The application of Bayesian inference for the purpose of model selection is very popular nowadays. In this framework, models are compared through their marginal likelihoods, or their quotients, called Bayes factors. However, marginal likelihoods depends on the prior choice. For model selection, even diffuse priors can be actually very informative, unlike for the parameter estimation problem. Furthermore, when the prior is improper, the marginal likelihood of the corresponding model is undetermined. In this work, we discuss the issue of prior sensitivity of the marginal likelihood and its role in model selection. We also comment on the use of uninformative priors, which are very common choices in practice. Several practical suggestions are discussed and many possible solutions, proposed in the literature, to design objective priors for model selection are described. Some of them also allow the use of improper priors. The connection between the marginal likelihood approach and the well-known information criteria is also presented. We describe the main issues and possible solutions by illustrative numerical examples, providing also some related code. One of them involving a real-world application on exoplanet detection.
Machine learning methods on graphs have proven useful in many applications due to their ability to handle generally structured data. The framework of Gaussian Markov Random Fields (GMRFs) provides a principled way to define Gaussian models on graphs by utilizing their sparsity structure. We propose a flexible GMRF model for general graphs built on the multi-layer structure of Deep GMRFs, originally proposed for lattice graphs only. By designing a new type of layer we enable the model to scale to large graphs. The layer is constructed to allow for efficient training using variational inference and existing software frameworks for Graph Neural Networks. For a Gaussian likelihood, close to exact Bayesian inference is available for the latent field. This allows for making predictions with accompanying uncertainty estimates. The usefulness of the proposed model is verified by experiments on a number of synthetic and real world datasets, where it compares favorably to other both Bayesian and deep learning methods.
Calculation of Bayesian posteriors and model evidences typically requires numerical integration. Bayesian quadrature (BQ), a surrogate-model-based approach to numerical integration, is capable of superb sample efficiency, but its lack of parallelisation has hindered its practical applications. In this work, we propose a parallelised (batch) BQ method, employing techniques from kernel quadrature, that possesses an empirically exponential convergence rate. Additionally, just as with Nested Sampling, our method permits simultaneous inference of both posteriors and model evidence. Samples from our BQ surrogate model are re-selected to give a sparse set of samples, via a kernel recombination algorithm, requiring negligible additional time to increase the batch size. Empirically, we find that our approach significantly outperforms the sampling efficiency of both state-of-the-art BQ techniques and Nested Sampling in various real-world datasets, including lithium-ion battery analytics.
Given some observed data and a probabilistic generative model, Bayesian inference aims at obtaining the distribution of a model's latent parameters that could have yielded the data. This task is challenging for large population studies where thousands of measurements are performed over a cohort of hundreds of subjects, resulting in a massive latent parameter space. This large cardinality renders off-the-shelf Variational Inference (VI) computationally impractical. In this work, we design structured VI families that can efficiently tackle large population studies. To this end, our main idea is to share the parameterization and learning across the different i.i.d. variables in a generative model -symbolized by the model's plates. We name this concept plate amortization, and illustrate the powerful synergies it entitles, resulting in expressive, parsimoniously parameterized and orders of magnitude faster to train large scale hierarchical variational distributions. We illustrate the practical utility of PAVI through a challenging Neuroimaging example featuring a million latent parameters, demonstrating a significant step towards scalable and expressive Variational Inference.
This paper presents a learning- and scenario-based model predictive control (MPC) design approach for systems modeled in linear parameter-varying (LPV) framework. Using input-output data collected from the system, a state-space LPV model with uncertainty quantification is first learned through the variational Bayesian inference Neural Network (BNN) approach. The learned probabilistic model is assumed to contain the true dynamics of the system with a high probability and used to generate scenarios which ensure safety for a scenario-based MPC. Moreover, to guarantee stability and enhance performance of the closed-loop system, a parameter-dependent terminal cost and controller, as well as a terminal robust positive invariant set are designed. Numerical examples will be used to demonstrate that the proposed control design approach can ensure safety and achieve desired control performance.
Extracting low-dimensional summary statistics from large datasets is essential for efficient (likelihood-free) inference. We characterize different classes of summaries and demonstrate their importance for correctly analysing dimensionality reduction algorithms. We demonstrate that minimizing the expected posterior entropy (EPE) under the prior predictive distribution of the model subsumes many existing methods. They are equivalent to or are special or limiting cases of minimizing the EPE. We offer a unifying framework for obtaining informative summaries, provide concrete recommendations for practitioners, and propose a practical method to obtain high-fidelity summaries whose utility we demonstrate for both benchmark and practical examples.
