Simulation plays a central role in scientific discovery. In many applications, the bottleneck is no longer running a simulator; it is choosing among large families of plausible simulators, each corresponding to different forward models/hypotheses consistent with observations. Over large model families, classical Bayesian workflows for model selection are impractical. Furthermore, amortized model selection methods typically hard-code a fixed model prior or complexity penalty at training time, requiring users to commit to a particular parsimony assumption before seeing the data. We introduce PRISM, a simulation-based encoder-decoder that infers a joint posterior over both discrete model structures and associated continuous parameters, while enabling test-time control of model complexity via a tunable model prior that the network is conditioned on. We show that PRISM scales to families with combinatorially many (up to billions) of model instantiations on a synthetic symbolic regression task. As a scientific application, we evaluate PRISM on biophysical modeling for diffusion MRI data, showing the ability to perform model selection across several multi-compartment models, on both synthetic and in vivo neuroimaging data.

Causal discovery from empirical data is a fundamental problem in many scientific domains. Observational data allows for identifiability only up to Markov equivalence class. In this paper we first propose a polynomial time algorithm for learning the exact correctly-oriented structure of the transitive reduction of any causal Bayesian network with high probability, by using interventional path queries. Each path query takes as input an origin node and a target node, and answers whether there is a directed path from the origin to the target. This is done by intervening on the origin node and observing samples from the target node. We theoretically show the logarithmic sample complexity for the size of interventional data per path query, for continuous and discrete networks. We then show how to learn the transitive edges using also logarithmic sample complexity (albeit in time exponential in the maximum number of parents for discrete networks), which allows us to learn the full network. We further extend our work by reducing the number of interventional path queries for learning rooted trees. We also provide an analysis of imperfect interventions.

We introduce a principled approach for unsupervised structure learning of deep neural networks. We propose a new interpretation for depth and inter-layer connectivity where conditional independencies in the input distribution are encoded hierarchically in the network structure. Thus, the depth of the network is determined inherently. The proposed method casts the problem of neural network structure learning as a problem of Bayesian network structure learning. Then, instead of directly learning the discriminative structure, it learns a generative graph, constructs its stochastic inverse, and then constructs a discriminative graph. We prove that conditional-dependency relations among the latent variables in the generative graph are preserved in the class-conditional discriminative graph. We demonstrate on image classification benchmarks that the deepest layers (convolutional and dense) of common networks can be replaced by significantly smaller learned structures, while maintaining classification accuracy---state-of-the-art on tested benchmarks. Our structure learning algorithm requires a small computational cost and runs efficiently on a standard desktop CPU.

Your Out-of-Distribution Detection Method is Not Robust!

Stochastic gradient Markov chain Monte Carlo (SGMCMC) has become a popular method for scalable Bayesian inference. These methods are based on sampling a discrete-time approximation to a continuous time process, such as the Langevin diffusion. When applied to distributions defined on a constrained space the time-discretization error can dominate when we are near the boundary of the space. We demonstrate that because of this, current SGMCMC methods for the simplex struggle with sparse simplex spaces; when many of the components are close to zero. Unfortunately, many popular large-scale Bayesian models, such as network or topic models, require inference on sparse simplex spaces. To avoid the biases caused by this discretization error, we propose the stochastic Cox-Ingersoll-Ross process (SCIR), which removes all discretization error and we prove that samples from the SCIR process are asymptotically unbiased. We discuss how this idea can be extended to target other constrained spaces. Use of the SCIR process within a SGMCMC algorithm is shown to give substantially better performance for a topic model and a Dirichlet process mixture model than existing SGMCMC approaches.

Implicit feedback is widely used in collaborative filtering methods for recommendation. It is well known that implicit feedback contains a large number of values that are \emph{missing not at random} (MNAR); and the missing data is a mixture of negative and unknown feedback, making it difficult to learn user's negative preferences. Recent studies modeled \emph{exposure}, a latent missingness variable which indicates whether an item is missing to a user, to give each missing entry a confidence of being negative feedback. However, these studies use static models and ignore the information in temporal dependencies among items, which seems to be a essential underlying factor to subsequent missingness. To model and exploit the dynamics of missingness, we propose a latent variable named ``\emph{user intent}'' to govern the temporal changes of item missingness, and a hidden Markov model to represent such a process. The resulting framework captures the dynamic item missingness and incorporate it into matrix factorization (MF) for recommendation. We also explore two types of constraints to achieve a more compact and interpretable representation of \emph{user intents}. Experiments on real-world datasets demonstrate the superiority of our method against state-of-the-art recommender systems.

