We present a Bayesian nonparametric model for genetic sequence data in which a set of genetic sequences is modelled using a Markov model of partitions. The partitions at consecutive locations in the genome are related by their clusters first splitting and then merging. Our model can be thought of as a discrete time analogue of continuous time fragmentation-coagulation processes [Teh et al 2011], preserving the important properties of projectivity, exchangeability and reversibility, while being more scalable. We apply this model to the problem of genotype imputation, showing improved computational efficiency while maintaining the same accuracies as in [Teh et al 2011].

We develop a Bayesian nonparametric extension of the popular Plackett-Luce choice model that can handle an infinite number of choice items. Our framework is based on the theory of random atomic measures, with the prior specified by a gamma process. We derive a posterior characterization and a simple and effective Gibbs sampler for posterior simulation. We then develop a time-varying extension of our model, and apply our model to the New York Times lists of weekly bestselling books.

In this paper, we derive a novel algorithm to cluster hidden Markov models (HMMs) according to their probability distributions. We propose a variational hierarchical EM algorithm that i) clusters a given collection of HMMs into groups of HMMs that are similar, in terms of the distributions they represent, and ii) characterizes each group by a cluster center'', i.e., a novel HMM that is representative for the group. We illustrate the benefits of the proposed algorithm on hierarchical clustering of motion capture sequences as well as on automatic music tagging.

We describe how the pre-training algorithm for Deep Boltzmann Machines (DBMs) is related to the pre-training algorithm for Deep Belief Networks and we show that under certain conditions, the pre-training procedure improves the variational lower bound of a two-hidden-layer DBM. Based on this analysis, we develop a different method of pre-training DBMs that distributes the modelling work more evenly over the hidden layers. Our results on the MNIST and NORB datasets demonstrate that the new pre-training algorithm allows us to learn better generative models.

In this paper, we consider Bayesian reinforcement learning (BRL) where actions incur costs in addition to rewards, and thus exploration has to be constrained in terms of the expected total cost while learning to maximize the expected long-term total reward. In order to formalize cost-sensitive exploration, we use the constrained Markov decision process (CMDP) as the model of the environment, in which we can naturally encode exploration requirements using the cost function. We extend BEETLE, a model-based BRL method, for learning in the environment with cost constraints. We demonstrate the cost-sensitive exploration behaviour in a number of simulated problems.

How does the brain combine prior knowledge with sensory evidence when making decisions under uncertainty? Two competing descriptive models have been proposed based on experimental data. The first posits an additive offset to a decision variable, implying a static effect of the prior. However, this model is inconsistent with recent data from a motion discrimination task involving temporal integration of uncertain sensory evidence. To explain this data, a second model has been proposed which assumes a time-varying influence of the prior.

Active learning can substantially improve the yield of neurophysiology experiments by adaptively selecting stimuli to probe a neuron's receptive field (RF) in real time. Bayesian active learning methods maintain a posterior distribution over the RF, and select stimuli to maximally reduce posterior entropy on each time step. However, existing methods tend to rely on simple Gaussian priors, and do not exploit uncertainty at the level of hyperparameters when determining an optimal stimulus. This uncertainty can play a substantial role in RF characterization, particularly when RFs are smooth, sparse, or local in space and time. In this paper, we describe a novel framework for active learning under hierarchical, conditionally Gaussian priors.

This paper introduces timeline trees, which are partial models of partially observable environments. Timeline trees are given some specific predictions to make and learn a decision tree over history. The main idea of timeline trees is to use temporally abstract features to identify and split on features of key events, spread arbitrarily far apart in the past (whereas previous decision-tree-based methods have been limited to a finite suffix of history). Experiments demonstrate that timeline trees can learn to make high quality predictions in complex, partially observable environments with high-dimensional observations (e.g. an arcade game).

Bayesian model-based reinforcement learning is a formally elegant approach to learning optimal behaviour under model uncertainty, trading off exploration and exploitation in an ideal way. Unfortunately, finding the resulting Bayes-optimal policies is notoriously taxing, since the search space becomes enormous. In this paper we introduce a tractable, sample-based method for approximate Bayes-optimal planning which exploits Monte-Carlo tree search. Our approach outperformed prior Bayesian model-based RL algorithms by a significant margin on several well-known benchmark problems -- because it avoids expensive applications of Bayes rule within the search tree by lazily sampling models from the current beliefs. We illustrate the advantages of our approach by showing it working in an infinite state space domain which is qualitatively out of reach of almost all previous work in Bayesian exploration.

Partially-observable Markov decision processes (POMDPs) provide a powerful model for real-world sequential decision-making problems. In recent years, point- based value iteration methods have proven to be extremely effective techniques for finding (approximately) optimal dynamic programming solutions to POMDPs when an initial set of belief states is known. However, no point-based work has provided exact point-based backups for both continuous state and observation spaces, which we tackle in this paper. Our key insight is that while there may be an infinite number of possible observations, there are only a finite number of observation partitionings that are relevant for optimal decision-making when a finite, fixed set of reachable belief states is known. To this end, we make two important contributions: (1) we show how previous exact symbolic dynamic pro- gramming solutions for continuous state MDPs can be generalized to continu- ous state POMDPs with discrete observations, and (2) we show how this solution can be further extended via recently developed symbolic methods to continuous state and observations to derive the minimal relevant observation partitioning for potentially correlated, multivariate observation spaces.