NeurIPS 2025 Papers

Many critical applications, from autonomous scientific discovery to personalized medicine, demand systems that can both strategically acquire the most informative data and instantaneously perform inference based upon it. While amortized methods for Bayesian inference and experimental design offer part of the solution, neither approach is optimal in the most general and challenging task, where new data needs to be collected for instant inference. To tackle this issue, we introduce the Amortized Active Learning and Inference Engine (ALINE), a unified framework for amortized Bayesian inference and active data acquisition. ALINE leverages a transformer architecture trained via reinforcement learning with a reward based on self-estimated information gain provided by its own integrated inference component. This allows it to strategically query informative data points while simultaneously refining its predictions. Moreover, ALINE can selectively direct its querying strategy towards specific subsets of model parameters or designated predictive tasks, optimizing for posterior estimation, data prediction, or a mixture thereof. Empirical results on regression-based active learning, classical Bayesian experimental design benchmarks, and a psychometric model with selectively targeted parameters demonstrate that ALINE delivers both instant and accurate inference along with efficient selection of informative points.

Schrodinger Bridges (SBs) are diffusion processes that steer, in finite time, a given initial distribution to another final one while minimizing a suitable cost functional. Although various methods for computing SBs have recently been proposed in the literature, most of these approaches require computationally expensive training schemes, even for solving low-dimensional problems. In this work, we propose an analytic parametrization of a set of feasible policies for steering the distribution of a dynamical system from one Gaussian Mixture Model (GMM) to another. Instead of relying on standard non-convex optimization techniques, the optimal policy within the set can be approximated as the solution of a low-dimensional linear program whose dimension scales linearly with the number of components in each mixture. The proposed method generalizes naturally to more general classes of dynamical systems, such as controllable linear time-varying systems, enabling efficient solutions to multi-marginal momentum SBs between GMMs, a challenging distribution interpolation problem. We showcase the potential of this approach in low-to-moderate dimensional problems such as image-to-image translation in the latent space of an autoencoder, learning of cellular dynamics using multi-marginal momentum SBs, and various other examples. The implementation is publicly available at https://github.com/georgeRapa/GMMflow.

Explicit noise-level conditioning is widely regarded as essential for the effective operation of Graph Diffusion Models (GDMs). In this work, we challenge this assumption by investigating whether denoisers can implicitly infer noise levels directly from corrupted graph structures, potentially eliminating the need for explicit noise conditioning. To this end, we develop a theoretical framework centered on Bernoulli edge-flip corruptions and extend it to encompass more complex scenarios involving coupled structure-attribute noise. Extensive empirical evaluations on both synthetic and real-world graph datasets, using models such as GDSS and DiGress, provide strong support for our theoretical findings. Notably, unconditional GDMs achieve performance comparable or superior to their conditioned counterparts, while also offering reductions in parameters (4-6%) and computation time (8-10%). Our results suggest that the high-dimensional nature of graph data itself often encodes sufficient information for the denoising process, opening avenues for simpler, more efficient GDM architectures.

Understanding and explaining the behavior of machine learning models is essential for building transparent and trustworthy AI systems. We introduce DEXTER, a data-free framework that employs diffusion models and large language models to generate global, textual explanations of visual classifiers. DEXTER operates by optimizing text prompts to synthesize class-conditional images that strongly activate a target classifier. These synthetic samples are then used to elicit detailed natural language reports that describe class-specific decision patterns and biases. Unlike prior work, DEXTER enables natural language explanation about a classifier's decision process without access to training data or ground-truth labels. We demonstrate DEXTER's flexibility across three tasks—activation maximization, slice discovery and debiasing, and bias explanation—each illustrating its ability to uncover the internal mechanisms of visual classifiers. Quantitative and qualitative evaluations, including a user study, show that DEXTER produces accurate, interpretable outputs. Experiments on ImageNet, Waterbirds, CelebA, and FairFaces confirm that DEXTER outperforms existing approaches in global model explanation and class-level bias reporting. Code is available at https://github.com/perceivelab/dexter.

