Estimation of cardiovascular model parameters from electronic health records (EHR) poses a significant challenge primarily due to lack of identifiability. Structural non-identifiability arises when a manifold in the space of parameters is mapped to a common output, while practical non-identifiability can result due to limited data, model misspecification, or noise corruption. To address the resulting ill-posed inverse problem, optimization-based or Bayesian inference approaches typically use regularization, thereby limiting the possibility of discovering multiple solutions. In this study, we use inVAErt networks, a neural network-based, data-driven framework for enhanced digital twin analysis of stiff dynamical systems. We demonstrate the flexibility and effectiveness of inVAErt networks in the context of physiological inversion of a six-compartment lumped parameter hemodynamic model from synthetic data to real data with missing components.
Expected free energy (EFE) is a central quantity in active inference which has recently gained popularity due to its intuitive decomposition of the expected value of control into a pragmatic and an epistemic component. While numerous conjectures have been made to justify EFE as a decision making objective function, the most widely accepted is still its intuitiveness and resemblance to variational free energy in approximate Bayesian inference. In this work, we take a bottom up approach and ask: taking EFE as given, what's the resulting agent's optimality gap compared with a reward-driven reinforcement learning (RL) agent, which is well understood? By casting EFE under a particular class of belief MDP and using analysis tools from RL theory, we show that EFE approximates the Bayes optimal RL policy via information value. We discuss the implications for objective specification of active inference agents.
Unexpected stimuli induce "error" or "surprise" signals in the brain. The theory of predictive coding promises to explain these observations in terms of Bayesian inference by suggesting that the cortex implements variational inference in a probabilistic graphical model. However, when applied to machine learning tasks, this family of algorithms has yet to perform on par with other variational approaches in high-dimensional, structured inference problems. To address this, we introduce a novel predictive coding algorithm for structured generative models, that we call divide-and-conquer predictive coding (DCPC). DCPC differs from other formulations of predictive coding, as it respects the correlation structure of the generative model and provably performs maximum-likelihood updates of model parameters, all without sacrificing biological plausibility. Empirically, DCPC achieves better numerical performance than competing algorithms and provides accurate inference in a number of problems not previously addressed with predictive coding. We provide an open implementation of DCPC in Pyro on Github.
Traditional deep Gaussian processes model the data evolution using a discrete hierarchy, whereas differential Gaussian processes (DIFFGPs) represent the evolution as an infinitely deep Gaussian process. However, prior DIFFGP methods often overlook the uncertainty of kernel hyperparameters and assume them to be fixed and time-invariant, failing to leverage the unique synergy between continuous-time models and approximate inference. In this work, we propose a fully Bayesian approach that treats the kernel hyperparameters as random variables and constructs coupled stochastic differential equations (SDEs) to learn their posterior distribution and that of inducing points. By incorporating estimation uncertainty on hyperparameters, our method enhances the model's flexibility and adaptability to complex dynamics. Additionally, our approach provides a time-varying, comprehensive, and realistic posterior approximation through coupling variables using SDE methods. Experimental results demonstrate the advantages of our method over traditional approaches, showcasing its superior performance in terms of flexibility, accuracy, and other metrics. Our work opens up exciting research avenues for advancing Bayesian inference and offers a powerful modeling tool for continuous-time Gaussian processes.
The synthetic control method (SCM) is widely used for causal inference with panel data, particularly when there are few treated units. SCM assumes the stable unit treatment value assumption (SUTVA), which posits that potential outcomes are unaffected by the treatment status of other units. However, interventions often impact not only treated units but also untreated units, known as spillover effects. This study introduces a novel panel data method that extends SCM to allow for spillover effects and estimate both treatment and spillover effects. This method leverages a spatial autoregressive panel data model to account for spillover effects. We also propose Bayesian inference methods using Bayesian horseshoe priors for regularization. We apply the proposed method to two empirical studies: evaluating the effect of the California tobacco tax on consumption and estimating the economic impact of the 2011 division of Sudan on GDP per capita.
