TensorBNN is a new package based on TensorFlow that implements Bayesian inference for modern neural network models. The posterior density of neural network model parameters is represented as a point cloud sampled using Hamiltonian Monte Carlo. The TensorBNN package leverages TensorFlow's architecture and training features as well as its ability to use modern graphics processing units (GPU) in both the training and prediction stages.
We develop a novel data-driven approach to the inverse problem of classical statistical mechanics: given experimental data on the collective motion of a classical many-body system, how does one characterise the free energy landscape of that system? By combining non-parametric Bayesian inference with physically-motivated constraints, we develop an efficient learning algorithm which automates the construction of approximate free energy functionals. In contrast to optimisation-based machine learning approaches, which seek to minimise a cost function, the central idea of the proposed Bayesian inference is to propagate a set of prior assumptions through the model, derived from physical principles. The experimental data is used to probabilistically weigh the possible model predictions. This naturally leads to humanly interpretable algorithms with full uncertainty quantification of predictions. In our case, the output of the learning algorithm is a probability distribution over a family of free energy functionals, consistent with the observed particle data. We find that surprisingly small data samples contain sufficient information for inferring highly accurate analytic expressions of the underlying free energy functionals, making our algorithm highly data efficient. We consider excluded volume particle interactions, which are ubiquitous in nature, whilst being highly challenging for modelling in terms of free energy. To validate our approach we consider the paradigmatic case of one-dimensional fluid and develop inference algorithms for the canonical and grand-canonical statistical-mechanical ensembles. Extensions to higher-dimensional systems are conceptually straightforward, whilst standard coarse-graining techniques allow one to easily incorporate attractive interactions.
Manifold learning is a fundamental problem in machine learning with numerous applications. Most of the existing methods directly learn the low-dimensional embedding of the data in some high-dimensional space, and usually lack the flexibility of being directly applicable to down-stream applications. In this paper, we propose the concept of implicit manifold learning, where manifold information is implicitly obtained by learning the associated heat kernel. A heat kernel is the solution of the corresponding heat equation, which describes how "heat" transfers on the manifold, thus containing ample geometric information of the manifold. We provide both practical algorithm and theoretical analysis of our framework. The learned heat kernel can be applied to various kernel-based machine learning models, including deep generative models (DGM) for data generation and Stein Variational Gradient Descent for Bayesian inference. Extensive experiments show that our framework can achieve state-of-the-art results compared to existing methods for the two tasks.
We give methods for Bayesian inference of directed acyclic graphs, DAGs, and the induced causal effects from passively observed complete data. Our methods build on a recent Markov chain Monte Carlo scheme for learning Bayesian networks, which enables efficient approximate sampling from the graph posterior, provided that each node is assigned a small number $K$ of candidate parents. We present algorithmic techniques to significantly reduce the space and time requirements, which make the use of substantially larger values of $K$ feasible. Furthermore, we investigate the problem of selecting the candidate parents per node so as to maximize the covered posterior mass. Finally, we combine our sampling method with a novel Bayesian approach for estimating causal effects in linear Gaussian DAG models. Numerical experiments demonstrate the performance of our methods in detecting ancestor-descendant relations, and in causal effect estimation our Bayesian method is shown to outperform previous approaches.
Mathematical models in epidemiology are an indispensable tool to determine the dynamics and important characteristics of infectious diseases. Apart from their scientific merit, these models are often used to inform political decisions and intervention measures during an ongoing outbreak. However, reliably inferring the dynamics of ongoing outbreaks by connecting complex models to real data is still hard and requires either laborious manual parameter fitting or expensive optimization methods which have to be repeated from scratch for every application of a given model. In this work, we address this problem with a novel combination of epidemiological modeling with specialized neural networks. Our approach entails two computational phases: In an initial training phase, a mathematical model describing the epidemic is used as a coach for a neural network, which acquires global knowledge about the full range of possible disease dynamics. In the subsequent inference phase, the trained neural network processes the observed data of an actual outbreak and infers the parameters of the model in order to realistically reproduce the observed dynamics and reliably predict future progression. With its flexible framework, our simulation-based approach is applicable to a variety of epidemiological models. Moreover, since our method is fully Bayesian, it is designed to incorporate all available prior knowledge about plausible parameter values and returns complete joint posterior distributions over these parameters. Application of our method to the early Covid-19 outbreak phase in Germany demonstrates that we are able to obtain reliable probabilistic estimates for important disease characteristics, such as generation time, fraction of undetected infections, likelihood of transmission before symptom onset, and reporting delays using a very moderate amount of real-world observations.
