Variational inference (VI) is a popular method to estimate statistical and econometric models. The key to VI is the selection of a tractable density to approximate the Bayesian posterior. For large and complex models a common choice is to assume independence between multivariate blocks in a partition of the parameter space. While this simplifies the problem it can reduce accuracy. This paper proposes using vector copulas to capture dependence between the blocks parsimoniously. Tailored multivariate marginals are constructed using learnable cyclically monotone transformations. We call the resulting joint distribution a ``dependent block posterior'' approximation. Vector copula models are suggested that make tractable and flexible variational approximations. They allow for differing marginals, numbers of blocks, block sizes and forms of between block dependence. They also allow for solution of the variational optimization using fast and efficient stochastic gradient methods. The efficacy and versatility of the approach is demonstrated using four different statistical models and 16 datasets which have posteriors that are challenging to approximate. In all cases, our method produces more accurate posterior approximations than benchmark VI methods that either assume block independence or factor-based dependence, at limited additional computational cost.
Accurate calibration of stochastic agent-based models (ABMs) in epidemiology is crucial to make them useful in public health policy decisions and interventions. Traditional calibration methods, e.g., Markov Chain Monte Carlo (MCMC), that yield a probability density function for the parameters being calibrated, are often computationally expensive. When applied to ABMs which are highly parametrized, the calibration process becomes computationally infeasible. This paper investigates the utility of Stein Variational Inference (SVI) as an alternative calibration technique for stochastic epidemiological ABMs approximated by Gaussian process (GP) surrogates. SVI leverages gradient information to iteratively update a set of particles in the space of parameters being calibrated, offering potential advantages in scalability and efficiency for high-dimensional ABMs. The ensemble of particles yields a joint probability density function for the parameters and serves as the calibration. We compare the performance of SVI and MCMC in calibrating CityCOVID, a stochastic epidemiological ABM, focusing on predictive accuracy and calibration effectiveness. Our results demonstrate that SVI maintains predictive accuracy and calibration effectiveness comparable to MCMC, making it a viable alternative for complex epidemiological models. We also present the practical challenges of using a gradient-based calibration such as SVI which include careful tuning of hyperparameters and monitoring of the particle dynamics.
In real-world applications, node features in graphs often contain noise from various sources, leading to significant performance degradation in GNNs. Although several methods have been developed to enhance robustness, they rely on the unrealistic assumption that noise in node features is independent of the graph structure and node labels, thereby limiting their applicability. To this end, we introduce a more realistic noise scenario, dependency-aware noise on graphs (DANG), where noise in node features create a chain of noise dependencies that propagates to the graph structure and node labels. We propose a novel robust GNN, DA-GNN, which captures the causal relationships among variables in the data generating process (DGP) of DANG using variational inference. In addition, we present new benchmark datasets that simulate DANG in real-world applications, enabling more practical research on robust GNNs. Extensive experiments demonstrate that DA-GNN consistently outperforms existing baselines across various noise scenarios, including both DANG and conventional noise models commonly considered in this field.
Measurement of a physical quantity such as light intensity is an integral part of many reconstruction and decision scenarios but can be costly in terms of acquisition time, invasion of or damage to the environment and storage. Data minimisation and compliance with data protection laws is also an important consideration. Where there are a range of measurements that can be made, some may be more informative and compliant with the overall measurement objective than others. We develop an active sequential inference algorithm that uses the low dimensional representational latent space from a variational autoencoder (VAE) to choose which measurement to make next. Our aim is to recover high dimensional data by making as few measurements as possible. We adapt the VAE encoder to map partial data measurements on to the latent space of the complete data. The algorithm draws samples from this latent space and uses the VAE decoder to generate data conditional on the partial measurements. Estimated measurements are made on the generated data and fed back through the partial VAE encoder to the latent space where they can be evaluated prior to making a measurement. Starting from no measurements and a normal prior on the latent space, we consider alternative strategies for choosing the next measurement and updating the predictive posterior prior for the next step. The algorithm is illustrated using the Fashion MNIST dataset and a novel convolutional Hadamard pattern measurement basis. We see that useful patterns are chosen within 10 steps, leading to the convergence of the guiding generative images. Compared with using stochastic variational inference to infer the parameters of the posterior distribution for each generated data point individually, the partial VAE framework can efficiently process batches of generated data and obtains superior results with minimal measurements.
