Edward is a Python library for probabilistic modeling, inference, and criticism. It is a testbed for fast experimentation and research with probabilistic models, ranging from classical hierarchical models on small data sets to complex deep probabilistic models on large data sets. Edward is built on top of TensorFlow. It enables features such as computational graphs, distributed training, CPU/GPU integration, automatic differentiation, and visualization with TensorBoard. Edward is led by Dustin Tran with guidance by David Blei.

Over the last two years I've occasionally been giving a very basic tutorial to Bayesian statistics using R and Stan. At the end of the tutorial I hand out an exercise for those that want to flex their newly acquired skills. I call this exercise Bayesian computation with Stan and Farmer Jöns and it's pretty cool! Now, it's not cool because of me, but because the expressiveness of Stan allowed me to write a small number of data analytic questions that quickly takes you from running a simple binomial model up to running a linear regression. Throughout the exercise you work with the same model code and each question just requires you to make a minimal change to this code, yet you will cover most models taught in a basic statistics course!

Dirichlet process mixture models (DPMM) are a cornerstone of Bayesian non-parametrics. While these models free from choosing the number of components a-priori, computationally attractive variational inference often reintroduces the need to do so, via a truncation on the variational distribution. In this paper we present a truncation-free hybrid inference for DPMM, combining the advantages of sampling-based MCMC and variational methods. The proposed hybridization enables more efficient variational updates, while increasing model complexity only if needed. We evaluate the properties of the hybrid updates and their empirical performance in single- as well as mixed-membership models. Our method is easy to implement and performs favorably compared to existing schemas.

We study large-scale kernel methods for acoustic modeling in speech recognition and compare their performance to deep neural networks (DNNs). We perform experiments on four speech recognition datasets, including the TIMIT and Broadcast News benchmark tasks, and compare these two types of models on frame-level performance metrics (accuracy, cross-entropy), as well as on recognition metrics (word/character error rate). In order to scale kernel methods to these large datasets, we use the random Fourier feature method of Rahimi and Recht (2007). We propose two novel techniques for improving the performance of kernel acoustic models. First, in order to reduce the number of random features required by kernel models, we propose a simple but effective method for feature selection. The method is able to explore a large number of non-linear features while maintaining a compact model more efficiently than existing approaches. Second, we present a number of frame-level metrics which correlate very strongly with recognition performance when computed on the heldout set; we take advantage of these correlations by monitoring these metrics during training in order to decide when to stop learning. This technique can noticeably improve the recognition performance of both DNN and kernel models, while narrowing the gap between them. Additionally, we show that the linear bottleneck method of Sainath et al. (2013) improves the performance of our kernel models significantly, in addition to speeding up training and making the models more compact. Together, these three methods dramatically improve the performance of kernel acoustic models, making their performance comparable to DNNs on the tasks we explored.

An important problem for HCI researchers is to estimate the parameter values of a cognitive model from behavioral data. This is a difficult problem, because of the substantial complexity and variety in human behavioral strategies. We report an investigation into a new approach using approximate Bayesian computation (ABC) to condition model parameters to data and prior knowledge. As the case study we examine menu interaction, where we have click time data only to infer a cognitive model that implements a search behaviour with parameters such as fixation duration and recall probability. Our results demonstrate that ABC (i) improves estimates of model parameter values, (ii) enables meaningful comparisons between model variants, and (iii) supports fitting models to individual users. ABC provides ample opportunities for theoretical HCI research by allowing principled inference of model parameter values and their uncertainty.

Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose dynamics are governed by the Chemical Master Equation. Despite its simple structure, no analytic solutions to the Chemical Master Equation are known for most systems. Moreover, stochastic simulations are computationally expensive, making systematic analysis and statistical inference a challenging task. Consequently, significant effort has been spent in recent decades on the development of efficient approximation and inference methods. This article gives an introduction to basic modelling concepts as well as an overview of state of the art methods. First, we motivate and introduce deterministic and stochastic methods for modelling chemical networks, and give an overview of simulation and exact solution methods. Next, we discuss several approximation methods, including the chemical Langevin equation, the system size expansion, moment closure approximations, time-scale separation approximations and hybrid methods. We discuss their various properties and review recent advances and remaining challenges for these methods. We present a comparison of several of these methods by means of a numerical case study and highlight some of their respective advantages and disadvantages. Finally, we discuss the problem of inference from experimental data in the Bayesian framework and review recent methods developed the literature. In summary, this review gives a self-contained introduction to modelling, approximations and inference methods for stochastic chemical kinetics.

The approach is capable of learning correspondences between views as well as correspondences between individual data-points. The proposed method requires only a few aligned examples from which it is capable to recover a global alignment through a probabilistic model. The strong, yet flexible regularization provided by the generative model is sufficient to align the views. We provide experiments on both synthetic and real data to highlight the benefit of the proposed approach.

We propose a modified expectation-maximization algorithm by introducing the concept of quantum annealing, which we call the deterministic quantum annealing expectation-maximization (DQAEM) algorithm. The expectation-maximization (EM) algorithm is an established algorithm to compute maximum likelihood estimates and applied to many practical applications. However, it is known that EM heavily depends on initial values and its estimates are sometimes trapped by local optima. To solve such a problem, quantum annealing (QA) was proposed as a novel optimization approach motivated by quantum mechanics. By employing QA, we then formulate DQAEM and present a theorem that supports its stability. Finally, we demonstrate numerical simulations to confirm its efficiency.

The focus in this paper is Bayesian system identification based on noisy incomplete modal data where we can impose spatially-sparse stiffness changes when updating a structural model. To this end, based on a similar hierarchical sparse Bayesian learning model from our previous work, we propose two Gibbs sampling algorithms. The algorithms differ in their strategies to deal with the posterior uncertainty of the equation-error precision parameter, but both sample from the conditional posterior probability density functions (PDFs) for the structural stiffness parameters and system modal parameters. The effective dimension for the Gibbs sampling is low because iterative sampling is done from only three conditional posterior PDFs that correspond to three parameter groups, along with sampling of the equation-error precision parameter from another conditional posterior PDF in one of the algorithms where it is not integrated out as a "nuisance" parameter. A nice feature from a computational perspective is that it is not necessary to solve a nonlinear eigenvalue problem of a structural model. The effectiveness and robustness of the proposed algorithms are illustrated by applying them to the IASE-ASCE Phase II simulated and experimental benchmark studies. The goal is to use incomplete modal data identified before and after possible damage to detect and assess spatially-sparse stiffness reductions induced by any damage. Our past and current focus on meeting challenges arising from Bayesian inference of structural stiffness serve to strengthen the capability of vibration-based structural system identification but our methods also have much broader applicability for inverse problems in science and technology where system matrices are to be inferred from noisy partial information about their eigenquantities.

Crowdsourcing systems are popular for solving large-scale labelling tasks with low-paid workers. We study the problem of recovering the true labels from the possibly erroneous crowdsourced labels under the popular Dawid-Skene model. To address this inference problem, several algorithms have recently been proposed, but the best known guarantee is still significantly larger than the fundamental limit. We close this gap by introducing a tighter lower bound on the fundamental limit and proving that Belief Propagation (BP) exactly matches this lower bound. The guaranteed optimality of BP is the strongest in the sense that it is information-theoretically impossible for any other algorithm to correctly label a larger fraction of the tasks. Experimental results suggest that BP is close to optimal for all regimes considered and improves upon competing state-of-the-art algorithms.