In this paper we study speaker linking (a.k.a.\ partitioning) given constraints of the distribution of speaker identities over speech recordings. Specifically, we show that the intractable partitioning problem becomes tractable when the constraints pre-partition the data in smaller cliques with non-overlapping speakers. The surprisingly common case where speakers in telephone conversations are known, but the assignment of channels to identities is unspecified, is treated in a Bayesian way. We show that for the Dutch CGN database, where this channel assignment task is at hand, a lightweight speaker recognition system can quite effectively solve the channel assignment problem, with 93% of the cliques solved. We further show that the posterior distribution over channel assignment configurations is well calibrated.

Associating genetic markers with a multidimensional phenotype is an important yet challenging problem. In this work, we establish the equivalence between two popular methods: kernel-machine regression (KMR), and kernel distance covariance (KDC). KMR is a semiparametric regression frameworks that models the covariate effects parametrically, while the genetic markers are considered non-parametrically. KDC represents a class of methods that includes distance covariance (DC) and Hilbert-Schmidt Independence Criterion (HSIC), which are nonparametric tests of independence. We show the equivalence between the score test of KMR and the KDC statistic under certain conditions. This result leads to a novel generalization of the KDC test that incorporates the covariates. Our contributions are three-fold: (1) establishing the equivalence between KMR and KDC; (2) showing that the principles of kernel machine regression can be applied to the interpretation of KDC; (3) the development of a broader class of KDC statistics, that the members are the quantities of different kernels. We demonstrate the proposals using simulation studies. Data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) is used to explore the association between the genetic variants on gene \emph{FLJ16124} and phenotypes represented in 3D structural brain MR images adjusting for age and gender. The results suggest that SNPs of \emph{FLJ16124} exhibit strong pairwise interaction effects that are correlated to the changes of brain region volumes.

This work proposes a new method for simultaneous probabilistic identification and control of an observable, fully-actuated mechanical system. Identification is achieved by conditioning stochastic process priors on observations of configurations and noisy estimates of configuration derivatives. In contrast to previous work that has used stochastic processes for identification, we leverage the structural knowledge afforded by Lagrangian mechanics and learn the drift and control input matrix functions of the control-affine system separately. We utilise feedback-linearisation to reduce, in expectation, the uncertain nonlinear control problem to one that is easy to regulate in a desired manner. Thereby, our method combines the flexibility of nonparametric Bayesian learning with epistemological guarantees on the expected closed-loop trajectory. We illustrate our method in the context of torque-actuated pendula where the dynamics are learned with a combination of normal and log-normal processes.

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to both include biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer and the model-based search was more accurate than keyword search; it moreover recovered biologically meaningful relationships that are not straightforwardly visible from annotations, for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

Representations in the auditory cortex might be based on mechanisms similar to the visual ventral stream; modules for building invariance to transformations and multiple layers for compositionality and selectivity. In this paper we propose the use of such computational modules for extracting invariant and discriminative audio representations. Building on a theory of invariance in hierarchical architectures, we propose a novel, mid-level representation for acoustical signals, using the empirical distributions of projections on a set of templates and their transformations. Under the assumption that, by construction, this dictionary of templates is composed from similar classes, and samples the orbit of variance-inducing signal transformations (such as shift and scale), the resulting signature is theoretically guaranteed to be unique, invariant to transformations and stable to deformations. Modules of projection and pooling can then constitute layers of deep networks, for learning composite representations. We present the main theoretical and computational aspects of a framework for unsupervised learning of invariant audio representations, empirically evaluated on music genre classification. This work was supported by the Center for Brains, Minds and Machines (CBMM), funded by NSF STC award CCF - 1231216.

Recent research has shown that a single arbitrarily efficient solver can be significantly outperformed by a portfolio of possibly slower on-average solvers. The solver selection is usually done by means of (un)supervised learning techniques which exploit features extracted from the problem specification. In this paper we present an useful and flexible framework that is able to extract an extensive set of features from a Constraint (Satisfaction/Optimization) Problem defined in possibly different modeling languages: MiniZinc, FlatZinc or XCSP. We also report some empirical results showing that the performances that can be obtained using these features are effective and competitive with state of the art CSP portfolio techniques.

