NeurIPS 2025 Papers

Latent component identification from unknown *nonlinear* mixtures is a foundational challenge in machine learning, with applications in tasks such as self-supervised learning and causal representation learning. Prior work in *nonlinear independent component analysis* (nICA) has shown that auxiliary signals---such as weak supervision---can support *identifiability* of conditionally independent latent components. More recent approaches explore structural assumptions, like sparsity in the Jacobian of the mixing function, to relax such requirements. In this work, we introduce *Diverse Influence Component Analysis* (DICA), a framework that exploits the convex geometry of the mixing function’s Jacobian. We propose a *Jacobian Volume Maximization* (J-VolMax) criterion, which enables latent component identification by encouraging diversity in their influence on the observed variables. Under suitable conditions, this approach achieves identifiability without relying on auxiliary information, latent component independence, or Jacobian sparsity assumptions. These results extend the scope of identifiability analysis and offer a complementary perspective to existing methods.

A reliable estimate of the full conditional distribution of a multivariate response given a set of covariates is essential in many decision-making applications. However, misspecified or miscalibrated models can lead to poor approximations of the joint distribution, resulting in unreliable predictions and suboptimal decisions. Standard recalibration methods are largely restricted to univariate settings, and while conformal prediction techniques yield multivariate regions with coverage guarantees, they do not provide an explicit form of the underlying probability distribution. We address this gap by first introducing a novel notion of latent calibration, which assesses probabilistic calibration in the latent space of conditional invertible generative models such as normalizing flows and flow matching. Second, we propose latent recalibration (LR), a post-hoc model recalibration method that learns a transformation of the latent space with finite-sample bounds on latent calibration. Unlike existing recalibration methods, LR produces a recalibrated distribution with an explicit multivariate density function while remaining computationally efficient. Extensive experiments on both tabular and image datasets show that LR consistently improves latent calibration error and the negative log-likelihood of the recalibrated models.

The do-calculus is a sound and complete tool for identifying causal effects in acyclic directed mixed graphs (ADMGs) induced by structural causal models (SCMs). However, in many real-world applications, especially in high-dimensional settings, constructing a fully specified ADMG is often infeasible. This limitation has led to growing interest in partially specified causal representations, particularly through cluster-directed mixed graphs (C-DMGs), which group variables into clusters and offer a more abstract yet practical view of causal dependencies. While these representations can include cycles, recent work has shown that the do-calculus remains sound and complete for identifying macro-level causal effects in C-DMGs over ADMGs under the assumption that all clusters sizes are greater than 1. Nevertheless, real-world systems often exhibit cyclic causal dynamics at the structural level. To account for this, input-output structural causal models (ioSCMs) have been introduced as a generalization of SCMs that allow for cycles. ioSCMs induce another type of graph structure known as a directed mixed graph (DMG). Analogous to the ADMG setting, one can define C-DMGs over DMGs as high-level representations of causal relations among clusters of variables. In this paper, we prove that, unlike in the ADMG setting, the do-calculus is unconditionally sound and complete for identifying macro causal effects in C-DMGs over DMGs. Furthermore, we show that the graphical criteria for non-identifiability of macro causal effects previously established C-DMGs over ADMGs naturally extends to a subset of C-DMGs over DMGs.

We consider the problem of sampling distributions stemming from non-convex potentials with Unadjusted Langevin Algorithm (ULA). We prove the stability of the discrete-time ULA to drift approximations under the assumption that the potential is strongly convex at infinity. In many context, e.g. imaging inverse problems, potentials are non-convex and non-smooth. Proximal Stochastic Gradient Langevin Algorithm (PSGLA) is a popular algorithm to handle such potentials. It combines the forward-backward optimization algorithm with a ULA step. Our main stability result combined with properties of the Moreau envelope allows us to derive the first proof of convergence of the PSGLA for non-convex potentials. We empirically validate our methodology on synthetic data and in the context of imaging inverse problems. In particular, we observe that PSGLA exhibits faster convergence rates than Stochastic Gradient Langevin Algorithm for posterior sampling while preserving its restoration properties.

