Designing optimal treatment plans for patients with comorbidities requires accurate cause-specific mortality prognosis. Motivated by the recent availability of linked electronic health records, we develop a nonparametric Bayesian model for survival analysis with competing risks, which can be used for jointly assessing a patient's risk of multiple (competing) adverse outcomes. The model views a patient's survival times with respect to the competing risks as the outputs of a deep multi-task Gaussian process (DMGP), the inputs to which are the patients' covariates. Unlike parametric survival analysis methods based on Cox and Weibull models, our model uses DMGPs to capture complex non-linear interactions between the patients' covariates and cause-specific survival times, thereby learning flexible patient-specific and cause-specific survival curves, all in a data-driven fashion without explicit parametric assumptions on the hazard rates. We propose a variational inference algorithm that is capable of learning the model parameters from time-to-event data while handling right censoring. Experiments on synthetic and real data show that our model outperforms the state-of-the-art survival models.

Bayesian models are established as one of the main successful paradigms for complex problems in machine learning. To handle intractable inference, research in this area has developed new approximation methods that are fast and effective. However, theoretical analysis of the performance of such approximations is not well developed. The paper furthers such analysis by providing bounds on the excess risk of variational inference algorithms and related regularized loss minimization algorithms for a large class of latent variable models with Gaussian latent variables. We strengthen previous results for variational algorithms by showing that they are competitive with any point-estimate predictor. Unlike previous work, we provide bounds on the risk of the Bayesian predictor and not just the risk of the Gibbs predictor for the same approximate posterior. The bounds are applied in complex models including sparse Gaussian processes and correlated topic models. Theoretical results are complemented by identifying novel approximations to the Bayesian objective that attempt to minimize the risk directly. An empirical evaluation compares the variational and new algorithms shedding further light on their performance.

We propose a generalized Gibbs sampler algorithm for obtaining samples approximately distributed from a high-dimensional Gaussian distribution. Similarly to Hogwild methods, our approach does not target the original Gaussian distribution of interest, but an approximation to it. Contrary to Hogwild methods, a single parameter allows us to trade bias for variance. We show empirically that our method is very flexible and performs well compared to Hogwild-type algorithms.

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 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.

The simple closed-form screening rule is a necessary and sufficient condition for exactly recovering the blockwise structure of a solution under any given regularization parameters. With enough sparsity, the screening rule can be combined with various optimization procedures to deliver solutions efficiently in practice. The screening rule is especially suitable for large-scale exploratory data analysis, where the number of variables in the dataset can be thousands while we are only interested in the relationship among a handful of variables within moderate-size clusters for interpretability. Experimental results on various datasets demonstrate the efficiency and insights gained from the introduction of the screening rule.

Implicit probabilistic models are a flexible class of models defined by a simulation process for data. They form the basis for theories which encompass our understanding of the physical world. Despite this fundamental nature, the use of implicit models remains limited due to challenges in specifying complex latent structure in them, and in performing inferences in such models with large data sets.

Predicated on the increasing abundance of electronic health records, we investigate the problem of inferring individualized treatment effects using observational data. Stemming from the potential outcomes model, we propose a novel multitask learning framework in which factual and counterfactual outcomes are modeled as the outputs of a function in a vector-valued reproducing kernel Hilbert space (vvRKHS). We develop a nonparametric Bayesian method for learning the treatment effects using a multi-task Gaussian process (GP) with a linear coregionalization kernel as a prior over the vvRKHS. The Bayesian approach allows us to compute individualized measures of confidence in our estimates via pointwise credible intervals, which are crucial for realizing the full potential of precision medicine. The impact of selection bias is alleviated via a risk-based empirical Bayes method for adapting the multi-task GP prior, which jointly minimizes the empirical error in factual outcomes and the uncertainty in (unobserved) counterfactual outcomes. We conduct experiments on observational datasets for an interventional social program applied to premature infants, and a left ventricular assist device applied to cardiac patients wait-listed for a heart transplant. In both experiments, we show that our method significantly outperforms the state-of-the-art.

Compression and computational efficiency in deep learning have become a problem of great significance. In this work, we argue that the most principled and effective way to attack this problem is by adopting a Bayesian point of view, where through sparsity inducing priors we prune large parts of the network. We introduce two novelties in this paper: 1) we use hierarchical priors to prune nodes instead of individual weights, and 2) we use the posterior uncertainties to determine the optimal fixed point precision to encode the weights. Both factors significantly contribute to achieving the state of the art in terms of compression rates, while still staying competitive with methods designed to optimize for speed or energy efficiency.

Calcium imaging permits optical measurement of neural activity. Since intracellular calcium concentration is an indirect measurement of neural activity, computational tools are necessary to infer the true underlying spiking activity from fluorescence measurements. Bayesian model inversion can be used to solve this problem, but typically requires either computationally expensive MCMC sampling, or faster but approximate maximum-a-posteriori optimization. Here, we introduce a flexible algorithmic framework for fast, efficient and accurate extraction of neural spikes from imaging data. Using the framework of variational autoencoders, we propose to amortize inference by training a deep neural network to perform model inversion efficiently.

We revisit the classical analysis of generative vs discriminative models for general exponential families, and high-dimensional settings.