We describe a class of algorithms for amortized inference in Bayesian networks. In this setting, we invest computation upfront to support rapid online inference for a wide range of queries. Our approach is based on learning an inverse factorization of a model's joint distribution: a factorization that turns observations into root nodes. Our algorithms accumulate information to estimate the local conditional distributions that constitute such a factorization. These stochastic inverses can be used to invert each of the computation steps leading to an observation, sampling backwards in order to quickly find a likely explanation. We show that estimated inverses converge asymptotically in number of (prior or posterior) training samples. To make use of inverses before convergence, we describe the Inverse MCMC algorithm, which uses stochastic inverses to make block proposals for a Metropolis-Hastings sampler. We explore the efficiency of this sampler for a variety of parameter regimes and Bayes nets.

Shannon's entropy is a basic quantity in information theory, and a fundamental building block for the analysis of neural codes. Estimating the entropy of a discrete distribution from samples is an important and difficult problem that has received considerable attention in statistics and theoretical neuroscience. However, neural responses have characteristic statistical structure that generic entropy estimators fail to exploit. For example, existing Bayesian entropy estimators make the naive assumption that all spike words are equally likely a priori, which makes for an inefficient allocation of prior probability mass in cases where spikes are sparse. Here we develop Bayesian estimators for the entropy of binary spike trains using priors designed to flexibly exploit the statistical structure of simultaneously-recorded spike responses. We define two prior distributions over spike words using mixtures of Dirichlet distributions centered on simple parametric models. The parametric model captures high-level statistical features of the data, such as the average spike count in a spike word, which allows the posterior over entropy to concentrate more rapidly than with standard estimators (e.g., in cases where the probability of spiking differs strongly from 0.5). Conversely, the Dirichlet distributions assign prior mass to distributions far from the parametric model, ensuring consistent estimates for arbitrary distributions. We devise a compact representation of the data and prior that allow for computationally efficient implementations of Bayesian least squares and empirical Bayes entropy estimators with large numbers of neurons. We apply these estimators to simulated and real neural data and show that they substantially outperform traditional methods.

EDML is a recently proposed algorithm for learning parameters in Bayesian networks. It was originally derived in terms of approximate inference on a meta-network, which underlies the Bayesian approach to parameter estimation. While this initial derivation helped discover EDML in the first place and provided a concrete context for identifying some of its properties (e.g., in contrast to EM), the formal setting was somewhat tedious in the number of concepts it drew on. In this paper, we propose a greatly simplified perspective on EDML, which casts it as a general approach to continuous optimization. The new perspective has several advantages. First, it makes immediate some results that were non-trivial to prove initially. Second, it facilitates the design of EDML algorithms for new graphical models, leading to a new algorithm for learning parameters in Markov networks. We derive this algorithm in this paper, and show, empirically, that it can sometimes learn better estimates from complete data, several times faster than commonly used optimization methods, such as conjugate gradient and L-BFGS.

Reliance on computationally expensive algorithms for inference has been limiting the use of Bayesian nonparametric models in large scale applications. To tackle this problem, we propose a Bayesian learning algorithm for DP mixture models. Instead of following the conventional paradigm -- random initialization plus iterative update, we take an progressive approach. Starting with a given prior, our method recursively transforms it into an approximate posterior through sequential variational approximation. In this process, new components will be incorporated on the fly when needed. The algorithm can reliably estimate a DP mixture model in one pass, making it particularly suited for applications with massive data. Experiments on both synthetic data and real datasets demonstrate remarkable improvement on efficiency -- orders of magnitude speed-up compared to the state-of-the-art.

We address the problem of learning a sparse Bayesian network structure for continuous variables in a high-dimensional space. The constraint that the estimated Bayesian network structure must be a directed acyclic graph (DAG) makes the problem challenging because of the huge search space of network structures. Most previous methods were based on a two-stage approach that prunes the search space in the first stage and then searches for a network structure that satisfies the DAG constraint in the second stage. Although this approach is effective in a low-dimensional setting, it is difficult to ensure that the correct network structure is not pruned in the first stage in a high-dimensional setting. In this paper, we propose a single-stage method, called A* lasso, that recovers the optimal sparse Bayesian network structure by solving a single optimization problem with A* search algorithm that uses lasso in its scoring system. Our approach substantially improves the computational efficiency of the well-known exact methods based on dynamic programming. We also present a heuristic scheme that further improves the efficiency of A* lasso without significantly compromising the quality of solutions and demonstrate this on benchmark Bayesian networks and real data.

