensible, and how such policy decisions can be made via simple checks executable on each site before any data transfer ever happens. With a focus on Alzheimer's disease studies, we present empirical results showing that in regimes suggested by our analysis, pooling a local dataset with data from an international study improves power.

Consider samples from two different data sources $\{\mathbf{x_s^i}\} \sim P_{\rm source}$ and $\{\mathbf{x_t^i}\} \sim P_{\rm target}$. We only observe their transformed versions $h(\mathbf{x_s^i})$ and $g(\mathbf{x_t^i})$, for some known function class $h(\cdot)$ and $g(\cdot)$. Our goal is to perform a statistical test checking if $P_{\rm source}$ = $P_{\rm target}$ while removing the distortions induced by the transformations. This problem is closely related to concepts underlying numerous domain adaptation algorithms, and in our case, is motivated by the need to combine clinical and imaging based biomarkers from multiple sites and/or batches, where this problem is fairly common and an impediment in the conduct of analyses with much larger sample sizes. We develop a framework that addresses this problem using ideas from hypothesis testing on the transformed measurements, where in the distortions need to be estimated {\it in tandem} with the testing. We derive a simple algorithm and study its convergence and consistency properties in detail, and we also provide lower-bound strategies based on recent work in continuous optimization. On a dataset of individuals at risk for neurological disease, our results are competitive with alternative procedures that are twice as expensive and in some cases operationally infeasible to implement.

Although recovering an Euclidean distance matrix from noisy observations is a common problem in practice, how well this could be done remains largely unknown. To fill in this void, we study a simple distance matrix estimate based upon the so-called regularized kernel estimate. We show that such an estimate can be characterized as simply applying a constant amount of shrinkage to all observed pairwise distances. This fact allows us to establish risk bounds for the estimate implying that the true distances can be estimated consistently in an average sense as the number of objects increases. In addition, such a characterization suggests an efficient algorithm to compute the distance matrix estimator, as an alternative to the usual second order cone programming known not to scale well for large problems. Numerical experiments and an application in visualizing the diversity of Vpu protein sequences from a recent HIV-1 study further demonstrate the practical merits of the proposed method.

In this paper, we consider the multivariate Bernoulli distribution as a model to estimate the structure of graphs with binary nodes. This distribution is discussed in the framework of the exponential family, and its statistical properties regarding independence of the nodes are demonstrated. Importantly the model can estimate not only the main effects and pairwise interactions among the nodes but also is capable of modeling higher order interactions, allowing for the existence of complex clique effects. We compare the multivariate Bernoulli model with existing graphical inference models - the Ising model and the multivariate Gaussian model, where only the pairwise interactions are considered. On the other hand, the multivariate Bernoulli distribution has an interesting property in that independence and uncorrelatedness of the component random variables are equivalent. Both the marginal and conditional distributions of a subset of variables in the multivariate Bernoulli distribution still follow the multivariate Bernoulli distribution. Furthermore, the multivariate Bernoulli logistic model is developed under generalized linear model theory by utilizing the canonical link function in order to include covariate information on the nodes, edges and cliques. We also consider variable selection techniques such as LASSO in the logistic model to impose sparsity structure on the graph. Finally, we discuss extending the smoothing spline ANOVA approach to the multivariate Bernoulli logistic model to enable estimation of non-linear effects of the predictor variables.

In discrete undirected graphical models, the conditional independence of node labels Y is specified by the graph structure. We study the case where there is another input random vector X (e.g. observed features) such that the distribution P (Y | X) is determined by functions of X that characterize the (higher-order) interactions among the Y ’s. The main contribution of this paper is to learn the graph structure and the functions conditioned on X at the same time. We prove that discrete undirected graphical models with feature X are equivalent to mul- tivariate discrete models. The reparameterization of the potential functions in graphical models by conditional log odds ratios of the latter offers advantages in representation of the conditional independence structure. The functional spaces can be flexibly determined by kernels. Additionally, we impose a Structure Lasso (SLasso) penalty on groups of functions to learn the graph structure. These groups with overlaps are designed to enforce hierarchical function selection. In this way, we are able to shrink higher order interactions to obtain a sparse graph structure.

We propose a new in-sample cross validation based method (randomized GACV) for choosing smoothing or bandwidth parameters that govern the bias-variance or fit-complexity tradeoff in'soft' classification. Soft classification refers to a learning procedure which estimates the probability that an example with a given attribute vector is in class 1 vs class O. The target for optimizing the the tradeoff is the Kullback-Liebler distance between the estimated probability distribution and the'true' probability distribution, representing knowledge of an infinite population. The method uses a randomized estimate of the trace of a Hessian and mimics cross validation at the cost of a single relearning with perturbed outcome data.

We propose a new in-sample cross validation based method (randomized GACV) for choosing smoothing or bandwidth parameters that govern the bias-variance or fit-complexity tradeoff in'soft' classification. Soft classification refers to a learning procedure which estimates the probability that an example with a given attribute vector is in class 1 vs class O. The target for optimizing the the tradeoff is the Kullback-Liebler distance between the estimated probability distribution and the'true' probability distribution, representing knowledge of an infinite population. The method uses a randomized estimate of the trace of a Hessian and mimics cross validation at the cost of a single relearning with perturbed outcome data.

We propose a new in-sample cross validation based method (randomized GACV) for choosing smoothing or bandwidth parameters that govern the bias-variance or fit-complexity tradeoff in'soft' classification. Soft classification refersto a learning procedure which estimates the probability that an example with a given attribute vector is in class 1 vs class O. The target for optimizing the the tradeoff is the Kullback-Liebler distance between the estimated probability distribution and the'true' probability distribution,representing knowledge of an infinite population.

We describe the use of smoothing spline analysis of variance (SS ANOVA) in the penalized log likelihood context, for learning (estimating) the probability p of a '1' outcome, given a training set with attribute vectors and outcomes.