Amortized Bayesian inference trains neural networks to solve stochastic inference problems using model simulations, thereby making it possible to rapidly perform Bayesian inference for any newly observed data. However, current simulation-based amortized inference methods are simulation-hungry and inflexible: They require the specification of a fixed parametric prior, simulator, and inference tasks ahead of time. Here, we present a new amortized inference method---the Simformer---which overcomes these limitations. By training a probabilistic diffusion model with transformer architectures, the Simformer outperforms current state-of-the-art amortized inference approaches on benchmark tasks and is substantially more flexible: It can be applied to models with function-valued parameters, it can handle inference scenarios with missing or unstructured data, and it can sample arbitrary conditionals of the joint distribution of parameters and data, including both posterior and likelihood. We showcase the performance and flexibility of the Simformer on simulators from ecology, epidemiology, and neuroscience, and demonstrate that it opens up new possibilities and application domains for amortized Bayesian inference on simulation-based models.

We introduce a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model’s performance, in terms of both training time and final accuracy. Our code can be found at https://github.com/plai-group/gsdm.

We propose a new class of generative model that naturally handles data of varying dimensionality by jointly modeling the state and dimension of each datapoint. The generative process is formulated as a jump diffusion process that makes jumps between different dimensional spaces. We first define a dimension destroying forward noising process, before deriving the dimension creating time-reversed generative process along with a novel evidence lower bound training objective for learning to approximate it. Simulating our learned approximation to the time-reversed generative process then provides an effective way of sampling data of varying dimensionality by jointly generating state values and dimensions. We demonstrate our approach on molecular and video datasets of varying dimensionality, reporting better compatibility with test-time diffusion guidance imputation tasks and improved interpolation capabilities versus fixed dimensional models that generate state values and dimensions separately.

We present a framework for video modeling based on denoising diffusion probabilistic models that produces long-duration video completions in a variety of realistic environments. We introduce a generative model that can at test-time sample any arbitrary subset of video frames conditioned on any other subset and present an architecture adapted for this purpose. Doing so allows us to efficiently compare and optimize a variety of schedules for the order in which frames in a long video are sampled and use selective sparse and long-range conditioning on previously sampled frames. We demonstrate improved video modeling over prior work on a number of datasets and sample temporally coherent videos over 25 minutes in length. We additionally release a new video modeling dataset and semantically meaningful metrics based on videos generated in the CARLA autonomous driving simulator.

Sequential Monte Carlo (SMC) is a general-purpose methodology for recursive Bayesian inference, and is widely used in state space modeling and probabilistic programming. Its resample-move variant reduces the variance of posterior estimates by interleaving Markov chain Monte Carlo (MCMC) steps for particle “rejuvenation”; but this requires accessing all past observations and leads to linearly growing memory size and quadratic computation cost. Under the assumption of exchangeability, we introduce sequential core-set Monte Carlo (SCMC), which achieves constant space and linear time by rejuvenating based on sparse, weighted subsets of past data. In contrast to earlier approaches, which uniformly subsample or throw away observations, SCMC uses a novel online version of a state-of-the-art Bayesian core-set algorithm to incrementally construct a nonparametric, data- and model-dependent variational representation of the unnormalized target density. Experiments demonstrate significantly reduced approximation errors at negligible additional cost.

We exploit minimally faithful inversion of graphical model structures to specify sparse continuous normalizing flows (CNFs) for amortized inference. We find that the sparsity of this factorization can be exploited to reduce the numbers of parameters in the neural network, adaptive integration steps of the flow, and consequently FLOPs at both training and inference time without decreasing performance in comparison to unconstrained flows. By expressing the structure inversion as a compilation pass in a probabilistic programming language, we are able to apply it in a novel way to models as complex as convolutional neural networks. Furthermore, we extend the training objective for CNFs in the context of inference amortization to the symmetric Kullback-Leibler divergence, and demonstrate its theoretical and practical advantages.