One of the primary goals of systems neuroscience is to relate the structure of neural circuits to their function, yet patterns of connectivity are difficult to establish when recording from large populations in behaving organisms. Many previous approaches have attempted to estimate functional connectivity between neurons using statistical modeling of observational data, but these approaches rely heavily on parametric assumptions and are purely correlational. Recently, however, holographic photostimulation techniques have made it possible to precisely target selected ensembles of neurons, offering the possibility of establishing direct causal links. Here, we propose a method based on noisy group testing that drastically increases the efficiency of this process in sparse networks. By stimulating small ensembles of neurons, we show that it is possible to recover binarized network connectivity with a number of tests that grows only logarithmically with population size under minimal statistical assumptions. Moreover, we prove that our approach, which reduces to an efficiently solvable convex optimization problem, can be related to Variational Bayesian inference on the binary connection weights, and we derive rigorous bounds on the posterior marginals. This allows us to extend our method to the streaming setting, where continuously updated posteriors allow for optional stopping, and we demonstrate the feasibility of inferring connectivity for networks of up to tens of thousands of neurons online. Finally, we show how our work can be theoretically linked to compressed sensing approaches, and compare results for connectivity inference in different settings.
Human collaborators can effectively communicate with their partners to finish a common task by inferring each other's mental states (e.g., goals, beliefs, and desires). Such mind-aware communication minimizes the discrepancy among collaborators' mental states, and is crucial to the success in human ad-hoc teaming. We believe that robots collaborating with human users should demonstrate similar pedagogic behavior. Thus, in this paper, we propose a novel explainable AI (XAI) framework for achieving human-like communication in human-robot collaborations, where the robot builds a hierarchical mind model of the human user and generates explanations of its own mind as a form of communications based on its online Bayesian inference of the user's mental state. To evaluate our framework, we conduct a user study on a real-time human-robot cooking task. Experimental results show that the generated explanations of our approach significantly improves the collaboration performance and user perception of the robot. Code and video demos are available on our project website: https://xfgao.github.io/xCookingWeb/.
In identifying infected patients in a population, group testing is an effective method to reduce the number of tests and correct the test errors. In the group testing procedure, tests are performed on pools of specimens collected from patients, where the number of pools is lower than that of patients. The performance of group testing heavily depends on the design of pools and algorithms that are used in inferring the infected patients from the test outcomes. In this paper, an adaptive design method of pools based on the predictive distribution is proposed in the framework of Bayesian inference. The proposed method executed using the belief propagation algorithm results in more accurate identification of the infected patients, as compared to the group testing performed on random pools determined in advance.
Modeling stochastic traffic behaviors at the microscopic level, such as car-following and lane-changing, is a crucial task to understand the interactions between individual vehicles in traffic streams. Leveraging a recently developed theory named physics regularized Gaussian process (PRGP), this study presents a stochastic microscopic traffic model that can capture the randomness and measure errors in the real world. Physical knowledge from classical car-following models is converted as physics regularizers, in the form of shadow Gaussian process (GP), of a multivariate PRGP for improving the modeling accuracy. More specifically, a Bayesian inference algorithm is developed to estimate the mean and kernel of GPs, and an enhanced latent force model is formulated to encode physical knowledge into stochastic processes. Also, based on the posterior regularization inference framework, an efficient stochastic optimization algorithm is developed to maximize the evidence lower-bound of the system likelihood. To evaluate the performance of the proposed models, this study conducts empirical studies on real-world vehicle trajectories from the NGSIM dataset. Since one unique feature of the proposed framework is the capability of capturing both car-following and lane-changing behaviors with one single model, numerical tests are carried out with two separated datasets, one contains lane-changing maneuvers and the other doesn't. The results show the proposed method outperforms the previous influential methods in estimation precision.
Scientists and engineers employ stochastic numerical simulators to model empirically observed phenomena. In contrast to purely statistical models, simulators express scientific principles that provide powerful inductive biases, improve generalization to new data or scenarios and allow for fewer, more interpretable and domain-relevant parameters. Despite these advantages, tuning a simulator's parameters so that its outputs match data is challenging. Simulation-based inference (SBI) seeks to identify parameter sets that a) are compatible with prior knowledge and b) match empirical observations. Importantly, SBI does not seek to recover a single 'best' data-compatible parameter set, but rather to identify all high probability regions of parameter space that explain observed data, and thereby to quantify parameter uncertainty. In Bayesian terminology, SBI aims to retrieve the posterior distribution over the parameters of interest. In contrast to conventional Bayesian inference, SBI is also applicable when one can run model simulations, but no formula or algorithm exists for evaluating the probability of data given parameters, i.e. the likelihood. We present $\texttt{sbi}$, a PyTorch-based package that implements SBI algorithms based on neural networks. $\texttt{sbi}$ facilitates inference on black-box simulators for practising scientists and engineers by providing a unified interface to state-of-the-art algorithms together with documentation and tutorials.
