Graphs have been commonly used to represent complex data structures. In models dealing with graph-structured data, multivariate parameters may not only exhibit sparse patterns but have structured sparsity and smoothness in the sense that both zero and non-zero parameters tend to cluster together. We propose a new prior for high-dimensional parameters with graphical relations, referred to as the Tree-based Low-rank Horseshoe (T-LoHo) model, that generalizes the popular univariate Bayesian horseshoe shrinkage prior to the multivariate setting to detect structured sparsity and smoothness simultaneously. The T-LoHo prior can be embedded in many high-dimensional hierarchical models. To illustrate its utility, we apply it to regularize a Bayesian high-dimensional regression problem where the regression coefficients are linked by a graph, so that the resulting clusters have flexible shapes and satisfy the cluster contiguity constraint with respect to the graph. We design an efficient Markov chain Monte Carlo algorithm that delivers full Bayesian inference with uncertainty measures for model parameters such as the number of clusters. We offer theoretical investigations of the clustering effects and posterior concentration results. Finally, we illustrate the performance of the model with simulation studies and a real data application for anomaly detection on a road network. The results indicate substantial improvements over other competing methods such as the sparse fused lasso.
Many common machine learning methods involve the geometric annealing path, a sequence of intermediate densities between two distributions of interest constructed using the geometric average. While alternatives such as the moment-averaging path have demonstrated performance gains in some settings, their practical applicability remains limited by exponential family endpoint assumptions and a lack of closed form energy function. In this work, we introduce $q$-paths, a family of paths which is derived from a generalized notion of the mean, includes the geometric and arithmetic mixtures as special cases, and admits a simple closed form involving the deformed logarithm function from nonextensive thermodynamics. Following previous analysis of the geometric path, we interpret our $q$-paths as corresponding to a $q$-exponential family of distributions, and provide a variational representation of intermediate densities as minimizing a mixture of $\alpha$-divergences to the endpoints. We show that small deviations away from the geometric path yield empirical gains for Bayesian inference using Sequential Monte Carlo and generative model evaluation using Annealed Importance Sampling.
Deep ensembles have recently gained popularity in the deep learning community for their conceptual simplicity and efficiency. However, maintaining functional diversity between ensemble members that are independently trained with gradient descent is challenging. This can lead to pathologies when adding more ensemble members, such as a saturation of the ensemble performance, which converges to the performance of a single model. Moreover, this does not only affect the quality of its predictions, but even more so the uncertainty estimates of the ensemble, and thus its performance on out-of-distribution data. We hypothesize that this limitation can be overcome by discouraging different ensemble members from collapsing to the same function. To this end, we introduce a kernelized repulsive term in the update rule of the deep ensembles. We show that this simple modification not only enforces and maintains diversity among the members but, even more importantly, transforms the maximum a posteriori inference into proper Bayesian inference. Namely, we show that the training dynamics of our proposed repulsive ensembles follow a Wasserstein gradient flow of the KL divergence with the true posterior. We study repulsive terms in weight and function space and empirically compare their performance to standard ensembles and Bayesian baselines on synthetic and real-world prediction tasks.
Approximate Bayesian inference for neural networks is considered a robust alternative to standard training, often providing good performance on out-of-distribution data. However, Bayesian neural networks (BNNs) with high-fidelity approximate inference via full-batch Hamiltonian Monte Carlo achieve poor generalization under covariate shift, even underperforming classical estimation. We explain this surprising result, showing how a Bayesian model average can in fact be problematic under covariate shift, particularly in cases where linear dependencies in the input features cause a lack of posterior contraction. We additionally show why the same issue does not affect many approximate inference procedures, or classical maximum a-posteriori (MAP) training. Finally, we propose novel priors that improve the robustness of BNNs to many sources of covariate shift.
Recent machine learning advances have proposed black-box estimation of unknown continuous-time system dynamics directly from data. However, earlier works are based on approximative ODE solutions or point estimates. We propose a novel Bayesian nonparametric model that uses Gaussian processes to infer posteriors of unknown ODE systems directly from data. We derive sparse variational inference with decoupled functional sampling to represent vector field posteriors. We also introduce a probabilistic shooting augmentation to enable efficient inference from arbitrarily long trajectories. The method demonstrates the benefit of computing vector field posteriors, with predictive uncertainty scores outperforming alternative methods on multiple ODE learning tasks.
