NeurIPS 2025 Papers

Expanding on neural operators, we propose a novel framework for stochastic process learning across arbitrary domains. In particular, we develop operator flow matching (OFM) for learning stochastic process priors on function spaces. OFM provides the probability density of the values of any collection of points and enables mathematically tractable functional regression at new points with mean and density estimation. Our method outperforms state-of-the-art models in stochastic process learning, functional regression, and prior learning.

Learning disentangled representations in sequential data is a key goal in deep learning, with broad applications in vision, audio, and time series. While real-world data involves multiple interacting semantic factors over time, prior work has mostly focused on simpler two-factor static and dynamic settings, primarily because such settings make data collection easier, thereby overlooking the inherently multi-factor nature of real-world data. We introduce the first standardized benchmark for evaluating multi-factor sequential disentanglement across six diverse datasets spanning video, audio, and time series. Our benchmark includes modular tools for dataset integration, model development, and evaluation metrics tailored to multi-factor analysis. We additionally propose a post-hoc Latent Exploration Stage to automatically align latent dimensions with semantic factors, and introduce a Koopman-inspired model that achieves state-of-the-art results. Moreover, we show that Vision-Language Models can automate dataset annotation and serve as zero-shot disentanglement evaluators, removing the need for manual labels and human intervention. Together, these contributions provide a robust and scalable foundation for advancing multi-factor sequential disentanglement. Our code is available on GitHub, and the datasets and trained models are available on Hugging Face.

This paper studies the black-box optimization task which aims to find the maxima of a black-box function using a static set of its observed input-output pairs. This is often achieved via learning and optimizing a surrogate function with that offline data. Alternatively, it can also be framed as an inverse modeling task that maps a desired performance to potential input candidates that achieve it. Both approaches are constrained by the limited amount of offline data. To mitigate this limitation, we introduce a new perspective that casts offline optimization as a distributional translation task. This is formulated as learning a probabilistic bridge transforming an implicit distribution of low-value inputs (i.e., offline data) into another distribution of high-value inputs (i.e., solution candidates). Such probabilistic bridge can be learned using low- and high-value inputs sampled from synthetic functions that resemble the target function. These synthetic functions are constructed as the mean posterior of multiple Gaussian processes fitted with different parameterizations on the offline data, alleviating the data bottleneck. The proposed approach is evaluated on an extensive benchmark comprising most recent methods, demonstrating significant improvement and establishing a new state-of-the-art performance. Our code is publicly available at https://github.com/cuong-dm/ROOT.

Pseudo label based semi-supervised learning (SSL) for single-label and multi-label classification tasks has been extensively studied; however, semi-supervised label distribution learning (SSLDL) remains a largely unexplored area. Existing SSL methods fail in SSLDL because the pseudo-labels they generate only ensure overall similarity to the ground truth but do not preserve the ranking relationships between true labels, as they rely solely on KL divergence as the loss function during training. These skewed pseudo-labels lead the model to learn incorrect semantic relationships, resulting in reduced performance accuracy. To address these issues, we propose a novel SSLDL method called \textit{RankMatch}. \textit{RankMatch} fully considers the ranking relationships between different labels during the training phase with labeled data to generate higher-quality pseudo-labels. Furthermore, our key observation is that a flexible utilization of pseudo-labels can enhance SSLDL performance. Specifically, focusing solely on the ranking relationships between labels while disregarding their margins helps prevent model overfitting. Theoretically, we prove that incorporating ranking correlations enhances SSLDL performance and establish generalization error bounds for \textit{RankMatch}. Finally, extensive real-world experiments validate its effectiveness.