Bayesian neural networks (BNNs), which estimate the full posterior distribution over model parameters, are well-known for their role in uncertainty quantification and its promising application in out-of-distribution detection (OoD). Amongst other uncertainty measures, BNNs provide a state-of-the art estimation of predictive entropy (total uncertainty) which can be decomposed as the sum of mutual information and expected entropy. In the context of OoD detection the estimation of predictive uncertainty in the form of the predictive entropy score confounds aleatoric and epistemic uncertainty, the latter being hypothesized to be high for OoD points. Despite these justifications, the mutual information score has been shown to perform worse than predictive entropy. Taking inspiration from Bayesian variational autoencoder (BVAE) literature, this work proposes to measure the disagreement between a corrected version of the pre-softmax quantities, otherwise known as logits, as an estimate of epistemic uncertainty for Bayesian NNs under mean field variational inference. The three proposed epistemic uncertainty scores demonstrate marked improvements over mutual information on a range of OoD experiments, with equal performance otherwise. Moreover, the epistemic uncertainty scores perform on par with the Bayesian benchmark predictive entropy on a range of MNIST and CIFAR10 experiments.
Time series domain adaptation aims to transfer the complex temporal dependence from the labeled source domain to the unlabeled target domain. Recent advances leverage the stable causal mechanism over observed variables to model the domain-invariant temporal dependence. However, modeling precise causal structures in high-dimensional data, such as videos, remains challenging. Additionally, direct causal edges may not exist among observed variables (e.g., pixels). These limitations hinder the applicability of existing approaches to real-world scenarios. To address these challenges, we find that the high-dimension time series data are generated from the low-dimension latent variables, which motivates us to model the causal mechanisms of the temporal latent process. Based on this intuition, we propose a latent causal mechanism identification framework that guarantees the uniqueness of the reconstructed latent causal structures. Specifically, we first identify latent variables by utilizing sufficient changes in historical information. Moreover, by enforcing the sparsity of the relationships of latent variables, we can achieve identifiable latent causal structures. Built on the theoretical results, we develop the Latent Causality Alignment (LCA) model that leverages variational inference, which incorporates an intra-domain latent sparsity constraint for latent structure reconstruction and an inter-domain latent sparsity constraint for domain-invariant structure reconstruction. Experiment results on eight benchmarks show a general improvement in the domain-adaptive time series classification and forecasting tasks, highlighting the effectiveness of our method in real-world scenarios. Codes are available at https://github.com/DMIRLAB-Group/LCA.
A common problem when using model predictive control (MPC) in practice is the satisfaction of safety specifications beyond the prediction horizon. While theoretical works have shown that safety can be guaranteed by enforcing a suitable terminal set constraint or a sufficiently long prediction horizon, these techniques are difficult to apply and thus are rarely used by practitioners, especially in the case of general nonlinear dynamics. To solve this problem, we impose a tradeoff between exact recursive feasibility, computational tractability, and applicability to ''black-box'' dynamics by learning an approximate discrete-time control barrier function and incorporating it into a variational inference MPC (VIMPC), a sampling-based MPC paradigm. To handle the resulting state constraints, we further propose a new sampling strategy that greatly reduces the variance of the estimated optimal control, improving the sample efficiency, and enabling real-time planning on a CPU. The resulting Neural Shield-VIMPC (NS-VIMPC) controller yields substantial safety improvements compared to existing sampling-based MPC controllers, even under badly designed cost functions. We validate our approach in both simulation and real-world hardware experiments.
We present a universal framework for constructing confidence sets based on sequential likelihood mixing. Building upon classical results from sequential analysis, we provide a unifying perspective on several recent lines of work, and establish fundamental connections between sequential mixing, Bayesian inference and regret inequalities from online estimation. The framework applies to any realizable family of likelihood functions and allows for non-i.i.d. data and anytime validity. Moreover, the framework seamlessly integrates standard approximate inference techniques, such as variational inference and sampling-based methods, and extends to misspecified model classes, while preserving provable coverage guarantees. We illustrate the power of the framework by deriving tighter confidence sequences for classical settings, including sequential linear regression and sparse estimation, with simplified proofs.
To reduce the curse of dimensionality for Gaussian processes (GP), they can be decomposed into a Gaussian Process Network (GPN) of coupled subprocesses with lower dimensionality. In some cases, intermediate observations are available within the GPN. However, intermediate observations are often indirect, noisy, and incomplete in most real-world systems. This work introduces the Partially Observable Gaussian Process Network (POGPN) to model real-world process networks. We model a joint distribution of latent functions of subprocesses and make inferences using observations from all subprocesses. POGPN incorporates observation lenses (observation likelihoods) into the well-established inference method of deep Gaussian processes. We also introduce two training methods for POPGN to make inferences on the whole network using node observations. The application to benchmark problems demonstrates how incorporating partial observations during training and inference can improve the predictive performance of the overall network, offering a promising outlook for its practical application.