When and why representations learned by different deep neural networks are similar is an active research topic. We choose to address these questions from the perspective of identifiability theory, which suggests that a measure of representational similarity should be invariant to transformations that leave the model distribution unchanged. Focusing on a model family which includes several popular pre-training approaches, e.g., autoregressive language models, we explore when models which generate distributions that are close have similar representations. We prove that a small Kullback--Leibler divergence between the model distributions does not guarantee that the corresponding representations are similar. This has the important corollary that models with near-maximum data likelihood can still learn dissimilar representations---a phenomenon mirrored in our experiments with models trained on CIFAR-10. We then define a distributional distance for which closeness implies representational similarity, and in synthetic experiments, we find that wider networks learn distributions which are closer with respect to our distance and have more similar representations. Our results thus clarify the link between closeness in distribution and representational similarity.

We introduce DeCaFlow, a deconfounding causal generative model. Training once per dataset using just observational data and the underlying causal graph, DeCaFlow enables accurate causal inference on continuous variables under the presence of hidden confounders. Specifically, we extend previous results on causal estimation under hidden confounding to show that a single instance of DeCaFlow provides correct estimates for all causal queries identifiable with do-calculus, leveraging proxy variables to adjust for the causal effects when do-calculus alone is insufficient. Moreover, we show that counterfactual queries are identifiable as long as their interventional counterparts are identifiable, and thus are also correctly estimated by DeCaFlow. Our empirical results on diverse settings—including the Ecoli70 dataset, with 3 independent hidden confounders, tens of observed variables and hundreds of causal queries—show that DeCaFlow outperforms existing approaches, while demonstrating its out-of-the-box applicability to any given causal graph.

Estimating associations between spatial covariates and responses — rather than merely predicting responses — is central to environmental science, epidemiology, and economics. For instance, public health officials might be interested in whether air pollution has a strictly positive association with a health outcome, and the magnitude of any effect. Standard machine learning methods often provide accurate predictions but offer limited insight into covariate-response relationships. And we show that existing methods for constructing confidence (or credible) intervals for associations can fail to provide nominal coverage in the face of model misspecification and nonrandom locations — despite both being essentially always present in spatial problems. We introduce a method that constructs valid frequentist confidence intervals for associations in spatial settings. Our method requires minimal assumptions beyond a form of spatial smoothness and a homoskedastic Gaussian error assumption. In particular, we do not require model correctness or covariate overlap between training and target locations. Our approach is the first to guarantee nominal coverage in this setting and outperforms existing techniques in both real and simulated experiments. Our confidence intervals are valid in finite samples when the noise of the Gaussian error is known, and we provide an asymptotically consistent estimation procedure for this noise variance when it is unknown.

Multi-arm bandit experimental designs are increasingly being adopted over standard randomized trials due to their potential to improve outcomes for study participants, enable faster identification of the best-performing options, and/or enhance the precision of estimating key parameters. Current approaches for inference after adaptive sampling either rely on asymptotic normality under restricted experiment designs or underpowered martingale concentration inequalities that lead to weak power in practice. To bypass these limitations, we propose a simulation-based approach for conducting hypothesis tests and constructing confidence intervals for arm specific means and their differences. Our simulation-based approach uses positively biased nuisances to generate additional trajectories of the experiment, which we call \textit{simulation with optimism}. Using these simulations, we characterize the distribution potentially non-normal sample mean test statistic to conduct inference. We provide guarantees for (i) asymptotic type I error control, (ii) convergence of our confidence intervals, and (iii) asymptotic strong consistency of our estimator over a wide variety of common bandit designs. Our empirical results show that our approach achieves the desired coverage while reducing confidence interval widths by up to 50\%, with drastic improvements for arms not targeted by the design.

