We present a novel mathematical formalism for the idea of a local model,'' a model of a potentially complex dynamical system that makes only certain predictions in only certain situations. As a result of its restricted responsibilities, a local model may be far simpler than a complete model of the system. We then show how one might combine several local models to produce a more detailed model. We demonstrate our ability to learn a collection of local models on a large-scale example and do a preliminary empirical comparison of learning a collection of local models and some other model learning methods."

We introduces a new probability distribution over a potentially infinite number of binary Markov chains which we call the Markov Indian buffet process. This process extends the IBP to allow temporal dependencies in the hidden variables. We use this stochastic process to build a nonparametric extension of the factorial hidden Markov model. After working out an inference scheme which combines slice sampling and dynamic programming we demonstrate how the infinite factorial hidden Markov model can be used for blind source separation.

We present a mixture model whose components are Restricted Boltzmann Machines (RBMs). This possibility has not been considered before because computing the partition function of an RBM is intractable, which appears to make learning a mixture of RBMs intractable as well. Surprisingly, when formulated as a third-order Boltzmann machine, such a mixture model can be learned tractably using contrastive divergence. The energy function of the model captures three-way interactions among visible units, hidden units, and a single hidden multinomial unit that represents the cluster labels. The distinguishing feature of this model is that, unlike other mixture models, the mixing proportions are not explicitly parameterized. Instead, they are defined implicitly via the energy function and depend on all the parameters in the model. We present results for the MNIST and NORB datasets showing that the implicit mixture of RBMs learns clusters that reflect the class structure in the data.

This paper considers a sensitivity analysis in Hidden Markov Models with continuous state and observation spaces. We propose an Infinitesimal Perturbation Analysis (IPA) on the filtering distribution with respect to some parameters of the model. We describe a methodology for using any algorithm that estimates the filtering density, such as Sequential Monte Carlo methods, to design an algorithm that estimates its gradient. The resulting IPA estimator is proven to be asymptotically unbiased, consistent and has computational complexity linear in the number of particles. We consider an application of this analysis to the problem of identifying unknown parameters of the model given a sequence of observations. We derive an IPA estimator for the gradient of the log-likelihood, which may be used in a gradient method for the purpose of likelihood maximization. We illustrate the method with several numerical experiments.

Metal binding is important for the structural and functional characterization of proteins. Previous prediction efforts have only focused on bonding state, i.e. deciding which protein residues act as metal ligands in some binding site. Identifying the geometry of metal-binding sites, i.e. deciding which residues are jointly involved in the coordination of a metal ion is a new prediction problem that has been never attempted before from protein sequence alone. In this paper, we formulate it in the framework of learning with structured outputs. Our solution relies on the fact that, from a graph theoretical perspective, metal binding has the algebraic properties of a matroid, enabling the application of greedy algorithms for learning structured outputs. On a data set of 199 non-redundant metalloproteins, we obtained precision/recall levels of 75\%/46\% correct ligand-ion assignments, which improves to 88\%/88\% in the setting where the metal binding state is known.

The Partially Observable Markov Decision Process (POMDP) framework has proven useful in planning domains that require balancing actions that increase an agents knowledge and actions that increase an agents reward. Unfortunately, most POMDPs are complex structures with a large number of parameters. In many realworld problems, both the structure and the parameters are difficult to specify from domain knowledge alone. Recent work in Bayesian reinforcement learning has made headway in learning POMDP models; however, this work has largely focused on learning the parameters of the POMDP model. We define an infinite POMDP (iPOMDP) model that does not require knowledge of the size of the state space; instead, it assumes that the number of visited states will grow as the agent explores its world and explicitly models only visited states. We demonstrate the iPOMDP utility on several standard problems.

We consider the problem of estimating the graph structure associated with a Gaussian Markov random field (GMRF) from i.i.d.

For undiscounted reinforcement learning in Markov decision processes (MDPs) we consider the total regret of a learning algorithm with respect to an optimal policy. In order to describe the transition structure of an MDP we propose a new parameter: An MDP has diameter D if for any pair of states s1,s2 there is a policy which moves from s1 to s2 in at most D steps (on average). We present a reinforcement learning algorithm with total regret O(DSAT) after T steps for any unknown MDP with S states, A actions per state, and diameter D. This bound holds with high probability. We also present a corresponding lower bound of Omega(DSAT) on the total regret of any learning algorithm. Both bounds demonstrate the utility of the diameter as structural parameter of the MDP.

We describe a new algorithmic framework for inference in probabilistic models, and apply it to inference for latent Dirichlet allocation. Our framework adopts the methodology of variational inference, but unlike existing variational methods such as mean field and expectation propagation it is not restricted to tractable classes of approximating distributions. Our approach can also be viewed as a sequential Monte Carlo (SMC) method, but unlike existing SMC methods there is no need to design the artificial sequence of distributions. Notably, our framework offers a principled means to exchange the variance of an importance sampling estimate for the bias incurred through variational approximation. Experiments on a challenging inference problem in population genetics demonstrate improvements in stability and accuracy over existing methods, and at a comparable cost.

Our setting is a Partially Observable Markov Decision Process with continuous state, observation and action spaces. Decisions are based on a Particle Filter for estimating the belief state given past observations. We consider a policy gradient approach for parameterized policy optimization. For that purpose, we investigate sensitivity analysis of the performance measure with respect to the parameters of the policy, focusing on Finite Difference (FD) techniques. We show that the naive FD is subject to variance explosion because of the non-smoothness of the resampling procedure. We propose a more sophisticated FD method which overcomes this problem and establish its consistency.