As a model for an on-line classification setting we consider a stochastic process $(X_{-n},Y_{-n})_{n}$, the present time-point being denoted by 0, with observables $ \ldots,X_{-n},X_{-n+1},\ldots, X_{-1}, X_0$ from which the pattern $Y_0$ is to be inferred. So in this classification setting, in addition to the present observation $X_0$ a number $l$ of preceding observations may be used for classification, thus taking a possible dependence structure into account as it occurs e.g. in an ongoing classification of handwritten characters. We treat the question how the performance of classifiers is improved by using such additional information. For our analysis, a hidden Markov model is used. Letting $R_l$ denote the minimal risk of misclassification using $l$ preceding observations we show that the difference $\sup_k |R_l - R_{l+k}|$ decreases exponentially fast as $l$ increases. This suggests that a small $l$ might already lead to a noticeable improvement. To follow this point we look at the use of past observations for kernel classification rules. Our practical findings in simulated hidden Markov models and in the classification of handwritten characters indicate that using $l=1$, i.e. just the last preceding observation in addition to $X_0$, can lead to a substantial reduction of the risk of misclassification. So, in the presence of stochastic dependencies, we advocate to use $ X_{-1},X_0$ for finding the pattern $Y_0$ instead of only $X_0$ as one would in the independent situation.

A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function relationships in biology are quantitative, but only recently have experimental techniques for effectively measuring these relationships been developed. The advent of such "massively parallel" experiments presents an exciting opportunity for the concepts and methods of statistical physics to inform the study of biological systems. After reviewing these recent experimental advances, we focus on the problem of how to infer parametric models of sequence-function relationships from the data produced by these experiments. Specifically, we retrace and extend recent theoretical work showing that inference based on mutual information, not the standard likelihood-based approach, is often necessary for accurately learning the parameters of these models. Closely connected with this result is the emergence of "diffeomorphic modes" -- directions in parameter space that are far less constrained by data than likelihood-based inference would suggest. Analogous to Goldstone modes in physics, diffeomorphic modes arise from an arbitrarily broken symmetry of the inference problem. An analytically tractable model of a massively parallel experiment is then described, providing an explicit demonstration of these fundamental aspects of statistical inference. This paper concludes with an outlook on the theoretical and computational challenges currently facing studies of quantitative sequence-function relationships.

We propose a Conditional Density Filtering (C-DF) algorithm for efficient online Bayesian inference. C-DF adapts MCMC sampling to the online setting, sampling from approximations to conditional posterior distributions obtained by propagating surrogate conditional sufficient statistics (a function of data and parameter estimates) as new data arrive. These quantities eliminate the need to store or process the entire dataset simultaneously and offer a number of desirable features. Often, these include a reduction in memory requirements and runtime and improved mixing, along with state-of-the-art parameter inference and prediction. These improvements are demonstrated through several illustrative examples including an application to high dimensional compressed regression. Finally, we show that C-DF samples converge to the target posterior distribution asymptotically as sampling proceeds and more data arrives.

We consider the problem of group testing with sum observations and noiseless answers, in which we aim to locate multiple objects by querying the number of objects in each of a sequence of chosen sets. We study a probabilistic setting with entropy loss, in which we assume a joint Bayesian prior density on the locations of the objects and seek to choose the sets queried to minimize the expected entropy of the Bayesian posterior distribution after a fixed number of questions. We present a new non-adaptive policy, called the dyadic policy, show it is optimal among non-adaptive policies, and is within a factor of two of optimal among adaptive policies. This policy is quick to compute, its nonadaptive nature makes it easy to parallelize, and our bounds show it performs well even when compared with adaptive policies. We also study an adaptive greedy policy, which maximizes the one-step expected reduction in entropy, and show that it performs at least as well as the dyadic policy, offering greater query efficiency but reduced parallelism. Numerical experiments demonstrate that both procedures outperform a divide-and-conquer benchmark policy from the literature, called sequential bifurcation, and show how these procedures may be applied in a stylized computer vision problem.

In this paper, several modifications are introduced to the functional approximation method iterLap to reduce the approximation error, including stopping rule adjustment, proposal of new residual function, starting point selection for numerical optimisation, scaling of Hessian matrix. Illustrative examples are also provided to show the trade-off between running time and accuracy of the original and modified methods.