AI planning can be cast as inference in probabilistic models, and probabilistic programming was shown to be capable of policy search in partially observable domains. Prior work introduces policy search through Markov chain Monte Carlo in deterministic domains, as well as adapts black-box variational inference to stochastic domains, however not in the strictly Bayesian sense. In this work, we cast policy search in stochastic domains as a Bayesian inference problem and provide a scheme for encoding such problems as nested probabilistic programs. We argue that probabilistic programs for policy search in stochastic domains should involve nested conditioning, and provide an adaption of Lightweight Metropolis-Hastings (LMH) for robust inference in such programs. We apply the proposed scheme to stochastic domains and show that policies of similar quality are learned, despite a simpler and more general inference algorithm. We believe that the proposed variant of LMH is novel and applicable to a wider class of probabilistic programs with nested conditioning.
Bayesian regression remains a simple but effective tool based on Bayesian inference techniques. For large-scale applications, with complicated posterior distributions, Markov Chain Monte Carlo methods are applied. To improve the well-known computational burden of Markov Chain Monte Carlo approach for Bayesian regression, we developed a multilevel Gibbs sampler for Bayesian regression of linear mixed models. The level hierarchy of data matrices is created by clustering the features and/or samples of data matrices. Additionally, the use of correlated samples is investigated for variance reduction to improve the convergence of the Markov Chain. Testing on a diverse set of data sets, speed-up is achieved for almost all of them without significant loss in predictive performance.
We consider online change detection of high dimensional data streams with sparse changes, where only a subset of data streams can be observed at each sensing time point due to limited sensing capacities. On the one hand, the detection scheme should be able to deal with partially observable data and meanwhile have efficient detection power for sparse changes. On the other, the scheme should be able to adaptively and actively select the most important variables to observe to maximize the detection power. To address these two points, in this paper, we propose a novel detection scheme called CDSSD. In particular, it describes the structure of high dimensional data with sparse changes by smooth-sparse decomposition, whose parameters can be learned via spike-slab variational Bayesian inference. Then the posterior Bayes factor, which incorporates the learned parameters and sparse change information, is formulated as a detection statistic. Finally, by formulating the statistic as the reward of a combinatorial multi-armed bandit problem, an adaptive sampling strategy based on Thompson sampling is proposed. The efficacy and applicability of our method in practice are demonstrated with numerical studies and a real case study.
Transportation of measure provides a versatile approach for modeling complex probability distributions, with applications in density estimation, Bayesian inference, generative modeling, and beyond. Monotone triangular transport maps$\unicode{x2014}$approximations of the Knothe$\unicode{x2013}$Rosenblatt (KR) rearrangement$\unicode{x2014}$are a canonical choice for these tasks. Yet the representation and parameterization of such maps have a significant impact on their generality and expressiveness, and on properties of the optimization problem that arises in learning a map from data (e.g., via maximum likelihood estimation). We present a general framework for representing monotone triangular maps via invertible transformations of smooth functions. We establish conditions on the transformation such that the associated infinite-dimensional minimization problem has no spurious local minima, i.e., all local minima are global minima; and we show for target distributions satisfying certain tail conditions that the unique global minimizer corresponds to the KR map. Given a sample from the target, we then propose an adaptive algorithm that estimates a sparse semi-parametric approximation of the underlying KR map. We demonstrate how this framework can be applied to joint and conditional density estimation, likelihood-free inference, and structure learning of directed graphical models, with stable generalization performance across a range of sample sizes.
Remote sensing image fusion technology (pan-sharpening) is an important means to improve the information capacity of remote sensing images. Inspired by the efficient arameter space posteriori sampling of Bayesian neural networks, in this paper we propose a Bayesian Generative Adversarial Network based on Preconditioned Stochastic Gradient Langevin Dynamics (PGSLD-BGAN) to improve pan-sharpening tasks. Unlike many traditional generative models that consider only one optimal solution (might be locally optimal), the proposed PGSLD-BGAN performs Bayesian inference on the network parameters, and explore the generator posteriori distribution, which assists selecting the appropriate generator parameters. First, we build a two-stream generator network with PAN and MS images as input, which consists of three parts: feature extraction, feature fusion and image reconstruction. Then, we leverage Markov discriminator to enhance the ability of generator to reconstruct the fusion image, so that the result image can retain more details. Finally, introducing Preconditioned Stochastic Gradient Langevin Dynamics policy, we perform Bayesian inference on the generator network. Experiments on QuickBird and WorldView datasets show that the model proposed in this paper can effectively fuse PAN and MS images, and be competitive with even superior to state of the arts in terms of subjective and objective metrics.
