NeurIPS 2025 论文列表

In this work, we prove that agents capable of adapting to distribution shifts must have learned the causal model of their environment even in the presence of mediation. This term describes situations where an agent's actions affect its environment, a dynamic common to most real-world settings. For example, a robot in an industrial plant might interact with tools, move through space, and transform products to complete its task. We introduce an algorithm for eliciting causal knowledge from robust agents using optimal policy oracles, with the flexibility to incorporate prior causal knowledge. We further demonstrate its effectiveness in mediated single-agent scenarios and multi-agent environments. We identify conditions under which the presence of a single robust agent is sufficient to recover the full causal model and derive optimal policies for other agents in the same environment. Finally, we show how to apply these results to sequential decision-making tasks modeled as Partially Observable Markov Decision Processes (POMDPs).

In multi-objective black-box optimization, the goal is typically to find solutions that optimize a set of $T$ black-box objective functions, $f_1, \ldots f_T$, simultaneously. Traditional approaches often seek a single Pareto-optimal set that balances trade-offs among all objectives. In contrast, we consider a problem setting that departs from this paradigm: finding a small set of $K < T$ solutions, that collectively "cover" the $T$ objectives. A set of solutions is defined as "covering" if, for each objective $f_1, \ldots f_T$, there is at least one good solution. A motivating example for this problem setting occurs in drug design. For example, we may have $T$ pathogens and aim to identify a set of $K < T$ antibiotics such that at least one antibiotic can be used to treat each pathogen. This problem, known as coverage optimization, has yet to be tackled with the Bayesian optimization (BO) framework. To fill this void, we develop Multi-Objective Coverage Bayesian Optimization (MOCOBO), a BO algorithm for solving coverage optimization. Our approach is based on a new acquisition function reminiscent of expected improvement in the vanilla BO setup. We demonstrate the performance of our method on high-dimensional black-box optimization tasks, including applications in peptide and molecular design. Results show that the coverage of the $K < T$ solutions found by MOCOBO matches or nearly matches the coverage of $T$ solutions obtained by optimizing each objective individually. Furthermore, in *in vitro* experiments, the peptides found by MOCOBO exhibited high potency against drug-resistant pathogens, further demonstrating the potential of MOCOBO for drug discovery. All of our code is publicly available at the following link: https://github.com/nataliemaus/mocobo.

Graph convolutional neural networks (GCNNs) have emerged as powerful tools for analyzing graph-structured data, achieving remarkable success across diverse applications. However, the theoretical understanding of the stability of these models, i.e., their sensitivity to small changes in the graph structure, remains in rather limited settings, hampering the development and deployment of robust and trustworthy models in practice. To fill this gap, we study how small perturbations in the graph topology affect GCNN outputs and propose a novel formulation for analyzing model stability. Unlike prior studies that focus only on worst-case perturbations, our distribution-aware formulation characterizes output perturbations across a broad range of input data. This way, our framework enables, for the first time, a probabilistic perspective on the interplay between the statistical properties of the node data and perturbations in the graph topology. We conduct extensive experiments to validate our theoretical findings and demonstrate their benefits over existing baselines, in terms of both representation stability and adversarial attacks on downstream tasks. Our results demonstrate the practical significance of the proposed formulation and highlight the importance of incorporating data distribution into stability analysis.

The mean of a random variable can be understood as a *linear* functional on the space of probability distributions. Quantum computing is known to provide a quadratic speedup over classical Monte Carlo methods for mean estimation. In this paper, we investigate whether a similar quadratic speedup is achievable for estimating *non-linear* functionals of probability distributions. We propose a \textit{quantum-inside-quantum} algorithm that achieves this speedup for the broad class of nonlinear estimation problems known as nested expectations. Our algorithm improves upon the direct application of the quantum-accelerated multilevel Monte Carlo algorithm introduced by An et. al.. The existing lower bound indicates that our algorithm is optimal up to polylogarithmic factors. A key innovation of our approach is a new sequence of multilevel Monte Carlo approximations specifically designed for quantum computing, which is central to the algorithm's improved performance.

