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.

We study the estimation of the latent variable Gaussian graphical model (LVGGM), where the precision matrix is the superposition of a sparse matrix and a low-rank matrix. In order to speed up the estimation of the sparse plus low-rank components, we propose a sparsity constrained maximum likelihood estimator based on matrix factorization and an efficient alternating gradient descent algorithm with hard thresholding to solve it. Our algorithm is orders of magnitude faster than the convex relaxation based methods for LVGGM. In addition, we prove that our algorithm is guaranteed to linearly converge to the unknown sparse and low-rank components up to the optimal statistical precision. Experiments on both synthetic and genomic data demonstrate the superiority of our algorithm over the state-of-the-art algorithms and corroborate our theory.

We present a factorized hierarchical variational autoencoder, which learns disentangled and interpretable representations from sequential data without supervision. Specifically, we exploit the multi-scale nature of information in sequential data by formulating it explicitly within a factorized hierarchical graphical model that imposes sequence-dependent priors and sequence-independent priors to different sets of latent variables. The model is evaluated on two speech corpora to demonstrate, qualitatively, its ability to transform speakers or linguistic content by manipulating different sets of latent variables; and quantitatively, its ability to outperform an i-vector baseline for speaker verification and reduce the word error rate by as much as 35% in mismatched train/test scenarios for automatic speech recognition tasks.

We present a new algorithmic approach for the task of finding a chordal Markov network structure that maximizes a given scoring function. The algorithm is based on branch and bound and integrates dynamic programming for both domain pruning and for obtaining strong bounds for search-space pruning. Empirically, we show that the approach dominates in terms of running times a recent integer programming approach (and thereby also a recent constraint optimization approach) for the problem.

The marginal likelihood, or model evidence, is a key quantity in Bayesian parameter estimation and model comparison. For many probabilistic models, computation of the marginal likelihood is challenging, because it involves a sum or integral over an enormous parameter space. Markov chain Monte Carlo (MCMC) is a powerful approach to compute marginal likelihoods. Various MCMC algorithms and evidence estimators have been proposed in the literature. Here we discuss the use of nonequilibrium techniques for estimating the marginal likelihood. Nonequilibrium estimators build on recent developments in statistical physics and are known as annealed importance sampling (AIS) and reverse AIS in probabilistic machine learning. We introduce estimators for the model evidence that combine forward and backward simulations and show for various challenging models that the evidence estimators outperform forward and reverse AIS.

We explore the top-K rank aggregation problem in which one aims to recover a consistent ordering that focuses on top-K ranked items based on partially revealed preference information. We examine an M-wise comparison model that builds on the Plackett-Luce (PL) model where for each sample, M items are ranked according to their perceived utilities modeled as noisy observations of their underlying true utilities. As our result, we characterize the minimax optimality on the sample size for top-K ranking. The optimal sample size turns out to be inversely proportional to M. We devise an algorithm that effectively converts M-wise samples into pairwise ones and employs a spectral method using the refined data. In demonstrating its optimality, we develop a novel technique for deriving tight $\ell_\infty$ estimation error bounds, which is key to accurately analyzing the performance of top-K ranking algorithms, but has been challenging. Recent work relied on an additional maximum-likelihood estimation (MLE) stage merged with a spectral method to attain good estimates in $\ell_\infty$ error to achieve the limit for the pairwise model. In contrast, although it is valid in slightly restricted regimes, our result demonstrates a spectral method alone to be sufficient for the general M-wise model. We run numerical experiments using synthetic data and confirm that the optimal sample size decreases at the rate of 1/M. Moreover, running our algorithm on real-world data, we find that its applicability extends to settings that may not fit the PL model.

A new model, named as deep dynamic poisson factorization model, is proposed in this paper for analyzing sequential count vectors. The model based on the Poisson Factor Analysis method captures dependence among time steps by neural networks, representing the implicit distributions. Local complicated relationship is obtained from local implicit distribution, and deep latent structure is exploited to get the long-time dependence. Variational inference on latent variables and gradient descent based on the loss functions derived from variational distribution is performed in our inference. Synthetic datasets and real-world datasets are applied to the proposed model and our results show good predicting and fitting performance with interpretable latent structure.

Point processes are powerful tools to model user activities and have a plethora of applications in social sciences. Predicting user activities based on point processes is a central problem. However, existing works are mostly problem specific, use heuristics, or simplify the stochastic nature of point processes. In this paper, we propose a framework that provides an efficient estimator of the probability mass function of point processes. In particular, we design a key reformulation of the prediction problem, and further derive a differential-difference equation to compute a conditional probability mass function. Our framework is applicable to general point processes and prediction tasks, and achieves superb predictive and efficiency performance in diverse real-world applications compared to the state of the art.

Deep networks trained on large-scale data can learn transferable features to promote learning multiple tasks. Since deep features eventually transition from general to specific along deep networks, a fundamental problem of multi-task learning is how to exploit the task relatedness underlying parameter tensors and improve feature transferability in the multiple task-specific layers. This paper presents Multilinear Relationship Networks (MRN) that discover the task relationships based on novel tensor normal priors over parameter tensors of multiple task-specific layers in deep convolutional networks. By jointly learning transferable features and multilinear relationships of tasks and features, MRN is able to alleviate the dilemma of negative-transfer in the feature layers and under-transfer in the classifier layer. Experiments show that MRN yields state-of-the-art results on three multi-task learning datasets.

Mechanistic models of single-neuron dynamics have been extensively studied in computational neuroscience. However, identifying which models can quantitatively reproduce empirically measured data has been challenging. We propose to overcome this limitation by using likelihood-free inference approaches (also known as Approximate Bayesian Computation, ABC) to perform full Bayesian inference on single-neuron models. Our approach builds on recent advances in ABC by learning a neural network which maps features of the observed data to the posterior distribution over parameters. We learn a Bayesian mixture-density network approximating the posterior over multiple rounds of adaptively chosen simulations. Furthermore, we propose an efficient approach for handling missing features and parameter settings for which the simulator fails, as well as a strategy for automatically learning relevant features using recurrent neural networks. On synthetic data, our approach efficiently estimates posterior distributions and recovers ground-truth parameters. On in-vitro recordings of membrane voltages, we recover multivariate posteriors over biophysical parameters, which yield model-predicted voltage traces that accurately match empirical data. Our approach will enable neuroscientists to perform Bayesian inference on complex neuron models without having to design model-specific algorithms, closing the gap between mechanistic and statistical approaches to single-neuron modelling.