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 Uncertainty


A Kernel Approach for Semi-implicit Variational Inference

arXiv.org Machine Learning

Semi-implicit variational inference (SIVI) enhances the expressiveness of variational families through hierarchical semi-implicit distributions, but the intractability of their densities makes standard ELBO-based optimization biased. Recent score-matching approaches to SIVI (SIVI-SM) address this issue via a minimax formulation, at the expense of an additional lower-level optimization problem. In this paper, we propose kernel semi-implicit variational inference (KSIVI), a principled and tractable alternative that eliminates the lower-level optimization by leveraging kernel methods. We show that when optimizing over a reproducing kernel Hilbert space, the lower-level problem admits an explicit solution, reducing the objective to the kernel Stein discrepancy (KSD). Exploiting the hierarchical structure of semi-implicit distributions, the resulting KSD objective can be efficiently optimized using stochastic gradient methods. We establish optimization guarantees via variance bounds on Monte Carlo gradient estimators and derive statistical generalization bounds of order $\tilde{\mathcal{O}}(1/\sqrt{n})$. We further introduce a multi-layer hierarchical extension that improves expressiveness while preserving tractability. Empirical results on synthetic and real-world Bayesian inference tasks demonstrate the effectiveness of KSIVI.


Irreversible Kinetics Emerges from Bayesian Inference over Admissible Histories

arXiv.org Machine Learning

A probabilistic formulation of irreversible kinetics is introduced in which incrementally admissible histories are weighted by a Gibbs-type measure built from an energy-dissipation action and observation constraints, with Theta controlling epistemic uncertainty. This measure can be interpreted as a Bayesian posterior over histories. In the zero-uncertainty limit, it concentrates on maximum-a-posteriori (MAP) histories, recovering classical deterministic evolution by incremental minimization in the convex generalized-standard-material setting, while allowing multiple competing MAP histories for non-convex energies or temporally coupled constraints. This emergence is demonstrated across seven distinct forward-in-time examples and an inverse inference problem of unknown histories from sparse observations via a global constrained minimum-action principle.


Coarsening Causal DAG Models

arXiv.org Machine Learning

Directed acyclic graphical (DAG) models are a powerful tool for representing causal relationships among jointly distributed random variables, especially concerning data from across different experimental settings. However, it is not always practical or desirable to estimate a causal model at the granularity of given features in a particular dataset. There is a growing body of research on causal abstraction to address such problems. We contribute to this line of research by (i) providing novel graphical identifiability results for practically-relevant interventional settings, (ii) proposing an efficient, provably consistent algorithm for directly learning abstract causal graphs from interventional data with unknown intervention targets, and (iii) uncovering theoretical insights about the lattice structure of the underlying search space, with connections to the field of causal discovery more generally. As proof of concept, we apply our algorithm on synthetic and real datasets with known ground truths, including measurements from a controlled physical system with interacting light intensity and polarization.


Riesz Representer Fitting under Bregman Divergence: A Unified Framework for Debiased Machine Learning

arXiv.org Machine Learning

Estimating the Riesz representer is central to debiased machine learning for causal and structural parameter estimation. We propose generalized Riesz regression, a unified framework that estimates the Riesz representer by fitting a representer model via Bregman divergence minimization. This framework includes the squared loss and the Kullback--Leibler (KL) divergence as special cases: the former recovers Riesz regression, while the latter recovers tailored loss minimization. Under suitable model specifications, the dual problems correspond to covariate balancing, which we call automatic covariate balancing. Moreover, under the same specifications, outcome averages weighted by the estimated Riesz representer satisfy Neyman orthogonality even without estimating the regression function, a property we call automatic Neyman orthogonalization. This property not only reduces the estimation error of Neyman orthogonal scores but also clarifies a key distinction between debiased machine learning and targeted maximum likelihood estimation. Our framework can also be viewed as a generalization of density ratio fitting under Bregman divergences to Riesz representer estimation, and it applies beyond density ratio estimation. We provide convergence analyses for both reproducing kernel Hilbert space (RKHS) and neural network model classes. A Python package for generalized Riesz regression is available at https://github.com/MasaKat0/grr.


Constraint- and Score-Based Nonlinear Granger Causality Discovery with Kernels

arXiv.org Machine Learning

Granger causality (GC) [15] is a time series causal discovery framework that uses predictive modeling to identify the underlying causal structure of a time series system. Relying on the assumption that cause precedes effect, GC assesses whether including the lagged information from one time series in the autoregressive model of a second time series enhances its predictions. This improvement indicates a predictive relationship between the time series variables, where one time series provides supplemental information about the future of another time series, thereby signifying the presence of a (Granger) causal relationship. GC requires only observational data, and has been used for time series causal discovery across diverse domains, including climate science [33], political and social sciences [17], econometrics [4], and biological systems studies [13]. The original formulation of GC requires several assumptions to be satisfied for causal identifiability. In regards to the candidate time series system, it is assumed that the time series variables are stationary, and that all variables are observed (absence of latent confounders). GC was initially proposed for bivariate time series systems, but was generalised for the multivariate setting to accommodate the assumption that all relevant variables are included in the analysis [15]. Additional assumptions are made with regard to the types of causal relationships that can be identified within the time series system. GC cannot estimate a causal relationship between time series at an instantaneous time point, relying on the relationship between the lags and predicted values to determine a GC relationship.