We propose a generalized score-based diffusion framework for learning multivariate Gaussian mixture models with homoscedastic or heteroscedastic noise. Our goal is to nonparametrically estimate the latent location distribution and denoise the observations. Departing from the conventional maximum likelihood approach, we reinterpret each observation as a temporal slice of a family of stochastic diffusion processes. This modeling choice enables a principled characterization of the additive noise structure and supports a multi-step denoising procedure grounded in reverse-time dynamics. We introduce a score-based objective that explicitly models the latent distribution and accommodates observation-specific noise covariances. Theoretically, we establish that the score estimation error with $n$ independent observations achieves a near-parametric error rate of $\frac{\mathrm{polylog}(n)}{n}$, improving upon existing results in the diffusion literature. Empirically, our method outperforms the nonparametric maximum likelihood estimator in both density estimation and denoising fidelity, especially in high-dimensional settings. These findings suggest a promising direction for integrating nonparametric empirical Bayes with diffusion-based generative modeling for latent structure recovery.

Simulation-based inference (SBI) offers a flexible and general approach to performing Bayesian inference: In SBI, a neural network is trained on synthetic data simulated from a model and used to rapidly infer posterior distributions for observed data. A key goal for SBI is to achieve accurate inference with as few simulations as possible, especially for expensive simulators. In this work, we address this challenge by repurposing recent probabilistic foundation models for tabular data: We show how tabular foundation models---specifically TabPFN---can be used as pre-trained autoregressive conditional density estimators for SBI. We propose Neural Posterior Estimation with Prior-data Fitted Networks (NPE-PFN) and show that it is competitive with current SBI approaches in terms of accuracy for both benchmark tasks and two complex scientific inverse problems. Crucially, it often substantially outperforms them in terms of simulation efficiency, sometimes requiring orders of magnitude fewer simulations. NPE-PFN eliminates the need for selecting and training an inference network and tuning its hyperparameters. We also show that it exhibits superior robustness to model misspecification and can be scaled to simulation budgets that exceed the context size limit of TabPFN. NPE-PFN provides a new direction for SBI, where training-free, general-purpose inference models offer efficient, easy-to-use, and flexible solutions for a wide range of stochastic inverse problems.

Existing methods for differentiable structure learning in discrete data typically assume that the data are generated from specific structural equation models. However, these assumptions may not align with the true data-generating process, which limits the general applicability of such methods. Furthermore, current approaches often ignore the complex dependence structure inherent in discrete data and consider only linear effects. We propose a differentiable structure learning framework that is capable of capturing arbitrary dependencies among discrete variables. We show that although general discrete models are unidentifiable from purely observational data, it is possible to characterize the complete set of compatible parameters and structures. Additionally, we establish identifiability up to the Markov equivalence class (MEC) under mild assumptions. We formulate the learning problem as a single differentiable optimization task in the most general form, thereby avoiding the unrealistic simplifications adopted by previous methods. Empirical results demonstrate that our approach effectively captures complex relationships in discrete data.

Expected information gain (EIG) is a crucial quantity in Bayesian optimal experimental design (BOED), quantifying how useful an experiment is by the amount we expect the posterior to differ from the prior. However, evaluating the EIG can be computationally expensive since it generally requires estimating the posterior normalizing constant. In this work, we leverage two idiosyncrasies of BOED to improve efficiency of EIG estimation via sequential Monte Carlo (SMC). First, in BOED we simulate the data and thus know the true underlying parameters. Second, we ultimately care about the EIG, not the individual normalizing constants. Often we observe that the Monte Carlo variance of standard SMC estimators for the normalizing constant of a single dataset are significantly lower than the variance of the normalizing constants across datasets; the latter thus contributes the majority of the variance for EIG estimates. This suggests the potential to slightly increase variance while drastically decreasing computation time by reducing the SMC population size, which leads us to an EIG-specific SMC estimator that starts with a only a single sample from the posterior and tempers \textit{backwards} towards the prior. Using this single-sample estimator, which we call reverse-annealed SMC (RA-SMC), we show that it is possible to estimate EIG with orders of magnitude fewer likelihood evaluations in three models: a four-dimensional spring-mass, a six-dimensional Johnson-Cook model and a four-dimensional source-finding problem.

