NeurIPS 2025 Papers

Medical time-series data play a vital role in disease diagnosis but suffer from limited labeled samples and single-center bias, which hinder model generalization and lead to overfitting. To address these challenges, we propose DAAC (Discrepancy-Aware Adaptive Contrastive learning), a learnable multi-view contrastive framework that integrates external normal samples and enhances feature learning through adaptive contrastive strategies. DAAC consists of two key modules: (1) a Discrepancy Estimator, built upon a GAN-enhanced encoder-decoder architecture, captures the distribution of normal data and computes reconstruction errors as indicators of abnormality. These discrepancy features augment the target dataset to mitigate overfitting. (2) an Adaptive Contrastive Learner uses multi-head attention to extract discriminative representations by contrasting embeddings across multiple views and data granularities (subject, trial, epoch, and temporal levels), eliminating the need for handcrafted positive-negative sample pairs. Extensive experiments on three clinical datasets—covering Alzheimer’s disease, Parkinson’s disease, and myocardial infarction—demonstrate that DAAC significantly outperforms existing methods, even when only 10\% of labeled data is available, showing strong generalization and diagnostic performance. Our code is available at https://github.com/CUHKSZ-MED-BioE/DAAC.

Accurately simulating physics is crucial across scientific domains, with applications spanning from robotics to materials science. While traditional mesh-based simulations are precise, they are often computationally expensive and require knowledge of physical parameters, such as material properties. In contrast, data-driven approaches like Graph Network Simulators (GNSs) offer faster inference but suffer from two key limitations: Firstly, they must be retrained from scratch for even minor variations in physical parameters, and secondly they require labor-intensive data collection for each new parameter setting. This is inefficient, as simulations with varying parameters often share a common underlying latent structure. In this work, we address these challenges by learning this shared structure through meta-learning, enabling fast adaptation to new physical parameters without retraining. To this end, we propose a novel architecture that generates a latent representation by encoding graph trajectories using conditional neural processes (CNPs). To mitigate error accumulation over time, we combine CNPs with a novel neural operator architecture. We validate our approach, Meta Neural Graph Operator (MaNGO), on several dynamics prediction tasks with varying material properties, demonstrating superior performance over existing GNS methods. Notably, MaNGO achieves accuracy on unseen material properties close to that of an oracle model.

Analysis of noninvasive microvascular blood flow can improve the diagnosis, prognosis, and management of many medical conditions, including cardiovascular, peripheral vascular, and sickle cell disease. This paper introduces SAM2Flow, an interactive optical flow estimation model to analyze long Oblique Back-illumination Microscopy (OBM) videos of *in vivo* microvascular flow. Inspired by the Segment Anything Model (SAM2), SAM2Flow enables users to specify regions of interest through user prompts for focused flow estimation. SAM2Flow also incorporates a dual memory attention mechanism, comprising both motion and context memory, to achieve efficient and stable flow estimations over extended video sequences. According to our experiments, SAM2Flow achieves SOTA accuracy in foreground optical flow estimation on both microvascular flow and public datasets, with a fast inference speed of over $20$ fps on $512\times512$ inputs. Based on the temporally robust flow estimation, SAM2Flow demonstrated superior performance in downstream physiological applications compared to existing models. The code and dataset will be published with this paper.

Evaluating preference optimization (PO) algorithms on LLM alignment is a challenging task that presents prohibitive costs, noise, and several variables like model size and hyper-parameters. In this work, we show that it is possible to gain insights on the efficacy of PO algorithm on much simpler benchmarks. We design a diagnostic suite of MuJoCo tasks and datasets, which we use to systematically evaluate PO algorithms, establishing a more controlled and cheaper benchmark. We then propose a novel family of PO algorithms based on mirror descent, which we call Mirror Preference Optimization (MPO). Through evolutionary strategies, we search this class to discover algorithms specialized to specific properties of preference datasets, such as mixed-quality or noisy data. We demonstrate that our discovered PO algorithms outperform all known algorithms in the targeted MuJoCo settings. Finally, based on the insights gained from our MuJoCo experiments, we design a novel PO algorithm that significantly outperforms existing baselines in an LLM alignment task.

We study channel simulation and distributed matching, two fundamental problems with several applications to machine learning, using a recently introduced generalization of the standard rejection sampling (RS) algorithm known as Ensemble Rejection Sampling (ERS). For channel simulation, we propose a new coding scheme based on ERS that achieves a near-optimal coding rate. In this process, we demonstrate that standard RS can also achieve a near-optimal coding rate and generalize the result of Braverman and Garg (2014) to the continuous alphabet setting. Next, as our main contribution, we present a distributed matching lemma for ERS, which serves as the rejection sampling counterpart to the Poisson Matching Lemma (PML) introduced by Li and Anantharam (2021). Our result also generalizes a recent work on importance matching lemma (Phan et al, 2024) and, to our knowledge, is the first result on distributed matching in the family of rejection sampling schemes where the matching probability is close to PML. We demonstrate the practical significance of our approach over prior works by applying it to distributed compression. The effectiveness of our proposed scheme is validated through experiments involving synthetic Gaussian sources and distributed image compression using the MNIST dataset.

