NeurIPS 2025 Papers

Diffusion Transformers (DiTs) have demonstrated strong performance in generative modeling, particularly in image synthesis, making them a compelling choice for molecular conformer generation. However, applying DiTs to molecules introduces novel challenges, such as integrating discrete molecular graph information with continuous 3D geometry, handling Euclidean symmetries, and designing conditioning mechanisms that generalize across molecules of varying sizes and structures. We propose DiTMC, a framework that adapts DiTs to address these challenges through a modular architecture that separates the processing of 3D coordinates from conditioning on atomic connectivity. To this end, we introduce two complementary graph-based conditioning strategies that integrate seamlessly with the DiT architecture. These are combined with different attention mechanisms, including both standard non-equivariant and SO(3)-equivariant formulations, enabling flexible control over the trade-off between between accuracy and computational efficiency. Experiments on standard conformer generation benchmarks (GEOM-QM9, -DRUGS, -XL) demonstrate that DiTMC achieves state-of-the-art precision and physical validity. Our results highlight how architectural choices and symmetry priors affect sample quality and efficiency, suggesting promising directions for large-scale generative modeling of molecular structures. Code is available at [https://github.com/ML4MolSim/dit_mc](https://github.com/ML4MolSim/dit_mc).

Object–context shortcuts remain a persistent challenge in vision‑language models, undermining zero‑shot reliability when test-time scenes diverge from familiar training co-occurrences. We recast this issue as a causal inference problem and ask: Would the prediction remain if the object appeared in a different environment? To answer it at inference time, we estimate object and background expectations within CLIP’s representation space, and synthesize counterfactual embeddings by recombining object features with diverse alternative contexts sampled from external datasets, batch neighbors, or text-derived descriptions. By estimating the Total Direct Effect and simulating intervention, we further subtract background‑only activation, preserving beneficial object–context interactions while mitigating hallucinated scores. Without retraining or prompt design, our method substantially improves both worst-group and average accuracy on context-sensitive benchmarks, establishing a new zero‑shot state of the art. Beyond performance, our framework provides a lightweight representation-level counterfactual approach, offering a practical causal avenue for debiased and reliable multimodal reasoning.

We propose a practical sequential test for auditing differential privacy guarantees of black-box mechanisms. The test processes streams of mechanisms' outputs providing anytime-valid inference while controlling Type I error, overcoming the fixed sample size limitation of previous batch auditing methods. Experiments show this test detects violations with sample sizes that are orders of magnitude smaller than existing methods, reducing this number from 50K to a few hundred examples, across diverse realistic mechanisms. Notably, it identifies DP-SGD privacy violations in \textit{under} one training run, unlike prior methods needing full model training.

Large Vision-Language Models (LVLMs) have shown impressive performance across multi-modal tasks by encoding images into thousands of tokens. However, the large number of image tokens results in significant computational overhead, and the use of dynamic high-resolution inputs further increases this burden. Previous approaches have attempted to reduce the number of image tokens through token pruning, typically by selecting tokens based on attention scores or image token diversity. Through empirical studies, we observe that existing methods often overlook the joint impact of pruning on both the current layer's output (local) and the outputs of subsequent layers (global), leading to suboptimal pruning decisions. To address this challenge, we propose Balanced Token Pruning (BTP), a plug-and-play method for pruning vision tokens. Specifically, our method utilizes a small calibration set to divide the pruning process into multiple stages. In the early stages, our method emphasizes the impact of pruning on subsequent layers, whereas in the deeper stages, the focus shifts toward preserving the consistency of local outputs. Extensive experiments across various LVLMs demonstrate the broad effectiveness of our approach on multiple benchmarks. Our method achieves a 78\% compression rate while preserving 96.7\% of the original models' performance on average. Our code is available at https://github.com/EmbodiedCity/NeurIPS2025-Balanced-Token-Pruning.