Intelligent agents must be able to articulate its own uncertainty. In this work, we show that pre-trained sequence models are naturally capable of probabilistic reasoning over exchangeable data points -- forming informed beliefs and sharpening them as it gathers more information. A sequence model learns the relationship between observations, which differs from typical Bayesian models that quantify uncertainty over latent parameters through priors and likelihoods (e.g., topic models). Despite the apparent difference, we illustrate how exchangeable sequence modeling provides a valid Bayesian model by going back to De Finetti's classical predictive view of probabilistic reasoning: uncertainty comes from data that has not been observed yet, rather than latent parameters. From this perspective, pre-training autoregressive models is equivalent to formulating informed beliefs based on prior observations ("empirical Bayes"), and forward generation is equivalent to simulating instantiations of an environment ("posterior inference"). In particular, exchangeable sequence models can explicitly perform statistical inference; epistemic uncertainty over latent environments is captured by variation in predicted future observations. Formally, we show the sequence prediction loss controls the quality of uncertainty quantification, and propose several approaches for encoding exchangeability in sequence model architectures: data augmentation, regularization, and causal masking.
Because of its strong predictive skills, deep learning has emerged as an essential tool in many industries, including healthcare. Traditional deep learning models, on the other hand, frequently lack interpretability and omit to take prediction uncertainty into account two crucial components of clinical decision making. In order to produce explainable and uncertainty aware predictions, this study presents a novel framework called Bayesian Kolmogorov Arnold Networks (BKANs), which combines the expressive capacity of Kolmogorov Arnold Networks with Bayesian inference. We employ BKANs on two medical datasets, which are widely used benchmarks for assessing machine learning models in medical diagnostics: the Pima Indians Diabetes dataset and the Cleveland Heart Disease dataset. Our method provides useful insights into prediction confidence and decision boundaries and outperforms traditional deep learning models in terms of prediction accuracy. Moreover, BKANs' capacity to represent aleatoric and epistemic uncertainty guarantees doctors receive more solid and trustworthy decision support. Our Bayesian strategy improves the interpretability of the model and considerably minimises overfitting, which is important for tiny and imbalanced medical datasets, according to experimental results. We present possible expansions to further use BKANs in more complicated multimodal datasets and address the significance of these discoveries for future research in building reliable AI systems for healthcare. This work paves the way for a new paradigm in deep learning model deployment in vital sectors where transparency and reliability are crucial.
The vast majority of the literature on learning dynamical systems or stochastic processes from time series has focused on stable or ergodic systems, for both Bayesian and frequentist inference procedures. However, most real-world systems are only metastable, that is, the dynamics appear to be stable on some time scale, but are in fact unstable over longer time scales. Consistency of inference for metastable systems may not be possible, but one can ask about metaconsistency: Do inference procedures converge when observations are taken over a large but finite time interval, but diverge on longer time scales? In this paper we introduce, discuss, and quantify metaconsistency in a Bayesian framework. We discuss how metaconsistency can be exploited to efficiently infer a model for a sub-system of a larger system, where inference on the global behavior may require much more data. We also discuss the relation between meta-consistency and the spectral properties of the model dynamical system in the case of uniformly ergodic diffusions.
Bayesian Inference with Markov Chain Monte Carlo requires efficient computation of the likelihood function. In some scientific applications, the likelihood must be computed by numerically solving a partial differential equation, which can be prohibitively expensive. We demonstrate that some such problems can be made tractable by amortizing the computation with a surrogate likelihood function implemented by a neural network. We show that this has two additional benefits: reducing noise in the likelihood evaluations and providing fast gradient calculations. In experiments, the approach is applied to a model of heliospheric transport of galactic cosmic rays, where it enables efficient sampling from the posterior of latent parameters in the Parker equation.