In this paper we investigate the use of Langevin Monte Carlo methods on the probability simplex and propose a new method, Stochastic gradient Riemannian Langevin dynamics, which is simple to implement and can be applied to large scale data. We apply this method to latent Dirichlet allocation in an online minibatch setting,and demonstrate that it achieves substantial performance improvements overthe state of the art online variational Bayesian methods.

Movement Primitives (MP) are a well-established approach for representing modular and re-usable robot movement generators. Many state-of-the-art robot learning successes are based MPs, due to their compact representation of the inherently continuous and high dimensional robot movements. A major goal in robot learning is to combine multiple MPs as building blocks in a modular control architecture to solve complex tasks. To this effect, a MP representation has to allow for blending between motions, adapting to altered task variables, and co-activating multiple MPs in parallel. We present a probabilistic formulation of the MP concept that maintains a distribution over trajectories. Our probabilistic approach allows for the derivation of new operations which are essential for implementing all aforementioned properties in one framework. In order to use such a trajectory distribution for robot movement control, we analytically derive a stochastic feedback controller which reproduces the given trajectory distribution. We evaluate and compare our approach to existing methods on several simulated as well as real robot scenarios.

We describe a set of fast, tractable methods for characterizing neural responses to high-dimensional sensory stimuli using a model we refer to as the generalized quadratic model (GQM). The GQM consists of a low-rank quadratic form followed by a point nonlinearity and exponential-family noise. The quadratic form characterizes the neuron's stimulus selectivity in terms of a set linear receptive fields followed by a quadratic combination rule, and the invertible nonlinearity maps this output to the desired response range. Special cases of the GQM include the 2nd-order Volterra model (Marmarelis and Marmarelis 1978, Koh and Powers 1985) and the elliptical Linear-Nonlinear-Poisson model (Park and Pillow 2011). Here we show that for canonical form" GQMs, spectral decomposition of the first two response-weighted moments yields approximate maximum-likelihood estimators via a quantity called the expected log-likelihood. The resulting theory generalizes moment-based estimators such as the spike-triggered covariance, and, in the Gaussian noise case, provides closed-form estimators under a large class of non-Gaussian stimulus distributions. We show that these estimators are fast and provide highly accurate estimates with far lower computational cost than full maximum likelihood. Moreover, the GQM provides a natural framework for combining multi-dimensional stimulus sensitivity and spike-history dependencies within a single model. We show applications to both analog and spiking data using intracellular recordings of V1 membrane potential and extracellular recordings of retinal spike trains."

The Bayesian online change point detection (BOCPD) algorithm provides an efficient way to do exact inference when the parameters of an underlying model may suddenly change over time. BOCPD requires computation of the underlying model's posterior predictives, which can only be computed online in $O(1)$ time and memory for exponential family models. We develop variational approximations to the posterior on change point times (formulated as run lengths) for efficient inference when the underlying model is not in the exponential family, and does not have tractable posterior predictive distributions. In doing so, we develop improvements to online variational inference. We apply our methodology to a tracking problem using radar data with a signal-to-noise feature that is Rice distributed. We also develop a variational method for inferring the parameters of the (non-exponential family) Rice distribution.

We investigate the problem of learning the structure of a Markov network from data. It is shown that the structure of such networks can be described in terms of constraints which enables the use of existing solver technology with optimization capabilities to compute optimal networks starting from initial scores computed from the data. To achieve efficient encodings, we develop a novel characterization of Markov network structure using a balancing condition on the separators between cliques forming the network. The resulting translations into propositional satisfiability and its extensions such as maximum satisfiability, satisfiability modulo theories, and answer set programming, enable us to prove the optimality of networks which have been previously found by stochastic search.