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.

Neural Information Processing Systems http://nips.cc/

Neural Information Processing Systems http://nips.cc/

The use of Bayesian methods in large-scale data settings is attractive because of the rich hierarchical models, uncertainty quantification, and prior specification they provide. Standard Bayesian inference algorithms are computationally expensive, however, making their direct application to large datasets difficult or infeasible. Recent work on scaling Bayesian inference has focused on modifying the underlying algorithms to, for example, use only a random data subsample at each iteration. We leverage the insight that data is often redundant to instead obtain a weighted subset of the data (called a coreset) that is much smaller than the original dataset. We can then use this small coreset in any number of existing posterior inference algorithms without modification.

Recent work on scaling up Gaussian process regression (GPR) to large datasets has primarily focused on sparse GPR, which leverages a small set of basis functions to approximate the full Gaussian process during inference. However, the majority of these approaches are batch methods that operate on the entire training dataset at once, precluding the use of datasets that are streaming or too large to fit into memory. Although previous work has considered incrementally solving variational sparse GPR, most algorithms fail to update the basis functions and therefore perform suboptimally. We propose a novel incremental learning algorithm for variational sparse GPR based on stochastic mirror ascent of probability densities in reproducing kernel Hilbert space. This new formulation allows our algorithm to update basis functions online in accordance with the manifold structure of probability densities for fast convergence. We conduct several experiments and show that our proposed approach achieves better empirical performance in terms of prediction error than the recent state-of-the-art incremental solutions to variational sparse GPR.

Variational methods that rely on a recognition network to approximate the posterior of directed graphical models offer better inference and learning than previous methods. Recent advances that exploit the capacity and flexibility in this approach have expanded what kinds of models can be trained. However, as a proposal for the posterior, the capacity of the recognition network is limited, which can constrain the representational power of the generative model and increase the variance of Monte Carlo estimates. To address these issues, we introduce an iterative refinement procedure for improving the approximate posterior of the recognition network and show that training with the refined posterior is competitive with state-of-the-art methods. The advantages of refinement are further evident in an increased effective sample size, which implies a lower variance of gradient estimates.

Neural Information Processing Systems http://nips.cc/

Random projections constitute a simple, yet effective technique for dimensionality reduction with applications in learning and search problems. In the present paper, we consider the problem of estimating cosine similarities when the projected data undergo scalar quantization to b bits. We here argue that the maximum likelihood estimator (MLE) is a principled approach to deal with the non-linearity resulting from quantization, and subsequently study its computational and statistical properties. A specific focus is on the on the trade-off between bit depth and the number of projections given a fixed budget of bits for storage or transmission. Along the way, we also touch upon the existence of a qualitative counterpart to the Johnson-Lindenstrauss lemma in the presence of quantization.

Neural Information Processing Systems http://nips.cc/

Markov chain Monte Carlo (MCMC) is one of the main workhorses of probabilistic inference, but it is notoriously hard to measure the quality of approximate posterior samples. This challenge is particularly salient in black box inference methods, which can hide details and obscure inference failures. In this work, we extend the recently introduced bidirectional Monte Carlo [GGA15] technique to evaluate MCMC-based posterior inference algorithms. By running annealed importance sampling (AIS) chains both from prior to posterior and vice versa on simulated data, we upper bound in expectation the symmetrized KL divergence between the true posterior distribution and the distribution of approximate samples. We integrate our method into two probabilistic programming languages, WebPPL [GS] and Stan [CGHL+ p], and validate it on several models and datasets. As an example of how our method be used to guide the design of inference algorithms, we apply it to study the effectiveness of different model representations in WebPPL and Stan.