Bayesian Inference

We present Causal Posterior Estimation (CPE), a novel method for Bayesian inference in simulator models, where evaluating the likelihood function is intractable or computationally expensive, but generating outputs given parameter values is straightforward. CPE approximates the posterior distribution using flow matching while directly incorporating the conditional dependence structure induced by the model's graphical representation into the neural network architecture. Across extensive experiments, we demonstrate that hard-coding these conditional dependencies into the network, rather than requiring them to be learned from data, enables CPE to achieve highly accurate posterior inference that matches or outperforms state-of-the-art baselines.

Discrete choice models (DCMs) are used to analyze individual decision-making in contexts such as transportation choices, political elections, and consumer preferences. DCMs play a central role in applied econometrics by enabling inference on key economic variables, such as marginal rates of substitution, rather than focusing solely on predicting choices on new unlabeled data. However, while traditional DCMs offer high interpretability and support for point and interval estimation of economic quantities, these models often underperform in predictive tasks compared to deep learning (DL) models. Despite their predictive advantages, DL models remain largely underutilized in discrete choice due to concerns about their lack of interpretability, unstable parameter estimates, and the absence of established methods for uncertainty quantification. Here, we introduce a deep learning model architecture specifically designed to integrate with approximate Bayesian inference methods, such as Stochastic Gradient Langevin Dynamics (SGLD). Our proposed model collapses to behaviorally informed hypotheses when data is limited, mitigating overfitting and instability in underspecified settings while retaining the flexibility to capture complex nonlinear relationships when sufficient data is available. We demonstrate our approach using SGLD through a Monte Carlo simulation study, evaluating both predictive metrics--such as out-of-sample balanced accuracy--and inferential metrics--such as empirical coverage for marginal rates of substitution interval estimates. Additionally, we present results from two empirical case studies: one using revealed mode choice data in NYC, and the other based on the widely used Swiss train choice stated preference data.

Magnetic resonance spectroscopy (MRS) is a non-invasive technique to measure the metabolic composition of tissues, offering valuable insights into neurological disorders, tumor detection, and other metabolic dysfunctions. However, accurate metabolite quantification is hindered by challenges such as spectral overlap, low signal-to-noise ratio, and various artifacts. Traditional methods like linear-combination modeling are susceptible to ambiguities and commonly only provide a theoretical lower bound on estimation accuracy in the form of the Cramér-Rao bound. This work introduces a Bayesian inference framework using Sylvester normalizing flows (SNFs) to approximate posterior distributions over metabolite concentrations, enhancing quantification reliability. A physics-based decoder incorporates prior knowledge of MRS signal formation, ensuring realistic distribution representations. We validate the method on simulated 7T proton MRS data, demonstrating accurate metabolite quantification, well-calibrated uncertainties, and insights into parameter correlations and multi-modal distributions.

Pareto fronts are useful to find good task-mixing strategies for multitask finetuning, but they are also costly to compute. To reduce costs, recent works have used existing model merging methods to help train cheap surrogate models to estimate the Pareto fronts. However, no work has yet considered designing new model-merging methods to directly, and provably, improve the quality of Pareto fronts. Here, we fill this gap by proposing a new Bayesian approach called Variational Model Merging. In this approach, existing model-merging methods are obtained as special cases of "posterior-merging" when Gaussian posteriors are used and new model-merging strategies can be derived by using non-Gaussian posteriors. Our main theoretical result is to show that more flexible posteriors necessarily yield better estimates of Pareto fronts. For instance, a Pareto front estimate obtained by merging full-Gaussian posteriors is expected to be better than that obtained by using isotropic Gaussian posteriors. We validate the theory through extensive empirical results on vision and language transformers where better Gaussian families consistently yields better or comparable Pareto fronts. Our work is a rare instance where Bayesian ideas are used to improve Pareto analysis.

