The standard approach to fitting an autoregressive spike train model is to maximize the likelihood for one-step prediction. This maximum likelihood estimation (MLE) often leads to models that perform poorly when generating samples recursively for more than one time step. Moreover, the generated spike trains can fail to capture important features of the data and even show diverging firing rates. To alleviate this, we propose to directly minimize the divergence between neural recorded and model generated spike trains using spike train kernels. We develop a method that stochastically optimizes the maximum mean discrepancy induced by the kernel. Experiments performed on both real and synthetic neural data validate the proposed approach, showing that it leads to well-behaving models. Using different combinations of spike train kernels, we show that we can control the trade-off between different features which is critical for dealing with model-mismatch.

Missing data can be informative. Ignoring this information can lead to misleading conclusions when the data model does not allow information to be extracted from the missing data. We propose a co-clustering model, based on the Latent Block Model, that aims to take advantage of this nonignorable nonresponses, also known as Missing Not At Random data (MNAR). A variational expectation-maximization algorithm is derived to perform inference and a model selection criterion is presented. We assess the proposed approach on a simulation study, before using our model on the voting records from the lower house of the French Parliament, where our analysis brings out relevant groups of MPs and texts, together with a sensible interpretation of the behavior of non-voters.

Despite recent advances, goal-directed generation of structured discrete data remains challenging. For problems such as program synthesis (generating source code) and materials design (generating molecules), finding examples which satisfy desired constraints or exhibit desired properties is difficult. In practice, expensive heuristic search or reinforcement learning algorithms are often employed. In this paper we investigate the use of conditional generative models which directly attack this inverse problem, by modeling the distribution of discrete structures given properties of interest. Unfortunately, maximum likelihood training of such models often fails with the samples from the generative model inadequately respecting the input properties. To address this, we introduce a novel approach to directly optimize a reinforcement learning objective, maximizing an expected reward. We avoid high-variance score-function estimators that would otherwise be required by sampling from an approximation to the normalized rewards, allowing simple Monte Carlo estimation of model gradients. We test our methodology on two tasks: generating molecules with user-defined properties, and identifying short python expressions which evaluate to a given target value. In both cases we find improvements over maximum likelihood estimation and other baselines.

Existing methods for estimating uncertainty in deep learning tend to require multiple forward passes, making them unsuitable for applications where computational resources are limited. To solve this, we perform probabilistic reasoning over the depth of neural networks. Different depths correspond to subnetworks which share weights and whose predictions are combined via marginalisation, yielding model uncertainty. By exploiting the sequential structure of feed-forward networks, we are able to both evaluate our training objective and make predictions with a single forward pass. We validate our approach on real-world regression and image classification tasks. Our approach provides uncertainty calibration, robustness to dataset shift, and accuracies competitive with more computationally expensive baselines.

Undirected graphical models are compact representations of joint probability distributions over random variables. To solve inference tasks of interest, graphical models of arbitrary topology can be trained using empirical risk minimization. However, to solve inference tasks that were not seen during training, these models (EGMs) often need to be re-trained. Instead, we propose an inference-agnostic adversarial training framework which produces an infinitely-large ensemble of graphical models (AGMs). The ensemble is optimized to generate data within the GAN framework, and inference is performed using a finite subset of these models. AGMs perform comparably with EGMs on inference tasks that the latter were specifically optimized for. Most importantly, AGMs show significantly better generalization to unseen inference tasks compared to EGMs, as well as deep neural architectures like GibbsNet and VAEAC which allow arbitrary conditioning. Finally, AGMs allow fast data sampling, competitive with Gibbs sampling from EGMs.

In order to construct accurate proposers for Metropolis-Hastings Markov Chain Monte Carlo, we integrate ideas from probabilistic graphical models and neural networks in an open-source framework we call Lightweight Inference Compilation (LIC). LIC implements amortized inference within an open-universe declarative probabilistic programming language (PPL). Graph neural networks are used to parameterize proposal distributions as functions of Markov blankets, which during "compilation" are optimized to approximate single-site Gibbs sampling distributions. Unlike prior work in inference compilation (IC), LIC forgoes importance sampling of linear execution traces in favor of operating directly on Bayesian networks. Through using a declarative PPL, the Markov blankets of nodes (which may be non-static) are queried at inference-time to produce proposers Experimental results show LIC can produce proposers which have less parameters, greater robustness to nuisance random variables, and improved posterior sampling in a Bayesian logistic regression and $n$-schools inference application.