With the ever increasing complexity of specifications, manual sizing for analog circuits recently became very challenging. Especially for innovative, large-scale circuits designs, with tens of design variables, operating conditions and conflicting objectives to be optimized, design engineers spend many weeks, running time-consuming simulations, in their attempt at finding the right configuration. Recent years brought machine learning and optimization techniques to the field of analog circuits design, with evolutionary algorithms and Bayesian models showing good results for circuit sizing. In this context, we introduce a design optimization method based on Generalized Differential Evolution 3 (GDE3) and Gaussian Processes (GPs). The proposed method is able to perform sizing for complex circuits with a large number of design variables and many conflicting objectives to be optimized. While state-of-the-art methods reduce multi-objective problems to single-objective optimization and potentially induce a prior bias, we search directly over the multi-objective space using Pareto dominance and ensure that diverse solutions are provided to the designers to choose from. To the best of our knowledge, the proposed method is the first to specifically address the diversity of the solutions, while also focusing on minimizing the number of simulations required to reach feasible configurations. We evaluate the introduced method on two voltage regulators showing different levels of complexity and we highlight that the proposed innovative candidate selection method and survival policy leads to obtaining feasible solutions, with a high degree of diversity, much faster than with GDE3 or Bayesian Optimization-based algorithms.
We define the information threshold as the point of maximum curvature in the prior vs. posterior Bayesian curve, both of which are described as a function of the true positive and negative rates of the classification system in question. The nature of the threshold is such that for sufficiently adequate binary classification systems, retrieving excess information beyond the threshold does not significantly alter the reliability of our classification assessment. We hereby introduce the "marital status thought experiment" to illustrate this idea and report a previously undefined mathematical relationship between the Bayesian prior and posterior, which may have significant philosophical and epistemological implications in decision theory. Where the prior probability is a scalar between 0 and 1 given by $\phi$ and the posterior is a scalar between 0 and 1 given by $\rho$, then at the information threshold, $\phi_e$: $\phi_e + \rho_e = 1$ Otherwise stated, given some degree of prior belief, we may assert its persuasiveness when sufficient quality evidence yields a posterior so that their combined sum equals 1. Retrieving further evidence beyond this point does not significantly improve the posterior probability, and may serve as a benchmark for confidence in decision-making.
Multimodal groupwise registration aligns internal structures in a group of medical images. Current approaches to this problem involve developing similarity measures over the joint intensity profile of all images, which may be computationally prohibitive for large image groups and unstable under various conditions. To tackle these issues, we propose BInGo, a general unsupervised hierarchical Bayesian framework based on deep learning, to learn intrinsic structural representations to measure the similarity of multimodal images. Particularly, a variational auto-encoder with a novel posterior is proposed, which facilitates the disentanglement learning of structural representations and spatial transformations, and characterizes the imaging process from the common structure with shape transition and appearance variation. Notably, BInGo is scalable to learn from small groups, whereas being tested for large-scale groupwise registration, thus significantly reducing computational costs. We compared BInGo with five iterative or deep learning methods on three public intrasubject and intersubject datasets, i.e. BraTS, MS-CMR of the heart, and Learn2Reg abdomen MR-CT, and demonstrated its superior accuracy and computational efficiency, even for very large group sizes (e.g., over 1300 2D images from MS-CMR in each group).
Bayesian models have many desirable properties, most notable is their ability to generalize from limited data and to properly estimate the uncertainty in their predictions. However, these benefits come at a steep computational cost as Bayesian inference, in most cases, is computationally intractable. One popular approach to alleviate this problem is using a Monte-Carlo estimation with an ensemble of models sampled from the posterior. However, this approach still comes at a significant computational cost, as one needs to store and run multiple models at test time. In this work, we investigate how to best distill an ensemble's predictions using an efficient model. First, we argue that current approaches that simply return distribution over predictions cannot compute important properties, such as the covariance between predictions, which can be valuable for further processing. Second, in many limited data settings, all ensemble members achieve nearly zero training loss, namely, they produce near-identical predictions on the training set which results in sub-optimal distilled models. To address both problems, we propose a novel and general distillation approach, named Functional Ensemble Distillation (FED), and we investigate how to best distill an ensemble in this setting. We find that learning the distilled model via a simple augmentation scheme in the form of mixup augmentation significantly boosts the performance. We evaluated our method on several tasks and showed that it achieves superior results in both accuracy and uncertainty estimation compared to current approaches.
