Nonlocal, integral operators have become an efficient surrogate for bottom-up homogenization, due to their ability to represent long-range dependence and multiscale effects. However, the nonlocal homogenized model has unavoidable discrepancy from the microscale model. Such errors accumulate and propagate in long-term simulations, making the resultant prediction unreliable. To develop a robust and reliable bottom-up homogenization framework, we propose a new framework, which we coin Embedded Nonlocal Operator Regression (ENOR), to learn a nonlocal homogenized surrogate model and its structural model error. This framework provides discrepancy-adaptive uncertainty quantification for homogenized material response predictions in long-term simulations. The method is built on Nonlocal Operator Regression (NOR), an optimization-based nonlocal kernel learning approach, together with an embedded model error term in the trainable kernel. Then, Bayesian inference is employed to infer the model error term parameters together with the kernel parameters. To make the problem computationally feasible, we use a multilevel delayed acceptance Markov chain Monte Carlo (MLDA-MCMC) method, enabling efficient Bayesian model calibration and model error estimation. We apply this technique to predict long-term wave propagation in a heterogeneous one-dimensional bar, and compare its performance with additive noise models. Owing to its ability to capture model error, the learned ENOR achieves improved estimation of posterior predictive uncertainty.
Modeling distributions that depend on external control parameters is a common scenario in diverse applications like molecular simulations, where system properties like temperature affect molecular configurations. Despite the relevance of these applications, existing solutions are unsatisfactory as they require severely restricted model architectures or rely on backward training, which is prone to unstable training. We introduce TRADE, which overcomes these limitations by formulating the learning process as a boundary value problem. By initially training the model for a specific condition using either i.i.d. samples or backward KL training, we establish a boundary distribution. We then propagate this information across other conditions using the gradient of the unnormalized density with respect to the external parameter. This formulation, akin to the principles of physics-informed neural networks, allows us to efficiently learn parameter-dependent distributions without restrictive assumptions. Experimentally, we demonstrate that TRADE achieves excellent results in a wide range of applications, ranging from Bayesian inference and molecular simulations to physical lattice models.
Differential privacy (DP) provides robust privacy guarantees for statistical inference, but this can lead to unreliable results and biases in downstream applications. While several noise-aware approaches have been proposed which integrate DP perturbation into the inference, they are limited to specific types of simple probabilistic models. In this work, we propose a novel method for noise-aware approximate Bayesian inference based on stochastic gradient variational inference which can also be applied to high-dimensional and non-conjugate models. We also propose a more accurate evaluation method for noise-aware posteriors. Empirically, our inference method has similar performance to existing methods in the domain where they are applicable. Outside this domain, we obtain accurate coverages on high-dimensional Bayesian linear regression and well-calibrated predictive probabilities on Bayesian logistic regression with the UCI Adult dataset.
In scenarios with limited training data or where explainability is crucial, conventional neural network-based machine learning models often face challenges. In contrast, Bayesian inference-based algorithms excel in providing interpretable predictions and reliable uncertainty estimation in these scenarios. While many state-of-the-art in-memory computing (IMC) architectures leverage emerging non-volatile memory (NVM) technologies to offer unparalleled computing capacity and energy efficiency for neural network workloads, their application in Bayesian inference is limited. This is because the core operations in Bayesian inference differ significantly from the multiplication-accumulation (MAC) operations common in neural networks, rendering them generally unsuitable for direct implementation in most existing IMC designs. In this paper, we propose FeBiM, an efficient and compact Bayesian inference engine powered by multi-bit ferroelectric field-effect transistor (FeFET)-based IMC. FeBiM effectively encodes the trained probabilities of a Bayesian inference model within a compact FeFET-based crossbar. It maps quantized logarithmic probabilities to discrete FeFET states. As a result, the accumulated outputs of the crossbar naturally represent the posterior probabilities, i.e., the Bayesian inference model's output given a set of observations. This approach enables efficient in-memory Bayesian inference without the need for additional calculation circuitry. As the first FeFET-based in-memory Bayesian inference engine, FeBiM achieves an impressive storage density of 26.32 Mb/mm$^{2}$ and a computing efficiency of 581.40 TOPS/W in a representative Bayesian classification task. These results demonstrate 10.7$\times$/43.4$\times$ improvement in compactness/efficiency compared to the state-of-the-art hardware implementation of Bayesian inference.