The relative similarity testing aims to determine which of the distributions, $P$ or $Q$, is closer to an anchor distribution $U$. Existing kernel-based approaches often test the relative similarity with a fixed kernel in a manually specified alternative hypothesis, e.g., $Q$ is closer to $U$ than $P$. Although kernel selection is known to be important to kernel-based testing methods, the manually specified hypothesis poses a significant challenge for kernel selection in relative similarity testing: Once the hypothesis is specified first, we can always find a kernel such that the hypothesis is rejected. This challenge makes relative similarity testing ill-defined when we want to select a good kernel after the hypothesis is specified. In this paper, we cope with this challenge via learning a proper hypothesis and a kernel simultaneously, instead of learning a kernel after manually specifying the hypothesis. We propose an anchor-based maximum discrepancy (AMD), which defines the relative similarity as the maximum discrepancy between the distances of $(U, P)$ and $(U, Q)$ in a space of deep kernels. Based on AMD, our testing incorporates two phases. In Phase I, we estimate the AMD over the deep kernel space and infer the potential hypothesis. In Phase II, we assess the statistical significance of the potential hypothesis, where we propose a unified testing framework to derive thresholds for tests over different possible hypotheses from Phase I. Lastly, we validate our method theoretically and demonstrate its effectiveness via extensive experiments on benchmark datasets. Codes are publicly available at: https://github.com/zhijianzhouml/AMD.

Pseudo-labeling is a commonly used paradigm in semi-supervised learning, yet its application to semi-supervised regression (SSR) remains relatively under-explored. Unlike classification, where pseudo-labels are discrete and confidence-based filtering is effective, SSR involves continuous outputs with heteroscedastic noise, making it challenging to assess pseudo-label reliability. As a result, naive pseudo-labeling can lead to error accumulation and overfitting to incorrect labels. To address this, we propose an uncertainty-aware pseudo-labeling framework that dynamically adjusts pseudo-label influence from a bi-level optimization perspective. By jointly minimizing empirical risk over all data and optimizing uncertainty estimates to enhance generalization on labeled data, our method effectively mitigates the impact of unreliable pseudo-labels. We provide theoretical insights and extensive experiments to validate our approach across various benchmark SSR datasets, and the results demonstrate superior robustness and performance compared to existing methods.

Self-Supervised Learning (SSL) has become a powerful solution to extract rich representations from unlabeled data. Yet, SSL research is mostly focused on clean, curated and high-quality datasets. As a result, applying SSL on noisy data remains a challenge, despite being crucial to applications such as astrophysics, medical imaging, geophysics or finance. In this work, we present a fully self-supervised framework that enables noise-robust representation learning without requiring a denoiser at inference or downstream fine-tuning. Our method first trains an SSL denoiser on noisy data, then uses it to construct a denoised-to-noisy data curriculum (i.e., training first on denoised, then noisy samples) for pretraining a SSL backbone (e.g., DINOv2), combined with a teacher-guided regularization that anchors noisy embeddings to their denoised counterparts. This process encourages the model to internalize noise robustness. Notably, the denoiser can be discarded after pretraining, simplifying deployment. On ImageNet-1k with ViT-B under extreme Gaussian noise ($\sigma=255$, SNR = 0.72 dB), our method improves linear probing accuracy by 4.8\% over DINOv2, demonstrating that denoiser-free robustness can emerge from noise-aware pretraining. The code is available at https://github.com/wenquanlu/noisy_dinov2.

Recent advances in vision-language-action (VLA) models have shown promise in integrating image generation with action prediction to improve generalization and reasoning in robot manipulation. However, existing methods are limited to challenging image-based forecasting, which suffers from redundant information and lacks comprehensive and critical world knowledge, including geometry, semantics and spatial information. To address these limitations, we propose DreamVLA, a novel VLA framework that integrates comprehensive world knowledge forecasting to enable inverse dynamics modeling, thereby establishing an action-forecasting loop for manipulation tasks. Specifically, DreamVLA introduces a dynamic-region-guided world knowledge prediction mechanism, which anticipates visual, depth, geometric, semantic, and segmentation cues to provide compact yet comprehensive representations for action planning. This design aligns with how humans interact with the world by first forming abstract multimodal reasoning chains before acting. Moreover, to model the conditional distribution over future actions, we employ a diffusion-based transformer that disentangles action representations from shared latent features and better captures multimodal uncertainty. Extensive experiments on both real-world and simulation environments demonstrate that DreamVLA achieves 76.7% success rate on real robot tasks and 4.45 average length on the CALVIN ABC-D benchmarks.

