OpenRaiser/Intern-Atlas huggingface dataset:
PolyPose: Deformable 2D/3D Registration via Polyrigid Transformations
Venue: Conference NeurIPS 2025
Year: 2025

Determining the 3D pose of a patient from a limited set of 2D X-ray images is a critical task in interventional settings. While preoperative volumetric imaging (e.g., CT and MRI) provides precise 3D localization and visualization of anatomical targets, these modalities cannot be acquired during procedures, where fast 2D imaging (X-ray) is used instead. To integrate volumetric guidance into intraoperative procedures, we present PolyPose, a simple and robust method for deformable 2D/3D registration. PolyPose parameterizes complex 3D deformation fields as a composition of rigid transforms, leveraging the biological constraint that individual bones do not bend in typical motion. Unlike existing methods that either assume no inter-joint movement or fail outright in this under-determined setting, our polyrigid formulation enforces anatomically plausible priors that respect the piecewise-rigid nature of human movement. This approach eliminates the need for expensive deformation regularizers that require patient- and procedure-specific hyperparameter optimization. Across extensive experiments on diverse datasets from orthopedic surgery and radiotherapy, we show that this strong inductive bias enables PolyPose to successfully align the patient's preoperative volume to as few as two X-rays, thereby providing crucial 3D guidance in challenging sparse-view and limited-angle settings where current registration methods fail. Additional visualizations, tutorials, and code are available at https://polypose.csail.mit.edu.
Traversal Verification for Speculative Tree Decoding
Venue: Conference NeurIPS 2025
Year: 2025

Speculative decoding is a promising approach for accelerating large language models. The primary idea is to use a lightweight draft model to speculate the output of the target model for multiple subsequent timesteps, and then verify them in parallel to determine whether the drafted tokens should be accepted or rejected. To enhance acceptance rates, existing frameworks typically construct token trees containing multiple candidates in each timestep. However, their reliance on token-level verification mechanisms introduces two critical limitations: First, the probability distribution of a sequence differs from that of individual tokens, leading to suboptimal acceptance length. Second, current verification schemes begin from the root node and proceed layer by layer in a top-down manner. Once a parent node is rejected, all its child nodes should be discarded, resulting in inefficient utilization of speculative candidates. This paper introduces Traversal Verification, a novel speculative decoding algorithm that fundamentally rethinks the verification paradigm through leaf-to-root traversal. Our approach considers the acceptance of the entire token sequence from the current node to the root, and preserves potentially valid subsequences that would be prematurely discarded by existing methods. We theoretically prove that the probability distribution obtained through Traversal Verification is identical to that of the target model, guaranteeing lossless inference while achieving substantial acceleration gains. Experimental results across different large language models and multiple tasks show that our method consistently improves acceptance length and throughput over existing methods.
Ultrametric Cluster Hierarchies: I Want ‘em All!
Venue: Conference NeurIPS 2025
Year: 2025

Hierarchical clustering is a powerful tool for exploratory data analysis, organizing data into a tree of clusterings from which a partition can be chosen. This paper generalizes these ideas by proving that, for any reasonable hierarchy, one can optimally solve any center-based clustering objective over it (such as $k$-means). Moreover, these solutions can be found exceedingly quickly and are themselves necessarily hierarchical. Thus, given a cluster tree, we show that one can quickly access a plethora of new, equally meaningful hierarchies. Just as in standard hierarchical clustering, one can then choose any desired partition from these new hierarchies. We conclude by verifying the utility of our proposed techniques across datasets, hierarchies, and partitioning schemes.
On the $O(\frac{\sqrt{d}}{K^{1/4}})$ Convergence Rate of AdamW Measured by $\ell_1$ Norm
Venue: Conference NeurIPS 2025
Year: 2025