Starting from flow- and diffusion-based transformers, Multi-modal Diffusion Transformers (MM-DiTs) have reshaped text-to-vision generation, gaining acclaim for exceptional visual fidelity. As these models advance, users continually push the boundary with imaginative or rare prompts, which advanced models still falter in generating, since their concepts are often too scarce to leave a strong imprint during pre-training. In this paper, we propose a simple yet effective intervention that surfaces rare semantics inside MM-DiTs without additional training steps, data, denoising-time optimization, or reliance on external modules (e.g., large language models). In particular, the joint-attention mechanism intrinsic to MM-DiT sequentially updates text embeddings alongside image embeddings throughout transformer blocks. We find that by mathematically expanding representational basins around text token embeddings via variance scale-up before the joint-attention blocks, rare semantics clearly emerge in MM-DiT’s outputs. Furthermore, our results generalize effectively across text-to-vision tasks, including text-to-image, text-to-video, and text-driven image editing. Our work invites generative models to reveal the semantics that users intend, once hidden yet ready to surface.

Recent advances in reinforcement learning (RL) methods such as Grouped Relative Policy Optimization (GRPO) have strengthened the reasoning capabilities of Large Vision-Language Models (LVLMs). However, due to the inherent entanglement between visual and textual modalities, applying GRPO to LVLMs often leads to reward convergence across different responses to the same sample as training progresses, hindering effective gradient updates and causing the enhancement of chain-of-thought reasoning to stagnate or even collapse. To address this issue, we propose a progressive instruction evolution framework, EvolvedGRPO, to gradually generate more complex questions via editing instructions in an adversarial way, progressively aligned with the model’s evolving capabilities. Specifically, we design two instruction editing strategies across modalities, incorporating incrementally increasing editing instructions and RL-based adversarial data augmentation to improve the effectiveness of model training. To address GRPO's limitations on overly difficult problems, we first train on basic subproblem versions of complex multi-modal questions in both the visual and textual modalities, progressively increasing difficulty to enable prefix-style process rewards, effectively combining the strengths of both process rewards and group-wise relative rewards. Finally, EvolvedGRPO achieves state-of-the-art performance among open-source RL models on multi-modal reasoning tasks, even approaching the closed-source GPT-4o in reasoning capabilities, and demonstrates better performance on unseen LVLM general benchmarks. The Code for EvolvedGRPO is available at https://github.com/SHENZHEBEI/EvolvedGRPO.

We study the noise-free Gaussian Process (GP) bandit problem, in which a learner seeks to minimize regret through noise-free observations of a black-box objective function that lies in a known reproducing kernel Hilbert space (RKHS). The Gaussian Process Upper Confidence Bound (GP-UCB) algorithm is a well-known approach for GP bandits, where query points are adaptively selected based on the GP-based upper confidence bound score. While several existing works have reported the practical success of GP-UCB, its theoretical performance remains suboptimal. However, GP-UCB often empirically outperforms other nearly-optimal noise-free algorithms that use non-adaptive sampling schemes. This paper resolves the gap between theoretical and empirical performance by establishing a nearly-optimal regret upper bound for noise-free GP-UCB. Specifically, our analysis provides the first constant cumulative regret bounds in the noise-free setting for both the squared exponential kernel and the Matérn kernel with some degree of smoothness.

Finding low-rank matrix weights is a key technique for addressing the high memory usage and computational demands of large models. Most existing algorithms rely on the factorization of the low-rank matrix weights, which is non-unique and redundant. Their convergence is slow especially when the target low-rank matrices are ill-conditioned, because the convergence rate depends on the condition number of the Jacobian operator for the factorization and the Hessian of the loss function with respect to the weight matrix. To address this challenge, we adopt the Riemannian gradient descent (RGD) algorithm on the Riemannian manifold of fixed-rank matrices to update the entire low-rank weight matrix. This algorithm completely avoids the factorization, thereby eliminating the negative impact of the Jacobian condition number. Furthermore, by leveraging the geometric structure of the Riemannian manifold and selecting an appropriate metric, it mitigates the negative impact of the Hessian condition number. Ultimately, this results in our two plug-and-play optimizers: RAdaGrad and RAdamW, which are RGD with metrics adapted from AdaGrad and AdamW and restricted to the manifold. Our algorithms can be seamlessly integrated with various deep neural network architectures without any modifications. We evaluate the effectiveness of our algorithms through fine-tuning experiments on large language models and diffusion models. Experimental results consistently demonstrate that our algorithms provide superior performance compared to state-of-the-art methods. Additionally, our algorithm is not only effective for fine-tuning large models but is also applicable to deep neural network (DNN) compression.