Neural posterior estimation (NPE), a simulation-based computational approach for Bayesian inference, has shown great success in approximating complex posterior distributions. Existing NPE methods typically rely on normalizing flows, which approximate a distribution by composing many simple, invertible transformations. But flow-based models, while state of the art for NPE, are known to suffer from several limitations, including training instability and sharp trade-offs between representational power and computational cost. In this work, we demonstrate the effectiveness of conditional diffusions coupled with high-capacity summary networks for amortized NPE. Conditional diffusions address many of the challenges faced by flow-based methods. Our results show that, across a highly varied suite of benchmarking problems for NPE architectures, diffusions offer improved stability, superior accuracy, and faster training times, even with simpler, shallower models. Building on prior work on diffusions for NPE, we show that these gains persist across a variety of different summary network architectures. Code is available at https://github.com/TianyuCodings/cDiff.
This paper presents a Bayesian inference framework for a linear index threshold-crossing binary choice model that satisfies a median independence restriction. The key idea is that the model is observationally equivalent to a probit model with nonparametric heteroskedasticity. Consequently, Gibbs sampling techniques from Albert and Chib (1993) and Chib and Greenberg (2013) lead to a computationally attractive Bayesian inference procedure in which a Gaussian process forms a conditionally conjugate prior for the natural logarithm of the skedastic function.
Random feature latent variable models (RFLVMs) represent the state-of-the-art in latent variable models, capable of handling non-Gaussian likelihoods and effectively uncovering patterns in high-dimensional data. However, their heavy reliance on Monte Carlo sampling results in scalability issues which makes it difficult to use these models for datasets with a massive number of observations. To scale up RFLVMs, we turn to the optimization-based variational Bayesian inference (VBI) algorithm which is known for its scalability compared to sampling-based methods. However, implementing VBI for RFLVMs poses challenges, such as the lack of explicit probability distribution functions (PDFs) for the Dirichlet process (DP) in the kernel learning component, and the incompatibility of existing VBI algorithms with RFLVMs. To address these issues, we introduce a stick-breaking construction for DP to obtain an explicit PDF and a novel VBI algorithm called ``block coordinate descent variational inference" (BCD-VI). This enables the development of a scalable version of RFLVMs, or in short, SRFLVM. Our proposed method shows scalability, computational efficiency, superior performance in generating informative latent representations and the ability of imputing missing data across various real-world datasets, outperforming state-of-the-art competitors.
Dimensionality reduction (DR) offers a useful representation of complex high-dimensional data. Recent DR methods focus on hyperbolic geometry to derive a faithful low-dimensional representation of hierarchical data. However, existing methods are based on neighbor embedding, frequently ruining the continual relation of the hierarchies. This paper presents hyperboloid Gaussian process (GP) latent variable models (hGP-LVMs) to embed high-dimensional hierarchical data with implicit continuity via nonparametric estimation. We adopt generative modeling using the GP, which brings effective hierarchical embedding and executes ill-posed hyperparameter tuning. This paper presents three variants that employ original point, sparse point, and Bayesian estimations. We establish their learning algorithms by incorporating the Riemannian optimization and active approximation scheme of GP-LVM. For Bayesian inference, we further introduce the reparameterization trick to realize Bayesian latent variable learning. In the last part of this paper, we apply hGP-LVMs to several datasets and show their ability to represent high-dimensional hierarchies in low-dimensional spaces.
Bayesian inference offers a robust framework for updating prior beliefs based on new data using Bayes' theorem, but exact inference is often computationally infeasible, necessitating approximate methods. Though widely used, these methods struggle to estimate marginal likelihoods accurately, particularly due to the rigid functional structures of deterministic models like Gaussian processes and the limitations of small sample sizes in stochastic models like the ensemble Kalman method. In this work, we introduce BI-EqNO, an equivariant neural operator framework for generalized approximate Bayesian inference, designed to enhance both deterministic and stochastic approaches. BI-EqNO transforms priors into posteriors conditioned on observation data through data-driven training. The framework is flexible, supporting diverse prior and posterior representations with arbitrary discretizations and varying numbers of observations. Crucially, BI-EqNO's architecture ensures (1) permutation equivariance between prior and posterior representations, and (2) permutation invariance with respect to observational data. We demonstrate BI-EqNO's utility through two examples: (1) as a generalized Gaussian process (gGP) for regression, and (2) as an ensemble neural filter (EnNF) for sequential data assimilation. Results show that gGP outperforms traditional Gaussian processes by offering a more flexible representation of covariance functions. Additionally, EnNF not only outperforms the ensemble Kalman filter in small-ensemble settings but also has the potential to function as a "super" ensemble filter, capable of representing and integrating multiple ensemble filters for enhanced assimilation performance. This study highlights BI-EqNO's versatility and effectiveness, improving Bayesian inference through data-driven training while reducing computational costs across various applications.