Latent stochastic differential equation (SDE) models are important tools for the unsupervised discovery of dynamical systems from data, with applications ranging from engineering to neuroscience. In these complex domains, exact posterior inference of the latent state path is typically intractable, motivating the use of approximate methods such as variational inference (VI). However, existing VI methods for inference in latent SDEs often suffer from slow convergence and numerical instability. Here, we propose SDE Inference via Natural Gradients (SING), a method that leverages natural gradient VI to efficiently exploit the underlying geometry of the model and variational posterior. SING enables fast and reliable inference in latent SDE models by approximating intractable integrals and parallelizing computations in time. We provide theoretical guarantees that SING will approximately optimize the intractable, continuous-time objective of interest. Moreover, we demonstrate that better state inference enables more accurate estimation of nonlinear drift functions using, for example, Gaussian process SDE models. SING outperforms prior methods in state inference and drift estimation on a variety of datasets, including a challenging application to modeling neural dynamics in freely behaving animals. Altogether, our results illustrate the potential of SING as a tool for accurate inference in complex dynamical systems, especially those characterized by limited prior knowledge and non-conjugate structure.

We introduce active generation of Pareto sets (A-GPS), a new framework for online discrete black-box multi-objective optimization (MOO). A-GPS learns a generative model of the Pareto set that supports a-posteriori conditioning on user preferences. The method employs a class probability estimator (CPE) to predict non-dominance relations and to condition the generative model toward high-performing regions of the search space. We also show that this non-dominance CPE implicitly estimates the probability of hypervolume improvement (PHVI). To incorporate subjective trade-offs, A-GPS introduces _preference direction vectors_ that encode user-specified preferences in objective space. At each iteration, the model is updated using both Pareto membership and alignment with these preference directions, producing an amortized generative model capable of sampling across the Pareto front without retraining. The result is a simple yet powerful approach that achieves high-quality Pareto set approximations, avoids explicit hypervolume computation, and flexibly captures user preferences. Empirical results on synthetic benchmarks and protein design tasks demonstrate strong sample efficiency and effective preference incorporation.

Estimating the uncertainty of responses from Large Language Models (LLMs) remains a critical challenge. While recent Bayesian methods have demonstrated effectiveness in quantifying uncertainty through low-rank weight updates, they typically require complex fine-tuning or post-training procedures. In this paper, we propose **T**raining-**F**ree **B**ayesianization (**TFB**), a simple yet theoretically grounded framework that efficiently transforms trained low-rank adapters into Bayesian ones without additional training. TFB systematically searches for the maximally acceptable level of variance in the weight posterior, constrained within a family of low-rank isotropic Gaussian distributions. Our theoretical analysis shows that under mild conditions, this search process is equivalent to KL-regularized variational optimization, a generalized form of variational inference. Through comprehensive experiments, we show that TFB achieves superior uncertainty estimation and generalization compared to existing methods while eliminating the need for complex Bayesianization training procedures.

Counterfactual inference is a powerful tool for analysing and evaluating autonomous agents, but its application to language model (LM) agents remains challenging. Existing work on counterfactuals in LMs has primarily focused on token-level counterfactuals, which are often inadequate for LM agents due to their open-ended action spaces. Unlike traditional agents with fixed, clearly defined action spaces, the actions of LM agents are often implicit in the strings they output, making their action spaces difficult to define and interpret. Furthermore, the meanings of individual tokens can shift depending on the context, adding complexity to token-level reasoning and sometimes leading to biased or meaningless counterfactuals. We introduce \emph{Abstract Counterfactuals}, a framework that emphasises high-level characteristics of actions and interactions within an environment, enabling counterfactual reasoning tailored to user-relevant features. Our experiments demonstrate that the approach produces consistent and meaningful counterfactuals while minimising the undesired side effects of token-level methods. We conduct experiments on text-based games and counterfactual text generation, while considering both token-level and latent-space interventions.

