Learning-based outlier (mismatched correspondence) rejection for robust 3D registration generally formulates the outlier removal as an inlier/outlier classification problem. The core for this to be successful is to learn the discriminative inlier/outlier feature representations. In this paper, we develop a novel variational non-local network-based outlier rejection framework for robust alignment. By reformulating the non-local feature learning with variational Bayesian inference, the Bayesian-driven long-range dependencies can be modeled to aggregate discriminative geometric context information for inlier/outlier distinction. Specifically, to achieve such Bayesian-driven contextual dependencies, each query/key/value component in our non-local network predicts a prior feature distribution and a posterior one. Embedded with the inlier/outlier label, the posterior feature distribution is label-dependent and discriminative. Thus, pushing the prior to be close to the discriminative posterior in the training step enables the features sampled from this prior at test time to model high-quality long-range dependencies. Notably, to achieve effective posterior feature guidance, a specific probabilistic graphical model is designed over our non-local model, which lets us derive a variational low bound as our optimization objective for model training. Finally, we propose a voting-based inlier searching strategy to cluster the high-quality hypothetical inliers for transformation estimation. Extensive experiments on 3DMatch, 3DLoMatch, and KITTI datasets verify the effectiveness of our method.
We present a hierarchical Bayesian learning approach to infer jointly sparse parameter vectors from multiple measurement vectors. Our model uses separate conditionally Gaussian priors for each parameter vector and common gamma-distributed hyper-parameters to enforce joint sparsity. The resulting joint-sparsity-promoting priors are combined with existing Bayesian inference methods to generate a new family of algorithms. Our numerical experiments, which include a multi-coil magnetic resonance imaging application, demonstrate that our new approach consistently outperforms commonly used hierarchical Bayesian methods.
This study aims to comprehensively investigate the deep ensemble approach, an approximate Bayesian inference, in the multi-output regression task for predicting the aerodynamic performance of a missile configuration. To this end, the effect of the number of neural networks used in the ensemble, which has been blindly adopted in previous studies, is scrutinized. As a result, an obvious trend towards underestimation of uncertainty as it increases is observed for the first time, and in this context, we propose the deep ensemble framework that applies the post-hoc calibration method to improve its uncertainty quantification performance. It is compared with Gaussian process regression and is shown to have superior performance in terms of regression accuracy ($\uparrow55\sim56\%$), reliability of estimated uncertainty ($\uparrow38\sim77\%$), and training efficiency ($\uparrow78\%$). Finally, the potential impact of the suggested framework on the Bayesian optimization is briefly examined, indicating that deep ensemble without calibration may lead to unintended exploratory behavior. This UQ framework can be seamlessly applied and extended to any regression task, as no special assumptions have been made for the specific problem used in this study.
Pretrained language models often generate outputs that are not in line with human preferences, such as harmful text or factually incorrect summaries. Recent work approaches the above issues by learning from a simple form of human feedback: comparisons between pairs of model-generated outputs. However, comparison feedback only conveys limited information about human preferences. In this paper, we introduce Imitation learning from Language Feedback (ILF), a new approach that utilizes more informative language feedback. ILF consists of three steps that are applied iteratively: first, conditioning the language model on the input, an initial LM output, and feedback to generate refinements. Second, selecting the refinement incorporating the most feedback. Third, finetuning the language model to maximize the likelihood of the chosen refinement given the input. We show theoretically that ILF can be viewed as Bayesian Inference, similar to Reinforcement Learning from human feedback. We evaluate ILF's effectiveness on a carefully-controlled toy task and a realistic summarization task. Our experiments demonstrate that large language models accurately incorporate feedback and that finetuning with ILF scales well with the dataset size, even outperforming finetuning on human summaries. Learning from both language and comparison feedback outperforms learning from each alone, achieving human-level summarization performance.
Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common continuous-time Markov chain models into a richer class of processes capable of capturing a wider variety of substitution dynamics. As these random-effects substitution models often require many more parameters than their usual counterparts, inference can be both statistically and computationally challenging. Thus, we also propose an efficient approach to compute an approximation to the gradient of the data likelihood with respect to all unknown substitution model parameters. We demonstrate that this approximate gradient enables scaling of sampling-based inference, namely Bayesian inference via Hamiltonian Monte Carlo, under random-effects substitution models across large trees and state-spaces. Applied to a dataset of 583 SARS-CoV-2 sequences, an HKY model with random-effects shows strong signals of nonreversibility in the substitution process, and posterior predictive model checks clearly show that it is a more adequate model than a reversible model. When analyzing the pattern of phylogeographic spread of 1441 influenza A virus (H3N2) sequences between 14 regions, a random-effects phylogeographic substitution model infers that air travel volume adequately predicts almost all dispersal rates. A random-effects state-dependent substitution model reveals no evidence for an effect of arboreality on the swimming mode in the tree frog subfamily Hylinae. Simulations reveal that random-effects substitution models can accommodate both negligible and radical departures from the underlying base substitution model. We show that our gradient-based inference approach is over an order of magnitude more time efficient than conventional approaches.