Within epidemiological modeling, the majority of analyses assume a single epidemic process for generating ground-truth data. However, this assumed data generation process can be unrealistic, since data sources for epidemics are often aggregated across geographic regions and communities. As a result, state-of-the-art models for estimating epidemiological parameters, e.g.~transmission rates, can be inappropriate when faced with complex systems. Our work empirically demonstrates some limitations of applying epidemiological models to aggregated datasets. We generate three complex outbreak scenarios by combining incidence curves from multiple epidemics that are independently simulated via SEIR models with different sets of parameters. Using these scenarios, we assess the robustness of a state-of-the-art Bayesian inference method that estimates the epidemic trajectory from viral load surveillance data. We evaluate two data-generating models within this Bayesian inference framework: a simple exponential growth model and a highly flexible Gaussian process prior model. Our results show that both models generate accurate transmission rate estimates for the combined incidence curve at the cost of generating biased estimates for each underlying epidemic, reflecting highly heterogeneous underlying population dynamics. The exponential growth model, while interpretable, is unable to capture the complexity of the underlying epidemics. With sufficient surveillance data, the Gaussian process prior model captures the shape of complex trajectories, but is imprecise for periods of low data coverage. Thus, our results highlight the potential pitfalls of neglecting complexity and heterogeneity in the data generation process, which can mask underlying location- and population-specific epidemic dynamics.
Despite their compelling theoretical properties, Bayesian neural networks (BNNs) tend to perform worse than frequentist methods in classification-based uncertainty quantification (UQ) tasks such as out-of-distribution (OOD) detection. In this paper, based on empirical findings in prior works, we hypothesize that this issue is because even recent Bayesian methods have never considered OOD data in their training processes, even though this "OOD training" technique is an integral part of state-of-the-art frequentist UQ methods. To validate this, we treat OOD data as a first-class citizen in BNN training by exploring four different ways of incorporating OOD data into Bayesian inference. We show in extensive experiments that OOD-trained BNNs are competitive to recent frequentist baselines. This work thus provides strong baselines for future work in Bayesian UQ.
Recent years have witnessed an upsurge of interest in employing flexible machine learning models for instrumental variable (IV) regression, but the development of uncertainty quantification methodology is still lacking. In this work we present a novel quasi-Bayesian procedure for IV regression, building upon the recently developed kernelized IV models and the dual/minimax formulation of IV regression. We analyze the frequentist behavior of the proposed method, by establishing minimax optimal contraction rates in $L_2$ and Sobolev norms, and discussing the frequentist validity of credible balls. We further derive a scalable inference algorithm which can be extended to work with wide neural network models. Empirical evaluation shows that our method produces informative uncertainty estimates on complex high-dimensional problems.
Lifelong Learning (LL) refers to the ability to continually learn and solve new problems with incremental available information over time while retaining previous knowledge. Much attention has been given lately to Supervised Lifelong Learning (SLL) with a stream of labelled data. In contrast, we focus on resolving challenges in Unsupervised Lifelong Learning (ULL) with streaming unlabelled data when the data distribution and the unknown class labels evolve over time. Bayesian framework is natural to incorporate past knowledge and sequentially update the belief with new data. We develop a fully Bayesian inference framework for ULL with a novel end-to-end Deep Bayesian Unsupervised Lifelong Learning (DBULL) algorithm, which can progressively discover new clusters without forgetting the past with unlabelled data while learning latent representations. To efficiently maintain past knowledge, we develop a novel knowledge preservation mechanism via sufficient statistics of the latent representation for raw data. To detect the potential new clusters on the fly, we develop an automatic cluster discovery and redundancy removal strategy in our inference inspired by Nonparametric Bayesian statistics techniques. We demonstrate the effectiveness of our approach using image and text corpora benchmark datasets in both LL and batch settings.
Learning the causal structure that underlies data is a crucial step towards robust real-world decision making. The majority of existing work in causal inference focuses on determining a single directed acyclic graph (DAG) or a Markov equivalence class thereof. However, a crucial aspect to acting intelligently upon the knowledge about causal structure which has been inferred from finite data demands reasoning about its uncertainty. For instance, planning interventions to find out more about the causal mechanisms that govern our data requires quantifying epistemic uncertainty over DAGs. While Bayesian causal inference allows to do so, the posterior over DAGs becomes intractable even for a small number of variables. Aiming to overcome this issue, we propose a form of variational inference over the graphs of Structural Causal Models (SCMs). To this end, we introduce a parametric variational family modelled by an autoregressive distribution over the space of discrete DAGs. Its number of parameters does not grow exponentially with the number of variables and can be tractably learned by maximising an Evidence Lower Bound (ELBO). In our experiments, we demonstrate that the proposed variational posterior is able to provide a good approximation of the true posterior.