Conditional moment equality models are regularly encountered in empirical economics, yet they are difficult to estimate. These models map a conditional distribution of data to a structural parameter via the restriction that a conditional mean equals zero. Using this observation, I introduce a Bayesian inference framework in which an unknown conditional distribution is replaced with a nonparametric posterior, and structural parameter inference is then performed using an implied posterior. The method has the same flexibility as frequentist semiparametric estimators and does not require converting conditional moments to unconditional moments. Importantly, I prove a semiparametric Bernstein-von Mises theorem, providing conditions under which, in large samples, the posterior for the structural parameter is approximately normal, centered at an efficient estimator, and has variance equal to the Chamberlain (1987) semiparametric efficiency bound. As byproducts, I show that Bayesian uncertainty quantification methods are asymptotically optimal frequentist confidence sets and derive low-level sufficient conditions for Gaussian process priors. The latter sheds light on a key prior stability condition and relates to the numerical aspects of the paper in which these priors are used to predict the welfare effects of price changes.
As large language models (LLMs) continue to evolve, understanding and quantifying the uncertainty in their predictions is critical for enhancing application credibility. However, the existing literature relevant to LLM uncertainty estimation often relies on heuristic approaches, lacking systematic classification of the methods. In this survey, we clarify the definitions of uncertainty and confidence, highlighting their distinctions and implications for model predictions. On this basis, we integrate theoretical perspectives, including Bayesian inference, information theory, and ensemble strategies, to categorize various classes of uncertainty estimation methods derived from heuristic approaches. Additionally, we address challenges that arise when applying these methods to LLMs. We also explore techniques for incorporating uncertainty into diverse applications, including out-of-distribution detection, data annotation, and question clarification. Our review provides insights into uncertainty estimation from both definitional and theoretical angles, contributing to a comprehensive understanding of this critical aspect in LLMs. We aim to inspire the development of more reliable and effective uncertainty estimation approaches for LLMs in real-world scenarios.
Bayesian inference provides a principled probabilistic framework for quantifying uncertainty by updating beliefs based on prior knowledge and observed data through Bayes' theorem. In Bayesian deep learning, neural network weights are treated as random variables with prior distributions, allowing for a probabilistic interpretation and quantification of predictive uncertainty. However, Bayesian methods lack theoretical generalization guarantees for unseen data. PAC-Bayesian analysis addresses this limitation by offering a frequentist framework to derive generalization bounds for randomized predictors, thereby certifying the reliability of Bayesian methods in machine learning. Temperature $T$, or inverse-temperature $\lambda = \frac{1}{T}$, originally from statistical mechanics in physics, naturally arises in various areas of statistical inference, including Bayesian inference and PAC-Bayesian analysis. In Bayesian inference, when $T < 1$ (``cold'' posteriors), the likelihood is up-weighted, resulting in a sharper posterior distribution. Conversely, when $T > 1$ (``warm'' posteriors), the likelihood is down-weighted, leading to a more diffuse posterior distribution. By balancing the influence of observed data and prior regularization, temperature adjustments can address issues of underfitting or overfitting in Bayesian models, bringing improved predictive performance.
Stein variational inference (SVI) is a sample-based approximate Bayesian inference technique that generates a sample set by jointly optimizing the samples' locations to minimize an information-theoretic measure of discrepancy with the target probability distribution. SVI thus provides a fast and significantly more sample-efficient approach to Bayesian inference than traditional (random-sampling-based) alternatives. However, the optimization techniques employed in existing SVI methods struggle to address problems in which the target distribution is high-dimensional, poorly-conditioned, or non-convex, which severely limits the range of their practical applicability. In this paper, we propose a novel trust-region optimization approach for SVI that successfully addresses each of these challenges. Our method builds upon prior work in SVI by leveraging conditional independences in the target distribution (to achieve high-dimensional scaling) and second-order information (to address poor conditioning), while additionally providing an effective adaptive step control procedure, which is essential for ensuring convergence on challenging non-convex optimization problems. Experimental results show our method achieves superior numerical performance, both in convergence rate and sample accuracy, and scales better in high-dimensional distributions, than previous SVI techniques.