Sequential Monte Carlo (SMC) samplers are powerful tools for Bayesian inference but suffer from high computational costs due to their reliance on large particle ensembles for accurate estimates. We introduce persistent sampling (PS), an extension of SMC that systematically retains and reuses particles from all prior iterations to construct a growing, weighted ensemble. By leveraging multiple importance sampling and resampling from a mixture of historical distributions, PS mitigates the need for excessively large particle counts, directly addressing key limitations of SMC such as particle impoverishment and mode collapse. Crucially, PS achieves this without additional likelihood evaluations-weights for persistent particles are computed using cached likelihood values. This framework not only yields more accurate posterior approximations but also produces marginal likelihood estimates with significantly lower variance, enhancing reliability in model comparison. Furthermore, the persistent ensemble enables efficient adaptation of transition kernels by leveraging a larger, decorrelated particle pool. Experiments on high-dimensional Gaussian mixtures, hierarchical models, and non-convex targets demonstrate that PS consistently outperforms standard SMC and related variants, including recycled and waste-free SMC, achieving substantial reductions in mean squared error for posterior expectations and evidence estimates, all at reduced computational cost. PS thus establishes itself as a robust, scalable, and efficient alternative for complex Bayesian inference tasks.
A new gradient-based particle sampling method, MPM-ParVI, based on material point method (MPM), is proposed for variational inference. MPM-ParVI simulates the deformation of a deformable body (e.g. a solid or fluid) under external effects driven by the target density; transient or steady configuration of the deformable body approximates the target density. The continuum material is modelled as an interacting particle system (IPS) using MPM, each particle carries full physical properties, interacts and evolves following conservation dynamics. This easy-to-implement ParVI method offers deterministic sampling and inference for a class of probabilistic models such as those encountered in Bayesian inference (e.g. intractable densities) and generative modelling (e.g. score-based).
Infinitely wide or deep neural networks (NNs) with independent and identically distributed (i.i.d.) parameters have been shown to be equivalent to Gaussian processes. Because of the favorable properties of Gaussian processes, this equivalence is commonly employed to analyze neural networks and has led to various breakthroughs over the years. However, neural networks and Gaussian processes are equivalent only in the limit; in the finite case there are currently no methods available to approximate a trained neural network with a Gaussian model with bounds on the approximation error. In this work, we present an algorithmic framework to approximate a neural network of finite width and depth, and with not necessarily i.i.d. parameters, with a mixture of Gaussian processes with error bounds on the approximation error. In particular, we consider the Wasserstein distance to quantify the closeness between probabilistic models and, by relying on tools from optimal transport and Gaussian processes, we iteratively approximate the output distribution of each layer of the neural network as a mixture of Gaussian processes. Crucially, for any NN and $\epsilon >0$ our approach is able to return a mixture of Gaussian processes that is $\epsilon$-close to the NN at a finite set of input points. Furthermore, we rely on the differentiability of the resulting error bound to show how our approach can be employed to tune the parameters of a NN to mimic the functional behavior of a given Gaussian process, e.g., for prior selection in the context of Bayesian inference. We empirically investigate the effectiveness of our results on both regression and classification problems with various neural network architectures. Our experiments highlight how our results can represent an important step towards understanding neural network predictions and formally quantifying their uncertainty.
We investigate the problem of recovering a structured sparse signal from a linear observation model with an uncertain dynamic grid in the sensing matrix. The state-of-the-art expectation maximization based compressed sensing (EM-CS) methods, such as turbo compressed sensing (Turbo-CS) and turbo variational Bayesian inference (Turbo-VBI), have a relatively slow convergence speed due to the double-loop iterations between the E-step and M-step. Moreover, each inner iteration in the E-step involves a high-dimensional matrix inverse in general, which is unacceptable for problems with large signal dimensions or real-time calculation requirements. Although there are some attempts to avoid the high-dimensional matrix inverse by majorization minimization, the convergence speed and accuracy are often sacrificed. To better address this problem, we propose an alternating estimation framework based on a novel subspace constrained VBI (SC-VBI) method, in which the high-dimensional matrix inverse is replaced by a low-dimensional subspace constrained matrix inverse (with the dimension equal to the sparsity level). We further prove the convergence of the SC-VBI to a stationary solution of the Kullback-Leibler divergence minimization problem. Simulations demonstrate that the proposed SC-VBI algorithm can achieve a much better tradeoff between complexity per iteration, convergence speed, and performance compared to the state-of-the-art algorithms.