We propose a novel method for maximum likelihood-based parameter inference in nonlinear and/or non-Gaussian state space models. The method is an iterative procedure with three steps. At each iteration a particle filter is used to estimate the value of the log-likelihood function at the current parameter iterate. Using these log-likelihood estimates, a surrogate objective function is created by utilizing a Gaussian process model. Finally, we use a heuristic procedure to obtain a revised parameter iterate, providing an automatic trade-off between exploration and exploitation of the surrogate model. The method is profiled on two state space models with good performance both considering accuracy and computational cost.

Sparse clustering, which aims to find a proper partition of an extremely high-dimensional data set with redundant noise features, has been attracted more and more interests in recent years. The existing studies commonly solve the problem in a framework of maximizing the weighted feature contributions subject to a $\ell_2/\ell_1$ penalty. Nevertheless, this framework has two serious drawbacks: One is that the solution of the framework unavoidably involves a considerable portion of redundant noise features in many situations, and the other is that the framework neither offers intuitive explanations on why this framework can select relevant features nor leads to any theoretical guarantee for feature selection consistency. In this article, we attempt to overcome those drawbacks through developing a new sparse clustering framework which uses a $\ell_{\infty}/\ell_0$ penalty. First, we introduce new concepts on optimal partitions and noise features for the high-dimensional data clustering problems, based on which the previously known framework can be intuitively explained in principle. Then, we apply the suggested $\ell_{\infty}/\ell_0$ framework to formulate a new sparse k-means model with the $\ell_{\infty}/\ell_0$ penalty ($\ell_0$-k-means for short). We propose an efficient iterative algorithm for solving the $\ell_0$-k-means. To deeply understand the behavior of $\ell_0$-k-means, we prove that the solution yielded by the $\ell_0$-k-means algorithm has feature selection consistency whenever the data matrix is generated from a high-dimensional Gaussian mixture model. Finally, we provide experiments with both synthetic data and the Allen Developing Mouse Brain Atlas data to support that the proposed $\ell_0$-k-means exhibits better noise feature detection capacity over the previously known sparse k-means with the $\ell_2/\ell_1$ penalty ($\ell_1$-k-means for short).

We describe Venture, an interactive virtual machine for probabilistic programming that aims to be sufficiently expressive, extensible, and efficient for general-purpose use. Like Church, probabilistic models and inference problems in Venture are specified via a Turing-complete, higher-order probabilistic language descended from Lisp. Unlike Church, Venture also provides a compositional language for custom inference strategies built out of scalable exact and approximate techniques. We also describe four key aspects of Venture's implementation that build on ideas from probabilistic graphical models. First, we describe the stochastic procedure interface (SPI) that specifies and encapsulates primitive random variables. The SPI supports custom control flow, higher-order probabilistic procedures, partially exchangeable sequences and ``likelihood-free'' stochastic simulators. It also supports external models that do inference over latent variables hidden from Venture. Second, we describe probabilistic execution traces (PETs), which represent execution histories of Venture programs. PETs capture conditional dependencies, existential dependencies and exchangeable coupling. Third, we describe partitions of execution histories called scaffolds that factor global inference problems into coherent sub-problems. Finally, we describe a family of stochastic regeneration algorithms for efficiently modifying PET fragments contained within scaffolds. Stochastic regeneration linear runtime scaling in cases where many previous approaches scaled quadratically. We show how to use stochastic regeneration and the SPI to implement general-purpose inference strategies such as Metropolis-Hastings, Gibbs sampling, and blocked proposals based on particle Markov chain Monte Carlo and mean-field variational inference techniques.

A formal framework is given for the characterizability of a class of belief revision operators, defined using minimization over a class of partial preorders, by postulates. It is shown that for partial orders characterizability implies a definability property of the class of partial orders in monadic second-order logic. Based on a non-definability result for a class of partial orders, an example is given of a non-characterizable class of revision operators. This appears to be the first non-characterizability result in belief revision.