We introduce a semi-parametric Bayesian model for survival analysis. The model is centred on a parametric baseline hazard, and uses a Gaussian process to model variations away from it nonparametrically, as well as dependence on covariates. As opposed to many other methods in survival analysis, our framework does not impose unnecessary constraints in the hazard rate or in the survival function. Furthermore, our model handles left, right and interval censoring mechanisms common in survival analysis. We propose a MCMC algorithm to perform inference and an approximation scheme based on random Fourier features to make computations faster. We report experimental results on synthetic and real data, showing that our model performs better than competing models such as Cox proportional hazards, ANOVA-DDP and random survival forests.

We propose Confusions over Time (CoT), a novel generative framework which facilitates a multi-granular analysis of the decision making process. The CoT not only models the confusions or error properties of individual decision makers and their evolution over time, but also allows us to obtain diagnostic insights into the collective decision making process in an interpretable manner. To this end, the CoT models the confusions of the decision makers and their evolution over time via time-dependent confusion matrices. Interpretable insights are obtained by grouping similar decision makers (and items being judged) into clusters and representing each such cluster with an appropriate prototype and identifying the most important features characterizing the cluster via a subspace feature indicator vector. Experimentation with real world data on bail decisions, asthma treatments, and insurance policy approval decisions demonstrates that CoT can accurately model and explain the confusions of decision makers and their evolution over time.

Many statistical models can be simulated forwards but have intractable likelihoods. Approximate Bayesian Computation (ABC) methods are used to infer properties of these models from data. Traditionally these methods approximate the posterior over parameters by conditioning on data being inside an ε-ball around the observed data, which is only correct in the limit ε→0. Monte Carlo methods can then draw samples from the approximate posterior to approximate predictions or error bars on parameters. These algorithms critically slow down as ε→0, and in practice draw samples from a broader distribution than the posterior. We propose a new approach to likelihood-free inference based on Bayesian conditional density estimation. Preliminary inferences based on limited simulation data are used to guide later simulations. In some cases, learning an accurate parametric representation of the entire true posterior distribution requires fewer model simulations than Monte Carlo ABC methods need to produce a single sample from an approximate posterior.

The softmax representation of probabilities for categorical variables plays a prominent role in modern machine learning with numerous applications in areas such as large scale classification, neural language modeling and recommendation systems. However, softmax estimation is very expensive for large scale inference because of the high cost associated with computing the normalizing constant. Here, we introduce an efficient approximation to softmax probabilities which takes the form of a rigorous lower bound on the exact probability. This bound is expressed as a product over pairwise probabilities and it leads to scalable estimation based on stochastic optimization. It allows us to perform doubly stochastic estimation by subsampling both training instances and class labels. We show that the new bound has interesting theoretical properties and we demonstrate its use in classification problems.

We present the first general purpose framework for marginal maximum a posteriori estimation of probabilistic program variables. By using a series of code transformations, the evidence of any probabilistic program, and therefore of any graphical model, can be optimized with respect to an arbitrary subset of its sampled variables. To carry out this optimization, we develop the first Bayesian optimization package to directly exploit the source code of its target, leading to innovations in problem-independent hyperpriors, unbounded optimization, and implicit constraint satisfaction; delivering significant performance improvements over prominent existing packages. We present applications of our method to a number of tasks including engineering design and parameter optimization.

We introduce a new dynamical system for sequentially observed multivariate count data. This model is based on the gamma-Poisson construction--a natural choice for count data--and relies on a novel Bayesian nonparametric prior that ties and shrinks the model parameters, thus avoiding overfitting. We present an efficient MCMC inference algorithmthat advances recent work on augmentation schemes for inference in negative binomial models. Finally, we demonstrate the model's inductive bias using a variety of real-world data sets, showing that it exhibits superior predictive performance over other models and infers highly interpretable latent structure.

Utilizing the structure of a probabilistic model can significantly increase its learning speed. Motivated by several recent applications, in particular bigram models in language processing, we consider learning low-rank conditional probability matrices under expected KL-risk. This choice makes smoothing, that is the careful handling of low-probability elements, paramount. We derive an iterative algorithm that extends classical non-negative matrix factorization to naturally incorporate additive smoothing and prove that it converges to the stationary points of a penalized empirical risk. We then derive sample-complexity bounds for the global minimizer of the penalized risk and show that it is within a small factor of the optimal sample complexity. This framework generalizes to more sophisticated smoothing techniques, including absolute-discounting.

Adaptive schemes, where tasks are assigned based on the data collected thus far, are widely used in practical crowdsourcing systems to efficiently allocate the budget. However, existing theoretical analyses of crowdsourcing systems suggest that the gain of adaptive task assignments is minimal. To bridge this gap, we investigate this question under a strictly more general probabilistic model, which has been recently introduced to model practical crowdsourcing datasets. Under this generalized Dawid-Skene model, we characterize the fundamental tradeoff between budget and accuracy. We introduce a novel adaptive scheme that matches this fundamental limit. A given budget is allocated over multiple rounds. In each round, a subset of tasks with high enough confidence are classified, and increasing budget is allocated on remaining ones that are potentially more difficult. On each round, decisions are made based on the leading eigenvector of (weighted) non-backtracking operator corresponding to the bipartite assignment graph. We further quantify the gain of adaptivity, by comparing the tradeoff with the one for nonadaptive schemes, and confirm that the gain is significant and can be made arbitrarily large depending on the distribution of the difficulty level of the tasks at hand.

We propose a vector-valued regression problem whose solution is equivalent to the reproducing kernel Hilbert space (RKHS) embedding of the Bayesian posterior distribution. This equivalence provides a new understanding of kernel Bayesian inference. Moreover, the optimization problem induces a new regularization for the posterior embedding estimator, which is faster and has comparable performance to the squared regularization in kernel Bayes' rule. This regularization coincides with a former thresholding approach used in kernel POMDPs whose consistency remains to be established. Our theoretical work solves this open problem and provides consistency analysis in regression settings. Based on our optimizational formulation, we propose a flexible Bayesian posterior regularization framework which for the first time enables us to put regularization at the distribution level. We apply this method to nonparametric state-space filtering tasks with extremely nonlinear dynamics and show performance gains over all other baselines.

Medical researchers are coming to appreciate that many diseases are in fact complex, heterogeneous syndromes composed of subpopulations that express different variants of a related complication. Longitudinal data extracted from individual electronic health records (EHR) offer an exciting new way to study subtle differences in the way these diseases progress over time. In this paper, we focus on answering two questions that can be asked using these databases of longitudinal EHR data. First, we want to understand whether there are individuals with similar disease trajectories and whether there are a small number of degrees of freedom that account for differences in trajectories across the population. Second, we want to understand how important clinical outcomes are associated with disease trajectories. To answer these questions, we propose the Disease Trajectory Map (DTM), a novel probabilistic model that learns low-dimensional representations of sparse and irregularly sampled longitudinal data. We propose a stochastic variational inference algorithm for learning the DTM that allows the model to scale to large modern medical datasets. To demonstrate the DTM, we analyze data collected on patients with the complex autoimmune disease, scleroderma. We find that DTM learns meaningful representations of disease trajectories and that the representations are significantly associated with important clinical outcomes.