Expectation Maximization (EM) is among the most popular algorithms for maximum likelihood estimation, but it is generally only guaranteed to find its stationary points of the log-likelihood objective. The goal of this article is to present theoretical and empirical evidence that over-parameterization can help EM avoid spurious local optima in the log-likelihood. We consider the problem of estimating the mean vectors of a Gaussian mixture model in a scenario where the mixing weights are known. Our study shows that the global behavior of EM, when one uses an over-parameterized model in which the mixing weights are treated as unknown, is better than that when one uses the (correct) model with the mixing weights fixed to the known values. For symmetric Gaussians mixtures with two components, we prove that introducing the (statistically redundant) weight parameters enables EM to find the global maximizer of the log-likelihood starting from almost any initial mean parameters, whereas EM without this over-parameterization may very often fail. For other Gaussian mixtures, we provide empirical evidence that shows similar behavior. Our results corroborate the value of over-parameterization in solving non-convex optimization problems, previously observed in other domains.

Understanding how humans and animals learn about statistical regularities in stable and volatile environments, and utilize these regularities to make predictions and decisions, is an important problem in neuroscience and psychology. Using a Bayesian modeling framework, specifically the Dynamic Belief Model (DBM), it has previously been shown that humans tend to make the {\it default} assumption that environmental statistics undergo abrupt, unsignaled changes, even when environmental statistics are actually stable. Because exact Bayesian inference in this setting, an example of switching state space models, is computationally intense, a number of approximately Bayesian and heuristic algorithms have been proposed to account for learning/prediction in the brain. Here, we examine a neurally plausible algorithm, a special case of leaky integration dynamics we denote as EXP (for exponential filtering), that is significantly simpler than all previously suggested algorithms except for the delta-learning rule, and which far outperforms the delta rule in approximating Bayesian prediction performance. We derive the theoretical relationship between DBM and EXP, and show that EXP gains computational efficiency by foregoing the representation of inferential uncertainty (as does the delta rule), but that it nevertheless achieves near-Bayesian performance due to its ability to incorporate a persistent prior influence unique to DBM and absent from the other algorithms. Furthermore, we show that EXP is comparable to DBM but better than all other models in reproducing human behavior in a visual search task, suggesting that human learning and prediction also incorporates an element of persistent prior. More broadly, our work demonstrates that when observations are information-poor, detecting changes or modulating the learning rate is both {\it difficult} and (thus) {\it unnecessary} for making Bayes-optimal predictions.

Interactive partially observable Markov decision processes (I-POMDPs) provide a principled framework for planning and acting in a partially observable, stochastic and multi-agent environment. It extends POMDPs to multi-agent settings by including models of other agents in the state space and forming a hierarchical belief structure. In order to predict other agents' actions using I-POMDPs, we propose an approach that effectively uses Bayesian inference and sequential Monte Carlo sampling to learn others' intentional models which ascribe to them beliefs, preferences and rationality in action selection. Empirical results show that our algorithm accurately learns models of the other agent and has superior performance than methods that use subintentional models. Our approach serves as a generalized Bayesian learning algorithm that learns other agents' beliefs, strategy levels, and transition, observation and reward functions.

The most widely used technology to identify the proteins present in a complex biological sample is tandem mass spectrometry, which quickly produces a large collection of spectra representative of the peptides (i.e., protein subsequences) present in the original sample. In this work, we greatly expand the parameter learning capabilities of a dynamic Bayesian network (DBN) peptide-scoring algorithm, Didea, by deriving emission distributions for which its conditional log-likelihood scoring function remains concave. We show that this class of emission distributions, called Convex Virtual Emissions (CVEs), naturally generalizes the log-sum-exp function while rendering both maximum likelihood estimation and conditional maximum likelihood estimation concave for a wide range of Bayesian networks. Utilizing CVEs in Didea allows efficient learning of a large number of parameters while ensuring global convergence, in stark contrast to Didea's previous parameter learning framework (which could only learn a single parameter using a costly grid search) and other trainable models (which only ensure convergence to local optima). The newly trained scoring function substantially outperforms the state-of-the-art in both scoring function accuracy and downstream Fisher kernel analysis. Furthermore, we significantly improve Didea's runtime performance through successive optimizations to its message passing schedule and derive explicit connections between Didea's new concave score and related MS/MS scoring functions.