The Mean Field Variational Bayes (MFVB) method is one of the most computationally efficient techniques for Bayesian inference. However, its use has been restricted to models with conjugate priors or those that require analytical calculations. This paper proposes a novel particle-based MFVB approach that greatly expands the applicability of the MFVB method. We establish the theoretical basis of the new method by leveraging the connection between Wasserstein gradient flows and Langevin diffusion dynamics, and demonstrate the effectiveness of this approach using Bayesian logistic regression, stochastic volatility, and deep neural networks.
The recent explosion of genetic and high dimensional biobank and 'omic' data has provided researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of hundreds to thousands of related phenotypes. However, existing methods for multi-phenotype genome-wide association studies (GWAS) do not model pleiotropy, are only applicable to a small number of phenotypes, or provide no way to perform inference. To add further complication, raw genetic and phenotype data are rarely observed, meaning analyses must be performed on GWAS summary statistics whose statistical properties in high dimensions are poorly understood. We therefore developed a novel model, theoretical framework, and set of methods to perform Bayesian inference in GWAS of high dimensional phenotypes using summary statistics that explicitly model pleiotropy, beget fast computation, and facilitate the use of biologically informed priors. We demonstrate the utility of our procedure by applying it to metabolite GWAS, where we develop new nonparametric priors for genetic effects on metabolite levels that use known metabolic pathway information and foster interpretable inference at the pathway level.
Understanding the gradient variance of black-box variational inference (BBVI) is a crucial step for establishing its convergence and developing algorithmic improvements. However, existing studies have yet to show that the gradient variance of BBVI satisfies the conditions used to study the convergence of stochastic gradient descent (SGD), the workhorse of BBVI. In this work, we show that BBVI satisfies a matching bound corresponding to the $ABC$ condition used in the SGD literature when applied to smooth and quadratically-growing log-likelihoods. Our results generalize to nonlinear covariance parameterizations widely used in the practice of BBVI. Furthermore, we show that the variance of the mean-field parameterization has provably superior dimensional dependence.
Multitemporal hyperspectral unmixing (MTHU) is a fundamental tool in the analysis of hyperspectral image sequences. It reveals the dynamical evolution of the materials (endmembers) and of their proportions (abundances) in a given scene. However, adequately accounting for the spatial and temporal variability of the endmembers in MTHU is challenging, and has not been fully addressed so far in unsupervised frameworks. In this work, we propose an unsupervised MTHU algorithm based on variational recurrent neural networks. First, a stochastic model is proposed to represent both the dynamical evolution of the endmembers and their abundances, as well as the mixing process. Moreover, a new model based on a low-dimensional parametrization is used to represent spatial and temporal endmember variability, significantly reducing the amount of variables to be estimated. We propose to formulate MTHU as a Bayesian inference problem. However, the solution to this problem does not have an analytical solution due to the nonlinearity and non-Gaussianity of the model. Thus, we propose a solution based on deep variational inference, in which the posterior distribution of the estimated abundances and endmembers is represented by using a combination of recurrent neural networks and a physically motivated model. The parameters of the model are learned using stochastic backpropagation. Experimental results show that the proposed method outperforms state of the art MTHU algorithms.
Background: In medical imaging, images are usually treated as deterministic, while their uncertainties are largely underexplored. Purpose: This work aims at using deep learning to efficiently estimate posterior distributions of imaging parameters, which in turn can be used to derive the most probable parameters as well as their uncertainties. Methods: Our deep learning-based approaches are based on a variational Bayesian inference framework, which is implemented using two different deep neural networks based on conditional variational auto-encoder (CVAE), CVAE-dual-encoder and CVAE-dual-decoder. The conventional CVAE framework, i.e., CVAE-vanilla, can be regarded as a simplified case of these two neural networks. We applied these approaches to a simulation study of dynamic brain PET imaging using a reference region-based kinetic model. Results: In the simulation study, we estimated posterior distributions of PET kinetic parameters given a measurement of time-activity curve. Our proposed CVAE-dual-encoder and CVAE-dual-decoder yield results that are in good agreement with the asymptotically unbiased posterior distributions sampled by Markov Chain Monte Carlo (MCMC). The CVAE-vanilla can also be used for estimating posterior distributions, although it has an inferior performance to both CVAE-dual-encoder and CVAE-dual-decoder. Conclusions: We have evaluated the performance of our deep learning approaches for estimating posterior distributions in dynamic brain PET. Our deep learning approaches yield posterior distributions, which are in good agreement with unbiased distributions estimated by MCMC. All these neural networks have different characteristics and can be chosen by the user for specific applications. The proposed methods are general and can be adapted to other problems.