Bayesian inference for inverse problems hinges critically on the choice of priors. In the absence of specific prior information, population-level distributions can serve as effective priors for parameters of interest. With the advent of machine learning, the use of data-driven population-level distributions (encoded, e.g., in a trained deep neural network) as priors is emerging as an appealing alternative to simple parametric priors in a variety of inverse problems. However, in many astrophysical applications, it is often difficult or even impossible to acquire independent and identically distributed samples from the underlying data-generating process of interest to train these models. In these cases, corrupted data or a surrogate, e.g. a simulator, is often used to produce training samples, meaning that there is a risk of obtaining misspecified priors. This, in turn, can bias the inferred posteriors in ways that are difficult to quantify, which limits the potential applicability of these models in real-world scenarios. In this work, we propose addressing this issue by iteratively updating the population-level distributions by retraining the model with posterior samples from different sets of observations, and we showcase the potential of this method on the problem of background image reconstruction in strong gravitational lensing when score-based models are used as data-driven priors. We show that, starting from a misspecified prior distribution, the updated distribution becomes progressively closer to the underlying population-level distribution, and the resulting posterior samples exhibit reduced bias after several updates.
The space of human goals is tremendously vast; and yet, from just a few moments of watching a scene or reading a story, we seem to spontaneously infer a range of plausible motivations for the people and characters involved. What explains this remarkable capacity for intuiting other agents' goals, despite the infinitude of ends they might pursue? And how does this cohere with our understanding of other people as approximately rational agents? In this paper, we introduce a sequential Monte Carlo model of open-ended goal inference, which combines top-down Bayesian inverse planning with bottom-up sampling based on the statistics of co-occurring subgoals. By proposing goal hypotheses related to the subgoals achieved by an agent, our model rapidly generates plausible goals without exhaustive search, then filters out goals that would be irrational given the actions taken so far. We validate this model in a goal inference task called Block Words, where participants try to guess the word that someone is stacking out of lettered blocks. In comparison to both heuristic bottom-up guessing and exact Bayesian inference over hundreds of goals, our model better predicts the mean, variance, efficiency, and resource rationality of human goal inferences, achieving similar accuracy to the exact model at a fraction of the cognitive cost, while also explaining garden-path effects that arise from misleading bottom-up cues. Our experiments thus highlight the importance of uniting top-down and bottom-up models for explaining the speed, accuracy, and generality of human theory-of-mind.
Estimating a distribution given access to its unnormalized density is pivotal in Bayesian inference, where the posterior is generally known only up to an unknown normalizing constant. Variational inference and Markov chain Monte Carlo methods are the predominant tools for this task; however, both are often challenging to apply reliably, particularly when the posterior has complex geometry. Here, we introduce Soft Contrastive Variational Inference (SoftCVI), which allows a family of variational objectives to be derived through a contrastive estimation framework. The approach parameterizes a classifier in terms of a variational distribution, reframing the inference task as a contrastive estimation problem aiming to identify a single true posterior sample among a set of samples. Despite this framing, we do not require positive or negative samples, but rather learn by sampling the variational distribution and computing ground truth soft classification labels from the unnormalized posterior itself. The objectives have zero variance gradient when the variational approximation is exact, without the need for specialized gradient estimators. We empirically investigate the performance on a variety of Bayesian inference tasks, using both simple (e.g. normal) and expressive (normalizing flow) variational distributions. We find that SoftCVI can be used to form objectives which are stable to train and mass-covering, frequently outperforming inference with other variational approaches.