Bayesian deep learning plays an important role especially for its ability evaluating epistemic uncertainty (EU). Due to computational complexity issues, approximation methods such as variational inference (VI) have been used in practice to obtain posterior distributions and their generalization abilities have been analyzed extensively, for example, by PAC-Bayesian theory; however, little analysis exists on EU, although many numerical experiments have been conducted on it. In this study, we analyze the EU of supervised learning in approximate Bayesian inference by focusing on its excess risk. First, we theoretically show the novel relations between generalization error and the widely used EU measurements, such as the variance and mutual information of predictive distribution, and derive their convergence behaviors. Next, we clarify how the objective function of VI regularizes the EU. With this analysis, we propose a new objective function for VI that directly controls the prediction performance and the EU based on the PAC-Bayesian theory. Numerical experiments show that our algorithm significantly improves the EU evaluation over the existing VI methods.
Multinomial probit (mnp) models are fundamental and widely-applied regression models for categorical data. Fasano and Durante (2022) proved that the class of unified skew-normal distributions is conjugate to several mnp sampling models. This allows to develop Monte Carlo samplers and accurate variational methods to perform Bayesian inference. In this paper, we adapt the abovementioned results for a popular special case: the discrete-choice mnp model under zero mean and independent Gaussian priors. This allows to obtain simplified expressions for the parameters of the posterior distribution and an alternative derivation for the variational algorithm that gives a novel understanding of the fundamental results in Fasano and Durante (2022) as well as computational advantages in our special settings.
Network inference has been extensively studied in several fields, such as systems biology and social sciences. Learning network topology and internal dynamics is essential to understand mechanisms of complex systems. In particular, sparse topologies and stable dynamics are fundamental features of many real-world continuous-time (CT) networks. Given that usually only a partial set of nodes are able to observe, in this paper, we consider linear CT systems to depict networks since they can model unmeasured nodes via transfer functions. Additionally, measurements tend to be noisy and with low and varying sampling frequencies. For this reason, we consider CT models since discrete-time approximations often require fine-grained measurements and uniform sampling steps. The developed method applies dynamical structure functions (DSFs) derived from linear stochastic differential equations (SDEs) to describe networks of measured nodes. A numerical sampling method, preconditioned Crank-Nicolson (pCN), is used to refine coarse-grained trajectories to improve inference accuracy. The convergence property of the developed method is robust to the dimension of data sources. Monte Carlo simulations indicate that the developed method outperforms state-of-the-art methods including group sparse Bayesian learning (GSBL), BINGO, kernel-based methods, dynGENIE3, GENIE3, and ARNI. The simulations include random and ring networks, and a synthetic biological network. These are challenging networks, suggesting that the developed method can be applied under a wide range of contexts, such as gene regulatory networks, social networks, and communication systems.
Along with Markov chain Monte Carlo (MCMC) methods, variational inference (VI) has emerged as a central computational approach to large-scale Bayesian inference. Rather than sampling from the true posterior $\pi$, VI aims at producing a simple but effective approximation $\hat \pi$ to $\pi$ for which summary statistics are easy to compute. However, unlike the well-studied MCMC methodology, algorithmic guarantees for VI are still relatively less well-understood. In this work, we propose principled methods for VI, in which $\hat \pi$ is taken to be a Gaussian or a mixture of Gaussians, which rest upon the theory of gradient flows on the Bures--Wasserstein space of Gaussian measures. Akin to MCMC, it comes with strong theoretical guarantees when $\pi$ is log-concave.
Recent progress in machine learning methods, and the emerging availability of programmable interfaces for scanning probe microscopes (SPMs), have propelled automated and autonomous microscopies to the forefront of attention of the scientific community. However, enabling automated microscopy requires the development of task-specific machine learning methods, understanding the interplay between physics discovery and machine learning, and fully defined discovery workflows. This, in turn, requires balancing the physical intuition and prior knowledge of the domain scientist with rewards that define experimental goals and machine learning algorithms that can translate these to specific experimental protocols. Here, we discuss the basic principles of Bayesian active learning and illustrate its applications for SPM. We progress from the Gaussian Process as a simple data-driven method and Bayesian inference for physical models as an extension of physics-based functional fits to more complex deep kernel learning methods, structured Gaussian Processes, and hypothesis learning. These frameworks allow for the use of prior data, the discovery of specific functionalities as encoded in spectral data, and exploration of physical laws manifesting during the experiment. The discussed framework can be universally applied to all techniques combining imaging and spectroscopy, SPM methods, nanoindentation, electron microscopy and spectroscopy, and chemical imaging methods, and can be particularly impactful for destructive or irreversible measurements.