Flexible Bayesian models are typically constructed using limits of large parametric models with a multitude of parameters that are often uninterpretable. In this article, we offer a novel alternative by constructing an exponentially tilted empirical likelihood carefully designed to concentrate near a parametric family of distributions of choice with respect to a novel variant of the Wasserstein metric, which is then combined with a prior distribution on model parameters to obtain a robustified posterior. The proposed approach finds applications in a wide variety of robust inference problems, where we intend to perform inference on the parameters associated with the centering distribution in presence of outliers. Our proposed transport metric enjoys great computational simplicity, exploiting the Sinkhorn regularization for discrete optimal transport problems, and being inherently parallelizable. We demonstrate superior performance of our methodology when compared against state-of-the-art robust Bayesian inference methods. We also demonstrate equivalence of our approach with a nonparametric Bayesian formulation under a suitable asymptotic framework, testifying to its flexibility. The constrained entropy maximization that sits at the heart of our likelihood formulation finds its utility beyond robust Bayesian inference; an illustration is provided in a trustworthy machine learning application.
PyVBMC is a Python implementation of the Variational Bayesian Monte Carlo (VBMC) algorithm for posterior and model inference for black-box computational models (Acerbi, 2018, 2020). VBMC is an approximate inference method designed for efficient parameter estimation and model assessment when model evaluations are mildly-to-very expensive (e.g., a second or more) and/or noisy. Specifically, VBMC computes: - a flexible (non-Gaussian) approximate posterior distribution of the model parameters, from which statistics and posterior samples can be easily extracted; - an approximation of the model evidence or marginal likelihood, a metric used for Bayesian model selection. PyVBMC can be applied to any computational or statistical model with up to roughly 10-15 continuous parameters, with the only requirement that the user can provide a Python function that computes the target log likelihood of the model, or an approximation thereof (e.g., an estimate of the likelihood obtained via simulation or Monte Carlo methods). PyVBMC is particularly effective when the model takes more than about a second per evaluation, with dramatic speed-ups of 1-2 orders of magnitude when compared to traditional approximate inference methods. Extensive benchmarks on both artificial test problems and a large number of real models from the computational sciences, particularly computational and cognitive neuroscience, show that VBMC generally - and often vastly - outperforms alternative methods for sample-efficient Bayesian inference, and is applicable to both exact and simulator-based models (Acerbi, 2018, 2019, 2020). PyVBMC brings this state-of-the-art inference algorithm to Python, along with an easy-to-use Pythonic interface for running the algorithm and manipulating and visualizing its results.
Bayesian inference provides a principled framework for learning from complex data and reasoning under uncertainty. It has been widely applied in machine learning tasks such as medical diagnosis, drug design, and policymaking. In these common applications, data can be highly sensitive. Differential privacy (DP) offers data analysis tools with powerful worst-case privacy guarantees and has been developed as the leading approach in privacy-preserving data analysis. In this paper, we study Metropolis-Hastings (MH), one of the most fundamental MCMC methods, for large-scale Bayesian inference under differential privacy. While most existing private MCMC algorithms sacrifice accuracy and efficiency to obtain privacy, we provide the first exact and fast DP MH algorithm, using only a minibatch of data in most iterations. We further reveal, for the first time, a three-way trade-off among privacy, scalability (i.e. the batch size), and efficiency (i.e. the convergence rate), theoretically characterizing how privacy affects the utility and computational cost in Bayesian inference. We empirically demonstrate the effectiveness and efficiency of our algorithm in various experiments.
Tensor decomposition is now being used for data analysis, information compression, and knowledge recovery. However, the mathematical property of tensor decomposition is not yet fully clarified because it is one of singular learning machines. In this paper, we give the upper bound of its real log canonical threshold (RLCT) of the tensor decomposition by using an algebraic geometrical method and derive its Bayesian generalization error theoretically. We also give considerations about its mathematical property through numerical experiments.
General robotic grippers are challenging to control because of their rich nonsmooth contact dynamics and the many sources of uncertainties due to the environment or sensor noise. In this work, we demonstrate how to compute 6-DoF grasp poses using simulation-based Bayesian inference through the full stochastic forward simulation of the robot in its environment while robustly accounting for many of the uncertainties in the system. A Riemannian manifold optimization procedure preserving the nonlinearity of the rotation space is used to compute the maximum a posteriori grasp pose. Simulation and physical benchmarks show the promising high success rate of the approach.
