This paper introduces the first set of PAC-Bayesian bounds for the batch reinforcement learning problem in finite state spaces. These bounds hold regardless of the correctness of the prior distribution. We demonstrate how such bounds can be used for model-selection in control problems where prior information is available either on the dynamics of the environment, or on the value of actions. Our empirical results confirm that PAC-Bayesian model-selection is able to leverage prior distributions when they are informative and, unlike standard Bayesian RL approaches, ignores them when they are misleading.

Score Matching is a recently-proposed criterion for training high-dimensional density models for which maximum likelihood training is intractable. It has been applied to learning natural image statistics but has so-far been limited to simple models due to the difficulty of differentiating the loss with respect to the model parameters. We show how this differentiation can be automated with an extended version of the double-backpropagation algorithm. In addition, we introduce a regularization term for the Score Matching loss that enables its use for a broader range of problem by suppressing instabilities that occur with finite training sample sizes and quantized input values. Results are reported for image denoising and super-resolution.

When software developers modify one or more files in a large code base, they must also identify and update other related files. Many file dependencies can be detected by mining the development history of the code base: in essence, groups of related files are revealed by the logs of previous workflows. From data of this form, we show how to detect dependent files by solving a problem in binary matrix completion. We explore different latent variable models (LVMs) for this problem, including Bernoulli mixture models, exponential family PCA, restricted Boltzmann machines, and fully Bayesian approaches. We evaluate these models on the development histories of three large, open-source software systems: Mozilla Firefox, Eclipse Subversive, and Gimp. In all of these applications, we find that LVMs improve the performance of related file prediction over current leading methods.

Gaussian graphical models with sparsity in the inverse covariance matrix are of significant interest in many modern applications. For the problem of recovering the graphical structure, information criteria provide useful optimization objectives for algorithms searching through sets of graphs or for selection of tuning parameters of other methods such as the graphical lasso, which is a likelihood penalization technique. In this paper we establish the asymptotic consistency of an extended Bayesian information criterion for Gaussian graphical models in a scenario where both the number of variables p and the sample size n grow. Compared to earlier work on the regression case, our treatment allows for growth in the number of non-zero parameters in the true model, which is necessary in order to cover connected graphs. We demonstrate the performance of this criterion on simulated data when used in conjuction with the graphical lasso, and verify that the criterion indeed performs better than either cross-validation or the ordinary Bayesian information criterion when p and the number of non-zero parameters q both scale with n.

Many time-series such as human movement data consist of a sequence of basic actions, e.g., forehands and backhands in tennis. Automatically extracting and characterizing such actions is an important problem for a variety of different applications. In this paper, we present a probabilistic segmentation approach in which an observed time-series is modeled as a concatenation of segments corresponding to different basic actions. Each segment is generated through a noisy transformation of one of a few hidden trajectories representing different types of movement, with possible time re-scaling. We analyze three different approximation methods for dealing with model intractability, and demonstrate how the proposed approach can successfully segment table tennis movements recorded using a robot arm as haptic input device.

Since the discovery of sophisticated fully polynomial randomized algorithms for a range of #P problems (Karzanov et al., 1991; Jerrum et al., 2001; Wilson, 2004), theoretical work on approximate inference in combinatorial spaces has focused on Markov chain Monte Carlo methods. Despite their strong theoretical guarantees, the slow running time of many of these randomized algorithms and the restrictive assumptions on the potentials have hindered the applicability of these algorithms to machine learning. Because of this, in applications to combinatorial spaces simple exact models are often preferred to more complex models that require approximate inference (Siepel et al., 2004). Variational inference would appear to provide an appealing alternative, given the success of variational methods for graphical models (Wainwright et al., 2008); unfortunately, however, it is not obvious how to develop variational approximations for combinatorial objects such as matchings, partial orders, plane partitions and sequence alignments. We propose a new framework that extends variational inference to a wide range of combinatorial spaces. Our method is based on a simple assumption: the existence of a tractable measure factorization, which we show holds in many examples. Simulations on a range of matching models show that the algorithm is more general and empirically faster than a popular fully polynomial randomized algorithm. We also apply the framework to the problem of multiple alignment of protein sequences, obtaining state-of-the-art results on the BAliBASE dataset (Thompson et al., 1999).

This paper is concerned with rank aggregation, which aims to combine multiple input rankings to get a better ranking. A popular approach to rank aggregation is based on probabilistic models on permutations, e.g., the Luce model and the Mallows model. However, these models have their limitations in either poor expressiveness or high computational complexity. To avoid these limitations, in this paper, we propose a new model, which is defined with a coset-permutation distance, and models the generation of a permutation as a stagewise process. We refer to the new model as coset-permutation distance based stagewise (CPS) model. The CPS model has rich expressiveness and can therefore be used in versatile applications, because many different permutation distances can be used to induce the coset-permutation distance. The complexity of the CPS model is low because of the stagewise decomposition of the permutation probability and the efficient computation of most coset-permutation distances. We apply the CPS model to supervised rank aggregation, derive the learning and inference algorithms, and empirically study their effectiveness and efficiency. Experiments on public datasets show that the derived algorithms based on the CPS model can achieve state-of-the-art ranking accuracy, and are much more efficient than previous algorithms.

To understand the relationship between genomic variations among population and complex diseases, it is essential to detect eQTLs which are associated with phenotypic effects.However, detecting eQTLs remains a challenge due to complex underlying mechanisms and the very large number of genetic loci involved compared tothe number of samples. Thus, to address the problem, it is desirable to take advantage of the structure of the data and prior information about genomic locations such as conservation scores and transcription factor binding sites. In this paper, we propose a novel regularized regression approach for detecting eQTLs which takes into account related traits simultaneously while incorporating many regulatory features. We first present a Bayesian network for a multi-task learning problem that includes priors on SNPs, making it possible to estimate the significance of each covariate adaptively. Then we find the maximum a posteriori (MAP) estimation of regression coefficients and estimate weights of covariates jointly. This optimization procedure is efficient since it can be achieved by using aprojected gradient descent and a coordinate descent procedure iteratively. Experimental results on simulated and real yeast datasets confirm that our model outperforms previous methods for finding eQTLs.

We present a simple and effective approach to learning tractable conditional random fieldswith structure that depends on the evidence. Our approach retains the advantages of tractable discriminative models, namely efficient exact inference and arbitrarily accurate parameter learning in polynomial time. At the same time, our algorithm does not suffer a large expressive power penalty inherent to fixed tractable structures. On real-life relational datasets, our approach matches or exceeds stateof the art accuracy of the dense models, and at the same time provides an order of magnitude speedup.

We define a copula process which describes the dependencies between arbitrarily many random variables independently of their marginal distributions. As an example, we develop a stochastic volatility model, Gaussian Copula Process Volatility (GCPV), to predict the latent standard deviations of a sequence of random variables. To make predictions we use Bayesian inference, with the Laplace approximation, and with Markov chain Monte Carlo as an alternative. We find our model can outperform GARCH on simulated and financial data. And unlike GARCH, GCPV can easily handle missing data, incorporate covariates other than time, and model a rich class of covariance structures.