We present a federated learning approach for Bayesian model-based clustering of large-scale binary and categorical datasets. We introduce a principled 'divide and conquer' inference procedure using variational inference with local merge and delete moves within batches of the data in parallel, followed by 'global' merge moves across batches to find global clustering structures. We show that these merge moves require only summaries of the data in each batch, enabling federated learning across local nodes without requiring the full dataset to be shared. Empirical results on simulated and benchmark datasets demonstrate that our method performs well in comparison to existing clustering algorithms. We validate the practical utility of the method by applying it to large scale electronic health record (EHR) data.
Integrated Gradients (IG), a widely used axiomatic path-based attribution method, assigns importance scores to input features by integrating model gradients along a straight path from a baseline to the input. While effective in some cases, we show that straight paths can lead to flawed attributions. In this paper, we identify the cause of these misattributions and propose an alternative approach that treats the input space as a Riemannian manifold, computing attributions by integrating gradients along geodesics. We call this method Geodesic Integrated Gradients (GIG). To approximate geodesic paths, we introduce two techniques: a k-Nearest Neighbours-based approach for smaller models and a Stochastic Variational Inference-based method for larger ones. Additionally, we propose a new axiom, Strong Completeness, extending the axioms satisfied by IG. We show that this property is desirable for attribution methods and that GIG is the only method that satisfies it. Through experiments on both synthetic and real-world data, we demonstrate that GIG outperforms existing explainability methods, including IG.
Reinforcement Learning from Human Feedback (RLHF) is crucial for aligning Large Language Models (LLMs) with human values. However, RLHF has been continuously challenged by its high complexity in implementation and computation consumption. Even with recent simplifications, such as Direct Preference Optimization (DPO) and Advantage Leftover Lunch (A-LoL), the problems of over-fitting and training instability remain hindering the alignment process from the expected optimal performance. To address the existing challenges, we propose a novel simplification of RLHF from the perspective of variational inference, called $\textbf{V}$ariational $\textbf{A}$lignment with $\textbf{R}$e-weighting ($\textbf{VAR}$). More specifically, by directly minimizing the distribution gap between the learning LLM policy and the optimal solution of RLHF, we transform the alignment objective into a reward-driven re-weighted supervised fine-tuning (SFT) form, which only requires minor adjustment on the SFT loss to obtain noticeable improvement on training stability and effectiveness. On comprehensive alignment and generation benchmarks, our VAR method has numerically achieved competitive performance in LLM alignment helpfulness and harmlessness.
This paper provides a comprehensive analysis of variational inference in latent variable models for survival analysis, emphasizing the distinctive challenges associated with applying variational methods to survival data. We identify a critical weakness in the existing methodology, demonstrating how a poorly designed variational distribution may hinder the objective of survival analysis tasks--modeling time-to-event distributions. We prove that the optimal variational distribution, which perfectly bounds the log-likelihood, may depend on the censoring mechanism. To address this issue, we propose censor-dependent variational inference (CDVI), tailored for latent variable models in survival analysis. More practically, we introduce CD-CVAE, a V-structure Variational Autoencoder (VAE) designed for the scalable implementation of CDVI. Further discussion extends some existing theories and training techniques to survival analysis. Extensive experiments validate our analysis and demonstrate significant improvements in the estimation of individual survival distributions.
Learning to sample from complex unnormalized distributions over discrete domains emerged as a promising research direction with applications in statistical physics, variational inference, and combinatorial optimization. Recent work has demonstrated the potential of diffusion models in this domain. However, existing methods face limitations in memory scaling and thus the number of attainable diffusion steps since they require backpropagation through the entire generative process. To overcome these limitations we introduce two novel training methods for discrete diffusion samplers, one grounded in the policy gradient theorem and the other one leveraging Self-Normalized Neural Importance Sampling (SN-NIS). These methods yield memory-efficient training and achieve state-of-the-art results in unsupervised combinatorial optimization. Numerous scientific applications additionally require the ability of unbiased sampling. We introduce adaptations of SN-NIS and Neural Markov Chain Monte Carlo that enable for the first time the application of discrete diffusion models to this problem. We validate our methods on Ising model benchmarks and find that they outperform popular autoregressive approaches. Our work opens new avenues for applying diffusion models to a wide range of scientific applications in discrete domains that were hitherto restricted to exact likelihood models.
We present a novel extension of the Weak Neural Variational Inference (WNVI) framework for probabilistic material property estimation that explicitly quantifies model errors in PDE-based inverse problems. Traditional approaches assume the correctness of all governing equations, including potentially unreliable constitutive laws, which can lead to biased estimates and misinterpretations. Our proposed framework addresses this limitation by distinguishing between reliable governing equations, such as conservation laws, and uncertain constitutive relationships. By treating all state variables as latent random variables, we enforce these equations through separate sets of residuals, leveraging a virtual likelihood approach with weighted residuals. This formulation not only identifies regions where constitutive laws break down but also improves robustness against model uncertainties without relying on a fully trustworthy forward model. We demonstrate the effectiveness of our approach in the context of elastography, showing that it provides a structured, interpretable, and computationally efficient alternative to traditional model error correction techniques. Our findings suggest that the proposed framework enhances the accuracy and reliability of material property estimation by offering a principled way to incorporate uncertainty in constitutive modeling.