Real-world datasets typically exhibit long-tailed (LT) distributions, where a few head classes dominate and many tail classes are severely underrepresented. While recent work shows that parameter-efficient fine-tuning (PEFT) methods like LoRA and AdaptFormer preserve tail-class performance on foundation models such as CLIP, we find that they do so at the cost of head-class accuracy. We identify the head-tail ratio, the proportion of head to tail classes, as a crucial but overlooked factor influencing this trade-off. Through controlled experiments on CIFAR100 with varying imbalance ratio ($\rho$) and head-tail ratio ($\eta$), we show that PEFT excels in tail-heavy scenarios but degrades in more balanced and head-heavy distributions. To overcome these limitations, we propose LT-Soups, a two-stage model soups framework designed to generalize across diverse LT regimes. In the first stage, LT-Soups averages models fine-tuned on balanced subsets to reduce head-class bias; in the second, it fine-tunes only the classifier on the full dataset to restore head-class accuracy. Experiments across six benchmark datasets show that LT-Soups achieves superior trade-offs compared to both PEFT and traditional model soups across a wide range of imbalance regimes.

In recent years, Multimodal Large Language Models (MLLMs) have been extensively utilized for multimodal reasoning tasks, including Graphical User Interface (GUI) automation. Unlike general offline multimodal tasks, GUI automation is executed in online interactive environments, necessitating step-by-step decision-making based on the real-time status of the environment. This task has a lower tolerance for decision-making errors at each step, as any mistakes may cumulatively disrupt the process and potentially lead to irreversible outcomes like deletions or payments. To address these issues, we introduce a pre-operative critic mechanism that provides effective feedback prior to the actual execution, by reasoning about the potential outcome and correctness of actions. Specifically, we propose a Suggestion-aware Group Relative Policy Optimization (S-GRPO) strategy to construct our pre-operative critic model GUI-Critic-R1, incorporating a novel suggestion reward to enhance the reliability of the model's feedback. Furthermore, we develop a reasoning-bootstrapping based data collection pipeline to create a GUI-Critic-Train and a GUI-Critic-Test, filling existing gaps in GUI critic data. Static experiments on the GUI-Critic-Test across both mobile and web domains reveal that our GUI-Critic-R1 offers significant advantages in critic accuracy compared to current MLLMs. Dynamic evaluation on GUI automation benchmark further highlights the effectiveness and superiority of our model, as evidenced by improved success rates and operational efficiency. The code is available at https://github.com/X-PLUG/MobileAgent/tree/main/GUI-Critic-R1.

Conformal Prediction (CP) is a popular framework for constructing prediction bands with valid coverage in finite samples, while being free of any distributional assumption. A well-known limitation of conformal prediction is the lack of adaptivity, although several works introduced practically efficient alternate procedures. In this work, we build upon recent ideas that rely on recasting the CP problem as a statistical learning problem, directly targeting coverage and adaptivity. This statistical learning problem is based on reproducible kernel Hilbert spaces (RKHS) and kernel sum-of-squares (SoS) methods. First, we extend previous results with a general representer theorem and exhibit the dual formulation of the learning problem. Crucially, such dual formulation can be solved efficiently by accelerated gradient methods with several hundreds or thousands of samples, unlike previous strategies based on off-the-shelf semidefinite programming algorithms. Second, we introduce a new hyperparameter tuning strategy tailored specifically to target adaptivity through bounds on test-conditional coverage. This strategy, based on the Hilbert-Schmidt Independence Criterion (HSIC), is introduced here to tune kernel lengthscales in our framework, but has broader applicability since it could be used in any CP algorithm where the score function is learned. Finally, extensive experiments are conducted to show how our method compares to related work. All figures can be reproduced with the accompanying code at https://www.gitlab.com/drti/ksos-bands.

