Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop novel therapeutic agents as well as to understand the molecular mechanisms of various types of cancers better. Tri-matrix factorization is an efficient tool to learn associations between two different entities (e.g., cancer types and pathways in our case) from data. To successfully apply tri-matrix factorization methods to biomedical problems, biological prior knowledge such as pathway databases or protein-protein interaction (PPI) networks, should be taken into account in the factorization model. However, it is not straightforward in the Bayesian setting even though Bayesian methods are more appealing than point estimate methods, such as a maximum likelihood or a maximum posterior method, in the sense that they calculate distributions over variables and are robust against overfitting. We propose a Bayesian (semi-)nonnegative matrix factorization model for human cancer genomic data, where the biological prior knowledge represented by a pathway database and a PPI network is taken into account in the factorization model through a finite dependent Beta-Bernoulli prior. We tested our method on The Cancer Genome Atlas (TCGA) dataset and found that the pathways identified by our method can be used as a prognostic biomarkers for patient subgroup identification.

Within a supervised classification framework, labeled data are used to learn classifier parameters. Prior to that, it is generally required to perform dimensionality reduction via feature extraction. These preprocessing steps have motivated numerous research works aiming at recovering latent variables in an unsupervised context. This paper proposes a unified framework to perform classification and low-level modeling jointly. The main objective is to use the estimated latent variables as features for classification and to incorporate simultaneously supervised information to help latent variable extraction. The proposed hierarchical Bayesian model is divided into three stages: a first low-level modeling stage to estimate latent variables, a second stage clustering these features into statistically homogeneous groups and a last classification stage exploiting the (possibly badly) labeled data. Performance of the model is assessed in the specific context of hyperspectral image interpretation, unifying two standard analysis techniques, namely unmixing and classification. Keywords: Bayesian model, supervised learning, image interpretation, Markov Random Field 1. Introduction In the context of image interpretation, numerous methods have been developed to extract meaningful information.

Estimating the joint probability mass function (PMF) of a set of random variables lies at the heart of statistical learning and signal processing. Without structural assumptions, such as modeling the variables as a Markov chain, tree, or other graphical model, joint PMF estimation is often considered mission impossible - the number of unknowns grows exponentially with the number of variables. But who gives us the structural model? Is there a generic, 'non-parametric' way to control joint PMF complexity without relying on a priori structural assumptions regarding the underlying probability model? Is it possible to discover the operational structure without biasing the analysis up front? What if we only observe random subsets of the variables, can we still reliably estimate the joint PMF of all? This paper shows, perhaps surprisingly, that if the joint PMF of any three variables can be estimated, then the joint PMF of all the variables can be provably recovered under relatively mild conditions. The result is reminiscent of Kolmogorov's extension theorem - consistent specification of lower-order distributions induces a unique probability measure for the entire process. The difference is that for processes of limited complexity (rank of the high-order PMF) it is possible to obtain complete characterization from only third-order distributions. In fact not all third order PMFs are needed; and under more stringent conditions even second-order will do. Exploiting multilinear (tensor) algebra, this paper proves that such higher-order PMF completion can be guaranteed - several pertinent identifiability results are derived. It also provides a practical and efficient algorithm to carry out the recovery task. Judiciously designed simulations and real-data experiments on movie recommendation and data classification are presented to showcase the effectiveness of the approach.

In this work, we address the problem of solving a series of underdetermined linear inverse problemblems subject to a sparsity constraint. We generalize the spike-and-slab prior distribution to encode a priori correlation of the support of the solution in both space and time by imposing a transformed Gaussian process on the spike-and-slab probabilities. An expectation propagation (EP) algorithm for posterior inference under the proposed model is derived. For large scale problems, the standard EP algorithm can be prohibitively slow. We therefore introduce three different approximation schemes to reduce the computational complexity. Finally, we demonstrate the proposed model using numerical experiments based on both synthetic and real data sets.

In statistical dialogue management, the dialogue manager learns a policy that maps a belief state to an action for the system to perform. Efficient exploration is key to successful policy optimisation. Current deep reinforcement learning methods are very promising but rely on epsilon-greedy exploration, thus subjecting the user to a random choice of action during learning. Alternative approaches such as Gaussian Process SARSA (GPSARSA) estimate uncertainties and are sample efficient, leading to better user experience, but on the expense of a greater computational complexity. This paper examines approaches to extract uncertainty estimates from deep Q-networks (DQN) in the context of dialogue management. We perform an extensive benchmark of deep Bayesian methods to extract uncertainty estimates, namely Bayes-By-Backprop, dropout, its concrete variation, bootstrapped ensemble and alpha-divergences, combining it with DQN algorithm.