Deep neural networks, particularly neural operators, provide an efficient alternative to costly simulations in surrogate modeling. However, their performance is often constrained by the need for large-scale labeled datasets, which are costly and challenging to acquire in many scientific domains. Semi-supervised learning reduces label reliance by leveraging unlabeled data yet remains vulnerable to noisy pseudo-labels that mislead training and undermine robustness. To address these challenges, we propose a novel framework, Uncertainty-Informed Meta Pseudo Labeling (UMPL). The core mechenism is to refine pseudo-label quality through uncertainty-informed feedback signals. Specifically, the teacher model generates pseudo labels via epistemic uncertainty, while the student model learns from these labels and provides feedback based on aleatoric uncertainty. This interplay forms a meta-learning loop where enhanced generalization and improved pseudo-label quality reinforce each other, enabling the student model to achieve more stable uncertainty estimation and leading to more robust training. Notably, This framework is model-agnostic and can be seamlessly integrated into various neural architectures, facilitating effective exploitation of unlabeled data to enhance generalization in distribution shifts and out-of-distribution scenarios. Extensive evaluations of four models across seven tasks covering steady state and transient prediction problems demonstrate that UMPL consistently outperforms the best existing semi-supervised regression methods. When using only 10% of the fully supervised training data, UMPL achieves a 14.18% improvement, highlighting its strong effectiveness under limited supervision. Our codes are available at https://github.com/small-dumpling/UMPL.

The physical sciences are replete with dynamical systems that require the resolution of a wide range of length and time scales. This presents significant computational challenges since direct numerical simulation requires discretization at the finest relevant scales, leading to a high-dimensional state space. In this work, we propose an approach to learn stochastic multiscale models in the form of stochastic differential equations directly from observational data. Drawing inspiration from physics-based multiscale modeling approaches, we resolve the macroscale state on a coarse mesh while introducing a microscale latent state to explicitly model unresolved dynamics. We learn the parameters of the multiscale model using a simulator-free amortized variational inference method with a Product of Experts likelihood that enforces scale separation. We present detailed numerical studies to demonstrate that our learned multiscale models achieve superior predictive accuracy compared to under-resolved direct numerical simulation and closure-type models at equivalent resolution, as well as reduced-order modeling approaches.

Diffusion models have achieved significant success, yet their application to time series data, particularly with regard to efficient sampling, remains an active area of research. We describe an operator-learning approach for conditioned time-series diffusion models that gives efficient single-step generation by leveraging insights from the frequency-domain characteristics of both the time-series data and the diffusion process itself. The forward diffusion process induces a structured, frequency-dependent smoothing of the data's probability density function. However, this frequency smoothing is related (e.g., via likelihood function) to easily accessible frequency components of time-series data. This suggests that a module operating in the frequency space of the time-series can, potentially, more effectively learn to reverse the frequency-dependent smoothing of the data distribution induced by the diffusion process. We set up an operator learning task, based on frequency-aware building blocks, which satisfies semi-group properties, while exploiting the structure of time-series data. Evaluations on multiple datasets show that our single-step generation proposal achieves forecasting/imputation results comparable (or superior) to many multi-step diffusion schemes while significantly reducing inference costs.

Quantum computing is an emerging field recognized for the significant speedup it offers over classical computing through quantum algorithms. However, designing and implementing quantum algorithms pose challenges due to the complex nature of quantum mechanics and the necessity for precise control over quantum states. Despite the significant advancements in AI, there has been a lack of datasets specifically tailored for this purpose. In this work, we introduce QCircuitBench, the first benchmark dataset designed to evaluate AI's capability in designing and implementing quantum algorithms in the form of quantum circuit codes. Unlike using AI for writing traditional codes, this task is fundamentally more complicated due to highly flexible design space. Our key contributions include: 1. A general framework which formulates the key features of quantum algorithm design task for Large Language Models. 2. Implementation for quantum algorithms from basic primitives to advanced applications, spanning 3 task suites, 25 algorithms, and 120,290 data points. 3. Automatic validation and verification functions, allowing for iterative and interactive evaluation without human inspection. 4. Promising potential as a training dataset through primitive fine-tuning results. We observed several interesting experimental phenomena: fine-tuning does not always outperform few-shot learning, and LLMs tend to exhibit consistent error patterns. QCircuitBench provides a comprehensive benchmark for AI-driven quantum algorithm design, while also revealing some limitations of LLMs in this domain.

