OpenRaiser/Intern-Atlas huggingface dataset:
Inference-Time Personalized Alignment with a Few User Preference Queries
Venue: Conference NeurIPS 2025
Year: 2025

We study the problem of aligning a generative model's response with a user's preferences. Recent works have proposed several different formulations for personalized alignment; however, they either require a large amount of user preference queries or require that the preference be explicitly specified as a text input. In this paper, we propose a novel inference-time personalized alignment method, UserAlign, that elicits the user's preferences with a few queries as pairwise response comparisons. In particular, UserAlign builds on the theoretical framework of best-arm identification in logistic bandits and selects a personalized response from a fixed pool of the model's generated responses. The key idea is to consider the user's feedback consistent and noise-free, and incorporate it into the theoretical framework to identify the best response quickly. Experimental results across several tasks, involving personalized text and image generation, showcase the effectiveness of UserAlign in achieving personalized alignment.
Why Diffusion Models Don’t Memorize:  The Role of Implicit Dynamical Regularization in Training
Venue: Conference NeurIPS 2025
Year: 2025

Diffusion models have achieved remarkable success across a wide range of generative tasks. A key challenge is understanding the mechanisms that prevent their memorization of training data and allow generalization. In this work, we investigate the role of the training dynamics in the transition from generalization to memorization. Through extensive experiments and theoretical analysis, we identify two distinct timescales: an early time $τ_\mathrm{gen}$ at which models begin to generate high-quality samples, and a later time $τ_\mathrm{mem}$ beyond which memorization emerges. Crucially, we find that $τ_\mathrm{mem}$ increases linearly with the training set size $n$, while $τ_\mathrm{gen}$ remains constant. This creates a growing window of training times with $n$ where models generalize effectively, despite showing strong memorization if training continues beyond it. It is only when $n$ becomes larger than a model-dependent threshold that overfitting disappears at infinite training times. These findings reveal a form of implicit dynamical regularization in the training dynamics, which allow to avoid memorization even in highly overparameterized settings. Our results are supported by numerical experiments with standard U-Net architectures on realistic and synthetic datasets, and by a theoretical analysis using a tractable random features model studied in the high-dimensional limit.
KL Penalty Control via Perturbation for Direct Preference Optimization
Venue: Conference NeurIPS 2025
Year: 2025

Direct Preference Optimization (DPO) demonstrates the advantage of aligning a large language model with human preference using only an offline dataset. However, DPO has the limitation that the KL penalty, which prevents excessive deviation from the reference model, is static throughout the training process. Several methods claim to change this static KL penalty of DPO into a dynamic one, but no approach can adaptively assign different KL penalties for each preference pair. In this paper, we propose $\varepsilon$-Direct Preference Optimization ($\varepsilon$-DPO), which allows adaptive control of the KL penalty strength $β$ for each preference pair. Specifically, $\varepsilon$-DPO adaptively controls $β$ for each preference pair based on the monotonicity of logits as a preference model under the perturbation of $β$ during training. This is equivalent to adjusting the KL penalty by checking whether the change in training-time temperature can lead to better preference confidence as preference models by simply reusing the logit of the current policy and the reference policy. Experimental results show that the simple criterion of $\varepsilon$-DPO for KL penalty relaxation significantly improves DPO compared to most existing direct alignment algorithms on general chatbot benchmarks and reveal that this KL penalty control criterion can reflect confusion as a preference model and provide an efficient KL trade-off, highlighting the significance of instance-level adaptive KL penalty control in DPO.
BoltzNCE: Learning likelihoods for Boltzmann Generation with Stochastic Interpolants and Noise Contrastive Estimation
Venue: Conference NeurIPS 2025
Year: 2025

Efficient sampling from the Boltzmann distribution given its energy function is a key challenge for modeling complex physical systems such as molecules. Boltzmann Generators address this problem by leveraging continuous normalizing flows to transform a simple prior into a distribution that can be reweighted to match the target using sample likelihoods. Despite the elegance of this approach, obtaining these likelihoods requires computing costly Jacobians during integration, which is impractical for large molecular systems. To overcome this difficulty, we train an energy-based model (EBM) to approximate likelihoods using both noise contrastive estimation (NCE) and score matching, which we show outperforms the use of either objective in isolation. On 2d synthetic systems where failure can be easily visualized, NCE improves mode weighting relative to score matching alone. On alanine dipeptide, our method yields free energy profiles and energy distributions that closely match those obtained using exact likelihoods while achieving $100\times$ faster inference. By training on multiple dipeptide systems, we show that our approach also exhibits effective transfer learning, generalizing to new systems at inference time and achieving at least a $6\times$ speedup over standard MD. While many recent efforts in generative modeling have prioritized models with fast sampling, our work demonstrates the design of models with accelerated likelihoods, enabling the application of reweighting schemes that ensure unbiased Boltzmann statistics at scale. Our code is available at https://github.com/RishalAggarwal/BoltzNCE.
Better Estimation of the Kullback--Leibler Divergence Between Language Models
Venue: Conference NeurIPS 2025
Year: 2025