The scarcity of data annotated at the desired level of granularity is a recurring issue in many applications. Significant amounts of effort have been devoted to developing weakly supervised methods tailored to each individual setting, which are often carefully designed to take advantage of the particular properties of weak supervision regimes, form of available data and prior knowledge of the task at hand. Unfortunately, it is difficult to adapt these methods to new tasks and/or forms of data, which often require different weak supervision regimes or models. We present a general-purpose method that can solve any weakly supervised learning problem irrespective of the weak supervision regime or the model. The proposed method turns any off-the-shelf strongly supervised classifier into a weakly supervised classifier and allows the user to specify any arbitrary weakly supervision regime via a loss function. We apply the method to several different weak supervision regimes and demonstrate competitive results compared to methods specifically engineered for those settings.

We develop methods for parameter estimation in settings with large-scale data sets, where traditional methods are no longer tenable. Our methods rely on stochastic approximations, which are computationally efficient as they maintain one iterate as a parameter estimate, and successively update that iterate based on a single data point. When the update is based on a noisy gradient, the stochastic approximation is known as standard stochastic gradient descent, which has been fundamental in modern applications with large data sets. Additionally, our methods are numerically stable because they employ implicit updates of the iterates. Intuitively, an implicit update is a shrinked version of a standard one, where the shrinkage factor depends on the observed Fisher information at the corresponding data point. This shrinkage prevents numerical divergence of the iterates, which can be caused either by excess noise or outliers. Our sgd package in R offers the most extensive and robust implementation of stochastic gradient descent methods. We demonstrate that sgd dominates alternative software in runtime for several estimation problems with massive data sets. Our applications include the wide class of generalized linear models as well as M-estimation for robust regression.

In this paper, we look to address the problem of estimating the dynamic direction of arrival (DOA) of a narrowband signal impinging on a sensor array from the far field. The initial estimate is made using a Bayesian compressive sensing (BCS) framework and then tracked using a Bayesian compressed sensing Kalman filter (BCSKF). The BCS framework splits the angular region into N potential DOAs and enforces a belief that only a few of the DOAs will have a non-zero valued signal present. A BCSKF can then be used to track the change in the DOA using the same framework. There can be an issue when the DOA approaches the endfire of the array. In this angular region current methods can struggle to accurately estimate and track changes in the DOAs. To tackle this problem, we propose changing the traditional sparse belief associated with BCS to a belief that the estimated signals will match the predicted signals given a known DOA change. This is done by modelling the difference between the expected sparse received signals and the estimated sparse received signals as a Gaussian distribution. Example test scenarios are provided and comparisons made with the traditional BCS based estimation method. They show that an improvement in estimation accuracy is possible without a significant increase in computational complexity.

Applying standard Markov chain Monte Carlo (MCMC) algorithms to large data sets is computationally infeasible. The recently proposed stochastic gradient Langevin dynamics (SGLD) method circumvents this problem in three ways: it generates proposed moves using only a subset of the data, it skips the Metropolis-Hastings accept-reject step, and it uses sequences of decreasing step sizes. In \cite{TehThierryVollmerSGLD2014}, we provided the mathematical foundations for the decreasing step size SGLD, including consistency and a central limit theorem. However, in practice the SGLD is run for a relatively small number of iterations, and its step size is not decreased to zero. The present article investigates the behaviour of the SGLD with fixed step size. In particular we characterise the asymptotic bias explicitly, along with its dependence on the step size and the variance of the stochastic gradient. On that basis a modified SGLD which removes the asymptotic bias due to the variance of the stochastic gradients up to first order in the step size is derived. Moreover, we are able to obtain bounds on the finite-time bias, variance and mean squared error (MSE). The theory is illustrated with a Gaussian toy model for which the bias and the MSE for the estimation of moments can be obtained explicitly. For this toy model we study the gain of the SGLD over the standard Euler method in the limit of large data sets.

This paper addresses the problem of neighborhood selection for Gaussian graphical models. We present two heuristic algorithms: a forward-backward greedy algorithm for general Gaussian graphical models based on mutual information test, and a threshold-based algorithm for walk summable Gaussian graphical models. Both algorithms are shown to be structurally consistent, and efficient. Numerical results show that both algorithms work very well.