In scientific domains---from biology to the social sciences---many questions boil down to \textit{What effect will we observe if we intervene on a particular variable?} If the causal relationships (e.g.~a causal graph) are known, its possible to estimate the intervention distributions. In the absence of this domain knowledge, the causal structure must be discovered from the available observational data. However, observational data are often compatible with multiple causal graphs, making methods that commit to a single structure prone to overconfidence. A principled way to manage this structural uncertainty is via Bayesian inference, which averages over a posterior distribution on possible causal structures and functional mechanisms. Unfortunately, the number of causal structures grows super-exponentially with the number of nodes in the graph, making computations intractable. We propose to circumvent these challenges by using meta-learning to create an end-to-end model: the Model-Averaged Causal Estimation Transformer Neural Process (MACE-TNP). The model is trained to predict the Bayesian model-averaged interventional posterior distribution, and its end-to-end nature bypasses the need for expensive calculations. Empirically, we demonstrate that MACE-TNP outperforms strong Bayesian baselines. Our work established meta-learning as a flexible and scalable paradigm for approximating complex Bayesian causal inference, that can be scaled to increasingly challenging settings in the future.

Causal representation learning (CRL) is the process of disentangling the *latent* low-dimensional causally-related generating factors underlying high-dimensional observable data. Extensive recent studies have characterized CRL identifiability and *perfect* recovery of the latent variables and their attendant causal graph. This paper introduces the notion of *reward-oriented* CRL, the purpose of which is to move away from perfectly learning the latent representation and instead learning it to the extent needed for optimizing a desired downstream task (reward). In reward-oriented CRL, perfectly learning the latent representation can be excessive; instead, it must be learned at the *coarsest* level sufficient for optimizing the desired task. Reward-oriented CRL is formalized as the optimization of a desired function of the observable data over the space of all possible interventions and focuses on linear causal and transformation models. To sequentially identify the optimal subset of interventions, an adaptive exploration algorithm is designed that learns the latent causal graph and the variables needed to identify the best intervention. It is shown that for an $n$-dimensional latent space and a $d$-dimensional observation space, over a horizon $T$ the algorithm's regret scales as $\tilde O(d^{\frac{1}{3}}n^{\frac{1}{3}}u^{\frac{2}{3}}T^{\frac{2}{3}} + u\sqrt{T})$, where $u$ measures total uncertainty in the graph estimates. Furthermore, an almost-matching lower bound is shown to scale as $\Omega(d^{\frac{1}{3}}n^{\frac{1}{3}}p^{\frac{2}{3}}T^{\frac{2}{3}} + p\sqrt{T})$, in which $u$ is replaced by $p$ that counts the number of causal paths in the graph.

Conformal prediction has been explored as a general and efficient way to provide uncertainty quantification for time series. However, current methods struggle to handle time series data with change points — sudden shifts in the underlying data-generating process. In this paper, we propose a novel Conformal Prediction for Time-series with Change points (CPTC) algorithm, addressing this gap by integrating a model to predict the underlying state with online conformal prediction to model uncertainties in non-stationary time series. We prove CPTC's validity and improved adaptivity in the time series setting under minimum assumptions, and demonstrate CPTC's practical effectiveness on 6 synthetic and real-world datasets, showing improved validity and adaptivity compared to state-of-the-art baselines.

Neurosymbolic (NeSy) predictors combine neural perception with symbolic reasoning to solve tasks like visual reasoning. However, standard NeSy predictors assume conditional independence between the symbols they extract, thus limiting their ability to model interactions and uncertainty --- often leading to overconfident predictions and poor out-of-distribution generalisation. To overcome the limitations of the independence assumption, we introduce _neurosymbolic diffusion models_ (NeSyDMs), a new class of NeSy predictors that use discrete diffusion to model dependencies between symbols. Our approach reuses the independence assumption from NeSy predictors at each step of the diffusion process, enabling scalable learning while capturing symbol dependencies and uncertainty quantification. Across both synthetic and real-world benchmarks — including high-dimensional visual path planning and rule-based autonomous driving — NeSyDMs achieve state-of-the-art accuracy among NeSy predictors and demonstrate strong calibration.

In many scientific experiments, the data annotating cost constraints the pace for testing novel hypotheses. Yet, modern machine learning pipelines offer a promising solution—provided their predictions yield correct conclusions. We focus on Prediction-Powered Causal Inferences (PPCI), i.e., estimating the treatment effect in an unlabeled target experiment, relying on training data with the same outcome annotated but potentially different treatment or effect modifiers. We first show that conditional calibration guarantees valid PPCI at population level. Then, we introduce a sufficient representation constraint transferring validity across experiments, which we propose to enforce in practice in Deconfounded Empirical Risk Minimization, our new model-agnostic training objective. We validate our method on synthetic and real-world scientific data, solving impossible problem instances for Empirical Risk Minimization even with standard invariance constraints. In particular, for the first time, we achieve valid causal inference on a scientific experiment with complex recording and no human annotations, fine-tuning a foundational model on our similar annotated experiment.