Recent research is revealing how cognitive processes are supported by a complex interplay between the brain and the rest of the body, which can be investigated by the analysis of physiological features such as breathing rhythms, heart rate, and skin conductance. Heart rate dynamics are of particular interest as they provide a way to track the sympathetic and parasympathetic outflow from the autonomic nervous system, which is known to play a key role in modulating attention, memory, decision-making, and emotional processing. However, extracting useful information from heartbeats about the autonomic outflow is still challenging due to the noisy estimates that result from standard signal-processing methods. To advance this state of affairs, we propose a paradigm shift in how we conceptualise and model heart rate: instead of being a mere summary of the observed inter-beat intervals, we introduce a modelling framework that views heart rate as a hidden stochastic process that drives the observed heartbeats. Moreover, by leveraging the rich literature of state-space modelling and Bayesian inference, our proposed framework delivers a description of heart rate dynamics that is not a point estimate but a posterior distribution of a generative model. We illustrate the capabilities of our method by showing that it recapitulates linear properties of conventional heart rate estimators, while exhibiting a better discriminative power for metrics of dynamical complexity compared across different physiological states.
In applied Bayesian inference scenarios, users may have access to a large number of pre-existing model evaluations, for example from maximum-a-posteriori (MAP) optimization runs. However, traditional approximate inference techniques make little to no use of this available information. We propose the framework of post-process Bayesian inference as a means to obtain a quick posterior approximation from existing target density evaluations, with no further model calls. Within this framework, we introduce Variational Sparse Bayesian Quadrature (VSBQ), a method for post-process approximate inference for models with black-box and potentially noisy likelihoods. VSBQ reuses existing target density evaluations to build a sparse Gaussian process (GP) surrogate model of the log posterior density function. Subsequently, we leverage sparse-GP Bayesian quadrature combined with variational inference to achieve fast approximate posterior inference over the surrogate. We validate our method on challenging synthetic scenarios and real-world applications from computational neuroscience. The experiments show that VSBQ builds high-quality posterior approximations by post-processing existing optimization traces, with no further model evaluations.
Stochastic-gradient sampling methods are often used to perform Bayesian inference on neural networks. It has been observed that the methods in which notions of differential geometry are included tend to have better performances, with the Riemannian metric improving posterior exploration by accounting for the local curvature. However, the existing methods often resort to simple diagonal metrics to remain computationally efficient. This loses some of the gains. We propose two non-diagonal metrics that can be used in stochastic-gradient samplers to improve convergence and exploration but have only a minor computational overhead over diagonal metrics. We show that for fully connected neural networks (NNs) with sparsity-inducing priors and convolutional NNs with correlated priors, using these metrics can provide improvements. For some other choices the posterior is sufficiently easy also for the simpler metrics.
Social hierarchy in animal groups carries a crucial adaptive function by reducing conflict and injury while protecting valuable group resources. Social hierarchy is dynamic and can be altered by social conflict, agonistic interactions, and aggression. Understanding social conflict and aggressive behavior is of profound importance to our society and welfare. In this study, we developed a quantitative theory of social conflict. We modeled individual agonistic interactions as a normal-form game between two agents. We assumed that the agents use Bayesian inference to update their beliefs about their strength or their opponent's strength and to derive optimal actions. We compared the results of our model to behavioral and whole-brain neural activity data obtained for a large (n=116) population of mice engaged in agonistic interactions. We find that both types of data are consistent with the first-level Theory of Mind model (1-ToM) in which mice form both "primary" beliefs about their and their opponent's strengths as well as the "secondary" beliefs about the beliefs of their opponents. Our model helps identify brain regions that carry information about these levels of beliefs. Overall, we both propose a model to describe agonistic interactions and support our quantitative results with behavioral and neural activity data.
Federated learning (FL) is a promising framework that models distributed machine learning while protecting the privacy of clients. However, FL suffers performance degradation from heterogeneous and limited data. To alleviate the degradation, we present a novel personalized Bayesian FL approach named pFedBayes. By using the trained global distribution from the server as the prior distribution of each client, each client adjusts its own distribution by minimizing the sum of the reconstruction error over its personalized data and the KL divergence with the downloaded global distribution. Then, we propose a sparse personalized Bayesian FL approach named sFedBayes. To overcome the extreme heterogeneity in non-i.i.d. data, we propose a clustered Bayesian FL model named cFedbayes by learning different prior distributions for different clients. Theoretical analysis gives the generalization error bound of three approaches and shows that the generalization error convergence rates of the proposed approaches achieve minimax optimality up to a logarithmic factor. Moreover, the analysis presents that cFedbayes has a tighter generalization error rate than pFedBayes. Numerous experiments are provided to demonstrate that the proposed approaches have better performance than other advanced personalized methods on private models in the presence of heterogeneous and limited data.