Recent studies seek to provide Graph Neural Network (GNN) interpretability via multiple unsupervised learning models. Due to the scarcity of datasets, current methods easily suffer from learning bias. To solve this problem, we embed a Large Language Model (LLM) as knowledge into the GNN explanation network to avoid the learning bias problem. We inject LLM as a Bayesian Inference (BI) module to mitigate learning bias. The efficacy of the BI module has been proven both theoretically and experimentally. We conduct experiments on both synthetic and real-world datasets. The innovation of our work lies in two parts: 1. We provide a novel view of the possibility of an LLM functioning as a Bayesian inference to improve the performance of existing algorithms; 2. We are the first to discuss the learning bias issues in the GNN explanation problem.
In this work, we propose a tracking method for multiple extended targets or unresolvable group targets based on the Variational Bayesian Inference (VBI). Firstly, based on the most commonly used Random Matrix Model (RMM), the joint states of a single target are modeled as a Gamma Gaussian Inverse Wishart (GGIW) distribution, and the multi-target joint association variables are involved in the estimation together as unknown information with a prior distribution. A shape evolution model and VBI are employed to address the shortcomings of the RMM. Through the VBI, we can derive the approximate variational posterior for the exact multi-target posterior. Furthermore, to demonstrate the applicability of the method in real-world tracking scenarios, we present two potential lightweight schemes. The first is based on clustering, which effectively prunes the joint association events. The second is a simplification of the variational posterior through marginal association probabilities. We demonstrate the effectiveness of the proposed method using simulation experiments, and the proposed method outperforms current state-of-the-art methods in terms of accuracy and adaptability. This manuscript is only a preprint version, a completer and more official version will be uploaded as soon as possible
Since their initial introduction, score-based diffusion models (SDMs) have been successfully applied to solve a variety of linear inverse problems in finite-dimensional vector spaces due to their ability to efficiently approximate the posterior distribution. However, using SDMs for inverse problems in infinite-dimensional function spaces has only been addressed recently, primarily through methods that learn the unconditional score. While this approach is advantageous for some inverse problems, it is mostly heuristic and involves numerous computationally costly forward operator evaluations during posterior sampling. To address these limitations, we propose a theoretically grounded method for sampling from the posterior of infinite-dimensional Bayesian linear inverse problems based on amortized conditional SDMs. In particular, we prove that one of the most successful approaches for estimating the conditional score in finite dimensions - the conditional denoising estimator - can also be applied in infinite dimensions. A significant part of our analysis is dedicated to demonstrating that extending infinite-dimensional SDMs to the conditional setting requires careful consideration, as the conditional score typically blows up for small times, contrarily to the unconditional score. We conclude by presenting stylized and large-scale numerical examples that validate our approach, offer additional insights, and demonstrate that our method enables large-scale, discretization-invariant Bayesian inference.
Existing methods for graph out-of-distribution (OOD) generalization primarily rely on empirical studies on synthetic datasets. Such approaches tend to overemphasize the causal relationships between invariant sub-graphs and labels, thereby neglecting the non-negligible role of environment in real-world scenarios. In contrast to previous studies that impose rigid independence assumptions on environments and invariant sub-graphs, this paper presents the theorems of environment-label dependency and mutable rationale invariance, where the former characterizes the usefulness of environments in determining graph labels while the latter refers to the mutable importance of graph rationales. Based on analytic investigations, a novel variational inference based method named ``Probability Dependency on Environments and Rationales for OOD Graphs on Real-world Data'' (DEROG) is introduced. To alleviate the adverse effect of unknown prior knowledge on environments and rationales, DEROG utilizes generalized Bayesian inference. Further, DEROG employs an EM-based algorithm for optimization. Finally, extensive experiments on real-world datasets under different distribution shifts are conducted to show the superiority of DEROG. Our code is publicly available at https://anonymous.4open.science/r/DEROG-536B.