Spatio-temporal forecasting has numerous applications in analyzing wireless, traffic, and financial networks. Many classical statistical models often fall short in handling the complexity and high non-linearity present in time-series data. Recent advances in deep learning allow for better modelling of spatial and temporal dependencies. While most of these models focus on obtaining accurate point forecasts, they do not characterize the prediction uncertainty. In this work, we consider the time-series data as a random realization from a nonlinear state-space model and target Bayesian inference of the hidden states for probabilistic forecasting. We use particle flow as the tool for approximating the posterior distribution of the states, as it is shown to be highly effective in complex, high-dimensional settings. Thorough experimentation on several real world time-series datasets demonstrates that our approach provides better characterization of uncertainty while maintaining comparable accuracy to the state-of-the art point forecasting methods.
Effectively modeling phenomena present in highly nonlinear dynamical systems whilst also accurately quantifying uncertainty is a challenging task, which often requires problem-specific techniques. We present a novel, domain-agnostic approach to tackling this problem, using compositions of physics-informed random features, derived from ordinary differential equations. The architecture of our model leverages recent advances in approximate inference for deep Gaussian processes, such as layer-wise weight-space approximations which allow us to incorporate random Fourier features, and stochastic variational inference for approximate Bayesian inference. We provide evidence that our model is capable of capturing highly nonlinear behaviour in real-world multivariate time series data. In addition, we find that our approach achieves comparable performance to a number of other probabilistic models on benchmark regression tasks.
We present a novel offline-online method to mitigate the computational burden of the characterization of posterior random variables in statistical learning. In the offline phase, the proposed method learns the joint law of the parameter random variables and the observable random variables in the tensor-train (TT) format. In the online phase, the resulting order-preserving conditional transport can characterize the posterior random variables given newly observed data in real time. Compared with the state-of-the-art normalizing flow techniques, the proposed method relies on function approximation and is equipped with a thorough performance analysis. The function approximation perspective also allows us to further extend the capability of transport maps in challenging problems with high-dimensional observations and high-dimensional parameters. On the one hand, we present novel heuristics to reorder and/or reparametrize the variables to enhance the approximation power of TT. On the other hand, we integrate the TT-based transport maps and the parameter reordering/reparametrization into layered compositions to further improve the performance of the resulting transport maps. We demonstrate the efficiency of the proposed method on various statistical learning tasks in ordinary differential equations (ODEs) and partial differential equations (PDEs).
We consider the privacy-preserving machine learning (ML) setting where the trained model must satisfy differential privacy (DP) with respect to the labels of the training examples. We propose two novel approaches based on, respectively, the Laplace mechanism and the PATE framework, and demonstrate their effectiveness on standard benchmarks. While recent work by Ghazi et al. proposed Label DP schemes based on a randomized response mechanism, we argue that additive Laplace noise coupled with Bayesian inference (ALIBI) is a better fit for typical ML tasks. Moreover, we show how to achieve very strong privacy levels in some regimes, with our adaptation of the PATE framework that builds on recent advances in semi-supervised learning. We complement theoretical analysis of our algorithms' privacy guarantees with empirical evaluation of their memorization properties. Our evaluation suggests that comparing different algorithms according to their provable DP guarantees can be misleading and favor a less private algorithm with a tighter analysis. Code for implementation of algorithms and memorization attacks is available from https://github.com/facebookresearch/label_dp_antipodes.
The advent of comprehensive synaptic wiring diagrams of large neural circuits has created the field of connectomics and given rise to a number of open research questions. One such question is whether it is possible to reconstruct the information stored in a recurrent network of neurons, given its synaptic connectivity matrix. Here, we address this question by determining when solving such an inference problem is theoretically possible in specific attractor network models and by providing a practical algorithm to do so. The algorithm builds on ideas from statistical physics to perform approximate Bayesian inference and is amenable to exact analysis. We study its performance on three different models, compare the algorithm to standard algorithms such as PCA, and explore the limitations of reconstructing stored patterns from synaptic connectivity.
This paper aims to address few-shot segmentation. While existing prototype-based methods have achieved considerable success, they suffer from uncertainty and ambiguity caused by limited labeled examples. In this work, we propose attentional prototype inference (API), a probabilistic latent variable framework for few-shot segmentation. We define a global latent variable to represent the prototype of each object category, which we model as a probabilistic distribution. The probabilistic modeling of the prototype enhances the model's generalization ability by handling the inherent uncertainty caused by limited data and intra-class variations of objects. To further enhance the model, we introduce a local latent variable to represent the attention map of each query image, which enables the model to attend to foreground objects while suppressing the background. The optimization of the proposed model is formulated as a variational Bayesian inference problem, which is established by amortized inference networks. We conduct extensive experiments on four benchmarks, where our proposal obtains at least competitive and often better performance than state-of-the-art prototype-based methods. We also provide comprehensive analyses and ablation studies to gain insight into the effectiveness of our method for few-shot segmentation.
