Graph structured data are abundant in the real world. Among different graph types, directed acyclic graphs (DAGs) are of particular interest to machine learning researchers, as many machine learning models are realized as computations on DAGs, including neural networks and Bayesian networks. In this paper, we study deep generative models for DAGs, and propose a novel DAG variational autoencoder (D-VAE).

Continuous-time Bayesian Networks (CTBNs) represent a compact yet powerful framework for understanding multivariate time-series data. Given complete data, parameters and structure can be estimated efficiently in closed-form. However, if data is incomplete, the latent states of the CTBN have to be estimated by laboriously simulating the intractable dynamics of the assumed CTBN. This is a problem, especially for structure learning tasks, where this has to be done for each element of a super-exponentially growing set of possible structures. In order to circumvent this notorious bottleneck, we develop a novel gradient-based approach to structure learning. Instead of sampling and scoring all possible structures individually, we assume the generator of the CTBN to be composed as a mixture of generators stemming from different structures. In this framework, structure learning can be performed via a gradient-based optimization of mixture weights. We combine this approach with a new variational method that allows for a closed-form calculation of this mixture marginal likelihood. We show the scalability of our method by learning structures of previously inaccessible sizes from synthetic and real-world data.

To check the accuracy of Bayesian computations, it is common to use rank-based simulation-based calibration (SBC). However, SBC has drawbacks: The test statistic is somewhat ad-hoc, interactions are difficult to examine, multiple testing is a challenge, and the resulting p-value is not a divergence metric. We propose to replace the marginal rank test with a flexible classification approach that learns test statistics from data. This measure typically has a higher statistical power than the SBC test and returns an interpretable divergence measure of miscalibration, computed from classification accuracy. This approach can be used with different data generating processes to address simulation-based inference or traditional inference methods like Markov chain Monte Carlo or variational inference. We illustrate an automated implementation using neural networks and statistically-inspired features, and validate the method with numerical and real data experiments.

Determinantal point processes (DPPs) have attracted substantial attention as an elegant probabilistic model that captures the balance between quality and diversity within sets. DPPs are conventionally parameterized by a positive semi-definite kernel matrix, and this symmetric kernel encodes only repulsive interactions between items. These so-called symmetric DPPs have significant expressive power, and have been successfully applied to a variety of machine learning tasks, including recommendation systems, information retrieval, and automatic summarization, among many others. Efficient algorithms for learning symmetric DPPs and sampling from these models have been reasonably well studied. However, relatively little attention has been given to nonsymmetric DPPs, which relax the symmetric constraint on the kernel. Nonsymmetric DPPs allow for both repulsive and attractive item interactions, which can significantly improve modeling power, resulting in a model that may better fit for some applications. We present a method that enables a tractable algorithm, based on maximum likelihood estimation, for learning nonsymmetric DPPs from data composed of observed subsets. Our method imposes a particular decomposition of the nonsymmetric kernel that enables such tractable learning algorithms, which we analyze both theoretically and experimentally. We evaluate our model on synthetic and real-world datasets, demonstrating improved predictive performance compared to symmetric DPPs, which have previously shown strong performance on modeling tasks associated with these datasets.

Recent advances in optical voltage sensors have brought us closer to a critical goal in cellular neuroscience: imaging the full spatiotemporal voltage on a dendritic tree. However, current sensors and imaging approaches still face significant limitations in SNR and sampling frequency; therefore statistical denoising and interpolation methods remain critical for understanding single-trial spatiotemporal dendritic voltage dynamics. Previous denoising approaches were either based on an inadequate linear voltage model or scaled poorly to large trees. Here we introduce a scalable fully Bayesian approach. We develop a generative nonlinear model that requires few parameters per compartment of the cell but is nonetheless flexible enough to sample realistic spatiotemporal data. The model captures different dynamics in each compartment and leverages biophysical knowledge to constrain intra-and inter-compartmental dynamics. We obtain a full posterior distribution over spatiotemporal voltage via an augmented Gibbs sampling algorithm. The nonlinear smoother model outperforms previously developed linear methods, and scales to much larger systems than previous methods based on sequential Monte Carlo approaches.