We present an online method for embodied agents to learn and accomplish diverse user goals. While offline methods like RLHF can represent various goals but require large datasets, our approach achieves similar flexibility with online efficiency. We extract natural language goal representations from conversations with Large Language Models (LLMs). We prompt an LLM to role play as a human with different goals and use the corresponding likelihoods to run Bayesian inference over potential goals. As a result, our method can represent uncertainty over complex goals based on unrestricted dialog. We evaluate our method in grocery shopping and home robot assistance domains using a text-based interface and AI2Thor simulation respectively. Results show our method outperforms ablation baselines that lack either explicit goal representation or probabilistic inference.
Background: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of trait through time, while incorporating noises that represent different unobservable evolutionary pressures. Often times, a heterogeneous Gaussian process that consists of multiple parametric sub-processes is often used when the observed data come from a very diverse set of taxa. In the maximum likelihood setting, challenges can be found when exploring the involved likelihood surface and when interpreting the uncertainty around the parameters. Results: We extend the methods to tackle inference problems for mixed Gaussian phylogenetic models (MGPMs) by implementing a Bayesian scheme that can take into account biologically relevant priors. The posterior inference method is based on the Population Monte Carlo (PMC) algorithm that are easily parallelized, and using an efficient algorithm to calculate the likelihood of phylogenetically correlated observations. A model evaluation method that is based on the proximity of the posterior predictive distribution to the observed data is also implemented. Simulation study is done to test the inference and evaluation capability of the method. Finally, we test our method on a real-world dataset. Conclusion: We implement the method in the R package bgphy, available at github.com/bayubeta/bgphy. Simulation study demonstrates that the method is able to infer parameters and evaluate models properly, while its implementation on the real-world dataset indicates that a carefully selected model of evolution based on naturally occurring classifications results in a better fit to the observed data.
In recent years, Full-Waveform Inversion (FWI) has been extensively used to derive high-resolution subsurface velocity models from seismic data. However, due to the nonlinearity and ill-posed nature of the problem, FWI requires a good starting model to avoid producing non-physical solutions. Moreover, conventional optimization methods fail to quantify the uncertainty associated with the recovered solution, which is critical for decision-making processes. Bayesian inference offers an alternative approach as it directly or indirectly evaluates the posterior probability density function. For example, Markov Chain Monte Carlo (MCMC) methods generate multiple sample chains to characterize the solution's uncertainty. Despite their ability to theoretically handle any form of distribution, MCMC methods require many sampling steps; this limits their usage in high-dimensional problems with computationally intensive forward modeling, as is the FWI case. Variational Inference (VI), on the other hand, provides an approximate solution to the posterior distribution in the form of a parametric or non-parametric proposal distribution. Among the various algorithms used in VI, Stein Variational Gradient Descent (SVGD) is recognized for its ability to iteratively refine a set of samples to approximate the target distribution. However, mode and variance-collapse issues affect SVGD in high-dimensional inverse problems. This study aims to improve the performance of SVGD within the context of FWI by utilizing, for the first time, an annealed variant of SVGD and combining it with a multi-scale strategy. Additionally, we demonstrate that Principal Component Analysis (PCA) can be used to evaluate the performance of the optimization process. Clustering techniques are also employed to provide more rigorous and meaningful statistical analysis of the particles in the presence of multi-modal distributions.