We address the problem of incremental sequence classification, where predictions are updated as new elements in the sequence are revealed. Drawing on temporal-difference learning from reinforcement learning, we identify a temporal-consistency condition that successive predictions should satisfy. We leverage this condition to develop a novel loss function for training incremental sequence classifiers. Through a concrete example, we demonstrate that optimizing this loss can offer substantial gains in data efficiency. We apply our method to text classification tasks and show that it improves predictive accuracy over competing approaches on several benchmark datasets. We further evaluate our approach on the task of verifying large language model generations for correctness in grade-school math problems. Our results show that models trained with our method are better able to distinguish promising generations from unpromising ones after observing only a few tokens.

Vision Language Models (VLMs) excel at complex visual tasks such as VQA and chart understanding, yet recent work suggests they struggle with simple perceptual tests. We present an evaluation that tests vision-language models’ capacity for \emph{nonlocal visual reasoning}- reasoning that requires chaining evidence collected from multiple, possibly distant, regions of an image. We isolate three distinct forms of non‑local vision: \emph{comparative perception}, which demands holding two images in working memory and comparing them; \emph{saccadic search}, which requires making discrete, evidence‑driven jumps to locate successive targets; and \emph{smooth visual search}, which involves searching smoothly along a continuous contour. Flagship models (e.g. GPT-5, Gemini 2.5 Pro, Claude Sonnet 4), even those that perform well on prior primitive‑vision benchmarks, fail these tests and barely exceed random accuracy on two variants of our tasks that are trivial for humans. Our structured evaluation suite allows us to test if VLMs can perform similar visual algorithms to humans. Our findings show that despite gains in raw visual acuity, current models lack core visual reasoning capabilities.

Classifier-free guidance (CFG) is a core technique powering state-of-the-art image generation systems, yet its underlying mechanisms remain poorly understood. In this work, we first analyze CFG in a simplified linear diffusion model, where we show its behavior closely resembles that observed in the nonlinear case. Our analysis reveals that linear CFG improves generation quality via three distinct components: (i) a mean-shift term that approximately steers samples in the direction of class means, (ii) a positive Contrastive Principal Components (CPC) term that amplifies class-specific features, and (iii) a negative CPC term that suppresses generic features prevalent in unconditional data. We then verify that these insights in real-world, nonlinear diffusion models: over a broad range of noise levels, linear CFG resembles the behavior of its nonlinear counterpart. Although the two eventually diverge at low noise levels, we discuss how the insights from the linear analysis still shed light on the CFG's mechanism within the nonlinear regime.

Projection-free first-order methods, e.g., the celebrated Frank-Wolfe (FW) algorithms, have emerged as powerful tools for optimization over simple convex sets such as polyhedra, because of their scalability, fast convergence, and iteration-wise feasibility without costly projections. However, extending these methods effectively to general compact convex sets remains challenging and largely open, as FW methods rely on expensive linear optimization oracles (LOO), while penalty-based methods often struggle with poor feasibility. We tackle this open challenge by presenting **Hom-PGD**, a novel projection-free method without expensive (optimization) oracles. Our method constructs a homeomorphism between the convex constraint set and a unit ball, transforming the original problem into an equivalent ball-constrained formulation, thus enabling efficient gradient-based optimization while preserving the original problem structure. We prove that Hom-PGD attains *optimal* convergence rates matching gradient descent with constant step-size to find an $\epsilon$-approximate (stationary) solution: $\mathcal{O}(\log (1/\epsilon))$ for strongly convex objectives, $\mathcal{O}(\epsilon^{-1})$ for convex objectives, and $\mathcal{O}(\epsilon^{-2})$ for non-convex objectives. Meanwhile, Hom-PGD enjoys a low per-iteration complexity of $\mathcal{O}(n^2)$, without expensive oracles like LOO or projection, where $n$ is the input size. Our framework further extends to certain non-convex sets, broadening its applicability in practical optimization scenarios with complex constraints. Extensive numerical experiments demonstrate that Hom-PGD achieves comparable convergence rates to state-of-the-art projection-free methods, while significantly reducing per-iteration runtime (up to 5 orders of magnitude faster) and thus the total problem-solving time.

