In a causal graphical model, an instrument for a variable X and its effect Y is a random variable that is a cause of X and independent of all the causes of Y except X. (Pearl (1995), Spirtes et al (2000)). Instrumental variables can be used to estimate how the distribution of an effect will respond to a manipulation of its causes, even in the presence of unmeasured common causes (confounders). In typical instrumental variable estimation, instruments are chosen based on domain knowledge. There is currently no statistical test for validating a variable as an instrument. In this paper, we introduce the concept of semi-instrument, which generalizes the concept of instrument. We show that in the framework of additive models, under certain conditions, we can test whether a variable is semi-instrumental. Moreover, adding some distribution assumptions, we can test whether two semi-instruments are instrumental. We give algorithms to estimate the p-value that a random variable is semi-instrumental, and the p-value that two semi-instruments are both instrumental. These algorithms can be used to test the experts' choice of instruments, or to identify instruments automatically.

We present a general framework for defining priors on model structure and sampling from the posterior using the Metropolis-Hastings algorithm. The key idea is that structure priors are defined via a probability tree and that the proposal mechanism for the Metropolis-Hastings algorithm operates by traversing this tree, thereby defining a cheaply computable acceptance probability. We have applied this approach to Bayesian net structure learning using a number of priors and tree traversal strategies. Our results show that these must be chosen appropriately for this approach to be successful.

We propose an approach to multivariate nonparametric regression that generalizes reduced rank regression for linear models. An additive model is estimated for each dimension of a $q$-dimensional response, with a shared $p$-dimensional predictor variable. To control the complexity of the model, we employ a functional form of the Ky-Fan or nuclear norm, resulting in a set of function estimates that have low rank. Backfitting algorithms are derived and justified using a nonparametric form of the nuclear norm subdifferential. Oracle inequalities on excess risk are derived that exhibit the scaling behavior of the procedure in the high dimensional setting. The methods are illustrated on gene expression data.

We propose a spectral clustering method based on local principal components analysis (PCA). After performing local PCA in selected neighborhoods, the algorithm builds a nearest neighbor graph weighted according to a discrepancy between the principal subspaces in the neighborhoods, and then applies spectral clustering. As opposed to standard spectral methods based solely on pairwise distances between points, our algorithm is able to resolve intersections. We establish theoretical guarantees for simpler variants within a prototypical mathematical framework for multi-manifold clustering, and evaluate our algorithm on various simulated data sets.

Recent work in metric learning has significantly improved the state-of-the-art in k-nearest neighbor classification. Support vector machines (SVM), particularly with RBF kernels, are amongst the most popular classification algorithms that uses distance metrics to compare examples. This paper provides an empirical analysis of the efficacy of three of the most popular Mahalanobis metric learning algorithms as pre-processing for SVM training. We show that none of these algorithms generate metrics that lead to particularly satisfying improvements for SVM-RBF classification. As a remedy we introduce support vector metric learning (SVML), a novel algorithm that seamlessly combines the learning of a Mahalanobis metric with the training of the RBF-SVM parameters. We demonstrate the capabilities of SVML on nine benchmark data sets of varying sizes and difficulties. In our study, SVML outperforms all alternative state-of-the-art metric learning algorithms in terms of accuracy and establishes itself as a serious alternative to the standard Euclidean metric with model selection by cross validation.

We present some nonparametric methods for graphical modeling. In the discrete case, where the data are binary or drawn from a finite alphabet, Markov random fields are already essentially nonparametric, since the cliques can take only a finite number of values. Continuous data are different. The Gaussian graphical model is the standard parametric model for continuous data, but it makes distributional assumptions that are often unrealistic. We discuss two approaches to building more flexible graphical models. One allows arbitrary graphs and a nonparametric extension of the Gaussian; the other uses kernel density estimation and restricts the graphs to trees and forests. Examples of both methods are presented. We also discuss possible future research directions for nonparametric graphical modeling.

This paper describes a new online convex optimization method which incorporates a family of candidate dynamical models and establishes novel tracking regret bounds that scale with the comparator's deviation from the best dynamical model in this family. Previous online optimization methods are designed to have a total accumulated loss comparable to that of the best comparator sequence, and existing tracking or shifting regret bounds scale with the overall variation of the comparator sequence. In many practical scenarios, however, the environment is nonstationary and comparator sequences with small variation are quite weak, resulting in large losses. The proposed Dynamic Mirror Descent method, in contrast, can yield low regret relative to highly variable comparator sequences by both tracking the best dynamical model and forming predictions based on that model. This concept is demonstrated empirically in the context of sequential compressive observations of a dynamic scene and tracking a dynamic social network.

We consider the problem of simultaneously learning to linearly combine a very large number of kernels and learn a good predictor based on the learnt kernel. When the number of kernels $d$ to be combined is very large, multiple kernel learning methods whose computational cost scales linearly in $d$ are intractable. We propose a randomized version of the mirror descent algorithm to overcome this issue, under the objective of minimizing the group $p$-norm penalized empirical risk. The key to achieve the required exponential speed-up is the computationally efficient construction of low-variance estimates of the gradient. We propose importance sampling based estimates, and find that the ideal distribution samples a coordinate with a probability proportional to the magnitude of the corresponding gradient. We show the surprising result that in the case of learning the coefficients of a polynomial kernel, the combinatorial structure of the base kernels to be combined allows the implementation of sampling from this distribution to run in $O(\log(d))$ time, making the total computational cost of the method to achieve an $\epsilon$-optimal solution to be $O(\log(d)/\epsilon^2)$, thereby allowing our method to operate for very large values of $d$. Experiments with simulated and real data confirm that the new algorithm is computationally more efficient than its state-of-the-art alternatives.

We present a new algorithm for approximate inference in probabilistic programs, based on a stochastic gradient for variational programs. This method is efficient without restrictions on the probabilistic program; it is particularly practical for distributions which are not analytically tractable, including highly structured distributions that arise in probabilistic programs. We show how to automatically derive mean-field probabilistic programs and optimize them, and demonstrate that our perspective improves inference efficiency over other algorithms.

Mapping the topology of gene regulatory networks is a central problem in systems biology. The regulatory architecture controlling gene expression also controls consequent cellular behavior such as development, differentiation, homeostasis and response to stimuli, while deregulation of these networks has been implicated in oncogenesis and tumor progression (Pe'er and Hacohen, 2011). Experimental methods based e.g. on chromatin immunoprecepitation, DNaseI hypersensitivity or protein-binding assays are capable of determining the nature of gene regulation in a given system, but are time-consuming, expensive and require antibodies for each transcription factor (Elnitski et al., 2006). Accurate computational methods to infer gene regulatory networks, particularly methods that leverage genome-scale experimental data, are urgently required not only to supplement empirical approaches but also, if possible, to explore these data in new, moreintegrative ways. Many computational methods have been developed to infer regulatory networks from gene expression data, predominately employing unsupervised techniques. Several comparisons have been made of network inference methods, but a comprehensive evaluation that covers unsupervised, semi-supervised and supervised methods is lacking, and many questions remain open.