Markov decision processes (MDPs) are formal models commonly used in sequential decision-making. MDPs capture the stochasticity that may arise, for instance, from imprecise actuators via probabilities in the transition function. However, in data-driven applications, deriving precise probabilities from (limited) data introduces statistical errors that may lead to unexpected or undesirable outcomes. Uncertain MDPs (uMDPs) do not require precise probabilities but instead use so-called uncertainty sets in the transitions, accounting for such limited data. Tools from the formal verification community efficiently compute robust policies that provably adhere to formal specifications, like safety constraints, under the worst-case instance in the uncertainty set. We continuously learn the transition probabilities of an MDP in a robust anytime-learning approach that combines a dedicated Bayesian inference scheme with the computation of robust policies. In particular, our method (1) approximates probabilities as intervals, (2) adapts to new data that may be inconsistent with an intermediate model, and (3) may be stopped at any time to compute a robust policy on the uMDP that faithfully captures the data so far. Furthermore, our method is capable of adapting to changes in the environment. We show the effectiveness of our approach and compare it to robust policies computed on uMDPs learned by the UCRL2 reinforcement learning algorithm in an experimental evaluation on several benchmarks.
We propose a general purpose Bayesian inference algorithm for expensive likelihoods, replacing the stochastic term in the Langevin equation with a deterministic density gradient term. The particle density is evaluated from the current particle positions using a Normalizing Flow (NF), which is differentiable and has good generalization properties in high dimensions. We take advantage of NF preconditioning and NF based Metropolis-Hastings updates for a faster convergence. We show on various examples that the method is competitive against state of the art sampling methods.
In this paper, we introduce a probabilistic model for learning interpolative decomposition (ID), which is commonly used for feature selection, low-rank approximation, and identifying hidden patterns in data, where the matrix factors are latent variables associated with each data dimension. Prior densities with support on the specified subspace are used to address the constraint for the magnitude of the factored component of the observed matrix. Bayesian inference procedure based on Gibbs sampling is employed. We evaluate the model on a variety of real-world datasets including CCLE EC50, CCLE IC50, CTRP EC50,and MovieLens 100K datasets with different sizes, and dimensions, and show that the proposed Bayesian ID GBT and GBTN models lead to smaller reconstructive errors compared to existing randomized approaches.
Addressing the challenge of scaling-up epidemiological inference to complex and heterogeneous models, we introduce Poisson Approximate Likelihood (PAL) methods. In contrast to the popular ODE approach to compartmental modelling, in which a large population limit is used to motivate a deterministic model, PALs are derived from approximate filtering equations for finite-population, stochastic compartmental models, and the large population limit drives consistency of maximum PAL estimators. Our theoretical results appear to be the first likelihood-based parameter estimation consistency results which apply to a broad class of partially observed stochastic compartmental models and address the large population limit. PALs are simple to implement, involving only elementary arithmetic operations and no tuning parameters, and fast to evaluate, requiring no simulation from the model and having computational cost independent of population size. Through examples we demonstrate how PALs can be used to: fit an age-structured model of influenza, taking advantage of automatic differentiation in Stan; compare over-dispersion mechanisms in a model of rotavirus by embedding PALs within sequential Monte Carlo; and evaluate the role of unit-specific parameters in a meta-population model of measles.
The computation of Wasserstein gradient direction is essential for posterior sampling problems and scientific computing. The approximation of the Wasserstein gradient with finite samples requires solving a variational problem. We study the variational problem in the family of two-layer networks with squared-ReLU activations, towards which we derive a semi-definite programming (SDP) relaxation. This SDP can be viewed as an approximation of the Wasserstein gradient in a broader function family including two-layer networks. By solving the convex SDP, we obtain the optimal approximation of the Wasserstein gradient direction in this class of functions. Numerical experiments including PDE-constrained Bayesian inference and parameter estimation in COVID-19 modeling demonstrate the effectiveness of the proposed method.