Stein discrepancies (SDs) monitor convergence and non-convergence in approximate inference when exact integration and sampling are intractable. However, the computation of a Stein discrepancy can be prohibitive if the Stein operator - often a sum over likelihood terms or potentials - is expensive to evaluate. To address this deficiency, we show that stochastic Stein discrepancies (SSDs) based on subsampled approximations of the Stein operator inherit the convergence control properties of standard SDs with probability 1. Along the way, we establish the convergence of Stein variational gradient descent (SVGD) on unbounded domains, resolving an open question of Liu (2017). In our experiments with biased Markov chain Monte Carlo (MCMC) hyperparameter tuning, approximate MCMC sampler selection, and stochastic SVGD, SSDs deliver comparable inferences to standard SDs with orders of magnitude fewer likelihood evaluations.

Many practical tasks involve sampling sequentially without replacement (WoR) from a finite population of size $N$, in an attempt to estimate some parameter $\theta^\star$. Accurately quantifying uncertainty throughout this process is a nontrivial task, but is necessary because it often determines when we stop collecting samples and confidently report a result. We present a suite of tools for designing confidence sequences (CS) for $\theta^\star$. A CS is a sequence of confidence sets $(C_n)_{n=1}^N$, that shrink in size, and all contain $\theta^\star$ simultaneously with high probability. We first exploit a relationship between Bayesian posteriors and martingales to construct a (frequentist) CS for the parameters of a hypergeometric distribution. We then present Hoeffding- and empirical-Bernstein-type time-uniform CSs and fixed-time confidence intervals for sampling WoR which improve on previous bounds in the literature.

A central goal of probabilistic programming languages (PPLs) is to separate modelling from inference. However, this goal is hard to achieve in practice. Users are often forced to re-write their models in order to improve efficiency of inference or meet restrictions imposed by the PPL. Conditional independence (CI) relationships among parameters are a crucial aspect of probabilistic models that captures a qualitative summary of the specified model and can facilitate more efficient inference. We present an information flow type system for probabilistic programming that captures conditional independence (CI) relationships, and show that, for a well-typed program in our system, the distribution it implements is guaranteed to have certain CI-relationships. Further, by using type inference, we can statically \emph{deduce} which CI-properties are present in a specified model. As a practical application, we consider the problem of how to perform inference on models with mixed discrete and continuous parameters. Inference on such models is challenging in many existing PPLs, but can be improved through a workaround, where the discrete parameters are used \textit{implicitly}, at the expense of manual model re-writing. We present a source-to-source semantics-preserving transformation, which uses our CI-type system to automate this workaround by eliminating the discrete parameters from a probabilistic program. The resulting program can be seen as a hybrid inference algorithm on the original program, where continuous parameters can be drawn using efficient gradient-based inference methods, while the discrete parameters are drawn using variable elimination. We implement our CI-type system and its example application in SlicStan: a compositional variant of Stan.

A new class of Markov chain Monte Carlo (MCMC) algorithms, based on simulating piecewise deterministic Markov processes (PDMPs), have recently shown great promise: they are non-reversible, can mix better than standard MCMC algorithms, and can use subsampling ideas to speed up computation in big data scenarios. However, current PDMP samplers can only sample from posterior densities that are differentiable almost everywhere, which precludes their use for model choice. Motivated by variable selection problems, we show how to develop reversible jump PDMP samplers that can jointly explore the discrete space of models and the continuous space of parameters. Our framework is general: it takes any existing PDMP sampler, and adds two types of trans-dimensional moves that allow for the addition or removal of a variable from the model. We show how the rates of these trans-dimensional moves can be calculated so that the sampler has the correct invariant distribution. Simulations show that the new samplers can mix better than standard MCMC algorithms. Our empirical results show they are also more efficient than gradient-based samplers that avoid model choice through use of continuous spike-and-slab priors which replace a point mass at zero for each parameter with a density concentrated around zero.