Unlocking spatial reasoning in Multimodal Large Language Models (MLLMs) is crucial for enabling intelligent interaction with 3D environments. While prior efforts often rely on explicit 3D inputs or specialized model architectures, we ask: can MLLMs reason about 3D space using only structured 2D representations derived from perception? In this work, we introduce Struct2D, a perception-guided prompting framework that combines bird’s-eye-view (BEV) images with object marks and object-centric metadata, optionally incorporating egocentric keyframes when needed. Using Struct2D, we conduct an in-depth zero-shot analysis of closed-source MLLMs (e.g., GPT-o3) and find that they exhibit surprisingly strong spatial reasoning abilities when provided with projected 2D inputs, effectively handling tasks such as relative direction estimation and route planning. Motivated by these findings, we construct a large-scale instructional tuning dataset, \textbf{Struct2D-Set}, using an automated pipeline that generates fine-grained QA pairs grounded in 3D indoor scenes. We then fine-tune an open-source MLLM (Qwen2.5VL) using Struct2D-Set, relying on noisy 3D perception rather than ground-truth annotations. Despite this, the tuned model achieves strong performance across multiple spatial reasoning benchmarks, including 3D question answering, captioning, and object grounding, spanning eight diverse reasoning categories. Our approach demonstrates that structured 2D inputs can effectively bridge perception and language reasoning in MLLMs—without requiring explicit 3D representations as input. We will release both our code and dataset to support future research.

Despite their strengths, large language models (LLMs) often fail to communicate their confidence accurately, making it difficult to assess when they might be wrong and limiting their reliability. In this work, we demonstrate that reasoning models that engage in extended chain-of-thought (CoT) reasoning exhibit superior performance not only in problem-solving but also in accurately expressing their confidence. Specifically, we benchmark six reasoning models across six datasets and find that they achieve strictly better confidence calibration than their non-reasoning counterparts in 33 out of the 36 settings. Our detailed analysis reveals that these gains in calibration stem from the slow thinking behaviors of reasoning models (e.g., exploring alternative approaches and backtracking) which enable them to adjust their confidence dynamically throughout their CoT, making it progressively more accurate. In particular, we find that reasoning models become increasingly better calibrated as their CoT unfolds, a trend not observed in non-reasoning models. Moreover, removing slow thinking behaviors from the CoT leads to a significant drop in calibration. Lastly, we show that non-reasoning models also demonstrate enhanced calibration when simply guided to slow think via in-context learning, fully isolating slow thinking as the source of the calibration gains.

Standard Retrieval-Augmented Generation (RAG) relies on chunk-based retrieval, whereas GraphRAG advances this approach by graph-based knowledge representation. However, existing graph-based RAG approaches are constrained by binary relations, as each edge in an ordinary graph connects only two entities, limiting their ability to represent the n-ary relations (n >= 2) in real-world knowledge. In this work, we propose HyperGraphRAG, the first hypergraph-based RAG method that represents n-ary relational facts via hyperedges. HyperGraphRAG consists of a comprehensive pipeline, including knowledge hypergraph construction, retrieval, and generation. Experiments across medicine, agriculture, computer science, and law demonstrate that HyperGraphRAG outperforms both standard RAG and previous graph-based RAG methods in answer accuracy, retrieval efficiency, and generation quality.

Color plays an important role in human perception and usually provides critical clues in visual reasoning. However, it is unclear whether and how vision-language models (VLMs) can perceive, understand, and leverage color as humans. This paper introduces ColorBench, an innovative benchmark meticulously crafted to assess the capabilities of VLMs in color understanding, including color perception, reasoning, and robustness. By curating a suite of diverse test scenarios, with grounding in real applications, ColorBench evaluates how these models perceive colors, infer meanings from color-based cues, and maintain consistent performance under varying color transformations. Through an extensive evaluation of 32 VLMs with varying language models and vision encoders, our paper reveals some undiscovered findings: (i) The scaling law (larger models are better) still holds on ColorBench, while the language model plays a more important role than the vision encoder. (ii) However, the performance gaps across models are relatively small, indicating that color understanding has been largely neglected by existing VLMs. (iii) CoT reasoning improves color understanding accuracies and robustness, though they are vision-centric tasks. (iv) Color clues are indeed leveraged by VLMs on ColorBench but they can also mislead models in some tasks. These findings highlight the critical limitations of current VLMs and underscore the need to enhance color comprehension. Our ColorBench can serve as a foundational tool for advancing the study of human-level color understanding of multimodal AI.

