Ensemble-of-trees methods have become popular choices for forecasting in both regression and classification problems. Algorithms such as random forests (Breiman 2001) and stochastic gradient boosting (Friedman 2002) are two well-established and widely employed procedures. Recent advances in ensemble methods include dynamic trees (Taddy, Gramacy, and Polson 2011) and Bayesian additive regression trees (BART, Chipman, George, and McCulloch 2010), which depart from predecessors in that they rely on an underlying Bayesian probability model rather than a pure algorithm. BART has demonstrated substantial promise in a wide variety of simulations and real world applications such as predicting avalanches on mountain roads (Blattenberger and Fowles 2014), predicting how transcription factors interact with DNA (Zhou and Liu 2008) and predicting movie box office revenues (Eliashberg 2010). This paper introduces bartMachine, a new R (R Core Team 2014) package available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package

In this report paper we first present a report of the Advanced Machine Learning Course Project on the provided data set and then present a novel heuristic algorithm for exact Bayesian network (BN) structure discovery that uses decomposable scoring functions. Our algorithm follows a different approach to solve the problem of BN structure discovery than the previously used methods such as Dynamic Programming (DP) and Branch and Bound to reduce the search space and find the global optima space for the problem. The algorithm we propose has some degree of flexibility that can make it more or less greedy. The more the algorithm is set to be greedy, the more the speed of the algorithm will be, and the less optimal the final structure. Our algorithm runs in a much less time than the previously known methods and guarantees to have an optimality of close to 99%.

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.

Several problems such as network intrusion, community detection, and disease outbreak can be described by observations attributed to nodes or edges of a graph. In these applications presence of intrusion, community or disease outbreak is characterized by novel observations on some unknown connected subgraph. These problems can be formulated in terms of optimization of suitable objectives on connected subgraphs, a problem which is generally computationally difficult. We overcome the combinatorics of connectivity by embedding connected subgraphs into linear matrix inequalities (LMI). Computationally efficient tests are then realized by optimizing convex objective functions subject to these LMI constraints. We prove, by means of a novel Euclidean embedding argument, that our tests are minimax optimal for exponential family of distributions on 1-D and 2-D lattices. We show that internal conductance of the connected subgraph family plays a fundamental role in characterizing detectability.

We propose a novel diverse feature selection method based on determinantal point processes (DPPs). Our model enables one to flexibly define diversity based on the covariance of features (similar to orthogonal matching pursuit) or alternatively based on side information. We introduce our approach in the context of Bayesian sparse regression, employing a DPP as a variational approximation to the true spike and slab posterior distribution. We subsequently show how this variational DPP approximation generalizes and extends mean-field approximation, and can be learned efficiently by exploiting the fast sampling properties of DPPs. Our motivating application comes from bioinformatics, where we aim to identify a diverse set of genes whose expression profiles predict a tumor type where the diversity is defined with respect to a gene-gene interaction network. We also explore an application in spatial statistics. In both cases, we demonstrate that the proposed method yields significantly more diverse feature sets than classic sparse methods, without compromising accuracy.

Nonparametric two sample testing deals with the question of consistently deciding if two distributions are different, given samples from both, without making any parametric assumptions about the form of the distributions. The current literature is split into two kinds of tests - those which are consistent without any assumptions about how the distributions may differ (\textit{general} alternatives), and those which are designed to specifically test easier alternatives, like a difference in means (\textit{mean-shift} alternatives). The main contribution of this paper is to explicitly characterize the power of a popular nonparametric two sample test, designed for general alternatives, under a mean-shift alternative in the high-dimensional setting. Specifically, we explicitly derive the power of the linear-time Maximum Mean Discrepancy statistic using the Gaussian kernel, where the dimension and sample size can both tend to infinity at any rate, and the two distributions differ in their means. As a corollary, we find that if the signal-to-noise ratio is held constant, then the test's power goes to one if the number of samples increases faster than the dimension increases. This is the first explicit power derivation for a general nonparametric test in the high-dimensional setting, and also the first analysis of how tests designed for general alternatives perform when faced with easier ones.