Contact-tracing is an essential tool in order to mitigate the impact of pandemic such as the COVID-19. In order to achieve efficient and scalable contact-tracing in real time, digital devices can play an important role. While a lot of attention has been paid to analyzing the privacy and ethical risks of the associated mobile applications, so far much less research has been devoted to optimizing their performance and assessing their impact on the mitigation of the epidemic. We develop Bayesian inference methods to estimate the risk that an individual is infected. This inference is based on the list of his recent contacts and their own risk levels, as well as personal information such as results of tests or presence of syndromes. We propose to use probabilistic risk estimation in order to optimize testing and quarantining strategies for the control of an epidemic. Our results show that in some range of epidemic spreading (typically when the manual tracing of all contacts of infected people becomes practically impossible, but before the fraction of infected people reaches the scale where a lock-down becomes unavoidable), this inference of individuals at risk could be an efficient way to mitigate the epidemic. Our approaches translate into fully distributed algorithms that only require communication between individuals who have recently been in contact. Such communication may be encrypted and anonymized and thus compatible with privacy preserving standards. We conclude that probabilistic risk estimation is capable to enhance performance of digital contact tracing and should be considered in the currently developed mobile applications.
The neural attention mechanism plays an important role in many natural language processing applications. In particular, the use of multi-head attention extends single-head attention by allowing a model to jointly attend information from different perspectives. Without explicit constraining, however, multi-head attention may suffer from attention collapse, an issue that makes different heads extract similar attentive features, thus limiting the model's representation power. In this paper, for the first time, we provide a novel understanding of multi-head attention from a Bayesian perspective. Based on the recently developed particle-optimization sampling techniques, we propose a non-parametric approach that explicitly improves the repulsiveness in multi-head attention and consequently strengthens model's expressiveness. Remarkably, our Bayesian interpretation provides theoretical inspirations on the not-well-understood questions: why and how one uses multi-head attention. Extensive experiments on various attention models and applications demonstrate that the proposed repulsive attention can improve the learned feature diversity, leading to more informative representations with consistent performance improvement on various tasks.
Predictions for physical systems often rely upon knowledge acquired from ensembles of entities, e.g., ensembles of cells in biological sciences. For qualitative and quantitative analysis, these ensembles are simulated with parametric families of mechanistic models (MM). Two classes of methodologies, based on Bayesian inference and Population of Models, currently prevail in parameter estimation for physical systems. However, in Bayesian analysis, uninformative priors for MM parameters introduce undesirable bias. Here, we propose how to infer parameters within the framework of stochastic inverse problems (SIP), also termed data-consistent inversion, wherein the prior targets only uncertainties that arise due to MM non-invertibility. To demonstrate, we introduce new methods to solve SIP based on rejection sampling, Markov chain Monte Carlo, and generative adversarial networks (GANs). In addition, to overcome limitations of SIP, we reformulate SIP based on constrained optimization and present a novel GAN to solve the constrained optimization problem.
Biological neurons and their in-silico emulations for neuromorphic artificial intelligence (AI) use extraordinarily energy-efficient mechanisms, such as spike-based communication and local synaptic plasticity. It remains unclear whether these neuronal mechanisms only offer efficiency or also underlie the superiority of biological intelligence. Here, we prove rigorously that, indeed, the Bayes-optimal prediction and inference of randomly but continuously transforming environments, a common natural setting, relies on short-term spike-timing-dependent plasticity, a hallmark of biological synapses. Further, this dynamic Bayesian inference through plasticity enables circuits of the cerebral cortex in simulations to recognize previously unseen, highly distorted dynamic stimuli. Strikingly, this also introduces a biologically-modelled AI, the first to overcome multiple limitations of deep learning and outperform artificial neural networks in a visual task. The cortical-like network is spiking and event-based, trained only with unsupervised and local plasticity, on a small, narrow, and static training dataset, but achieves recognition of unseen, transformed, and dynamic data better than deep neural networks with continuous activations, trained with supervised backpropagation on the transforming data. These results link short-term plasticity to high-level cortical function, suggest optimality of natural intelligence for natural environments, and repurpose neuromorphic AI from mere efficiency to computational supremacy altogether.
This paper introduces Distributed Stein Variational Gradient Descent (DSVGD), a non-parametric generalized Bayesian inference framework for federated learning. DSVGD maintains a number of non-random and interacting particles at a central server to represent the current iterate of the model global posterior. The particles are iteratively downloaded and updated by one of the agents with the end goal of minimizing the global free energy. By varying the number of particles, DSVGD enables a flexible trade-off between per-iteration communication load and number of communication rounds. DSVGD is shown to compare favorably to benchmark frequentist and Bayesian federated learning strategies, also scheduling a single device per iteration, in terms of accuracy and scalability with respect to the number of agents, while also providing well-calibrated, and hence trustworthy, predictions.