Ultrasound (US) has the unique potential to offer access to medical imaging to anyone, everywhere. Devices have become ultra-portable and cost-effective, akin to the stethoscope. Nevertheless US image quality and diagnostic efficacy are still highly operator- and patient-dependent. In difficult-to-image patients, image quality is often insufficient for reliable diagnosis. In this paper, we put forth that US imaging systems can be recast as information-seeking agents that engage in reciprocal interactions with their anatomical environment. Such agents autonomously adapt their transmit-receive sequences to fully personalize imaging and actively maximize information gain in-situ. To that end, we will show that the sequence of pulse-echo experiments that a US system performs can be interpreted as a perception-action loop: the action is the data acquisition, probing tissue with acoustic waves and recording reflections at the detection array, and perception is the inference of the anatomical and or functional state, potentially including associated diagnostic quantities. We then equip systems with a mechanism to actively reduce uncertainty and maximize diagnostic value across a sequence of experiments, treating action and perception jointly using Bayesian inference given generative models of the environment and action-conditional pulse-echo observations. Since the representation capacity of the generative models dictates both the quality of inferred anatomical states and the effectiveness of inferred sequences of future imaging actions, we will be greatly leveraging the enormous advances in deep generative modelling that are currently disrupting many fields and society at large. Finally, we show some examples of cognitive, closed-loop, US systems that perform active beamsteering and adaptive scanline selection, based on deep generative models that track anatomical belief states.
Given an intractable target density $p$, variational inference (VI) attempts to find the best approximation $q$ from a tractable family $Q$. This is typically done by minimizing the exclusive Kullback-Leibler divergence, $\text{KL}(q||p)$. In practice, $Q$ is not rich enough to contain $p$, and the approximation is misspecified even when it is a unique global minimizer of $\text{KL}(q||p)$. In this paper, we analyze the robustness of VI to these misspecifications when $p$ exhibits certain symmetries and $Q$ is a location-scale family that shares these symmetries. We prove strong guarantees for VI not only under mild regularity conditions but also in the face of severe misspecifications. Namely, we show that (i) VI recovers the mean of $p$ when $p$ exhibits an \textit{even} symmetry, and (ii) it recovers the correlation matrix of $p$ when in addition~$p$ exhibits an \textit{elliptical} symmetry. These guarantees hold for the mean even when $q$ is factorized and $p$ is not, and for the correlation matrix even when~$q$ and~$p$ behave differently in their tails. We analyze various regimes of Bayesian inference where these symmetries are useful idealizations, and we also investigate experimentally how VI behaves in their absence.
The logit transform is arguably the most widely-employed link function beyond linear settings. This transformation routinely appears in regression models for binary data and provides, either explicitly or implicitly, a core building-block within state-of-the-art methodologies for both classification and regression. Its widespread use, combined with the lack of analytical solutions for the optimization of general losses involving the logit transform, still motivates active research in computational statistics. Among the directions explored, a central one has focused on the design of tangent lower bounds for logistic log-likelihoods that can be tractably optimized, while providing a tight approximation of these log-likelihoods. Although progress along these lines has led to the development of effective minorize-maximize (MM) algorithms for point estimation and coordinate ascent variational inference schemes for approximate Bayesian inference under several logit models, the overarching focus in the literature has been on tangent quadratic minorizers. In fact, it is still unclear whether tangent lower bounds sharper than quadratic ones can be derived without undermining the tractability of the resulting minorizer. This article addresses such a challenging question through the design and study of a novel piece-wise quadratic lower bound that uniformly improves any tangent quadratic minorizer, including the sharpest ones, while admitting a direct interpretation in terms of the classical generalized lasso problem. As illustrated in a ridge logistic regression, this unique connection facilitates more effective implementations than those provided by available piece-wise bounds, while improving the convergence speed of quadratic ones.
In sequential decision-making (SDM) tasks, methods like reinforcement learning (RL) and heuristic search have made notable advances in specific cases. However, they often require extensive exploration and face challenges in generalizing across diverse environments due to their limited grasp of the underlying decision dynamics. In contrast, large language models (LLMs) have recently emerged as powerful general-purpose tools, due to their capacity to maintain vast amounts of domain-specific knowledge. To harness this rich prior knowledge for efficiently solving complex SDM tasks, we propose treating LLMs as prior action distributions and integrating them into RL frameworks through Bayesian inference methods, making use of variational inference and direct posterior sampling. The proposed approaches facilitate the seamless incorporation of fixed LLM priors into both policy-based and value-based RL frameworks. Our experiments show that incorporating LLM-based action priors significantly reduces exploration and optimization complexity, substantially improving sample efficiency compared to traditional RL techniques, e.g., using LLM priors decreases the number of required samples by over 90% in offline learning scenarios.