We present Rectified Point Flow, a unified parameterization that formulates pairwise point cloud registration and multi-part shape assembly as a single conditional generative problem. Given unposed point clouds, our method learns a continuous point-wise velocity field that transports noisy points toward their target positions, from which part poses are recovered. In contrast to prior work that regresses part-wise poses with ad-hoc symmetry handling, our method intrinsically learns assembly symmetries without symmetry labels. Together with an overlap-aware encoder focused on inter-part contacts, Rectified Point Flow achieves a new state-of-the-art performance on six benchmarks spanning pairwise registration and shape assembly. Notably, our unified formulation enables effective joint training on diverse datasets, facilitating the learning of shared geometric priors and consequently boosting accuracy. Our code and models are available at https://rectified-pointflow.github.io/.

We investigate the mechanism underlying a previously identified phenomenon in Vision Transformers -- the emergence of high-norm tokens that lead to noisy attention maps (Darcet et al., 2024). We observe that in multiple models (e.g., CLIP, DINOv2), a sparse set of neurons is responsible for concentrating high-norm activations on outlier tokens, leading to irregular attention patterns and degrading downstream visual processing. While the existing solution for removing these outliers involves retraining models from scratch with additional learned $\textit{register tokens}$, we use our findings to create a training-free approach to mitigate these artifacts. By shifting the high-norm activations from our discovered $\textit{register neurons}$ into an additional untrained token, we can mimic the effect of register tokens on a model already trained without registers. We demonstrate that our method produces cleaner attention and feature maps, enhances performance over base models across multiple downstream visual tasks, and achieves results comparable to models explicitly trained with register tokens. We then extend test-time registers to off-the-shelf vision-language models, yielding cleaner attention-based, text-to-image attribution. Finally, we outline a simple mathematical model that reflects the observed behavior of register neurons and high norm tokens. Our results suggest that test-time registers effectively take on the role of register tokens at test-time, offering a training-free solution for any pre-trained model released without them.

Federated Learning has gained traction in privacy-sensitive collaborative environments, with local SGD emerging as a key optimization method in decentralized settings. While its convergence properties are well-studied, asymptotic statistical guarantees beyond convergence remain limited. In this paper, we present two generalized Gaussian approximation results for local SGD and explore their implications. First, we prove a Berry-Esseen theorem for the final local SGD iterates, enabling valid multiplier bootstrap procedures. Second, motivated by robustness considerations, we introduce two distinct time-uniform Gaussian approximations for the entire trajectory of local SGD. The time-uniform approximations support Gaussian bootstrap-based tests for detecting adversarial attacks. Extensive simulations are provided to support our theoretical results.

Unlike reasoning, which often entails a deep sequence of deductive steps, complex real-world planning is characterized by the need to synthesize a broad spectrum of parallel and potentially conflicting information and constraints. For example, in travel planning scenarios, it requires the integration of diverse real-world information and user preferences. While LLMs show promise, existing methods with long-horizon thinking struggle with handling multifaceted constraints, leading to suboptimal solutions. Motivated by the challenges of real-world travel planning, this paper introduces the Multiple Aspects of Planning (MAoP), empowering LLMs with "wide-horizon thinking" to solve planning problems with multifaceted constraints. Instead of direct planning, MAoP leverages the strategist to conduct pre-planning from various aspects and provide the planning blueprint for planners, enabling strong inference-time scalability by scaling aspects to consider various constraints. In addition, existing benchmarks for multi-constraint planning are flawed because they assess constraints in isolation, ignoring causal dependencies within the constraints, e.g, travel planning, where past activities dictate future itinerary. To address this, we propose Travel-Sim, an agent-based benchmark assessing plans via real-world simulation, thereby inherently resolving these causal dependencies. This paper advances LLM capabilities in complex planning and offers novel insights for evaluating sophisticated scenarios through simulation.

