Progress in probabilistic generative models has accelerated, developing richer models with neural architectures, implicit densities, and with scalable algorithms for their Bayesian inference. However, there has been limited progress in models that capture causal relationships, for example, how individual genetic factors cause major human diseases. In this work, we focus on two challenges in particular: How do we build richer causal models, which can capture highly nonlinear relationships and interactions between multiple causes? How do we adjust for latent confounders, which are variables influencing both cause and effect and which prevent learning of causal relationships? To address these challenges, we synthesize ideas from causality and modern probabilistic modeling. For the first, we describe implicit causal models, a class of causal models that leverages neural architectures with an implicit density. For the second, we describe an implicit causal model that adjusts for confounders by sharing strength across examples. In experiments, we scale Bayesian inference on up to a billion genetic measurements. We achieve state of the art accuracy for identifying causal factors: we significantly outperform existing genetics methods by an absolute difference of 15-45.3%.

This work constructs a hypothesis test for detecting whether an data-generating function $h: R^p \rightarrow R$ belongs to a specific reproducing kernel Hilbert space $\mathcal{H}_0$ , where the structure of $\mathcal{H}_0$ is only partially known. Utilizing the theory of reproducing kernels, we reduce this hypothesis to a simple one-sided score test for a scalar parameter, develop a testing procedure that is robust against the mis-specification of kernel functions, and also propose an ensemble-based estimator for the null model to guarantee test performance in small samples. To demonstrate the utility of the proposed method, we apply our test to the problem of detecting nonlinear interaction between groups of continuous features. We evaluate the finite-sample performance of our test under different data-generating functions and estimation strategies for the null model. Our results reveal interesting connections between notions in machine learning (model underfit/overfit) and those in statistical inference (i.e. Type I error/power of hypothesis test), and also highlight unexpected consequences of common model estimating strategies (e.g. estimating kernel hyperparameters using maximum likelihood estimation) on model inference.

Reward augmented maximum likelihood (RAML), a simple and effective learning framework to directly optimize towards the reward function in structured prediction tasks, has led to a number of impressive empirical successes. RAML incorporates task-specific reward by performing maximum-likelihood updates on candidate outputs sampled according to an exponentiated payoff distribution, which gives higher probabilities to candidates that are close to the reference output. While RAML is notable for its simplicity, efficiency, and its impressive empirical successes, the theoretical properties of RAML, especially the behavior of the exponentiated payoff distribution, has not been examined thoroughly. In this work, we introduce softmax Q-distribution estimation, a novel theoretical interpretation of RAML, which reveals the relation between RAML and Bayesian decision theory. The softmax Q-distribution can be regarded as a smooth approximation of the Bayes decision boundary, and the Bayes decision rule is achieved by decoding with this Q-distribution. We further show that RAML is equivalent to approximately estimating the softmax Q-distribution, with the temperature $\tau$ controlling approximation error. We perform two experiments, one on synthetic data of multi-class classification and one on real data of image captioning, to demonstrate the relationship between RAML and the proposed softmax Q-distribution estimation method, verifying our theoretical analysis. Additional experiments on three structured prediction tasks with rewards defined on sequential (named entity recognition), tree-based (dependency parsing) and irregular (machine translation) structures show notable improvements over maximum likelihood baselines.

This work addresses the problem of segmentation in time series data with respect to a statistical parameter of interest in Bayesian models. It is common to assume that the parameters are distinct within each segment. As such, many Bayesian change point detection models do not exploit the segment parameter patterns, which can improve performance. This work proposes a Bayesian mean-shift change point detection algorithm that makes use of repetition in segment parameters, by introducing segment class labels that utilise a Dirichlet process prior. The performance of the proposed approach was assessed on both synthetic and real world data, highlighting the enhanced performance when using parameter labelling.