Horseshoe Mixtures-of-Experts (HS-MoE)

arXiv.org Machine Learning

Horseshoe mixtures-of-experts (HS-MoE) models provide a Bayesian framework for sparse expert selection in mixture-of-experts architectures. We combine the horseshoe prior's adaptive global-local shrinkage with input-dependent gating, yielding data-adaptive sparsity in expert usage. Our primary methodological contribution is a particle learning algorithm for sequential inference, in which the filter is propagated forward in time while tracking only sufficient statistics. We also discuss how HS-MoE relates to modern mixture-of-experts layers in large language models, which are deployed under extreme sparsity constraints (e.g., activating a small number of experts per token out of a large pool).


MLCBART: Multilabel Classification with Bayesian Additive Regression Trees

arXiv.org Machine Learning

Multilabel Classification (MLC) deals with the simultaneous classification of multiple binary labels. The task is challenging because, not only may there be arbitrarily different and complex relationships between predictor variables and each label, but associations among labels may exist even after accounting for effects of predictor variables. In this paper, we present a Bayesian additive regression tree (BART) framework to model the problem. BART is a nonparametric and flexible model structure capable of uncovering complex relationships within the data. Our adaptation, MLCBART, assumes that labels arise from thresholding an underlying numeric scale, where a multivariate normal model allows explicit estimation of the correlation structure among labels. This enables the discovery of complicated relationships in various forms and improves MLC predictive performance. Our Bayesian framework not only enables uncertainty quantification for each predicted label, but our MCMC draws produce an estimated conditional probability distribution of label combinations for any predictor values. Simulation experiments demonstrate the effectiveness of the proposed model by comparing its performance with a set of models, including the oracle model with the correct functional form. Results show that our model predicts vectors of labels more accurately than other contenders and its performance is close to the oracle model. An example highlights how the method's ability to produce measures of uncertainty on predictions provides nuanced understanding of classification results.


Why are there many equally good models? An Anatomy of the Rashomon Effect

arXiv.org Machine Learning

The Rashomon effect -- the existence of multiple, distinct models that achieve nearly equivalent predictive performance -- has emerged as a fundamental phenomenon in modern machine learning and statistics. In this paper, we explore the causes underlying the Rashomon effect, organizing them into three categories: statistical sources arising from finite samples and noise in the data-generating process; structural sources arising from non-convexity of optimization objectives and unobserved variables that create fundamental non-identifiability; and procedural sources arising from limitations of optimization algorithms and deliberate restrictions to suboptimal model classes. We synthesize insights from machine learning, statistics, and optimization literature to provide a unified framework for understanding why the multiplicity of good models arises. A key distinction emerges: statistical multiplicity diminishes with more data, structural multiplicity persists asymptotically and cannot be resolved without different data or additional assumptions, and procedural multiplicity reflects choices made by practitioners. Beyond characterizing causes, we discuss both the challenges and opportunities presented by the Rashomon effect, including implications for inference, interpretability, fairness, and decision-making under uncertainty.


A Statistical Assessment of Amortized Inference Under Signal-to-Noise Variation and Distribution Shift

arXiv.org Machine Learning

Since the turn of the century, approximate Bayesian inference has steadily evolved as new computational techniques have been incorporated to handle increasingly complex and large-scale predictive problems. The recent success of deep neural networks and foundation models has now given rise to a new paradigm in statistical modeling, in which Bayesian inference can be amortized through large-scale learned predictors. In amortized inference, substantial computation is invested upfront to train a neural network that can subsequently produce approximate posterior or predictions at negligible marginal cost across a wide range of tasks. At deployment, amortized inference offers substantial computational savings compared with traditional Bayesian procedures, which generally require repeated likelihood evaluations or Monte Carlo simulations for predictions for each new dataset. Despite the growing popularity of amortized inference, its statistical interpretation and its role within Bayesian inference remain poorly understood. This paper presents statistical perspectives on the working principles of several major neural architectures, including feedforward networks, Deep Sets, and Transformers, and examines how these architectures naturally support amortized Bayesian inference. We discuss how these models perform structured approximation and probabilistic reasoning in ways that yield controlled generalization error across a wide range of deployment scenarios, and how these properties can be harnessed for Bayesian computation. Through simulation studies, we evaluate the accuracy, robustness, and uncertainty quantification of amortized inference under varying signal-to-noise ratios and distributional shifts, highlighting both its strengths and its limitations.


Robust low-rank estimation with multiple binary responses using pairwise AUC loss

arXiv.org Machine Learning

Multiple binary responses arise in many modern data-analytic problems. Although fitting separate logistic regressions for each response is computationally attractive, it ignores shared structure and can be statistically inefficient, especially in high-dimensional and class-imbalanced regimes. Low-rank models offer a natural way to encode latent dependence across tasks, but existing methods for binary data are largely likelihood-based and focus on pointwise classification rather than ranking performance. In this work, we propose a unified framework for learning with multiple binary responses that directly targets discrimination by minimizing a surrogate loss for the area under the ROC curve (AUC). The method aggregates pairwise AUC surrogate losses across responses while imposing a low-rank constraint on the coefficient matrix to exploit shared structure. We develop a scalable projected gradient descent algorithm based on truncated singular value decomposition. Exploiting the fact that the pairwise loss depends only on differences of linear predictors, we simplify computation and analysis. We establish non-asymptotic convergence guarantees, showing that under suitable regularity conditions, leading to linear convergence up to the minimax-optimal statistical precision. Extensive simulation studies demonstrate that the proposed method is robust in challenging settings such as label switching and data contamination and consistently outperforms likelihood-based approaches.