We explain how effective automatic probability density function estimates can be constructed using contemporary Bayesian inference engines such as those based on no-U-turn sampling and expectation propagation. Extensive simulation studies demonstrate that the proposed density estimates have excellent comparative performance and scale well to very large sample sizes due to a binning strategy. Moreover, the approach is fully Bayesian and all estimates are accompanied by pointwise credible intervals. An accompanying package in the R language facilitates easy use of the new density estimates.
The COVID-19 pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission during an outbreak (formally, the time-varying reproduction number) from case counts. While standard methods exist, they work best at coarse-grained national or state scales with abundant data, and struggle to accommodate the partial observability and sparse data common at finer scales (e.g., individual schools or towns). For example, case counts may be sparse when only a small fraction of infections are caught by a testing program. Or, whether an infected individual tests positive may depend on the kind of test and the point in time when they are tested. We propose a Bayesian framework which accommodates partial observability in a principled manner. Our model places a Gaussian process prior over the unknown reproduction number at each time step and models observations sampled from the distribution of a specific testing program. For example, our framework can accommodate a variety of kinds of tests (viral RNA, antibody, antigen, etc.) and sampling schemes (e.g., longitudinal or cross-sectional screening). Inference in this framework is complicated by the presence of tens or hundreds of thousands of discrete latent variables. To address this challenge, we propose an efficient stochastic variational inference method which relies on a novel gradient estimator for the variational objective. Experimental results for an example motivated by COVID-19 show that our method produces an accurate and well-calibrated posterior, while standard methods for estimating the reproduction number can fail badly.
To increase situational awareness and support evidence-based policy-making, we formulated two types of mathematical models for COVID-19 transmission within a regional population. One is a fitting function that can be calibrated to reproduce an epidemic curve with two timescales (e.g., fast growth and slow decay). The other is a compartmental model that accounts for quarantine, self-isolation, social distancing, a non-exponentially distributed incubation period, asymptomatic individuals, and mild and severe forms of symptomatic disease. Using Bayesian inference, we have been calibrating our models daily for consistency with new reports of confirmed cases from the 15 most populous metropolitan statistical areas in the United States and quantifying uncertainty in parameter estimates and predictions of future case reports. This online learning approach allows for early identification of new trends despite considerable variability in case reporting. We infer new significant upward trends for five of the metropolitan areas starting between 19-April-2020 and 12-June-2020.
Tensor rank learning for canonical polyadic decomposition (CPD) has long been deemed as an essential yet challenging problem. In particular, since the tensor rank controls the complexity of the CPD model, its inaccurate learning would cause overfitting to noise or underfitting to the signal sources, and even destroy the interpretability of model parameters. However, the optimal determination of a tensor rank is known to be a non-deterministic polynomial-time hard (NP-hard) task. Rather than exhaustively searching for the best tensor rank via trial-and-error experiments, Bayesian inference under the Gaussian-gamma prior was introduced in the context of probabilistic CPD modeling, and it was shown to be an effective strategy for automatic tensor rank determination. This triggered flourishing research on other structured tensor CPDs with automatic tensor rank learning. On the other side of the coin, these research works also reveal that the Gaussian-gamma model does not perform well for high-rank tensors and/or low signal-to-noise ratios (SNRs). To overcome these drawbacks, in this paper, we introduce a more advanced generalized hyperbolic (GH) prior to the probabilistic CPD model, which not only includes the Gaussian-gamma model as a special case, but also is more flexible to adapt to different levels of sparsity. Based on this novel probabilistic model, an algorithm is developed under the framework of variational inference, where each update is obtained in a closed-form. Extensive numerical results, using synthetic data and real-world datasets, demonstrate the significantly improved performance of the proposed method in learning both low as well as high tensor ranks even for low SNR cases.
Federated learning aims to collaboratively train a strong global model by accessing users' locally trained models but not their own data. A crucial step is therefore to aggregate local models into a global model, which has been shown challenging when users have non-i.i.d. data. In this paper, we propose a novel aggregation algorithm named FedBE, which takes a Bayesian inference perspective by sampling higher-quality global models and combining them via Bayesian model Ensemble, leading to much robust aggregation. We show that an effective model distribution can be constructed by simply fitting a Gaussian or Dirichlet distribution to the local models. Our empirical studies validate FedBE's superior performance, especially when users' data are not i.i.d. and when the neural networks go deeper. Moreover, FedBE is compatible with recent efforts in regularizing users' model training, making it an easily applicable module: you only need to replace the aggregation method but leave other parts of your federated learning algorithm intact. Our code is publicly available at https://github.com/hongyouc/FedBE.