In inverse problems, we often have access to data consisting of paired samples $(x,y)\sim p_{X,Y}(x,y)$ where $y$ are partial observations of a physical system, and $x$ represents the unknowns of the problem. Under these circumstances, we can employ supervised training to learn a solution $x$ and its uncertainty from the observations $y$. We refer to this problem as the "supervised" case. However, the data $y\sim p_{Y}(y)$ collected at one point could be distributed differently than observations $y'\sim p_{Y}'(y')$, relevant for a current set of problems. In the context of Bayesian inference, we propose a two-step scheme, which makes use of normalizing flows and joint data to train a conditional generator $q_{\theta}(x|y)$ to approximate the target posterior density $p_{X|Y}(x|y)$. Additionally, this preliminary phase provides a density function $q_{\theta}(x|y)$, which can be recast as a prior for the "unsupervised" problem, e.g.~when only the observations $y'\sim p_{Y}'(y')$, a likelihood model $y'|x$, and a prior on $x'$ are known. We then train another invertible generator with output density $q'_{\phi}(x|y')$ specifically for $y'$, allowing us to sample from the posterior $p_{X|Y}'(x|y')$. We present some synthetic results that demonstrate considerable training speedup when reusing the pretrained network $q_{\theta}(x|y')$ as a warm start or preconditioning for approximating $p_{X|Y}'(x|y')$, instead of learning from scratch. This training modality can be interpreted as an instance of transfer learning. This result is particularly relevant for large-scale inverse problems that employ expensive numerical simulations.
Multinomial probit models are routinely-implemented representations for learning how the class probabilities of categorical response data change with p observed predictors. Although several frequentist methods have been developed for estimation, inference and classification within such a class of models, Bayesian inference is still lagging behind. This is due to the apparent absence of a tractable class of conjugate priors, that may facilitate posterior inference on the multinomial probit coefficients. Such an issue has motivated increasing efforts toward the development of effective Markov chain Monte Carlo methods, but state-of-the-art solutions still face severe computational bottlenecks, especially in high dimensions. In this article, we show that the entire class of unified skew-normal (SUN) distributions is conjugate to several multinomial probit models. Leveraging this result and the SUN properties, we improve upon state-of-the-art solutions for posterior inference and classification both in terms of closed-form results for several functionals of interest, and also by developing novel computational methods relying either on independent and identically distributed samples from the exact posterior or on scalable and accurate variational approximations based on blocked partially-factorized representations. As illustrated in simulations and in a gastrointestinal lesions application, the magnitude of the improvements relative to current methods is particularly evident, in practice, when the focus is on high-dimensional studies.
Traditional training of deep classifiers yields overconfident models that are not reliable under dataset shift. We propose a Bayesian framework to obtain reliable uncertainty estimates for deep classifiers. Our approach consists of a plug-in "generator" used to augment the data with an additional class of points that lie on the boundary of the training data, followed by Bayesian inference on top of features that are trained to distinguish these "out-of-distribution" points.
We formulate approximate Bayesian inference in non-conjugate temporal and spatio-temporal Gaussian process models as a simple parameter update rule applied during Kalman smoothing. This viewpoint encompasses most inference schemes, including expectation propagation (EP), the classical (Extended, Unscented, etc.) Kalman smoothers, and variational inference. We provide a unifying perspective on these algorithms, showing how replacing the power EP moment matching step with linearisation recovers the classical smoothers. EP provides some benefits over the traditional methods via introduction of the so-called cavity distribution, and we combine these benefits with the computational efficiency of linearisation, providing extensive empirical analysis demonstrating the efficacy of various algorithms under this unifying framework. We provide a fast implementation of all methods in JAX.
Forecasting the effect of COVID-19 is essential to design policies that may prepare us to handle the pandemic. Many methods have already been proposed, particularly, to forecast reported cases and deaths at country-level and state-level. Many of these methods are based on traditional epidemiological model which rely on simulations or Bayesian inference to simultaneously learn many parameters at a time. This makes them prone to over-fitting and slow execution. We propose an extension to our model SIkJ$\alpha$ to forecast deaths and show that it can consider the effect of many complexities of the epidemic process and yet be simplified to a few parameters that are learned using fast linear regressions. We also present an evaluation of our method against seven approaches currently being used by the CDC, based on their two weeks forecast at various times during the pandemic. We demonstrate that our method achieves better root mean squared error compared to these seven approaches during majority of the evaluation period. Further, on a 2 core desktop machine, our approach takes only 3.18s to tune hyper-parameters, learn parameters and generate 100 days of forecasts of reported cases and deaths for all the states in the US. The total execution time for 184 countries is 11.83s and for all the US counties ($>$ 3000) is 101.03s.
