Detection of very short signal segments arise in a wide range of applications in many fields including engineering, genomics, and material science. For example, copy number variations (CNVs) play a significant role in the genetics of complex disease. Therefore the detection of CNVs due to duplication and deletion of a segment of DNA sequences is an important problem in genomics. In contrast to single-nucleotide polymorphisms which affects only one single nucleotide base, each CNV corresponds to a short segment of the genome, typically around 1000 nucleotide bases, that has been altered (see, e.g., Stankiewicz and Lupski, 2010). Although the length of these CNVs is much smaller than that of the whole genome, recognizing and accounting for such segment structure are critical in effective detection of CNVs (see, e.g., Jeng, Cai and Li, 2010).

A key problem in statistics and machine learning is the determination of network structure from data. We consider the case where the structure of the graph to be reconstructed is known to be scale-free. We show that in such cases it is natural to formulate structured sparsity inducing priors using submodular functions, and we use their Lov\'asz extension to obtain a convex relaxation. For tractable classes such as Gaussian graphical models, this leads to a convex optimization problem that can be efficiently solved. We show that our method results in an improvement in the accuracy of reconstructed networks for synthetic data. We also show how our prior encourages scale-free reconstructions on a bioinfomatics dataset.

Recent advances in large-margin classification of data residing in general metric spaces (rather than Hilbert spaces) enable classification under various natural metrics, such as string edit and earthmover distance. A general framework developed for this purpose by von Luxburg and Bousquet [JMLR, 2004] left open the questions of computational efficiency and of providing direct bounds on generalization error. We design a new algorithm for classification in general metric spaces, whose runtime and accuracy depend on the doubling dimension of the data points, and can thus achieve superior classification performance in many common scenarios. The algorithmic core of our approach is an approximate (rather than exact) solution to the classical problems of Lipschitz extension and of Nearest Neighbor Search. The algorithm's generalization performance is guaranteed via the fat-shattering dimension of Lipschitz classifiers, and we present experimental evidence of its superiority to some common kernel methods. As a by-product, we offer a new perspective on the nearest neighbor classifier, which yields significantly sharper risk asymptotics than the classic analysis of Cover and Hart [IEEE Trans. Info. Theory, 1967].

Schema Matching, i.e. the process of discovering semantic correspondences between concepts adopted in different data source schemas, has been a key topic in Database and Artificial Intelligence research areas for many years. In the past, it was largely investigated especially for classical database models (e.g., E/R schemas, relational databases, etc.). However, in the latest years, the widespread adoption of XML in the most disparate application fields pushed a growing number of researchers to design XML-specific Schema Matching approaches, called XML Matchers, aiming at finding semantic matchings between concepts defined in DTDs and XSDs. XML Matchers do not just take well-known techniques originally designed for other data models and apply them on DTDs/XSDs, but they exploit specific XML features (e.g., the hierarchical structure of a DTD/XSD) to improve the performance of the Schema Matching process. The design of XML Matchers is currently a well-established research area. The main goal of this paper is to provide a detailed description and classification of XML Matchers. We first describe to what extent the specificities of DTDs/XSDs impact on the Schema Matching task. Then we introduce a template, called XML Matcher Template, that describes the main components of an XML Matcher, their role and behavior. We illustrate how each of these components has been implemented in some popular XML Matchers. We consider our XML Matcher Template as the baseline for objectively comparing approaches that, at first glance, might appear as unrelated. The introduction of this template can be useful in the design of future XML Matchers. Finally, we analyze commercial tools implementing XML Matchers and introduce two challenging issues strictly related to this topic, namely XML source clustering and uncertainty management in XML Matchers.

In this paper, we propose a low-rank approximation method based on discrete least-squares for the approximation of a multivariate function from random, noisy-free observations. Sparsity inducing regularization techniques are used within classical algorithms for low-rank approximation in order to exploit the possible sparsity of low-rank approximations. Sparse low-rank approximations are constructed with a robust updated greedy algorithm which includes an optimal selection of regularization parameters and approximation ranks using cross validation techniques. Numerical examples demonstrate the capability of approximating functions of many variables even when very few function evaluations are available, thus proving the interest of the proposed algorithm for the propagation of uncertainties through complex computational models.

We develop a technique for generalising from data in which models are samplers represented as program text. We establish encouraging empirical results that suggest that Markov chain Monte Carlo probabilistic programming inference techniques coupled with higher-order probabilistic programming languages are now sufficiently powerful to enable successful inference of this kind in nontrivial domains. We also introduce a new notion of probabilistic program compilation and show how the same machinery might be used in the future to compile probabilistic programs for efficient reusable predictive inference.

One of the goals of probabilistic inference is to decide whether an empirically observed distribution is compatible with a candidate Bayesian network. However, Bayesian networks with hidden variables give rise to highly non-trivial constraints on the observed distribution. Here, we propose an information-theoretic approach, based on the insight that conditions on entropies of Bayesian networks take the form of simple linear inequalities. We describe an algorithm for deriving entropic tests for latent structures. The well-known conditional independence tests appear as a special case. While the approach applies for generic Bayesian networks, we presently adopt the causal view, and show the versatility of the framework by treating several relevant problems from that domain: detecting common ancestors, quantifying the strength of causal influence, and inferring the direction of causation from two-variable marginals.

We perform the first study of the tradeoff space of access methods and replication to support statistical analytics using first-order methods executed in the main memory of a Non-Uniform Memory Access (NUMA) machine. Statistical analytics systems differ from conventional SQL-analytics in the amount and types of memory incoherence they can tolerate. Our goal is to understand tradeoffs in accessing the data in row- or column-order and at what granularity one should share the model and data for a statistical task. We study this new tradeoff space, and discover there are tradeoffs between hardware and statistical efficiency. We argue that our tradeoff study may provide valuable information for designers of analytics engines: for each system we consider, our prototype engine can run at least one popular task at least 100x faster. We conduct our study across five architectures using popular models including SVMs, logistic regression, Gibbs sampling, and neural networks.

We consider the problem of learning overcomplete dictionaries in the context of sparse coding, where each sample selects a sparse subset of dictionary elements. Our main result is a strategy to approximately recover the unknown dictionary using an efficient algorithm. Our algorithm is a clustering-style procedure, where each cluster is used to estimate a dictionary element. The resulting solution can often be further cleaned up to obtain a high accuracy estimate, and we provide one simple scenario where $\ell_1$-regularized regression can be used for such a second stage.

The success of machine learning on a given task dependson, among other things, which learning algorithm is selected and its associated hyperparameters. Selecting an appropriate learning algorithm and setting its hyperparameters for a given data set can be a challenging task, especially for users who are not experts in machine learning. Previous work has examined using meta-features to predict which learning algorithm and hyperparameters should be used. However, choosing a set of meta-features that are predictive of algorithm performance is difficult. Here, we propose to apply collaborative filtering techniques to learning algorithm and hyperparameter selection, and find that doing so avoids determining which meta-features to use and outperforms traditional meta-learning approaches in many cases.