When can reliable inference be drawn in the "Big Data" context? This paper presents a framework for answering this fundamental question in the context of correlation mining, with implications for general large scale inference. In large scale data applications like genomics, connectomics, and eco-informatics the dataset is often variable-rich but sample-starved: a regime where the number $n$ of acquired samples (statistical replicates) is far fewer than the number $p$ of observed variables (genes, neurons, voxels, or chemical constituents). Much of recent work has focused on understanding the computational complexity of proposed methods for "Big Data." Sample complexity however has received relatively less attention, especially in the setting when the sample size $n$ is fixed, and the dimension $p$ grows without bound. To address this gap, we develop a unified statistical framework that explicitly quantifies the sample complexity of various inferential tasks. Sampling regimes can be divided into several categories: 1) the classical asymptotic regime where the variable dimension is fixed and the sample size goes to infinity; 2) the mixed asymptotic regime where both variable dimension and sample size go to infinity at comparable rates; 3) the purely high dimensional asymptotic regime where the variable dimension goes to infinity and the sample size is fixed. Each regime has its niche but only the latter regime applies to exa-scale data dimension. We illustrate this high dimensional framework for the problem of correlation mining, where it is the matrix of pairwise and partial correlations among the variables that are of interest. We demonstrate various regimes of correlation mining based on the unifying perspective of high dimensional learning rates and sample complexity for different structured covariance models and different inference tasks.

Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domains ranging in scale from intracellular biochemistry to human populations, literature mining has not been used to extract specific types of experimental evidence, which are reported differently for distinct experimental goals. We focus on pharmacokinetic evidence for DDI, essential for identifying causal mechanisms of putative interactions and as input for further pharmacological and pharmaco-epidemiology investigations. We used manually curated corpora of PubMed abstracts and annotated sentences to evaluate the efficacy of literature mining on two tasks: first, identifying PubMed abstracts containing pharmacokinetic evidence of DDIs; second, extracting sentences containing such evidence from abstracts. We implemented a text mining pipeline and evaluated it using several linear classifiers and a variety of feature transforms. The most important textual features in the abstract and sentence classification tasks were analyzed. We also investigated the performance benefits of using features derived from PubMed metadata fields, various publicly available named entity recognizers, and pharmacokinetic dictionaries. Several classifiers performed very well in distinguishing relevant and irrelevant abstracts (reaching F1~=0.93, MCC~=0.74, iAUC~=0.99) and sentences (F1~=0.76, MCC~=0.65, iAUC~=0.83). We found that word bigram features were important for achieving optimal classifier performance and that features derived from Medical Subject Headings (MeSH) terms significantly improved abstract classification. ...

Mini-batch optimization has proven to be a powerful paradigm for large-scale learning. However, the state of the art parallel mini-batch algorithms assume synchronous operation or cyclic update orders. When worker nodes are heterogeneous (due to different computational capabilities or different communication delays), synchronous and cyclic operations are inefficient since they will leave workers idle waiting for the slower nodes to complete their computations. In this paper, we propose an asynchronous mini-batch algorithm for regularized stochastic optimization problems with smooth loss functions that eliminates idle waiting and allows workers to run at their maximal update rates. We show that by suitably choosing the step-size values, the algorithm achieves a rate of the order $O(1/\sqrt{T})$ for general convex regularization functions, and the rate $O(1/T)$ for strongly convex regularization functions, where $T$ is the number of iterations. In both cases, the impact of asynchrony on the convergence rate of our algorithm is asymptotically negligible, and a near-linear speedup in the number of workers can be expected. Theoretical results are confirmed in real implementations on a distributed computing infrastructure.

We pose causal inference as the problem of learning to classify probability distributions. In particular, we assume access to a collection $\{(S_i,l_i)\}_{i=1}^n$, where each $S_i$ is a sample drawn from the probability distribution of $X_i \times Y_i$, and $l_i$ is a binary label indicating whether "$X_i \to Y_i$" or "$X_i \leftarrow Y_i$". Given these data, we build a causal inference rule in two steps. First, we featurize each $S_i$ using the kernel mean embedding associated with some characteristic kernel. Second, we train a binary classifier on such embeddings to distinguish between causal directions. We present generalization bounds showing the statistical consistency and learning rates of the proposed approach, and provide a simple implementation that achieves state-of-the-art cause-effect inference. Furthermore, we extend our ideas to infer causal relationships between more than two variables.

Tensor factorization arises in many machine learning applications, such as knowledge base modeling and parameter estimation in latent variable models. However, numerical methods for tensor factorization have not reached the level of maturity of matrix factorization methods. In this paper, we propose a new algorithm for CP tensor factorization that uses random projections to reduce the problem to simultaneous matrix diagonalization. Our method is conceptually simple and also applies to non-orthogonal and asymmetric tensors of arbitrary order. We prove that a small number random projections essentially preserves the spectral information in the tensor, allowing us to remove the dependence on the eigengap that plagued earlier tensor-to-matrix reductions. Experimentally, our method outperforms existing tensor factorization methods on both simulated data and two real datasets.