In this paper, we study the distributed convex-concave finite-sum minimax optimization over the network, and a decentralized variance-reduced optimistic gradient method with stochastic mini-batch sizes (DIVERSE) is proposed. For the strongly-convex-strongly-concave objective, it is shown that DIVERSE can achieve a linear convergence rate that depends on the global smoothness parameters, yielding sharper computation and communication complexity bounds than existing results. Furthermore, we also establish the lower complexity bounds, which show that our upper bounds are optimal up to a logarithmic factor in terms of the local incremental first-order oracle calls, the computation rounds, and the communication rounds. Numerical experiments demonstrate that our algorithm outperforms existing methods in practice.

Large Language Models (LLMs) have demonstrated remarkable performance in real-world applications. However, adapting LLMs to novel tasks via fine-tuning often requires substantial training data and computational resources that are impractical in few-shot scenarios. Existing approaches, such as In-context learning and Parameter-Efficient Fine-Tuning (PEFT), face key limitations: In-context learning introduces additional inference computational overhead with limited performance gains, while PEFT models are prone to overfitting on the few demonstration examples. In this work, we reinterpret the forward pass of LLMs as an optimization process, a sequence of preconditioned gradient descent steps refining internal representations. Based on this connection, we propose Optimization-Inspired Few-Shot Adaptation (OFA), integrating a parameterization that learns preconditioners without introducing additional trainable parameters, and an objective that improves optimization efficiency by learning preconditioners based on a convergence bound, while simultaneously steering the optimization path toward the flat local minimum. Our method overcomes both issues of ICL-based and PEFT-based methods, and demonstrates superior performance over the existing methods on a variety of few-shot adaptation tasks in experiments.

Test-time adaptation (TTA) enhances the zero-shot robustness under distribution shifts by leveraging unlabeled test data during inference. Despite notable advances, several challenges still limit its broader applicability. First, most methods rely on backpropagation or iterative optimization, which limits scalability and hinders real-time deployment. Second, they lack explicit modeling of class-conditional feature distributions. This modeling is crucial for producing reliable decision boundaries and calibrated predictions, but it remains underexplored due to the lack of both source data and supervision at test time. In this paper, we propose ADAPT, an Advanced Distribution-Aware and backPropagation-free Test-time adaptation method. We reframe TTA as a probabilistic inference task by modeling class-conditional likelihoods using gradually updated class means and a shared covariance matrix. This enables closed-form, training-free inference. To correct potential likelihood bias, we introduce lightweight regularization guided by CLIP priors and a historical knowledge bank. ADAPT requires no source data, no gradient updates, and no full access to target data, supporting both online and transductive settings. Extensive experiments across diverse benchmarks demonstrate that our method achieves state-of-the-art performance under a wide range of distribution shifts with superior scalability and robustness.

Neural Probabilistic Circuits (NPCs), a new class of concept bottleneck models, comprise an attribute recognition model and a probabilistic circuit for reasoning. By integrating the outputs from these two modules, NPCs produce compositional and interpretable predictions. While offering enhanced interpretability and high performance on downstream tasks, the neural-network-based attribute recognition model remains a black box. This vulnerability allows adversarial attacks to manipulate attribute predictions by introducing carefully crafted subtle perturbations to input images, potentially compromising the final predictions. In this paper, we theoretically analyze the adversarial robustness of NPC and demonstrate that it only depends on the robustness of the attribute recognition model and is independent of the robustness of the probabilistic circuit. Moreover, we propose RNPC, the first robust neural probabilistic circuit against adversarial attacks on the recognition module. RNPC introduces a novel class-wise integration for inference, ensuring a robust combination of outputs from the two modules. Our theoretical analysis demonstrates that RNPC exhibits provably improved adversarial robustness compared to NPC. Empirical results on image classification tasks show that RNPC achieves superior adversarial robustness compared to existing concept bottleneck models while maintaining high accuracy on benign inputs. The code is available at https://github.com/uiuctml/RNPC.

Discrete diffusion models have recently gained significant attention due to their ability to process complex discrete structures for language modeling. However, fine-tuning these models with policy gradient methods, as is commonly done in Reinforcement Learning from Human Feedback (RLHF), remains a challenging task. We propose an efficient, broadly applicable, and theoretically justified policy gradient algorithm, called Score Entropy Policy Optimization (SEPO), for fine-tuning discrete diffusion models over non-differentiable rewards. Our numerical experiments across several discrete generative tasks demonstrate the scalability and efficiency of our method.