Estimating the Kullback--Leibler (KL) divergence between language models has many applications, e.g., reinforcement learning from human feedback (RLHF), interpretability, and knowledge distillation. However, computing the exact KL divergence between two arbitrary language models is intractable. Thus, practitioners often resort to sampling-based estimators. While it is easy to fashion a simple Monte Carlo (MC) estimator that provides an unbiased estimate of the KL divergence between language models, this estimator notoriously suffers from high variance and can even result in a negative estimate of the KL divergence, a non-negative quantity. In this paper, we introduce a Rao--Blackwellized estimator that is unbiased and provably has variance less than or equal to that of the standard Monte Carlo estimator. In an empirical study on sentiment-controlled fine-tuning, we show that our estimator provides more stable KL estimates and reduces variance substantially. Additionally, we derive an analogous Rao--Blackwellized estimator of the gradient of the KL divergence, which leads to more stable training and produces models that more frequently appear on the Pareto frontier of reward vs. KL compared to the ones trained with the MC estimator of the gradient.
The Surprising Effectiveness of Negative Reinforcement in LLM Reasoning
Venue: Conference NeurIPS 2025
Year: 2025

Reinforcement learning with verifiable rewards (RLVR) is a promising approach for training language models (LMs) on reasoning tasks that elicit emergent long chains of thought (CoTs). Unlike supervised learning, it updates the model using both correct and incorrect samples via policy gradients. To better understand its mechanism, we decompose the learning signal into reinforcing correct responses and penalizing incorrect ones, referred to as Positive and Negative Sample Reinforcement (PSR and NSR), respectively. We train Qwen2.5-Math-7B, Qwen3-4B and Llama-3.1-8B-Instruct on a mathematical reasoning dataset and uncover a surprising result: training with only negative samples -- without reinforcing correct responses -- can be highly effective: it consistently improves performance over the base model across the entire Pass@$k$ spectrum $k$ up to 256), often matching or surpassing PPO and GRPO. In contrast, reinforcing only correct responses improves Pass@1 but degrades performance at higher $k$, due to reduced diversity. These inference-scaling trends highlight that solely penalizing incorrect responses may contribute more to performance than previously recognized. Through gradient analysis, we show that NSR works by suppressing incorrect generations and redistributing probability mass toward other plausible candidates, guided by the model's prior beliefs. It refines the model's existing knowledge rather than introducing entirely new behaviors. Building on this insight, we propose a simple variant of the RL objective that upweights NSR, and show that it consistently improves overall Pass@$k$ performance on MATH, AIME 2025, and AMC23. Our code is available at https://github.com/TianHongZXY/RLVR-Decomposed.
Ambient Diffusion Omni: Training Good Models with Bad Data
Venue: Conference NeurIPS 2025
Year: 2025

We show how to use low-quality, synthetic, and out-of-distribution images to improve the quality of a diffusion model. Typically, diffusion models are trained on curated datasets that emerge from highly filtered data pools from the Web and other sources. We show that there is immense value in the lower-quality images that are often discarded. We present Ambient Diffusion Omni, a simple, principled framework to train diffusion models that can extract signal from all available images during training. Our framework exploits two properties of natural images -- spectral power law decay and locality. We first validate our framework by successfully training diffusion models with images synthetically corrupted by Gaussian blur, JPEG compression, and motion blur. We then use our framework to achieve state-of-the-art ImageNet FID, and we show significant improvements in both image quality and diversity for text-to-image generative modeling. The core insight is that noise dampens the initial skew between the desired high-quality distribution and the mixed distribution we actually observe. We provide rigorous theoretical justification for our approach by analyzing the trade-off between learning from biased data versus limited unbiased data across diffusion times.
How Many Tokens Do 3D Point Cloud Transformer Architectures Really Need?
Venue: Conference NeurIPS 2025
Year: 2025