Extensive research has produced robust methods for unsupervised data visualization. Yet supervised visualization—where expert labels guide representations—remains underexplored, as most supervised approaches prioritize classification over visualization. Recently, RF-PHATE, a diffusion-based manifold learning method leveraging random forests and information geometry, marked significant progress in supervised visualization. However, its lack of an explicit mapping function limits scalability and its application to unseen data, posing challenges for large datasets and label-scarce scenarios. To overcome these limitations, we introduce Random Forest Autoencoders (RF-AE), a neural network-based framework for out-of-sample kernel extension that combines the flexibility of autoencoders with the supervised learning strengths of random forests and the geometry captured by RF-PHATE. RF-AE enables efficient out-of-sample supervised visualization and outperforms existing methods, including RF-PHATE's standard kernel extension, in both accuracy and interpretability. Additionally, RF-AE is robust to the choice of hyperparameters and generalizes to any kernel-based dimensionality reduction method.

Graph Neural Networks (GNNs) have achieved remarkable success in a wide range of applications. However, when trained on limited or low-diversity datasets, GNNs are prone to overfitting and memorization, which impacts their generalization. To address this, graph data augmentation (GDA) has become a crucial task to enhance the performance and generalization of GNNs. Traditional GDA methods employ simple transformations that result in limited performance gains. Although recent diffusion-based augmentation methods offer improved results, they are sparse, task-specific, and constrained by class labels. In this work, we propose a more general and effective diffusion-based GDA framework that is task-agnostic and label-free. For better training stability and reduced computational cost, we employ a graph variational auto-encoder (GVAE) to learn a compact latent graph representation. A diffusion model is used in the learned latent space to generate both consistent and diverse augmentations. For a fixed augmentation budget, our algorithm selects a subset of samples that would benefit the most from the augmentation. To further improve performance, we also perform test-time augmentation, leveraged by the label-free nature of our method. Thanks to the efficient utilization of GVAE and latent diffusion, our algorithm significantly enhances machine learning safety measures, including calibration, robustness to corruptions, and prediction consistency. Moreover, our method has shown improved robustness against four types of adversarial attacks and achieves better generalization performance. To demonstrate the effectiveness of the proposed method, we compare it with 30 existing methods on 12 benchmark datasets across node classification, link prediction, and graph classification in various learning settings, including semi-supervised, supervised, and long-tailed data distributions. The code will soon be made publicly available.

Adversarial examples crafted on one model often exhibit poor transferability to others, hindering their effectiveness in black-box settings. This limitation arises from two key factors: (i) \emph{decision-boundary variation} across models and (ii) \emph{representation drift} in feature space. We address these challenges through a new perspective that frames transferability for \emph{untargeted attacks} as a \emph{consensus-robust optimization} problem: adversarial perturbations should remain effective across a neighborhood of plausible target models. To model this uncertainty, we introduce two complementary perturbation channels: a \emph{parameter channel}, capturing boundary shifts via weight perturbations, and a \emph{representation channel}, addressing feature drift via stochastic blending of clean and adversarial activations. We then propose \emph{CORTA} (COnsensus--Robust Transfer Attack), a lightweight attack instantiated from this robust formulation using two first-order strategies: (i) sensitivity regularization based on the squared Frobenius norm of logits’ Jacobian with respect to weights, and (ii) Monte Carlo sampling for blended feature representations. Our theoretical analysis provides a certified lower bound linking these approximations to the robust objective. Extensive experiments on CIFAR-100 and ImageNet show that CORTA significantly outperforms state-of-the-art transfer-based methods---including ensemble approaches---across CNN and Vision Transformer targets. Notably, CORTA achieves a \emph{19.1 percentage-point gain in transfer success rate over the best prior method} while using only a single surrogate model.