According to Cobanoglu et al and Murphy, it is now widely acknowledged that the single target paradigm (one protein or target, one disease, one drug) that has been the dominant premise in drug development in the recent past is untenable. More often than not, a drug-like compound (ligand) can be promiscuous - that is, it can interact with more than one target protein. In recent years, in in silico target prediction methods the promiscuity issue has been approached computationally in different ways. In this study we confine attention to the so-called ligand-based target prediction machine learning approaches, commonly referred to as target-fishing. With a few exceptions, the target-fishing approaches that are currently ubiquitous in cheminformatics literature can be essentially viewed as single-label multi-classification schemes; these approaches inherently bank on the single target paradigm assumption that a ligand can home in on one specific target. In order to address the ligand promiscuity issue, one might be able to cast target-fishing as a multi-label multi-class classification problem. For illustrative and comparison purposes, single-label and multi-label Naive Bayes classification models (denoted here by SMM and MMM, respectively) for target-fishing were implemented. The models were constructed and tested on 65,587 compounds and 308 targets retrieved from the ChEMBL17 database. SMM and MMM performed differently: for 16,344 test compounds, the MMM model returned recall and precision values of 0.8058 and 0.6622, respectively; the corresponding recall and precision values yielded by the SMM model were 0.7805 and 0.7596, respectively. However, at a significance level of 0.05 and one degree of freedom McNemar test performed on the target prediction results returned by SMM and MMM for the 16,344 test ligands gave a chi-squared value of 15.656, in favour of the MMM approach.

This paper is about two related decision theoretic problems, nonparametric two-sample testing and independence testing. There is a belief that two recently proposed solutions, based on kernels and distances between pairs of points, behave well in high-dimensional settings. We identify different sources of misconception that give rise to the above belief. Specifically, we differentiate the hardness of estimation of test statistics from the hardness of testing whether these statistics are zero or not, and explicitly discuss a notion of "fair" alternative hypotheses for these problems as dimension increases. We then demonstrate that the power of these tests actually drops polynomially with increasing dimension against fair alternatives. We end with some theoretical insights and shed light on the \textit{median heuristic} for kernel bandwidth selection. Our work advances the current understanding of the power of modern nonparametric hypothesis tests in high dimensions.

Empirical risk minimization (ERM) is a fundamental learning rule for statistical learning problems where the data is generated according to some unknown distribution $\mathsf{P}$ and returns a hypothesis $f$ chosen from a fixed class $\mathcal{F}$ with small loss $\ell$. In the parametric setting, depending upon $(\ell, \mathcal{F},\mathsf{P})$ ERM can have slow $(1/\sqrt{n})$ or fast $(1/n)$ rates of convergence of the excess risk as a function of the sample size $n$. There exist several results that give sufficient conditions for fast rates in terms of joint properties of $\ell$, $\mathcal{F}$, and $\mathsf{P}$, such as the margin condition and the Bernstein condition. In the non-statistical prediction with expert advice setting, there is an analogous slow and fast rate phenomenon, and it is entirely characterized in terms of the mixability of the loss $\ell$ (there being no role there for $\mathcal{F}$ or $\mathsf{P}$). The notion of stochastic mixability builds a bridge between these two models of learning, reducing to classical mixability in a special case. The present paper presents a direct proof of fast rates for ERM in terms of stochastic mixability of $(\ell,\mathcal{F}, \mathsf{P})$, and in so doing provides new insight into the fast-rates phenomenon. The proof exploits an old result of Kemperman on the solution to the general moment problem. We also show a partial converse that suggests a characterization of fast rates for ERM in terms of stochastic mixability is possible.

Conditional Value at Risk (CVaR) is a prominent risk measure that is being used extensively in various domains. We develop a new formula for the gradient of the CVaR in the form of a conditional expectation. Based on this formula, we propose a novel sampling-based estimator for the gradient of the CVaR, in the spirit of the likelihood-ratio method. We analyze the bias of the estimator, and prove the convergence of a corresponding stochastic gradient descent algorithm to a local CVaR optimum. Our method allows to consider CVaR optimization in new domains. As an example, we consider a reinforcement learning application, and learn a risksensitive controller for the game of Tetris.