Obtaining a reliable estimate of the joint probability mass function (PMF) of a set of random variables from observed data is a significant objective in statistical signal processing and machine learning. Modelling the joint PMF as a tensor that admits a low-rank canonical polyadic decomposition (CPD) has enabled the development of efficient PMF estimation algorithms. However, these algorithms require the rank (model order) of the tensor to be specified beforehand. In real-world applications, the true rank is unknown. Therefore, an appropriate rank is usually selected from a candidate set either by observing validation errors or by computing various likelihood-based information criteria, a procedure that could be costly in terms of computational time or hardware resources, or could result in mismatched models which affect the model accuracy. This paper presents a novel Bayesian framework for estimating the low-rank components of a joint PMF tensor and simultaneously inferring its rank from the observed data. We specify a Bayesian PMF estimation model and employ appropriate prior distributions for the model parameters, allowing the rank to be inferred without cross-validation.We then derive a deterministic solution based on variational inference (VI) to approximate the posterior distributions of various model parameters. Numerical experiments involving both synthetic data and real classification and item recommendation data illustrate the advantages of our VI-based method in terms of estimation accuracy, automatic rank detection, and computational efficiency.

In applied statistics and machine learning, the gold standards used for training are often biased and almost always noisy. Dawid and Skene's justifiably popular crowdsourcing model adjusts for rater sensitivity and specificity, but fails to capture distributional properties of rating data gathered for training, which in turn biases training. In this study, we introduce a general purpose measurement-error model with which we can infer consensus categories by adding item-level effects for difficulty, discriminativeness, and guessability. We further show how to constrain the bimodal posterior of these models to avoid adversarial raters. We validate our model's goodness of fit with posterior predictive checks, the Bayesian analogue of $χ^2$ tests, and assess its predictive accuracy using leave-one-out cross-validation. We illustrate our new model with two well-studied data sets, binary rating data for caries in dental X-rays and implication in natural language.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Analyzing the behavior of complex interdependent networks requires complete information about the network topology and the interdependent links across networks. For many applications such as critical infrastructure systems, understanding network interdependencies is crucial to anticipate cascading failures and plan for disruptions. However, data on the topology of individual networks are often publicly unavailable due to privacy and security concerns. Additionally, interdependent links are often only revealed in the aftermath of a disruption as a result of cascading failures. We propose a scalable nonparametric Bayesian approach to reconstruct the topology of interdependent infrastructure networks from observations of cascading failures. Metropolis-Hastings algorithm coupled with the infrastructure-dependent proposal are employed to increase the efficiency of sampling possible graphs. Results of reconstructing a synthetic system of interdependent infrastructure networks demonstrate that the proposed approach outperforms existing methods in both accuracy and computational time. We further apply this approach to reconstruct the topology of one synthetic and two real-world systems of interdependent infrastructure networks, including gas-power-water networks in Shelby County, TN, USA, and an interdependent system of power-water networks in Italy, to demonstrate the general applicability of the approach.

Variational inference, as an alternative to Markov chain Monte Carlo sampling, has played a transformative role in enabling scalable computation for complex Bayesian models. Nevertheless, existing approaches often depend on either rigid model-specific formulations or stochastic black-box optimization routines. Tangent approximation is a principled class of structured variational methods that exploits the geometry of the underlying probability model. However, its utility has largely been confined to logistic regression and related modeling regimes. In this article, we propose a novel variational framework based on tangent transformation for a broad class of probability models characterized by strongly super-Gaussian likelihoods. Our method leverages convex duality to construct tangent minorants of the log-likelihood, thereby inducing conjugacy with Gaussian priors over model parameters in an otherwise intractable setup. Under mild assumptions on the data-generating mechanism, we establish algorithmic convergence guarantees, a contribution that stands in contrast to the limited theoretical assurances typically available for black-box variational methods. Additionally, we derive near-parametric variational risk bounds. Superior performance of our proposed methodology is illustrated on simulated and real-data scenarios that challenge state-of-the-art variational algorithms in terms of scalability and their ability to consistently capture complex underlying data structure.