Progress in a research field can be hard to assess, in particular when many concurrent methods are proposed in a short period of time. This is the case in digital pathology, where many foundation models have been released recently to serve as feature extractors for tile-level images, being used in a variety of downstream tasks, both for tile- and slide-level problems. Benchmarking available methods then becomes paramount to get a clearer view of the research landscape. In particular, in critical domains such as healthcare, a benchmark should not only focus on evaluating downstream performance, but also provide insights about the main differences between methods, and importantly, further consider uncertainty and robustness to ensure a reliable usage of proposed models. For these reasons, we introduce THUNDER, a tile-level benchmark for digital pathology foundation models, allowing for efficient comparison of many models on diverse datasets with a series of downstream tasks, studying their feature spaces and assessing the robustness and uncertainty of predictions informed by their embeddings. THUNDER is a fast, easy-to-use, dynamic benchmark that can already support a large variety of state-of-the-art foundation, as well as local user-defined models for direct tile-based comparison. In this paper, we provide a comprehensive comparison of 23 foundation models on 16 different datasets covering diverse tasks, feature analysis, and robustness. The code for THUNDER is publicly available at https://github.com/MICS-Lab/thunder.

Prompting is one of the main ways to adapt a pretrained model to target tasks. Besides manually constructing prompts, many prompt optimization methods have been proposed in the literature. Method development is mainly empirically driven, with less emphasis on a conceptual understanding of prompting. In this paper we discuss how optimal prompting can be understood through a Bayesian view, which also implies some fundamental limitations of prompting that can only be overcome by tuning weights. The paper explains in detail how meta-trained neural networks behave as Bayesian predictors over the pretraining distribution, whose hallmark feature is rapid in-context adaptation. Optimal prompting can be studied formally as conditioning these Bayesian predictors, yielding criteria for target tasks where optimal prompting is and is not possible. We support the theory with educational experiments on LSTMs and Transformers, where we compare different versions of prefix-tuning and different weight-tuning methods. We also confirm that soft prefixes, which are sequences of real-valued vectors outside the token alphabet, can lead to very effective prompts for trained and even untrained networks by manipulating activations in ways that are not achievable by hard tokens. This adds an important mechanistic aspect beyond the conceptual Bayesian theory.

Multimodal learning holds the promise for richer information extraction by capturing dependencies across data sources. Yet, current training methods often underperform due to modality competition, a phenomenon where modalities contend for training resources, leaving some underoptimized. This raises a pivotal question: how can we address training imbalances, ensure adequate optimization across all modalities, and achieve consistent performance improvements as we transition from unimodal to multimodal data? This paper proposes the Multimodal Competition Regularizer (MCR), inspired by a mutual information (MI) decomposition designed to prevent the adverse effects of competition in multimodal training. Our key contributions are: 1) A game-theoretic framework that adaptively balances modality contributions by encouraging each to maximize its informative role in the final prediction. 2) Refining lower and upper bounds for each MI term to enhance the extraction of both task-relevant unique and shared information across modalities. 3) Proposing latent space permutations for conditional MI estimation, significantly improving computational efficiency. MCR outperforms all previously suggested training strategies and simple baselines, demonstrating that training modalities jointly lead to important performance gains on synthetic and large real-world datasets. We release our code and models at https://github.com/kkontras/MCR.