Vision-language models (VLMs) as foundation models have significantly enhanced performance across a wide range of visual and textual tasks, without requiring large-scale training from scratch for downstream tasks. However, these deterministic VLMs fail to capture the inherent ambiguity and uncertainty in natural language and visual data. Recent probabilistic post-hoc adaptation methods address this by mapping deterministic embeddings onto probability distributions; however, existing approaches do not account for the asymmetric uncertainty between modalities, and the constraint that meaningful deterministic embeddings reside on a unit hypersphere, potentially leading to suboptimal performance. In this paper, we address the asymmetric uncertainty structure inherent in textual and visual data, and propose AsymVLM to build probabilistic embeddings from pre-trained VLMs on the unit hypersphere, enabling uncertainty quantification. We validate the effectiveness of the probabilistic embeddings on established benchmarks, and present comprehensive ablation studies demonstrating the inherent nature of asymmetry in the uncertainty structure of textual and visual data.

In this paper, we explore the asymptotically optimal tuning parameter choice in ridge regression for estimating nuisance functions of a statistical functional that has recently gained prominence in conditional independence testing and causal inference. Given a sample of size $n$, we study estimators of the Expected Conditional Covariance (ECC) between variables $Y$ and $A$ given a high-dimensional covariate $X \in \mathbb{R}^p$. Under linear regression models for $Y$ and $A$ on $X$ and the proportional asymptotic regime $p/n \to c \in (0, \infty)$, we evaluate three existing ECC estimators and two sample splitting strategies for estimating the required nuisance functions. Since no consistent estimator of the nuisance functions exists in the proportional asymptotic regime without imposing further structure on the problem, we first derive debiased versions of the ECC estimators that utilize the ridge regression nuisance function estimators. We show that our bias correction strategy yields $\sqrt{n}$-consistent estimators of the ECC across different sample splitting strategies and estimator choices. We then derive the asymptotic variances of these debiased estimators to illustrate the nuanced interplay between the sample splitting strategy, estimator choice, and tuning parameters of the nuisance function estimators for optimally estimating the ECC. Our analysis reveals that prediction-optimal tuning parameters (i.e., those that optimally estimate the nuisance functions) may not lead to the lowest asymptotic variance of the ECC estimator -- thereby demonstrating the need to be careful in selecting tuning parameters based on the final goal of inference. Finally, we verify our theoretical results through extensive numerical experiments.

Greedy Equivalence Search (GES) is a classic score-based algorithm for causal discovery from observational data. In the sample limit, it recovers the Markov equivalence class of graphs that describe the data. Still, it faces two challenges in practice: computational cost and finite-sample accuracy. In this paper, we develop Less Greedy Equivalence Search (LGES), a variant of GES that retains its theoretical guarantees while partially addressing these limitations. LGES modifies the greedy step; rather than always applying the highest-scoring insertion, it avoids edge insertions between variables for which the score implies some conditional independence. This more targeted search yields up to a $10$-fold speed-up and a substantial reduction in structural error relative to GES. Moreover, LGES can guide the search using prior knowledge, and can correct this knowledge when contradicted by data. Finally, LGES can use interventional data to refine the learned observational equivalence class. We prove that LGES recovers the true equivalence class in the sample limit, even with misspecified knowledge. Experiments demonstrate that LGES outperforms GES and other baselines in speed, accuracy, and robustness to misspecified knowledge. Our code is available at https://github.com/CausalAILab/lges}{https://github.com/CausalAILab/lges.