Recent advances in 3D point cloud transformers have led to state-of-the-art results in tasks such as semantic segmentation and reconstruction. However, these models typically rely on dense token representations, incurring high computational and memory costs during training and inference. In this work, we present the finding that tokens are remarkably redundant, leading to substantial inefficiency. We introduce gitmerge3D, a globally informed graph token merging method that can reduce the token count by up to 90-95% while maintaining competitive performance. This finding challenges the prevailing assumption that more tokens inherently yield better performance and highlights that many current models are over-tokenized and under-optimized for scalability. We validate our method across multiple 3D vision tasks and show consistent improvements in computational efficiency. This work is the first to assess redundancy in large-scale 3D transformer models, providing insights into the development of more efficient 3D foundation architectures. Our code and checkpoints are publicly available at https://gitmerge3d.github.io
Information Retrieval Induced Safety Degradation in AI Agents
Venue: Conference NeurIPS 2025
Year: 2025

Despite the growing integration of retrieval-enabled AI agents into society, their safety and ethical behavior remain inadequately understood. In particular, the integration of LLMs and AI agents with external information sources and real-world environments raises critical questions about how they engage with and are influenced by these external data sources and interactive contexts. This study investigates how expanding retrieval access -- from no external sources to Wikipedia-based retrieval and open web search -- affects model reliability, bias propagation, and harmful content generation. Through extensive benchmarking of censored and uncensored LLMs and AI agents, our findings reveal a consistent degradation in refusal rates, bias sensitivity, and harmfulness safeguards as models gain broader access to external sources, culminating in a phenomenon we term safety degradation. Notably, retrieval-enabled agents built on aligned LLMs often behave more unsafely than uncensored models without retrieval. This effect persists even under strong retrieval accuracy and prompt-based mitigation, suggesting that the mere presence of retrieved content reshapes model behavior in structurally unsafe ways. These findings underscore the need for robust mitigation strategies to ensure fairness and reliability in retrieval-enabled and increasingly autonomous AI systems.
Learning Reconfigurable Representations for Multimodal Federated Learning with Missing Data
Venue: Conference NeurIPS 2025
Year: 2025

Multimodal federated learning in real-world settings often encounters incomplete and heterogeneous data across clients. This results in misaligned local feature representations that limit the effectiveness of model aggregation. Unlike prior work that assumes either differing modality sets without missing input features or a shared modality set with missing features across clients, we consider a more general and realistic setting where each client observes a different subset of modalities and might also have missing input features within each modality. To address the resulting misalignment in learned representations, we propose a new federated learning framework featuring locally adaptive representations based on learnable client-side embedding controls that encode each client's data-missing patterns. These embeddings serve as reconfiguration signals that align the globally aggregated representation with each client's local context, enabling more effective use of shared information. Furthermore, the embedding controls can be algorithmically aggregated across clients with similar data-missing patterns to enhance the robustness of reconfiguration signals in adapting the global representation. Empirical results on multiple federated multimodal benchmarks with diverse data-missing patterns across clients demonstrate the efficacy of the proposed method, achieving up to 36.45\% performance improvement under severe data incompleteness. The method is also supported by a theoretical analysis with an explicit performance bound that matches our empirical observations. Our source codes are provided at https://github.com/nmduonggg/PEPSY
HiPoNet: A Multi-View Simplicial Complex Network for High Dimensional Point-Cloud and Single-Cell data
Venue: Conference NeurIPS 2025
Year: 2025

In this paper, we propose HiPoNet, an end-to-end differentiable neural network for regression, classification, and representation learning on high-dimensional point clouds. Our work is motivated by single-cell data which can have very high-dimensionality --exceeding the capabilities of existing methods for point clouds which are mostly tailored for 3D data. Moreover, modern single-cell and spatial experiments now yield entire cohorts of datasets (i.e., one data set for every patient), necessitating models that can process large, high-dimensional point-clouds at scale. Most current approaches build a single nearest-neighbor graph, discarding important geometric and topological information. In contrast, HiPoNet models the point-cloud as a set of higher-order simplicial complexes, with each particular complex being created using a reweighting of features. This method thus generates multiple constructs corresponding to different views of high-dimensional data, which in biology offers the possibility of disentangling distinct cellular processes. It then employs simplicial wavelet transforms to extract multiscale features, capturing both local and global topology from each view. We show that geometric and topological information is preserved in this framework both theoretically and empirically. We showcase the utility of HiPoNet on point-cloud level tasks, involving classification and regression of entire point-clouds in data cohorts. Experimentally, we find that HiPoNet outperforms other point-cloud and graph-based models on single-cell data. We also apply HiPoNet to spatial transcriptomics datasets using spatial coordinates as one of the views. Overall, HiPoNet offers a robust and scalable solution for high-dimensional data analysis.
SharpZO: Hybrid Sharpness-Aware Vision Language Model Prompt Tuning via Forward-Only Passes
Venue: Conference NeurIPS 2025
Year: 2025