Existing frameworks for evaluating long-context language models (LCLM) can be broadly categorized into real-world applications (e.g, document summarization) and synthetic tasks (e.g, needle-in-a-haystack). Despite their utility, both approaches are accompanied by certain intrinsic limitations. Real-world tasks often involve complexity that makes interpretation challenging and suffer from data contamination, whereas synthetic tasks frequently lack meaningful coherence between the target information ("needle") and its surrounding context ("haystack"), undermining their validity as proxies for realistic applications. In response to these challenges, we posit that an ideal long-context evaluation framework should be characterized by three essential features: 1) seamless context: coherent contextual integration between target information and its surrounding context; 2) controllable setting: an extensible task setup that enables controlled studies—for example, incorporating additional required abilities such as numerical reasoning; and 3) sound evaluation: avoiding LLM-as-Judge and conduct exact-match to ensure deterministic and reproducible evaluation results. This study introduces $\textbf{LongBioBench}$, a benchmark that utilizes artificially generated biographies as a controlled environment for assessing LCLMs across dimensions of $\textit{understanding}$, $\textit{reasoning}$, and $\textit{trustworthiness}$. Our experimental evaluation, which includes $\textbf{18}$ LCLMs in total, demonstrates that most models still exhibit deficiencies in semantic understanding and elementary reasoning over retrieved results and are less trustworthy as context length increases. Our further analysis indicates some design choices employed by existing synthetic benchmarks, such as contextual non-coherence, numerical needles, and the absence of distractors, rendering them vulnerable to test the model's long-context capabilities. Moreover, we also reveal that long-context continual pretraining primarily adjusts RoPE embedding to accommodate extended context lengths, which in turn yields only marginal improvements in the model’s true capabilities. To sum up, compared to previous synthetic benchmarks, LongBioBench achieves a better trade-off between mirroring authentic language tasks and maintaining controllability, and is highly interpretable and configurable.

High-dimensional data often conceal low-dimensional signals beneath structured background noise, limiting standard PCA. Motivated by contrastive learning, we address the problem of recovering shared signal subspaces from positive pairs--paired observations sharing the same signal but differing in background. Our baseline, PCA+, uses alignment-only contrastive learning and succeeds when background variation is mild, but fails under strong noise or high-dimensional regimes. To address this, we introduce PCA++, a hard uniformity-constrained contrastive PCA that enforces identity covariance on projected features. PCA++ has a closed-form solution via a generalized eigenproblem, remains stable in high dimensions, and provably regularizes against background interference. We provide exact high-dimensional asymptotics in both fixed-aspect-ratio and growing-spike regimes, showing uniformity’s role in robust signal recovery. Empirically, PCA++ outperforms standard PCA and alignment-only PCA+ on simulations, corrupted-MNIST, and single-cell transcriptomics, reliably recovering condition-invariant structure. More broadly, we clarify uniformity’s role in contrastive learning—showing that explicit feature dispersion defends against structured noise and enhances robustness.

Transfer learning is a key component of modern machine learning, enhancing the performance of target tasks by leveraging diverse data sources. Simultaneously, overparameterized models such as the minimum-$\ell_2$-norm interpolator (MNI) in high-dimensional linear regression have garnered significant attention for their remarkable generalization capabilities, a property known as *benign overfitting*. Despite their individual importance, the intersection of transfer learning and MNI remains largely unexplored. Our research bridges this gap by proposing a novel two-step Transfer MNI approach and analyzing its trade-offs. We characterize its non-asymptotic excess risk and identify conditions under which it outperforms the target-only MNI. Our analysis reveals *free-lunch* covariate shift regimes, where leveraging heterogeneous data yields the benefit of knowledge transfer at limited cost. To operationalize our findings, we develop a data-driven procedure to detect *informative* sources and introduce an ensemble method incorporating multiple informative Transfer MNIs. Finite-sample experiments demonstrate the robustness of our methods to model and data heterogeneity, confirming their advantage.

Modern foundation models often undergo iterative ``bootstrapping'' in their post-training phase: a model generates synthetic data, an external verifier filters out low-quality samples, and the high-quality subset is used for further fine-tuning. Over multiple iterations, the model performance improves, raising a crucial question: How should the total budget for generation and training be allocated across iterations to maximize final performance? In this work, we develop a theoretical framework for analyzing budget allocation strategies. Specifically, we show that constant policies fail to converge with high probability, while increasing policies---particularly exponential growth policies---exhibit significant theoretical advantages. Experiments on image denoising with diffusion probabilistic models and math reasoning with large language models show that both exponential and polynomial growth policies consistently outperform constant policies, with exponential policies often providing more stable performance.