Markov Chain Monte Carlo (MCMC) methods such as Gibbs sampling are finding widespread use in applied statistics and machine learning. These often lead to difficult computational problems, which are increasingly being solved on parallel and distributed systems such as compute clusters. Recent work has proposed running iterative algorithms such as gradient descent and MCMC in parallel asynchronously for increased performance, with good empirical results in certain problems. Unfortunately, for MCMC this parallelization technique requires new convergence theory, as it has been explicitly demonstrated to lead to divergence on some examples. Recent theory on Asynchronous Gibbs sampling describes why these algorithms can fail, and provides a way to alter them to make them converge. In this article, we describe how to apply this theory in a generic setting, to understand the asynchronous behavior of any MCMC algorithm, including those implemented using parameter servers, and those not based on Gibbs sampling.

The presence of noisy instances in mobile phone data is a fundamental issue for classifying user phone call behavior (i.e., accept, reject, missed and outgoing), with many potential negative consequences. The classification accuracy may decrease and the complexity of the classifiers may increase due to the number of redundant training samples. To detect such noisy instances from a training dataset, researchers use naive Bayes classifier (NBC) as it identifies misclassified instances by taking into account independence assumption and conditional probabilities of the attributes. However, some of these misclassified instances might indicate usages behavioral patterns of individual mobile phone users. Existing naive Bayes classifier based noise detection techniques have not considered this issue and, thus, are lacking in classification accuracy. In this paper, we propose an improved noise detection technique based on naive Bayes classifier for effectively classifying users' phone call behaviors. In order to improve the classification accuracy, we effectively identify noisy instances from the training dataset by analyzing the behavioral patterns of individuals. We dynamically determine a noise threshold according to individual's unique behavioral patterns by using both the naive Bayes classifier and Laplace estimator. We use this noise threshold to identify noisy instances. To measure the effectiveness of our technique in classifying user phone call behavior, we employ the most popular classification algorithm (e.g., decision tree). Experimental results on the real phone call log dataset show that our proposed technique more accurately identifies the noisy instances from the training datasets that leads to better classification accuracy.

This paper develops a novel methodology for using symbolic knowledge in deep learning. From first principles, we derive a semantic loss function that bridges between neural output vectors and logical constraints. This loss function captures how close the neural network is to satisfying the constraints on its output. An experimental evaluation shows that our semantic loss function effectively guides the learner to achieve (near-)state-of-the-art results on semi-supervised multi-class classification. Moreover, it significantly increases the ability of the neural network to predict structured objects, such as rankings and paths. These discrete concepts are tremendously difficult to learn, and benefit from a tight integration of deep learning and symbolic reasoning methods.

We propose stochastic, non-parametric activation functions that are fully learnable and individual to each neuron. Complexity and the risk of overfitting are controlled by placing a Gaussian process prior over these functions. The result is the Gaussian process neuron, a probabilistic unit that can be used as the basic building block for probabilistic graphical models that resemble the structure of neural networks. The proposed model can intrinsically handle uncertainties in its inputs and self-estimate the confidence of its predictions. Using variational Bayesian inference and the central limit theorem, a fully deterministic loss function is derived, allowing it to be trained as efficiently as a conventional neural network using mini-batch gradient descent. The posterior distribution of activation functions is inferred from the training data alongside the weights of the network. The proposed model favorably compares to deep Gaussian processes, both in model complexity and efficiency of inference. It can be directly applied to recurrent or convolutional network structures, allowing its use in audio and image processing tasks. As an preliminary empirical evaluation we present experiments on regression and classification tasks, in which our model achieves performance comparable to or better than a Dropout regularized neural network with a fixed activation function. Experiments are ongoing and results will be added as they become available.

Variational inference is a general approach for approximating complex density functions, such as those arising in latent variable models, popular in machine learning. It has been applied to approximate the maximum likelihood estimator and to carry out Bayesian inference, however, quantification of uncertainty with variational inference remains challenging from both theoretical and practical perspectives. This paper is concerned with developing uncertainty measures for variational inference by using bootstrap procedures. We first develop two general bootstrap approaches for assessing the uncertainty of a variational estimate and the study the underlying bootstrap theory in both fixed- and increasing-dimension settings. We then use the bootstrap approach and our theoretical results in the context of mixed membership modeling with multivariate binary data on functional disability from the National Long Term Care Survey. We carry out a two-sample approach to test for changes in the repeated measures of functional disability for the subset of individuals present in 1984 and 1994 waves.