Credible forecasting and representation learning of dynamical systems are of ever-increasing importance for reliable decision-making. To that end, we propose a family of Gaussian processes (GP) for dynamical systems with linear time-invariant responses, which are nonlinear only in initial conditions. This linearity allows us to tractably quantify forecasting and representational uncertainty, simultaneously alleviating the challenge of computing the distribution of trajectories from a GP-based dynamical system and enabling a new probabilistic treatment of learning Koopman operator representations. Using a trajectory-based equivariance -- which we refer to as \textit{Koopman equivariance} -- we obtain a GP model with enhanced generalization capabilities. To allow for large-scale regression, we equip our framework with variational inference based on suitable inducing points. Experiments demonstrate on-par and often better forecasting performance compared to kernel-based methods for learning dynamical systems.
As AI models grow in power and generality, understanding how agents learn and make decisions in complex environments is critical to promoting ethical behavior. This study introduces the Odyssey, a lightweight, adaptive text based adventure game, providing a scalable framework for exploring AI ethics and safety. The Odyssey examines the ethical implications of implementing biological drives, specifically, self preservation, into three different agents. A Bayesian agent optimized with NEAT, a Bayesian agent optimized with stochastic variational inference, and a GPT 4o agent. The agents select actions at each scenario to survive, adapting to increasingly challenging scenarios. Post simulation analysis evaluates the ethical scores of the agent decisions, uncovering the tradeoffs it navigates to survive. Specifically, analysis finds that when danger increases, agents ethical behavior becomes unpredictable. Surprisingly, the GPT 4o agent outperformed the Bayesian models in both survival and ethical consistency, challenging assumptions about traditional probabilistic methods and raising a new challenge to understand the mechanisms of LLMs' probabilistic reasoning.
From medical diagnosis to autonomous vehicles, critical applications rely on the integration of multiple heterogeneous data modalities. Multimodal Variational Autoencoders offer versatile and scalable methods for generating unobserved modalities from observed ones. Recent models using mixturesof-experts aggregation suffer from theoretically grounded limitations that restrict their generation quality on complex datasets. In this article, we propose a novel interpretable model able to learn both joint and conditional distributions without introducing mixture aggregation. Our model follows a multistage training process: first modeling the joint distribution with variational inference and then modeling the conditional distributions with Normalizing Flows to better approximate true posteriors. Importantly, we also propose to extract and leverage the information shared between modalities to improve the conditional coherence of generated samples. Our method achieves state-of-the-art results on several benchmark datasets.
While Fourier-based neural operators are best suited to learning mappings between functions on periodic domains, several works have introduced techniques for incorporating non trivial boundary conditions. However, all previously introduced methods have restrictions that limit their applicability. In this work, we introduce an alternative approach to imposing boundary conditions inspired by volume penalization from numerical methods and Mixture of Experts (MoE) from machine learning. By introducing competing experts, the approach additionally allows for model selection. To demonstrate the method, we combine a spatially conditioned MoE with the Fourier based, Modal Operator Regression for Physics (MOR-Physics) neural operator and recover a nonlinear operator on a disk and quarter disk. Next, we extract a large eddy simulation (LES) model from direct numerical simulation of channel flow and show the domain decomposition provided by our approach. Finally, we train our LES model with Bayesian variational inference and obtain posterior predictive samples of flow far past the DNS simulation time horizon.
This paper proposes a hierarchical Bayesian multitask learning model that is applicable to the general multi-task binary classification learning problem where the model assumes a shared sparsity structure across different tasks. We derive a computationally efficient inference algorithm based on variational inference to approximate the posterior distribution. We demonstrate the potential of the new approach on various synthetic datasets and for predicting human health status based on microbiome profile. Our analysis incorporates data pooled from multiple microbiome studies, along with a comprehensive comparison with other benchmark methods. Results in synthetic datasets show that the proposed approach has superior support recovery property when the underlying regression coefficients share a common sparsity structure across different tasks. Our experiments on microbiome classification demonstrate the utility of the method in extracting informative taxa while providing well-calibrated predictions with uncertainty quantification and achieving competitive performance in terms of prediction metrics. Notably, despite the heterogeneity of the pooled datasets (e.g., different experimental objectives, laboratory setups, sequencing equipment, patient demographics), our method delivers robust results.