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.

Bayesian model averaging, model selection and their approximations such as BIC are generally statistically consistent, but sometimes achieve slower rates of con- vergence than other methods such as AIC and leave-one-out cross-validation. On the other hand, these other methods can be inconsistent. We identify the catch-up phenomenon as a novel explanation for the slow convergence of Bayesian meth- ods. Based on this analysis we define the switch-distribution, a modification of the Bayesian model averaging distribution. We prove that in many situations model selection and prediction based on the switch-distribution is both consistent and achieves optimal convergence rates, thereby resolving the AIC-BIC dilemma. The method is practical; we give an efficient algorithm.

Learning in real-world domains often requires to deal with continuous state and action spaces. Although many solutions have been proposed to apply Reinforce- ment Learning algorithms to continuous state problems, the same techniques can be hardly extended to continuous action spaces, where, besides the computation of a good approximation of the value function, a fast method for the identification of the highest-valued action is needed. In this paper, we propose a novel actor-critic approach in which the policy of the actor is estimated through sequential Monte Carlo methods. The importance sampling step is performed on the basis of the values learned by the critic, while the resampling step modifies the actor's policy. The proposed approach has been empirically compared to other learning algo- rithms into several domains; in this paper, we report results obtained in a control problem consisting of steering a boat across a river.

We propose an extended probabilistic model for human perception. We argue that in many circumstances, human observers simultaneously evaluate sensory evidence under different hypotheses regarding the underlying physical process that might have generated the sensory information. Within this context, inference can be optimal if the observer weighs each hypothesis according to the correct belief in that hypothesis. But if the observer commits to a particular hypothesis, the belief in that hypothesis is converted into subjective certainty, and subsequent perceptual behavior is suboptimal, conditioned only on the chosen hypothesis. We demonstrate that this framework can explain psychophysical data of a recently reported decision-estimation experiment. The model well accounts for the data, predicting the same estimation bias as a consequence of the preceding decision step.

We present a new family of linear time algorithms based on sufficient statistics for string comparison with mismatches under the string kernels framework. Our algorithms improve theoretical complexity bounds of existing approaches while scaling well with respect to the sequence alphabet size, the number of allowed mismatches and the size of the dataset. In particular, on large alphabets with loose mismatch constraints our algorithms are several orders of magnitude faster than the existing algorithms for string comparison under the mismatch similarity measure. We evaluate our algorithms on synthetic data and real applications in music genre classification, protein remote homology detection and protein fold prediction. The scalability of the algorithms allows us to consider complex sequence transformations, modeled using longer string features and larger numbers of mismatches, leading to a state-of-the-art performance with significantly reduced running times.

Research in animal learning and behavioral neuroscience has distinguished between two forms of action control: a habit-based form, which relies on stored action values, and a goal-directed form, which forecasts and compares action outcomes based on a model of the environment. While habit-based control has been the subject of extensive computational research, the computational principles underlying goal-directed control in animals have so far received less attention. In the present paper, we advance a computational framework for goal-directed control in animals and humans. We take three empirically motivated points as founding premises: (1) Neurons in dorsolateral prefrontal cortex represent action policies, (2) Neurons in orbitofrontal cortex represent rewards, and (3) Neural computation, across domains, can be appropriately understood as performing structured probabilistic inference. On a purely computational level, the resulting account relates closely to previous work using Bayesian inference to solve Markov decision problems, but extends this work by introducing a new algorithm, which provably converges on optimal plans.

We show how improved sequences for magnetic resonance imaging can be found through automated optimization of Bayesian design scores. Combining recent advances in approximate Bayesian inference and natural image statistics with high-performance numerical computation, we propose the first scalable Bayesian experimental design framework for this problem of high relevance to clinical and brain research. Our solution requires approximate inference for dense, non-Gaussian models on a scale seldom addressed before. We propose a novel scalable variational inference algorithm, and show how powerful methods of numerical mathematics can be modified to compute primitives in our framework. Our approach is evaluated on a realistic setup with raw data from a 3T MR scanner.

We present a novel method for inducing synchronous context free grammars (SCFGs) from a corpus of parallel string pairs. SCFGs can model equivalence between strings in terms of substitutions, insertions and deletions, and the reordering of sub-strings. We develop a non-parametric Bayesian model and apply it to a machine translation task, using priors to replace the various heuristics commonly used in this field. Using a variational Bayes training procedure, we learn the latent structure of translation equivalence through the induction of synchronous grammar categories for phrasal translations, showing improvements in translation performance over previously proposed maximum likelihood models.

Many interesting problems, including Bayesian network structure-search, can be cast in terms of finding the optimum value of a function over the space of graphs. However, this function is often expensive to compute exactly. We here present a method derived from the study of reproducing-kernel Hilbert spaces which takes advantage of the regular structure of the space of all graphs on a fixed number of nodes to obtain approximations to the desired function quickly and with reasonable accuracy. We then test this method on both a small testing set and a real-world Bayesian network; the results suggest that not only is this method reasonably accurate, but that the BDe score itself varies quadratically over the space of all graphs.

Many nonlinear dynamical phenomena can be effectively modeled by a system that switches among a set of conditionally linear dynamical modes. We consider two such models: the switching linear dynamical system (SLDS) and the switching vector autoregressive (VAR) process. In this paper, we present a nonparametric approach to the learning of an unknown number of persistent, smooth dynamical modes by utilizing a hierarchical Dirichlet process prior. We develop a sampling algorithm that combines a truncated approximation to the Dirichlet process with an efficient joint sampling of the mode and state sequences. The utility and flexibility of our model are demonstrated on synthetic data, sequences of dancing honey bees, and the IBOVESPA stock index.