Monte Carlo (MC) dropout is one of the state-of-the-art approaches for uncertainty estimation in neural networks (NNs). It has been interpreted as approximately performing Bayesian inference. Based on previous work on the approximation of Gaussian processes by wide and deep neural networks with random weights, we study the limiting distribution of wide untrained NNs under dropout more rigorously and prove that they as well converge to Gaussian processes for fixed sets of weights and biases. We sketch an argument that this property might also hold for infinitely wide feed-forward networks that are trained with (full-batch) gradient descent. The theory is contrasted by an empirical analysis in which we find correlations and non-Gaussian behaviour for the pre-activations of finite width NNs. We therefore investigate how (strongly) correlated pre-activations can induce non-Gaussian behavior in NNs with strongly correlated weights.
Continuously-indexed flows (CIFs) have recently achieved improvements over baseline normalizing flows on a variety of density estimation tasks. CIFs do not possess a closed-form marginal density, and so, unlike standard flows, cannot be plugged in directly to a variational inference (VI) scheme in order to produce a more expressive family of approximate posteriors. However, we show here how CIFs can be used as part of an auxiliary VI scheme to formulate and train expressive posterior approximations in a natural way. We exploit the conditional independence structure of multi-layer CIFs to build the required auxiliary inference models, which we show empirically yield low-variance estimators of the model evidence. We then demonstrate the advantages of CIFs over baseline flows in VI problems when the posterior distribution of interest possesses a complicated topology, obtaining improved results in both the Bayesian inference and surrogate maximum likelihood settings.
While deep learning methods continue to improve in predictive accuracy on a wide range of application domains, significant issues remain with other aspects of their performance including their ability to quantify uncertainty and their robustness. Recent advances in approximate Bayesian inference hold significant promise for addressing these concerns, but the computational scalability of these methods can be problematic when applied to large-scale models. In this paper, we describe initial work on the development ofURSABench(the Uncertainty, Robustness, Scalability, and Accu-racy Benchmark), an open-source suite of bench-marking tools for comprehensive assessment of approximate Bayesian inference methods with a focus on deep learning-based classification tasks
We are interested in gradient-based Explicit Generative Modeling where samples can be derived from iterative gradient updates based on an estimate of the score function of the data distribution. Recent advances in Stochastic Gradient Langevin Dynamics (SGLD) demonstrates impressive results with energy-based models on high-dimensional and complex data distributions. Stein Variational Gradient Descent (SVGD) is a deterministic sampling algorithm that iteratively transports a set of particles to approximate a given distribution, based on functional gradient descent that decreases the KL divergence. SVGD has promising results on several Bayesian inference applications. However, applying SVGD on high dimensional problems is still under-explored. The goal of this work is to study high dimensional inference with SVGD. We first identify key challenges in practical kernel SVGD inference in high-dimension. We propose noise conditional kernel SVGD (NCK-SVGD), that works in tandem with the recently introduced Noise Conditional Score Network estimator. NCK is crucial for successful inference with SVGD in high dimension, as it adapts the kernel to the noise level of the score estimate. As we anneal the noise, NCK-SVGD targets the real data distribution. We then extend the annealed SVGD with an entropic regularization. We show that this offers a flexible control between sample quality and diversity, and verify it empirically by precision and recall evaluations. The NCK-SVGD produces samples comparable to GANs and annealed SGLD on computer vision benchmarks, including MNIST and CIFAR-10.
Variational inference (VI) plays an essential role in approximate Bayesian inference due to its computational efficiency and broad applicability. Crucial to the performance of VI is the selection of the associated divergence measure, as VI approximates the intractable distribution by minimizing this divergence. In this paper we propose a meta-learning algorithm to learn the divergence metric suited for the task of interest, automating the design of VI methods. In addition, we learn the initialization of the variational parameters without additional cost when our method is deployed in the few-shot learning scenarios. We demonstrate our approach outperforms standard VI on Gaussian mixture distribution approximation, Bayesian neural network regression, image generation with variational autoencoders and recommender systems with a partial variational autoencoder.