Model-free reinforcement learning (RL) combined with diffusion models has achieved significant progress in addressing complex continuous control tasks. However, a persistent challenge in RL remains the accurate estimation of Q-values, which critically governs the efficacy of policy optimization. Although recent advances employ parametric distributions to model value distributions for enhanced estimation accuracy, current methodologies predominantly rely on unimodal Gaussian assumptions or quantile representations. These constraints introduce distributional bias between the learned and true value distributions, particularly in some tasks with a nonstationary policy, ultimately degrading performance. To address these limitations, we propose value diffusion reinforcement learning (VDRL), a novel model-free online RL method that utilizes the generative capacity of diffusion models to represent multimodal value distributions. The core innovation of VDRL lies in the use of the variational loss of diffusion-based value distribution, which is theoretically proven to be a tight lower bound for the optimization objective under the KL-divergence measurement. Furthermore, we introduce double value diffusion learning with sample selection to enhance training stability and further improve value estimation accuracy. Extensive experiments conducted on the MuJoCo benchmark demonstrate that VDRL significantly outperforms some SOTA model-free online RL baselines, showcasing its effectiveness and robustness.

Transformers have gained attention in atmospheric time series forecasting (ATSF) for their ability to capture global spatial-temporal correlations. However, their complex architectures lead to excessive parameter counts and extended training times, limiting their scalability to large-scale forecasting. In this paper, we revisit ATSF from a theoretical perspective of atmospheric dynamics and uncover a key insight: spatial-temporal position embedding (STPE) can inherently model spatial-temporal correlations even without attention mechanisms. Its effectiveness arises from integrating geographical coordinates and temporal features, which are intrinsically linked to atmospheric dynamics. Based on this, we propose **STELLA**, a **S**patial-**T**emporal knowledge **E**mbedded **L**ightweight mode**L** for ASTF, utilizing only STPE and an MLP architecture in place of Transformer layers. With 10k parameters and one hour of training, STELLA achieves superior performance on five datasets compared to other advanced methods. The paper emphasizes the effectiveness of spatial-temporal knowledge integration over complex architectures, providing novel insights for ATSF.

Seeking high-quality representations with latent variable models (LVMs) to reveal the intrinsic correlation between neural activity and behavior or sensory stimuli has attracted much interest. In the study of the biological visual system, naturalistic visual stimuli are inherently high-dimensional and time-dependent, leading to intricate dynamics within visual neural activity. However, most work on LVMs has not explicitly considered neural temporal relationships. To cope with such conditions, we propose Time-Evolving Visual Dynamical System (TE-ViDS), a sequential LVM that decomposes neural activity into low-dimensional latent representations that evolve over time. To better align the model with the characteristics of visual neural activity, we split latent representations into two parts and apply contrastive learning to shape them. Extensive experiments on synthetic datasets and real neural datasets from the mouse visual cortex demonstrate that TE-ViDS achieves the best decoding performance on naturalistic scenes/movies, extracts interpretable latent trajectories that uncover clear underlying neural dynamics, and provides new insights into differences in visual information processing between subjects and between cortical regions. In summary, TE-ViDS is markedly competent in extracting stimulus-relevant embeddings from visual neural activity and contributes to the understanding of visual processing mechanisms. Our codes are available at https://github.com/Grasshlw/Time-Evolving-Visual-Dynamical-System.

Enhancing large language models by simply scaling up datasets has begun to yield diminishing returns, shifting the spotlight to data quality. Monte Carlo Tree Search (MCTS) has emerged as a powerful technique for generating high-quality chain-of-thought data, yet conventional approaches typically retain only the top-scoring trajectory from the search tree, discarding sibling nodes that often contain valuable partial insights, recurrent error patterns, and alternative reasoning strategies. This unconditional rejection of non-optimal reasoning branches may waste vast amounts of informative data in the whole search tree. We propose SIGMA (Sibling Guided Monte Carlo Augmentation), a novel framework that reintegrates these discarded sibling nodes to refine LLM reasoning. SIGMA forges semantic links among sibling nodes along each search path and applies a two-stage refinement: a critique model identifies overlooked strengths and weaknesses across the sibling set, and a revision model conducts text-based backpropagation to refine the top-scoring trajectory in light of this comparative feedback. By recovering and amplifying the underutilized but valuable signals from non-optimal reasoning branches, SIGMA substantially improves reasoning trajectories. On the challenging MATH benchmark, our SIGMA-tuned 7B model achieves 54.92\% accuracy using only 30K samples, outperforming state-of-the-art models trained on 590K samples. This result highlights that our sibling-guided optimization not only significantly reduces data usage but also significantly boosts LLM reasoning.