This paper investigates methods for quantifying similarity between audio signals, specifically for the task of of cover song detection. We consider an information-theoretic approach, where we compute pairwise measures of predictability between time series. We compare discrete-valued approaches operating on quantised audio features, to continuous-valued approaches. In the discrete case, we propose a method for computing the normalised compression distance, where we account for correlation between time series. In the continuous case, we propose to compute information-based measures of similarity as statistics of the prediction error between time series. We evaluate our methods on two cover song identification tasks using a data set comprised of 300 Jazz standards and using the Million Song Dataset. For both datasets, we observe that continuous-valued approaches outperform discrete-valued approaches. We consider approaches to estimating the normalised compression distance (NCD) based on string compression and prediction, where we observe that our proposed normalised compression distance with alignment (NCDA) improves average performance over NCD, for sequential compression algorithms. Finally, we demonstrate that continuous-valued distances may be combined to improve performance with respect to baseline approaches. Using a large-scale filter-and-refine approach, we demonstrate state-of-the-art performance for cover song identification using the Million Song Dataset.

We consider the problem of identifying the parameters of an unknown mixture of two arbitrary $d$-dimensional gaussians from a sequence of independent random samples. Our main results are upper and lower bounds giving a computationally efficient moment-based estimator with an optimal convergence rate, thus resolving a problem introduced by Pearson (1894). Denoting by $\sigma^2$ the variance of the unknown mixture, we prove that $\Theta(\sigma^{12})$ samples are necessary and sufficient to estimate each parameter up to constant additive error when $d=1.$ Our upper bound extends to arbitrary dimension $d>1$ up to a (provably necessary) logarithmic loss in $d$ using a novel---yet simple---dimensionality reduction technique. We further identify several interesting special cases where the sample complexity is notably smaller than our optimal worst-case bound. For instance, if the means of the two components are separated by $\Omega(\sigma)$ the sample complexity reduces to $O(\sigma^2)$ and this is again optimal. Our results also apply to learning each component of the mixture up to small error in total variation distance, where our algorithm gives strong improvements in sample complexity over previous work. We also extend our lower bound to mixtures of $k$ Gaussians, showing that $\Omega(\sigma^{6k-2})$ samples are necessary to estimate each parameter up to constant additive error.

In this paper we analyze boosting algorithms in linear regression from a new perspective: that of modern first-order methods in convex optimization. We show that classic boosting algorithms in linear regression, namely the incremental forward stagewise algorithm (FS$_\varepsilon$) and least squares boosting (LS-Boost($\varepsilon$)), can be viewed as subgradient descent to minimize the loss function defined as the maximum absolute correlation between the features and residuals. We also propose a modification of FS$_\varepsilon$ that yields an algorithm for the Lasso, and that may be easily extended to an algorithm that computes the Lasso path for different values of the regularization parameter. Furthermore, we show that these new algorithms for the Lasso may also be interpreted as the same master algorithm (subgradient descent), applied to a regularized version of the maximum absolute correlation loss function. We derive novel, comprehensive computational guarantees for several boosting algorithms in linear regression (including LS-Boost($\varepsilon$) and FS$_\varepsilon$) by using techniques of modern first-order methods in convex optimization. Our computational guarantees inform us about the statistical properties of boosting algorithms. In particular they provide, for the first time, a precise theoretical description of the amount of data-fidelity and regularization imparted by running a boosting algorithm with a prespecified learning rate for a fixed but arbitrary number of iterations, for any dataset.

We extend the Bayesian Information Criterion (BIC), an asymptotic approximation for the marginal likelihood, to Bayesian networks with hidden variables. This approximation can be used to select models given large samples of data. The standard BIC as well as our extension punishes the complexity of a model according to the dimension of its parameters. We argue that the dimension of a Bayesian network with hidden variables is the rank of the Jacobian matrix of the transformation between the parameters of the network and the parameters of the observable variables. We compute the dimensions of several networks including the naive Bayes model with a hidden root node.

We examine methods for clustering in high dimensions. In the first part of the paper, we perform an experimental comparison between three batch clustering algorithms: the Expectation-Maximization (EM) algorithm, a "winner take all" version of the EM algorithm reminiscent of the K-means algorithm, and model-based hierarchical agglomerative clustering. We learn naive-Bayes models with a hidden root node, using high-dimensional discrete-variable data sets (both real and synthetic). We find that the EM algorithm significantly outperforms the other methods, and proceed to investigate the effect of various initialization schemes on the final solution produced by the EM algorithm. The initializations that we consider are (1) parameters sampled from an uninformative prior, (2) random perturbations of the marginal distribution of the data, and (3) the output of hierarchical agglomerative clustering. Although the methods are substantially different, they lead to learned models that are strikingly similar in quality.