Variational inference seeks the best approximation of a target distribution within a chosen family, where "best" means minimizing Kullback-Leibler divergence. When the approximation family is exponential, the optimal approximation satisfies a fixed-point equation. We introduce LSVI (Least Squares Variational Inference), a gradient-free, Monte Carlo-based scheme for the fixed-point recursion, where each iteration boils down to performing ordinary least squares regression on tempered log-target evaluations under the variational approximation. We show that LSVI is equivalent to biased stochastic natural gradient descent and use this to derive convergence rates with respect to the numbers of samples and iterations. When the approximation family is Gaussian, LSVI involves inverting the Fisher information matrix, whose size grows quadratically with dimension $d$. We exploit the regression formulation to eliminate the need for this inversion, yielding $O(d^3)$ complexity in the full-covariance case and $O(d)$ in the mean-field case. Finally, we numerically demonstrate LSVI’s performance on various tasks, including logistic regression, discrete variable selection, and Bayesian synthetic likelihood, showing competitive results with state-of-the-art methods, even when gradients are unavailable.

Conformal prediction is a distribution-free uncertainty quantification method that has gained popularity in the machine learning community due to its finite-sample guarantees and ease of use. Its most common variant, dubbed split conformal prediction, is also computationally efficient as it boils down to collecting statistics of the model predictions on some calibration data not yet seen by the model. Nonetheless, these guarantees only hold if the calibration and test data are exchangeable, a condition that is difficult to verify and often violated in practice due to so-called distribution shifts. The literature is rife with methods to mitigate the loss in coverage in this non-exchangeable setting, but these methods require some prior information on the type of distribution shift to be expected at test time. In this work, we study this problem via a new perspective, through the lens of optimal transport, and show that it is possible to estimate the loss in coverage and mitigate arbitrary distribution shifts, offering a principled and broadly applicable solution.

Gaussian processes (GPs) play an essential role in biostatistics, scientific machine learning, and Bayesian optimization for their ability to provide probabilistic predictions and model uncertainty. However, GP inference struggles to scale to large datasets (which are common in modern applications), since it requires the solution of a linear system whose size scales quadratically with the number of samples in the dataset. We propose an approximate, distributed, accelerated sketch-and-project algorithm ($\texttt{ADASAP}$) for solving these linear systems, which improves scalability. We use the theory of determinantal point processes to show that the posterior mean induced by sketch-and-project rapidly converges to the true posterior mean. In particular, this yields the first efficient, condition number-free algorithm for estimating the posterior mean along the top spectral basis functions, showing that our approach is principled for GP inference. $\texttt{ADASAP}$ outperforms state-of-the-art solvers based on conjugate gradient and coordinate descent across several benchmark datasets and a large-scale Bayesian optimization task. Moreover, $\texttt{ADASAP}$ scales to a dataset with $> 3 \cdot 10^8$ samples, a feat which has not been accomplished in the literature.

We present Free energy Estimators with Adaptive Transport (FEAT), a novel framework for free energy estimation---a critical challenge across scientific domains. FEAT leverages learned transports implemented via stochastic interpolants and provides consistent, minimum-variance estimators based on escorted Jarzynski equality and controlled Crooks theorem, alongside variational upper and lower bounds on free energy differences. Unifying equilibrium and non-equilibrium methods under a single theoretical framework, FEAT establishes a principled foundation for neural free energy calculations. Experimental validation on toy examples, molecular simulations, and quantum field theory demonstrates promising improvements over existing learning-based methods. Our PyTorch implementation is available at https://github.com/jiajunhe98/FEAT.

We study a relaxation of the problem of coupling probability distributions — a list of samples is generated from one distribution and an *accept* is declared if any one of these samples is identical to the sample generated from the other distribution. We propose a novel method for generating samples, which extends the Gumbel-max sampling suggested in Daliri et al. (2025) for coupling probability distributions. We also establish a corresponding lower bound on the acceptance probability, which we call the \emph{list matching lemma}. We next discuss two applications of our setup. First, we develop a new mechanism for multi-draft speculative sampling that is simple to implement and achieves performance competitive with baselines such as SpecTr and SpecInfer across a range of language tasks. Our method also guarantees a certain degree of *drafter invariance* with respect to the output tokens which is not supported by existing schemes. We also provide a theoretical lower bound on the token level acceptance probability. As our second application, we consider distributed lossy compression with side information in a setting where a source sample is compressed and available to multiple decoders, each with independent side information. We propose a compression technique that is based on our generalization of Gumbel-max sampling and show that it provides significant gains in experiments involving synthetic Gaussian sources and the MNIST image dataset.

