The Bayesian approach to machine learning amounts to computing posterior distributions of random variables from a probabilistic model of how the variables are related (that is, a prior distribution) and a set of observations of variables. There is a trend in machine learning towards expressing Bayesian models as probabilistic programs. As a foundation for this kind of programming, we propose a core functional calculus with primitives for sampling prior distributions and observing variables. We define measure-transformer combinators inspired by theorems in measure theory, and use these to give a rigorous semantics to our core calculus. The original features of our semantics include its support for discrete, continuous, and hybrid measures, and, in particular, for observations of zero-probability events. We compile our core language to a small imperative language that is processed by an existing inference engine for factor graphs, which are data structures that enable many efficient inference algorithms. This allows efficient approximate inference of posterior marginal distributions, treating thousands of observations per second for large instances of realistic models.

We study the performance of a family of randomized parallel coordinate descent methods for minimizing the sum of a nonsmooth and separable convex functions. The problem class includes as a special case L1-regularized L1 regression and the minimization of the exponential loss ("AdaBoost problem"). We assume the input data defining the loss function is contained in a sparse $m\times n$ matrix $A$ with at most $\omega$ nonzeros in each row. Our methods need $O(n \beta/\tau)$ iterations to find an approximate solution with high probability, where $\tau$ is the number of processors and $\beta = 1 + (\omega-1)(\tau-1)/(n-1)$ for the fastest variant. The notation hides dependence on quantities such as the required accuracy and confidence levels and the distance of the starting iterate from an optimal point. Since $\beta/\tau$ is a decreasing function of $\tau$, the method needs fewer iterations when more processors are used. Certain variants of our algorithms perform on average only $O(\nnz(A)/n)$ arithmetic operations during a single iteration per processor and, because $\beta$ decreases when $\omega$ does, fewer iterations are needed for sparser problems.

Recent advances in high-throughput cDNA sequencing (RNA-Seq) technology have revolutionized transcriptome studies. A major motivation for RNA-Seq is to map the structure of expressed transcripts at nucleotide resolution. With accurate computational tools for transcript reconstruction, this technology may also become useful for genome (re-)annotation, which has mostly relied on de novo gene finding where gene structures are primarily inferred from the genome sequence. We developed a machine-learning method, called mTim (margin-based transcript inference method) for transcript reconstruction from RNA-Seq read alignments that is based on discriminatively trained hidden Markov support vector machines. In addition to features derived from read alignments, it utilizes characteristic genomic sequences, e.g. around splice sites, to improve transcript predictions. mTim inferred transcripts that were highly accurate and relatively robust to alignment errors in comparison to those from Cufflinks, a widely used transcript assembly method.

This work proposes a framework using temporal data and domain knowledge in order to analyze complex agronomical features. The expertise is first formalized in an ontology, under the form of concepts and relationships between them, and then used in conjunction with raw data and mathematical models to design a software sensor. Next the software sensor outputs are put in relation to product quality, assessed by quantitative measurements. This requires the use of advanced data analysis methods, such as functional regression. The methodology is applied to a case study involving an experimental design in French vineyards. The temporal data consist of sap flow measurements, and the goal is to explain fruit quality (sugar concentration and weight), using vine's water courses through the various vine phenological stages. The results are discussed, as well as the method genericity and robustness.

We present a complete finite axiomatization of the unrestricted implication problem for inclusion and conditional independence atoms in the context of dependence logic. For databases, our result implies a finite axiomatization of the unrestricted implication problem for inclusion, functional, and embedded multivalued dependencies in the unirelational case.

HOL(y)Hammer is an online AI/ATP service for formal (computer-understandable) mathematics encoded in the HOL Light system. The service allows its users to upload and automatically process an arbitrary formal development (project) based on HOL Light, and to attack arbitrary conjectures that use the concepts defined in some of the uploaded projects. For that, the service uses several automated reasoning systems combined with several premise selection methods trained on all the project proofs. The projects that are readily available on the server for such query answering include the recent versions of the Flyspeck, Multivariate Analysis and Complex Analysis libraries. The service runs on a 48-CPU server, currently employing in parallel for each task 7 AI/ATP combinations and 4 decision procedures that contribute to its overall performance. The system is also available for local installation by interested users, who can customize it for their own proof development. An Emacs interface allowing parallel asynchronous queries to the service is also provided. The overall structure of the service is outlined, problems that arise and their solutions are discussed, and an initial account of using the system is given.

We obtain a tight distribution-specific characterization of the sample complexity of large-margin classification with L2 regularization: We introduce the margin-adapted dimension, which is a simple function of the second order statistics of the data distribution, and show distribution-specific upper and lower bounds on the sample complexity, both governed by the margin-adapted dimension of the data distribution. The upper bounds are universal, and the lower bounds hold for the rich family of sub-Gaussian distributions with independent features. We conclude that this new quantity tightly characterizes the true sample complexity of large-margin classification. To prove the lower bound, we develop several new tools of independent interest. These include new connections between shattering and hardness of learning, new properties of shattering with linear classifiers, and a new lower bound on the smallest eigenvalue of a random Gram matrix generated by sub-Gaussian variables. Our results can be used to quantitatively compare large margin learning to other learning rules, and to improve the effectiveness of methods that use sample complexity bounds, such as active learning.

We introduce GP-FNARX: a new model for nonlinear system identification based on a nonlinear autoregressive exogenous model (NARX) with filtered regressors (F) where the nonlinear regression problem is tackled using sparse Gaussian processes (GP). We integrate data pre-processing with system identification into a fully automated procedure that goes from raw data to an identified model. Both pre-processing parameters and GP hyper-parameters are tuned by maximizing the marginal likelihood of the probabilistic model. We obtain a Bayesian model of the system's dynamics which is able to report its uncertainty in regions where the data is scarce. The automated approach, the modeling of uncertainty and its relatively low computational cost make of GP-FNARX a good candidate for applications in robotics and adaptive control.

Optimizing the acquisition matrix is useful for compressed sensing of signals that are sparse in overcomplete dictionaries, because the acquisition matrix can be adapted to the particular correlations of the dictionary atoms. In this paper a novel formulation of the optimization problem is proposed, in the form of a rank-constrained nearest correlation matrix problem. Furthermore, improvements for three existing optimization algorithms are introduced, which are shown to be particular instances of the proposed formulation. Simulation results show notable improvements and superior robustness in sparse signal recovery.

Qualitative spatial and temporal reasoning is based on so-called qualitative calculi. Algebraic properties of these calculi have several implications on reasoning algorithms. But what exactly is a qualitative calculus? And to which extent do the qualitative calculi proposed meet these demands? The literature provides various answers to the first question but only few facts about the second. In this paper we identify the minimal requirements to binary spatio-temporal calculi and we discuss the relevance of the according axioms for representation and reasoning. We also analyze existing qualitative calculi and provide a classification involving different notions of a relation algebra.