Knowledge in modern neural networks is often entangled and structurally opaque, making current transfer methods—typically based on reusing entire parameter sets—inefficient and inflexible. Efforts to improve flexibility by reusing partial parameters frequently depend on handcrafted heuristics or rigid structural assumptions, which constrain generalization. In contrast, biological evolution enables efficient knowledge transfer by encoding only essential information into genes through iterative refinement under environmental pressure. Inspired by this principle, we propose **ECO**, a framework that **E**volves **CO**re knowledge into modular, reusable neural components—termed *learngenes*—through similar evolutionary dynamics. To this end, we redefine learngenes as neural circuits and introduce Genetic Transfer Learning (GTL), a biologically inspired paradigm that establishes a genetic mechanism within neural networks in the context of supervised learning. GTL simulates evolutionary processes by generating diverse network populations, selecting high-performing individuals, and transferring their learngenes to subsequent generations. Through iterative refinement, GTL enables learngenes to accumulate transferable common knowledge. Extensive experiments show that ECO achieves efficient initialization and strong generalization across diverse models and tasks, while significantly reducing computational and memory costs compared to conventional methods.

Training reasoning language models (LMs) with reinforcement learning (RL) for one-hot correctness inherently relies on the LM being able to explore and solve its task with some chance at initialization. Furthermore, a key use case of reasoning LMs is to act as teachers for distilling new students and cold-starting future RL iterations rather than being deployed themselves. From these considerations, we introduce a new framework that avoids RL's exploration challenge by training a new class of Reinforcement-Learned Teachers (RLTs) focused on yielding the most effective downstream distillation. RLTs are prompted with both the question and solution to each problem, and tasked to simply "connect-the-dots" with detailed explanations tailored for their students. We train RLTs with dense rewards obtained by feeding each explanation to the student and testing its understanding of the problem's solution. In practice, the raw outputs of a 7B RLT provide higher final performance on competition and graduate-level tasks than existing distillation and cold-starting pipelines that collect and postprocess the reasoning traces of orders of magnitude larger LMs. Furthermore, RLTs maintain their effectiveness when training larger students and when applied zero-shot to out-of-distribution tasks, unlocking new levels of efficiency and re-usability for the RL reasoning framework.

The ability to selectively remove knowledge from LLMs is highly desirable. However, existing methods often struggle with balancing unlearning efficacy and retain model utility, and lack controllability at inference time to emulate base model behavior as if it had never seen the unlearned data. In this paper, we propose LUNAR, a novel unlearning method grounded in the Linear Representation Hypothesis and operates by redirecting the representations of unlearned data to activation regions that expresses its inability to answer. We show that contrastive features are not a prerequisite for effective activation redirection, and LUNAR achieves state-of-the-art unlearning performance and superior controllability. Specifically, LUNAR achieves between 2.9x and 11.7x improvement in the combined unlearning efficacy and model utility score (Deviation Score) across various base models and generates coherent, contextually appropriate responses post-unlearning. Moreover, LUNAR effectively reduces parameter updates to a single down-projection matrix, a novel design that significantly enhances efficiency by 20x and robustness. Finally, we demonstrate that LUNAR is robust to white-box adversarial attacks and versatile in real-world scenarios, including handling sequential unlearning requests.

Parameter-Efficient Fine-Tuning (PEFT) is a popular class of techniques that strive to adapt large models in a scalable and resource-efficient manner. Yet, the mechanisms underlying their training performance and generalization remain underexplored. In this paper, we provide several insights into such fine-tuning through the lens of linearization. Fine-tuned models are often implicitly encouraged to remain close to the pretrained model. By making this explicit, using an $\ell_2$-distance inductive bias in parameter space, we show that fine-tuning dynamics become equivalent to learning with the positive-definite neural tangent kernel (NTK). We specifically analyze how close the fully linear and the linearized fine-tuning optimizations are, based on the strength of the regularization. This allows us to be pragmatic about how good a model linearization is when fine-tuning large language models (LLMs). When linearization is a good model, our findings reveal a strong correlation between the eigenvalue spectrum of the NTK and the performance of model adaptation. Motivated by this, we give spectral perturbation bounds on the NTK induced by the choice of layers selected for fine-tuning. We empirically validate our theory on Low Rank Adaptation (LoRA) on LLMs. These insights not only characterize fine-tuning but also have the potential to enhance PEFT techniques, paving the way to better informed and more nimble adaptation in LLMs.