Agent-Based Models (ABMs) are powerful tools for studying emergent properties in complex systems. In ABMs, agent behaviors are governed by local interactions and stochastic rules. However, these rules are ad hoc and, in general, non-differentiable, limiting the use of gradient-based methods for optimization, and thus integration with real-world data. We propose a novel framework to learn a differentiable surrogate of any ABM by observing its generated data. Our method combines diffusion models to capture behavioral stochasticity and graph neural networks to model agent interactions. Distinct from prior surrogate approaches, our method introduces a fundamental shift: rather than approximating system-level outputs, it models individual agent behavior directly, preserving the decentralized, bottom-up dynamics that define ABMs. We validate our approach on two ABMs (Schelling's segregation model and a Predator-Prey ecosystem) showing that it replicates individual-level patterns and accurately forecasts emergent dynamics beyond training. Our results demonstrate the potential of combining diffusion models and graph learning for data-driven ABM simulation.

Missing values, frequently encountered in time series data, can significantly impair the effectiveness of analytical methods. While deep imputation models have emerged as the predominant approach due to their superior performance, explicitly incorporating inductive biases aligned with time-series characteristics offers substantial improvement potential. Taking advantage of non-stationarity and periodicity in time series, two domain-specific inductive biases are designed: (1) Non-Stationary Guidance, which operationalizes the proximity principle to address highly non-stationary series by emphasizing temporal neighbors, and (2) Periodic Guidance, which exploits periodicity patterns through learnable weight allocation across historical periods. Building upon these complementary mechanisms, the overall module, named Meta Guidance, dynamically fuses both guidances through data-adaptive weights learned from the specific input sample. Experiments on nine benchmark datasets demonstrate that integrating Meta Guidance into existing deep imputation architectures achieves an average 27.39\% reduction in imputation error compared to state-of-the-art baselines.

Contrastive Language-Image Pre-training (CLIP) generates versatile multimodal embeddings for diverse applications, yet the specific information captured within these representations is not fully understood. Current explainability techniques often target specific tasks, overlooking the rich, general semantics inherent in the representations. Our objective is to reveal the concepts encoded in CLIP embeddings by learning a surrogate representation, which is expressed as a linear combination of human-understandable concepts evident in the image. Our method, which we term EXPLAIN-R, introduces a novel approach that leverages CLIP's learned instance-instance similarity to train a surrogate model that faithfully mimics CLIP's behavior. From the trained surrogate, we derive concept scores for each input image; these scores quantify the contribution of each concept and act as the explanation for the representation. Quantitative evaluations on multiple datasets demonstrate our method's superior faithfulness over the baseline. Moreover, a user study confirms that our explanations are perceived as more relevant, complete, and useful. Our work provides a novel approach for interpreting CLIP image representations, enhancing the user interpretability of representations and fostering more trustworthy AI systems.

Pseudo-label-based Semi-Supervised Learning (SSL) often suffers from classifier bias, particularly under class imbalance, as inaccurate pseudo-labels tend to exacerbate existing biases towards majority classes. Existing methods, such as \textit{CDMAD}\cite{cdmad}, utilize simplistic reference inputs—typically uniform or blank-colored images—to estimate and correct this bias. However, such simplistic references fundamentally ignore realistic statistical information inherent to real datasets, specifically typical color distributions, texture details, and frequency characteristics. This lack of \emph{statistical representativeness} can lead the model to inaccurately estimate its inherent bias, limiting the effectiveness of bias correction, particularly under severe class imbalance or substantial distribution mismatches between labeled and unlabeled datasets. To overcome these limitations, we introduce the \textbf{FARAD} (Fourier-Adapted Reference for Accurate Debiasing) System. This system utilizes random-phase images, constructed by preserving the amplitude spectrum of real data while randomizing the phase spectrum. This strategy ensures two critical properties: (1) \textbf{Semantic Irrelevance}, as randomizing phase removes any structural or recognizable semantic cues, and (2) \textbf{Statistical Representativeness}, as preserving the amplitude spectrum maintains realistic textures, color distributions, and frequency characteristics. Grounded theoretically in classical Fourier analysis, the FARAD System provides a robust, accurate estimation of per-class biases. Furthermore, computational efficiency is enhanced through optimized real-to-complex (R2C) batched Fast Fourier Transforms (FFTs). Comprehensive experiments demonstrate that our approach, significantly improves minority-class accuracy and overall SSL performance, particularly under challenging imbalance scenarios, compared with existing reference-based bias correction methods.