When do diffusion models reproduce their training data, and when are they able to generate samples beyond it? A practically relevant theoretical understanding of this interplay between memorization and generalization may significantly impact real-world deployments of diffusion models with respect to issues such as copyright infringement and data privacy. In this paper, we propose a scientific and mathematical “laboratory” for investigating memorization and generalization in diffusion models trained on fully synthetic or natural image-like structured data. Within this setting, we theoretically characterize a crossover point wherein the weighted training loss of a fully generalizing model becomes greater than that of an underparameterized memorizing model at a critical value of model (under)parameterization. We then demonstrate via carefully-designed experiments that the location of this crossover predicts a phase transition in diffusion models trained via gradient descent, as our theory enables us to analytically predict the model size at which memorization becomes predominant. Our work provides an analytically tractable and practically meaningful setting for future theoretical and empirical investigations. Code for our experiments is available at https://github.com/DruvPai/diffusion_mem_gen.

Designing algorithms for solving high-dimensional Bayesian inverse problems directly in infinite‑dimensional function spaces – where such problems are naturally formulated – is crucial to ensure stability and convergence as the discretization of the underlying problem is refined. In this paper, we contribute to this line of work by analyzing a widely used sampler for linear inverse problems: Langevin dynamics driven by score‑based generative models (SGMs) acting as priors, formulated directly in function space. Building on the theoretical framework for SGMs in Hilbert spaces, we give a rigorous definition of this sampler in the infinite-dimensional setting and derive, for the first time, error estimates that explicitly depend on the approximation error of the score. As a consequence, we obtain sufficient conditions for global convergence in Kullback–Leibler divergence on the underlying function space. Preventing numerical instabilities requires preconditioning of the Langevin algorithm and we prove the existence and form of an optimal preconditioner. The preconditioner depends on both the score error and the forward operator and guarantees a uniform convergence rate across all posterior modes. Our analysis applies to both Gaussian and a general class of non‑Gaussian priors. Finally, we present examples that illustrate and validate our theoretical findings.

Zeroth-order optimization (ZOO) is an important framework for stochastic optimization when gradients are unavailable or expensive to compute. A potential limitation of existing ZOO methods is the bias inherent in most gradient estimators unless the perturbation stepsize vanishes. In this paper, we overcome this biasedness issue by proposing a novel family of *unbiased* gradient estimators based solely on function evaluations. By reformulating directional derivatives as a telescoping series and sampling from carefully designed distributions, we construct estimators that eliminate bias while maintaining favorable variance. We analyze their theoretical properties, derive optimal scaling distributions and perturbation stepsizes of four specific constructions, and prove that SGD using the proposed estimators achieves optimal complexity for smooth non-convex objectives. Experiments on synthetic tasks and language model fine-tuning confirm the superior accuracy and convergence of our approach compared to standard methods.

Quantum state tomography, the task of learning an unknown quantum state, is a fundamental problem in quantum information. In standard settings, the complexity of this problem depends significantly on the type of quantum state that one is trying to learn, with pure states being substantially easier to learn than general mixed states. A natural question is whether this separation holds for any quantum state learning setting. In this work, we consider the online learning framework and prove the surprising result that learning pure states in this setting is as hard as learning mixed states. More specifically, we show that both classes share almost the same sequential fat-shattering dimension, leading to identical regret scaling. We also generalize previous results on full quantum state tomography in the online setting to (i) the $\epsilon$-realizable setting and (ii) learning the density matrix only partially, using smoothed analysis.

In the classic expert problem, $\Phi$-regret measures the gap between the learner's total loss and that achieved by applying the best action transformation $\phi \in \Phi$. A recent work by Lu et al., [2025] introduced an adaptive algorithm whose regret against a comparator $\phi$ depends on a certain sparsity-based complexity measure of $\phi$, recovering and interpolating optimal bounds for standard regret notions such as external, internal, and swap regret. In this work, we propose a general idea to achieve an even better comparator-adaptive $\Phi$-regret bound via much simpler algorithms compared to Lu et al., [2025]. Specifically, we discover a prior distribution over all possible binary transformations and show that it suffices to achieve prior-dependent regret against these transformations. Then, we propose two concrete and efficient algorithms to achieve so, where the first one combines multiple copies of the kernelized Hedge algorithm of Farina et al., [2022], and the second one combines multiple copies of a variant of the BM-reduction [Blum and Mansour, 2007]. To further showcase the power of our methods and the advantages over Lu et al., [2025] besides the simplicity and better regret bounds, we also show that our second approach can be extended to the game setting to achieve accelerated and adaptive convergence rate to $\Phi$-equilibria for a class of general-sum games. When specified to the special case of correlated equilibria, our bound improves over the existing ones from Anagnostides et al., [2022a,b].