A general modeling framework is proposed that unifies nonparametric-Bayesian models, topic-models and Bayesian networks. This class of infinite state Bayes nets (ISBN) can be viewed as directed networks of'hierarchical Dirichlet processes' (HDPs) where the domain of the variables can be structured (e.g.

We introduce a hierarchical Bayesian model for the discovery of putative regulators from gene expression data only. The hierarchy incorporates the knowledge that there are just a few regulators that by themselves only regulate a handful of genes. This is implemented through a so-called spike-and-slab prior, a mixture of Gaussians with different widths, with mixing weights from a hierarchical Bernoulli model. For efficient inference we implemented expectation propagation. Running the model on a malaria parasite data set, we found four genes with significant homology to transcription factors in an amoebe, one RNA regulator and three genes of unknown function (out of the top ten genes considered).

In many structured prediction problems, the highest-scoring labeling is hard to compute exactly, leading to the use of approximate inference methods. However, when inference is used in a learning algorithm, a good approximation of the score may not be sufficient. We show in particular that learning can fail even with an approximate inference method with rigorous approximation guarantees. There are two reasons for this. First, approximate methods can effectively reduce the expressivity ofan underlying model by making it impossible to choose parameters that reliably give good predictions. Second, approximations can respond to parameter changes in such a way that standard learning algorithms are misled. In contrast, we give two positive results in the form of learning bounds for the use of LPrelaxed inference in structured perceptron and empirical risk minimization settings. We argue that without understanding combinations of inference and learning, such as these, that are appropriately compatible, learning performance under approximate inference cannot be guaranteed.

We introduce a new Bayesian model for hierarchical clustering based on a prior over trees called Kingman's coalescent. We develop novel greedy and sequential Monte Carlo inferences which operate in a bottom-up agglomerative fashion. We show experimentally the superiority of our algorithms over the state-of-the-art, and demonstrate our approach in document clustering and phylolinguistics.

Dynamic Bayesian networks are structured representations of stochastic processes. Despitetheir structure, exact inference in DBNs is generally intractable. One approach to approximate inference involves grouping the variables in the process into smaller factors and keeping independent beliefs over these factors. In this paper we present several techniques for decomposing a dynamic Bayesian network automatically to enable factored inference. We examine a number of features ofa DBN that capture different types of dependencies that will cause error in factored inference. An empirical comparison shows that the most useful of these is a heuristic that estimates the mutual information introduced between factors by one step of belief propagation.

Motivated by stochastic systems in which observed evidence and conditional dependencies betweenstates of the network change over time, and certain quantities of interest (marginal distributions, likelihood estimates etc.) must be updated, we study the problem of adaptive inference in tree-structured Bayesian networks. We describe an algorithm for adaptive inference that handles a broad range of changes to the network and is able to maintain marginal distributions, MAP estimates, and data likelihoods in all expected logarithmic time. We give an implementation of our algorithm and provide experiments that show that the algorithm can yield up to two orders of magnitude speedups on answering queries and responding to dynamic changesover the sum-product algorithm.

We present an efficient generalization of the sparse pseudo-input Gaussian process (SPGP)model developed by Snelson and Ghahramani [1], applying it to binary classification problems.

In transfer learning we aim to solve new problems using fewer examples using information gained from solving related problems. Transfer learning has been successful in practice, and extensive PAC analysis of these methods has been developed. Howeverit is not yet clear how to define relatedness between tasks. This is considered as a major problem as it is conceptually troubling and it makes it unclear how much information to transfer and when and how to transfer it. In this paper we propose to measure the amount of information one task contains about another using conditional Kolmogorov complexity between the tasks. We show how existing theory neatly solves the problem of measuring relatedness and transferring the'right' amount of information in sequential transfer learning in a Bayesian setting. The theory also suggests that, in a very formal and precise sense, no other reasonable transfer method can do much better than our Kolmogorov Complexity theoretic transfer method, and that sequential transfer is always justified. Wealso develop a practical approximation to the method and use it to transfer information between 8 arbitrarily chosen databases from the UCI ML repository.

We describe a novel noisy-logical distribution for representing the distribution of a binary output variable conditioned on multiple binary input variables. The distribution is represented in terms of noisy-or's and noisy-and-not's of causal features which are conjunctions of the binary inputs. The standard noisy-or and noisy-and-not models, used in causal reasoning and artificial intelligence, are special cases of the noisy-logical distribution. We prove that the noisy-logical distribution is complete in the sense that it can represent all conditional distributions provided a sufficient number of causal factors are used. We illustrate the noisy-logical distribution by showing that it can account for new experimental findings on how humans perform causal reasoning in more complex contexts. Finally, we speculate on the use of the noisy-logical distribution for causal reasoning and artificial intelligence.

Unsupervised learning algorithms aim to discover the structure hidden in the data, and to learn representations that are more suitable as input to a supervised machine than the raw input. Many unsupervised methods are based on reconstructing the input from the representation, while constraining the representation to have certain desirable properties (e.g. low dimension, sparsity, etc). Others are based on approximating density by stochastically reconstructing the input from the representation. We describe a novel and efficient algorithm to learn sparse representations, and compare it theoretically and experimentally with a similar machines trained probabilistically, namely a Restricted Boltzmann Machine. We propose a simple criterion to compare and select different unsupervised machines based on the trade-off between the reconstruction error and the information content of the representation. We demonstrate this method by extracting features from a dataset of handwritten numerals, and from a dataset of natural image patches. We show that by stacking multiple levels of such machines and by training sequentially, high-order dependencies between the input variables can be captured.