Fine-tuning vision language models (VLMs) has achieved remarkable performance across various downstream tasks; yet, it requires access to model gradients through backpropagation (BP), making them unsuitable for memory-constrained, inference-only edge devices. To address this limitation, previous work has explored various BP-free fine-tuning methods. However, these approaches often rely on high-variance evolutionary strategies (ES) or zeroth-order (ZO) optimization, and often fail to achieve satisfactory performance. In this paper, we propose a hybrid Sharpness-aware Zeroth-order optimization (SharpZO) approach, specifically designed to enhance the performance of ZO VLM fine-tuning via a sharpness-aware warm-up training. SharpZO features a two-stage optimization process: a sharpness-aware ES stage that globally explores and smooths the loss landscape to construct a strong initialization, followed by a fine-grained local search via sparse ZO optimization. The entire optimization relies solely on forward passes. Detailed theoretical analysis and extensive experiments on CLIP models demonstrate that SharpZO significantly improves accuracy and convergence speed, achieving up to 7% average gain over state-of-the-art forward-only methods.
Transfer Learning on Edge Connecting Probability Estimation Under Graphon Model
Venue: Conference NeurIPS 2025
Year: 2025

Graphon models provide a flexible nonparametric framework for estimating latent connectivity probabilities in networks, enabling a range of downstream applications such as link prediction and data augmentation. However, accurate graphon estimation typically requires a large graph, whereas in practice, one often only observes a small-sized network. One approach to addressing this issue is to adopt a transfer learning framework, which aims to improve estimation in a small target graph by leveraging structural information from a larger, related source graph. In this paper, we propose a novel method, namely GTRANS, a transfer learning framework that integrates neighborhood smoothing and Gromov-Wasserstein optimal transport to align and transfer structural patterns between graphs. To prevent negative transfer, GTRANS includes an adaptive debiasing mechanism that identifies and corrects for target-specific deviations via residual smoothing. We provide theoretical guarantees on the stability of the estimated alignment matrix and demonstrate the effectiveness of GTRANS in improving the accuracy of target graph estimation through extensive synthetic and real data experiments. These improvements translate directly to enhanced performance in downstream applications, such as the graph classification task and the link prediction task.
Learning Parameterized Skills from Demonstrations
Venue: Conference NeurIPS 2025
Year: 2025

We present DEPS, an end-to-end algorithm for discovering parameterized skills from expert demonstrations. Our method learns parameterized skill policies jointly with a meta-policy that selects the appropriate discrete skill and continuous parameters at each timestep. Using a combination of temporal variational inference and information-theoretic regularization methods, we address the challenge of degeneracy common in latent variable models, ensuring that the learned skills are temporally extended, semantically meaningful, and adaptable. We empirically show that learning parameterized skills from multitask expert demonstrations significantly improves generalization to unseen tasks. Our method outperforms multitask as well as skill learning baselines on both LIBERO and MetaWorld benchmarks. We also demonstrate that DEPS discovers interpretable parameterized skills, such as an object grasping skill whose continuous arguments define the grasp location.
The Rise of Parameter Specialization for Knowledge Storage in Large Language Models
Venue: Conference NeurIPS 2025
Year: 2025

Over time, a growing wave of large language models from various series has been introduced to the community. Researchers are striving to maximize the performance of language models with constrained parameter sizes. However, from a microscopic perspective, there has been limited research on how to better store knowledge in model parameters, particularly within MLPs, to enable more effective utilization of this knowledge by the model. In this work, we analyze twenty publicly available open-source large language models to investigate the relationship between their strong performance and the way knowledge is stored in their corresponding MLP parameters. Our findings reveal that as language models become more advanced and demonstrate stronger knowledge capabilities, their parameters exhibit increased specialization. Specifically, parameters in the MLPs tend to be more focused on encoding similar types of knowledge. We experimentally validate that this specialized distribution of knowledge contributes to improving the efficiency of knowledge utilization in these models. Furthermore, by conducting causal training experiments, we confirm that this specialized knowledge distribution plays a critical role in improving the model's efficiency in leveraging stored knowledge.
The Atlas of In-Context Learning: How Attention Heads Shape In-Context Retrieval Augmentation
Venue: Conference NeurIPS 2025
Year: 2025

Large language models are able to exploit in-context learning to access external knowledge beyond their training data through retrieval-augmentation. While promising, its inner workings remain unclear. In this work, we shed light on the mechanism of in-context retrieval augmentation for question answering by viewing a prompt as a composition of informational components. We propose an attribution-based method to identify specialized attention heads, revealing in-context heads that comprehend instructions and retrieve relevant contextual information, and parametric heads that store entities' relational knowledge. To better understand their roles, we extract function vectors and modify their attention weights to show how they can influence the answer generation process. Finally, we leverage the gained insights to trace the sources of knowledge used during inference, paving the way towards more safe and transparent language models.