In this contribution, we predict the wellhead protection area (WHPA, target), the shape and extent of which is influenced by the distribution of hydraulic conductivity (K), from a small number of tracing experiments (predictor). Our first objective is to make stochastic predictions of the WHPA within the Bayesian Evidential Learning (BEL) framework, which aims to find a direct relationship between predictor and target using machine learning. This relationship is learned from a small set of training models (400) sampled from the prior distribution of K. The associated 400 pairs of simulated predictors and targets are obtained through forward modelling. Newly collected field data can then be directly used to predict the approximate posterior distribution of the corresponding WHPA. The uncertainty range of the posterior WHPA distribution is affected by the number and position of data sources (injection wells). Our second objective is to extend BEL to identify the optimal design of data source locations that minimizes the posterior uncertainty of the WHPA. This can be done explicitly, without averaging or approximating because once trained, the BEL model allows the computation of the posterior uncertainty corresponding to any new input data. We use the Modified Hausdorff Distance and the Structural Similarity index metrics to estimate the posterior uncertainty range of the WHPA. Increasing the number of injection wells effectively reduces the derived posterior WHPA uncertainty. Our approach can also estimate which injection wells are more informative than others, as validated through a k-fold cross-validation procedure. Overall, the application of BEL to experimental design makes it possible to identify the data sources maximizing the information content of any measurement data.
Domain generalization is challenging due to the domain shift and the uncertainty caused by the inaccessibility of target domain data. In this paper, we address both challenges with a probabilistic framework based on variational Bayesian inference, by incorporating uncertainty into neural network weights. We couple domain invariance in a probabilistic formula with the variational Bayesian inference. This enables us to explore domain-invariant learning in a principled way. Specifically, we derive domain-invariant representations and classifiers, which are jointly established in a two-layer Bayesian neural network. We empirically demonstrate the effectiveness of our proposal on four widely used cross-domain visual recognition benchmarks. Ablation studies validate the synergistic benefits of our Bayesian treatment when jointly learning domain-invariant representations and classifiers for domain generalization. Further, our method consistently delivers state-of-the-art mean accuracy on all benchmarks.
Bayesian inference on non-Gaussian data is often non-analytic and requires computationally expensive approximations such as sampling or variational inference. We propose an approximate inference framework primarily designed to be computationally cheap while still achieving high approximation quality. The concept, which we call Laplace Matching, involves closed-form, approximate, bi-directional transformations between the parameter spaces of exponential families. These are constructed from Laplace approximations under custom-designed basis transformations. The mappings can then be leveraged to effectively turn a latent Gaussian distribution into an approximate conjugate prior to a rich class of observable variables. This allows us to train latent Gaussian models such as Gaussian Processes on non-Gaussian data at nearly no additional cost. The method can be thought of as a pre-processing step which can be implemented in <5 lines of code and runs in less than a second. Furthermore, Laplace Matching yields a simple way to group similar data points together, e.g. to produce inducing points for GPs. We empirically evaluate the method with experiments for four different exponential distributions, namely the Beta, Gamma, Dirichlet and inverse Wishart, showing approximation quality comparable to state-of-the-art approximate inference techniques at a drastic reduction in computational cost.
In a bag-of-words model, the senses of a word with multiple meanings, e.g. "bank" (used either in a river-bank or an institution sense), are represented as probability distributions over context words, and sense prevalence is represented as a probability distribution over senses. Both of these may change with time. Modelling and measuring this kind of sense change is challenging due to the typically high-dimensional parameter space and sparse datasets. A recently published corpus of ancient Greek texts contains expert-annotated sense labels for selected target words. Automatic sense-annotation for the word "kosmos" (meaning decoration, order or world) has been used as a test case in recent work with related generative models and Monte Carlo methods. We adapt an existing generative sense change model to develop a simpler model for the main effects of sense and time, and give MCMC methods for Bayesian inference on all these models that are more efficient than existing methods. We carry out automatic sense-annotation of snippets containing "kosmos" using our model, and measure the time-evolution of its three senses and their prevalence. As far as we are aware, ours is the first analysis of this data, within the class of generative models we consider, that quantifies uncertainty and returns credible sets for evolving sense prevalence in good agreement with those given by expert annotation.