Bayesian methods have proved powerful in many applications for the inference of model parameters from data. These methods are based on Bayes' theorem, which itself is deceptively simple. However, in practice the computations required are intractable even for simple cases. Hence methods for Bayesian inference have historically either been significantly approximate, e.g., the Laplace approximation, or achieve samples from the exact solution at significant computational expense, e.g., Markov Chain Monte Carlo methods. Since around the year 2000 so-called Variational approaches to Bayesian inference have been increasingly deployed. In its most general form Variational Bayes (VB) involves approximating the true posterior probability distribution via another more 'manageable' distribution, the aim being to achieve as good an approximation as possible. In the original FMRIB Variational Bayes tutorial we documented an approach to VB based that took a 'mean field' approach to forming the approximate posterior, required the conjugacy of prior and likelihood, and exploited the Calculus of Variations, to derive an iterative series of update equations, akin to Expectation Maximisation. In this tutorial we revisit VB, but now take a stochastic approach to the problem that potentially circumvents some of the limitations imposed by the earlier methodology. This new approach bears a lot of similarity to, and has benefited from, computational methods applied to machine learning algorithms. Although, what we document here is still recognisably Bayesian inference in the classic sense, and not an attempt to use machine learning as a black-box to solve the inference problem.
Variational Bayes (VB) has been used to facilitate the calculation of the posterior distribution in the context of Bayesian inference of the parameters of nonlinear models from data. Previously an analytical formulation of VB has been derived for nonlinear model inference on data with additive gaussian noise as an alternative to nonlinear least squares. Here a stochastic solution is derived that avoids some of the approximations required of the analytical formulation, offering a solution that can be more flexibly deployed for nonlinear model inference problems. The stochastic VB solution was used for inference on a biexponential toy case and the algorithmic parameter space explored, before being deployed on real data from a magnetic resonance imaging study of perfusion. The new method was found to achieve comparable parameter recovery to the analytic solution and be competitive in terms of computational speed despite being reliant on sampling.
Buildings consume over 40% of the total energy in modern societies, and improving their energy efficiency can significantly reduce our energy footprint. In this paper, we present \texttt{WattScale}, a data-driven approach to identify the least energy-efficient buildings from a large population of buildings in a city or a region. Unlike previous methods such as least-squares that use point estimates, \texttt{WattScale} uses Bayesian inference to capture the stochasticity in the daily energy usage by estimating the distribution of parameters that affect a building. Further, it compares them with similar homes in a given population. \texttt{WattScale} also incorporates a fault detection algorithm to identify the underlying causes of energy inefficiency. We validate our approach using ground truth data from different geographical locations, which showcases its applicability in various settings. \texttt{WattScale} has two execution modes -- (i) individual, and (ii) region-based, which we highlight using two case studies. For the individual execution mode, we present results from a city containing >10,000 buildings and show that more than half of the buildings are inefficient in one way or another indicating a significant potential from energy improvement measures. Additionally, we provide probable cause of inefficiency and find that 41\%, 23.73\%, and 0.51\% homes have poor building envelope, heating, and cooling system faults, respectively. For the region-based execution mode, we show that \texttt{WattScale} can be extended to millions of homes in the US due to the recent availability of representative energy datasets.
Determination of inspection and maintenance policies for minimizing long-term risks and costs in deteriorating engineering environments constitutes a complex optimization problem. Major computational challenges include the (i) curse of dimensionality, due to exponential scaling of state/action set cardinalities with the number of components; (ii) curse of history, related to exponentially growing decision-trees with the number of decision-steps; (iii) presence of state uncertainties, induced by inherent environment stochasticity and variability of inspection/monitoring measurements; (iv) presence of constraints, pertaining to stochastic long-term limitations, due to resource scarcity and other infeasible/undesirable system responses. In this work, these challenges are addressed within a joint framework of constrained Partially Observable Markov Decision Processes (POMDP) and multi-agent Deep Reinforcement Learning (DRL). POMDPs optimally tackle (ii)-(iii), combining stochastic dynamic programming with Bayesian inference principles. Multi-agent DRL addresses (i), through deep function parametrizations and decentralized control assumptions. Challenge (iv) is herein handled through proper state augmentation and Lagrangian relaxation, with emphasis on life-cycle risk-based constraints and budget limitations. The underlying algorithmic steps are provided, and the proposed framework is found to outperform well-established policy baselines and facilitate adept prescription of inspection and intervention actions, in cases where decisions must be made in the most resource- and risk-aware manner.
Low rank tensor ring model is powerful for image completion which recovers missing entries in data acquisition and transformation. The recently proposed tensor ring (TR) based completion algorithms generally solve the low rank optimization problem by alternating least squares method with predefined ranks, which may easily lead to overfitting when the unknown ranks are set too large and only a few measurements are available. In this paper, we present a Bayesian low rank tensor ring model for image completion by automatically learning the low rank structure of data. A multiplicative interaction model is developed for the low-rank tensor ring decomposition, where core factors are enforced to be sparse by assuming their entries obey Student-T distribution. Compared with most of the existing methods, the proposed one is free of parameter-tuning, and the TR ranks can be obtained by Bayesian inference. Numerical Experiments, including synthetic data, color images with different sizes and YaleFace dataset B with respect to one pose, show that the proposed approach outperforms state-of-the-art ones, especially in terms of recovery accuracy.