When maximum likelihood estimation is infeasible, one often turns to score matching, contrastive divergence, or minimum probability flow to obtain tractable parameter estimates. We provide a unifying perspective of these techniques as minimum Stein discrepancy estimators, and use this lens to design new diffusion kernel Stein discrepancy (DKSD) and diffusion score matching (DSM) estimators with complementary strengths. We establish the consistency, asymptotic normality, and robustness of DKSD and DSM estimators, then derive stochastic Riemannian gradient descent algorithms for their efficient optimisation. The main strength of our methodology is its flexibility, which allows us to design estimators with desirable properties for specific models at hand by carefully selecting a Stein discrepancy. We illustrate this advantage for several challenging problems for score matching, such as non-smooth, heavy-tailed or light-tailed densities.

We study the problem of fair binary classification using the notion of Equal Opportunity. It requires the true positive rate to distribute equally across the sensitive groups. Within this setting we show that the fair optimal classifier is obtained by recalibrating the Bayes classifier by a group-dependent threshold. We provide a constructive expression for the threshold. This result motivates us to devise a plug-in classification procedure based on both unlabeled and labeled datasets. While the latter is used to learn the output conditional probability, the former is used for calibration. The overall procedure can be computed in polynomial time and it is shown to be statistically consistent both in terms of the classification error and fairness measure. Finally, we present numerical experiments which indicate that our method is often superior or competitive with the state-of-the-art methods on benchmark datasets.

Tensor-network techniques have recently proven useful in machine learning, both as a tool for the formulation of new learning algorithms and for enhancing the mathematical understanding of existing methods. Inspired by these developments, and the natural correspondence between tensor networks and probabilistic graphical models, we provide a rigorous analysis of the expressive power of various tensor-network factorizations of discrete multivariate probability distributions. These factorizations include non-negative tensor-trains/MPS, which are in correspondence with hidden Markov models, and Born machines, which are naturally related to the probabilistic interpretation of quantum circuits. When used to model probability distributions, they exhibit tractable likelihoods and admit efficient learning algorithms. Interestingly, we prove that there exist probability distributions for which there are unbounded separations between the resource requirements of some of these tensor-network factorizations. Of particular interest, using complex instead of real tensors can lead to an arbitrarily large reduction in the number of parameters of the network. Additionally, we introduce locally purified states (LPS), a new factorization inspired by techniques for the simulation of quantum systems, with provably better expressive power than all other representations considered. The ramifications of this result are explored through numerical experiments.

A graphical model is a structured representation of the data generating process. The traditional method to reason over random variables is to perform inference in this graphical model. However, in many cases the generating process is only a poor approximation of the much more complex true data generating process, leading to suboptimal estimation. The subtleties of the generative process are however captured in the data itself and we can ``learn to infer'', that is, learn a direct mapping from observations to explanatory latent variables. In this work we propose a hybrid model that combines graphical inference with a learned inverse model, which we structure as in a graph neural network, while the iterative algorithm as a whole is formulated as a recurrent neural network. By using cross-validation we can automatically balance the amount of work performed by graphical inference versus learned inference. We apply our ideas to the Kalman filter, a Gaussian hidden Markov model for time sequences, and show, among other things, that our model can estimate the trajectory of a noisy chaotic Lorenz Attractor much more accurately than either the learned or graphical inference run in isolation.

A fundamental goal of systems neuroscience is to understand the relationship between neural activity and behavior. Behavior has traditionally been characterized by low-dimensional, task-related variables such as movement speed or response times. More recently, there has been a growing interest in automated analysis of high-dimensional video data collected during experiments. Here we introduce a probabilistic framework for the analysis of behavioral video and neural activity. This framework provides tools for compression, segmentation, generation, and decoding of behavioral videos.