Models of hybrid dynamical systems are widely used to answer questions about the causes and effects of dynamic events in time. Unfortunately, existing causal reasoning formalisms lack support for queries involving the dynamically triggered, discontinuous interventions that characterize hybrid dynamical systems. This mismatch can lead to ad-hoc and error-prone causal analysis workflows in practice. To bridge the gap between the needs of hybrid systems users and current causal inference capabilities, we develop a rigorous counterfactual semantics by formalizing interventions as transformations to the constraints of hybrid systems. Unlike interventions in a typical structural causal model, however, interventions in hybrid systems can easily render the model ill-posed. Thus, we identify mild conditions under which our interventions maintain solution existence, uniqueness, and measurability by making explicit connections to established hybrid systems theory. To illustrate the utility of our framework, we formalize a number of canonical causal estimands and explore a case study on the probabilities of causation with applications to fishery management. Our work simultaneously expands the modeling possibilities available to causal inference practitioners and begins to unlock decades of causality research for users of hybrid systems.

Autoregressive generative models naturally generate variable-length sequences, while non-autoregressive models struggle, often imposing rigid, token-wise structures. We propose Edit Flows, a non-autoregressive model that overcomes these limitations by defining a discrete flow over sequences through edit operations---insertions, deletions, and substitutions. By modeling these operations within a Continuous-time Markov Chain over the sequence space, Edit Flows enable flexible, position-relative generation that aligns more closely with the structure of sequence data. Our training method leverages an expanded state space with auxiliary variables, making the learning process efficient and tractable. Empirical results show that Edit Flows outperforms both autoregressive and mask models on image captioning and significantly outperforms the mask construction in text and code generation.

We study the estimation of distributional treatment effects in randomized experiments with imperfect compliance. When participants do not adhere to their assigned treatments, we leverage treatment assignment as an instrumental variable to identify the local distributional treatment effect—the difference in outcome distributions between treatment and control groups for the subpopulation of compliers. We propose a regression-adjusted estimator based on a distribution regression framework with Neyman-orthogonal moment conditions, enabling robustness and flexibility with high-dimensional covariates. Our approach accommodates continuous, discrete, and mixed discrete-continuous outcomes, and applies under a broad class of covariate-adaptive randomization schemes, including stratified block designs and simple random sampling. We derive the estimator’s asymptotic distribution and show that it achieves the semiparametric efficiency bound. Simulation results demonstrate favorable finite-sample performance, and we demonstrate the method’s practical relevance in an application to the Oregon Health Insurance Experiment.

We introduce BayeSQP, a novel algorithm for general black-box optimization that merges the structure of sequential quadratic programming with concepts from Bayesian optimization. BayeSQP employs second-order Gaussian process surrogates for both the objective and constraints to jointly model the function values, gradients, and Hessian from only zero-order information. At each iteration, a local subproblem is constructed using the GP posterior estimates and solved to obtain a search direction. Crucially, the formulation of the subproblem explicitly incorporates uncertainty in both the function and derivative estimates, resulting in a tractable second-order cone program for high probability improvements under model uncertainty. A subsequent one-dimensional line search via constrained Thompson sampling selects the next evaluation point. Empirical results show that BayeSQP outperforms state-of-the-art methods in specific high-dimensional settings. Our algorithm offers a principled and flexible framework that bridges classical optimization techniques with modern approaches to black-box optimization.

We study the problem of sequential decision-making in environments governed by evolving causal mechanisms. Prior work on structural causal bandits--formulations that integrate causal graphs into multi-armed bandit problems to guide intervention selection--has shown that leveraging the causal structure can reduce unnecessary interventions by identifying possibly-optimal minimal intervention sets (POMISs). However, such formulations fall short in dynamic settings where reward distributions may vary over time, as their static, hence myopic, nature focuses on immediate rewards and overlooks the long-term effects of interventions. In this work, we propose a non-stationary structural causal bandit framework that leverages temporal structural causal models to capture evolving dynamics over time. We characterize how interventions propagate over time by developing graphical tools and assumptions, which form the basis for identifying non-myopic intervention strategies. Within this framework, we devise POMIS$^+$, which captures the existence of variables that contribute to maximizing both immediate and long-term rewards. Our framework provides a principled way to reason about temporally-aware interventions by explicitly modeling information propagation across time. Empirical results validate the effectiveness of our approach, demonstrating improved performance over myopic baselines.