This paper examines fundamental error characteristics for a general class of matrix completion problems, where the matrix of interest is a product of two a priori unknown matrices, one of which is sparse, and the observations are noisy. Our main contributions come in the form of minimax lower bounds for the expected per-element squared error for this problem under under several common noise models. Specifically, we analyze scenarios where the corruptions are characterized by additive Gaussian noise or additive heavier-tailed (Laplace) noise, Poisson-distributed observations, and highly-quantized (e.g., one-bit) observations, as instances of our general result. Our results establish that the error bounds derived in (Soni et al., 2016) for complexity-regularized maximum likelihood estimators achieve, up to multiplicative constants and logarithmic factors, the minimax error rates in each of these noise scenarios, provided that the nominal number of observations is large enough, and the sparse factor has (on an average) at least one non-zero per column.

Many matching, tracking, sorting, and ranking problems require probabilistic reasoning about possible permutations, a set that grows factorially with dimension. Combinatorial optimization algorithms may enable efficient point estimation, but fully Bayesian inference poses a severe challenge in this high-dimensional, discrete space. To surmount this challenge, we start with the usual step of relaxing a discrete set (here, of permutation matrices) to its convex hull, which here is the Birkhoff polytope: the set of all doubly-stochastic matrices. We then introduce two novel transformations: first, an invertible and differentiable stick-breaking procedure that maps unconstrained space to the Birkhoff polytope; second, a map that rounds points toward the vertices of the polytope. Both transformations include a temperature parameter that, in the limit, concentrates the densities on permutation matrices. We then exploit these transformations and reparameterization gradients to introduce variational inference over permutation matrices, and we demonstrate its utility in a series of experiments.

The original problem of supervised classification considers the task of automatically assigning objects to their respective classes on the basis of numerical measurements derived from these objects. Classifiers are the tools that implement the actual functional mapping from these measurements---also called features or inputs---to the so-called class label---or output. The fields of pattern recognition and machine learning study ways of constructing such classifiers. The main idea behind supervised methods is that of learning from examples: given a number of example input-output relations, to what extent can the general mapping be learned that takes any new and unseen feature vector to its correct class? This chapter provides a basic introduction to the underlying ideas of how to come to a supervised classification problem. In addition, it provides an overview of some specific classification techniques, delves into the issues of object representation and classifier evaluation, and (very) briefly covers some variations on the basic supervised classification task that may also be of interest to the practitioner.

We consider the problem of accurately estimating the reliability of workers based on noisy labels they provide, which is a fundamental question in crowdsourcing. We propose a novel lower bound on the minimax estimation error which applies to any estimation procedure. We further propose Triangular Estimation (TE), an algorithm for estimating the reliability of workers. TE has low complexity, may be implemented in a streaming setting when labels are provided by workers in real time, and does not rely on an iterative procedure. We further prove that TE is minimax optimal and matches our lower bound. We conclude by assessing the performance of TE and other state-of-the-art algorithms on both synthetic and real-world data sets.

Prediction is a fundamental and difficult scientific problem. We limit the scope of our discussion by imposing, from the outset, two restrictions: we only want to predict one real number y R, and we want our prediction to satisfy a reasonable property of validity (under a natural assumption). It can be argued that the fullest prediction for y is a probability measure on R, which can be represented by its distribution function: see, e.g., [5, 6, 8]. We will refer to it as the predictive distribution. A standard property of validity for predictive distributions is being well-calibrated.

We present a new model-based integrative method for clustering objects given both vectorial data, which describes the feature of each object, and network data, which indicates the similarity of connected objects. The proposed general model is able to cluster the two types of data simultaneously within one integrative probabilistic model, while traditional methods can only handle one data type or depend on transforming one data type to another. Bayesian inference of the clustering is conducted based on a Markov chain Monte Carlo algorithm. A special case of the general model combining the Gaussian mixture model and the stochastic block model is extensively studied. We used both synthetic data and real data to evaluate this new method and compare it with alternative methods. The results show that our simultaneous clustering method performs much better. This improvement is due to the power of the model-based probabilistic approach for efficiently integrating information.