As the default optimizer for training large language models, AdamW has achieved remarkable success in deep learning. However, its convergence behavior is not theoretically well-understood. This paper establishes the convergence rate $\frac{1}{K}\sum_{k=1}^KE\left[||\nabla f(x^k)||_1\right]\leq O(\frac{\sqrt{d}C}{K^{1/4}})$ for AdamW measured by $\ell_1$ norm, where $K$ represents the iteration number, $d$ denotes the model dimension, and $C$ matches the constant in the optimal convergence rate of SGD. Theoretically, we have $||\nabla f(x)||_2\ll ||\nabla f(x)||_1\leq \sqrt{d}||\nabla f(x)||_2$ for any high-dimensional vector $x$ and $E\left[||\nabla f(x)||_1\right]\geq\sqrt{\frac{2d}π}E\left[||\nabla f(x)||_2\right]$ when each element of $\nabla f(x)$ is generated from Gaussian distribution $\mathcal N(0,1)$. Empirically, our experimental results on real-world deep learning tasks reveal $||\nabla f(x)||_1=\varTheta(\sqrt{d})||\nabla f(x)||_2$. Both support that our convergence rate can be considered to be analogous to the optimal $\frac{1}{K}\sum_{k=1}^KE\left[||\nabla f(x^k)||_2\right]\leq O(\frac{C}{K^{1/4}})$ convergence rate of SGD in the ideal case. We also extend our result to NAdamW, an AdamW variant that employs a double-momentum mechanism, and demonstrate that it maintains the same convergence rate.
A Theoretical Study on Bridging Internal Probability and Self-Consistency for LLM Reasoning
Venue: Conference NeurIPS 2025
Year: 2025

Test-time scaling seeks to improve the reasoning performance of large language models (LLMs) by adding computational resources. A prevalent approach within the field is sampling-based test-time scaling methods, which enhance reasoning by generating multiple reasoning paths for a given input during inference. However, despite its practical success, the theoretical foundations remain underexplored. In this paper, we provide the first theoretical framework for analyzing sampling-based test-time scaling methods, grounded in the perspective of confidence estimation. Based on the framework, we analyze two dominant paradigms: self-consistency and perplexity, and reveal key limitations: self-consistency suffers from high estimation error while perplexity exhibits substantial modeling error and possible degradation of the estimation error convergence. To address these limitations, we introduce RPC, a hybrid method that leverages our theoretical insights through two key components: Perplexity Consistency and Reasoning Pruning. Perplexity Consistency combines the strengths of self-consistency and perplexity, boosting the convergence rate of estimation error from linear to exponential while preserving model error. Reasoning Pruning prevents degradation by eliminating low-probability reasoning paths. Both theoretical analysis and empirical results across seven benchmark datasets demonstrate that RPC has a strong potential for reducing reasoning error. Notably, RPC achieves reasoning performance comparable to self-consistency while not only enhancing confidence reliability but also reducing sampling costs by 50%. The code and resources are available at https://wnjxyk.github.io/RPC.
Constructing an Optimal Behavior Basis for the Option Keyboard
Venue: Conference NeurIPS 2025
Year: 2025

Multi-task reinforcement learning aims to quickly identify solutions for new tasks with minimal or no additional interaction with the environment. Generalized Policy Improvement (GPI) addresses this by combining a set of base policies to produce a new one that is at least as good -- though not necessarily optimal -- as any individual base policy. Optimality can be ensured, particularly in the linear-reward case, via techniques that compute a Convex Coverage Set (CCS). However, these are computationally expensive and do not scale to complex domains. The Option Keyboard (OK) improves upon GPI by producing policies that are at least as good -- and often better. It achieves this through a learned meta-policy that dynamically combines base policies. However, its performance critically depends on the choice of base policies. This raises a key question: is there an optimal set of base policies -- an optimal behavior basis -- that enables zero-shot identification of optimal solutions for any linear tasks? We solve this open problem by introducing a novel method that efficiently constructs such an optimal behavior basis. We show that it significantly reduces the number of base policies needed to ensure optimality in new tasks. We also prove that it is strictly more expressive than a CCS, enabling particular classes of non-linear tasks to be solved optimally. We empirically evaluate our technique in challenging domains and show that it outperforms state-of-the-art approaches, increasingly so as task complexity increases.
Riemannian Flow Matching for Brain Connectivity Matrices via Pullback Geometry
Venue: Conference NeurIPS 2025
Year: 2025

Generating realistic brain connectivity matrices is key to analyzing population heterogeneity in brain organization, understanding disease, and augmenting data in challenging classification problems. Functional connectivity matrices lie in constrained spaces, such as the set of symmetric positive definite or correlation matrices, that can be modeled as Riemannian manifolds. However, using Riemannian tools typically requires redefining core operations (geodesics, norms, integration), making generative modeling computationally inefficient. In this work, we propose DiffeoCFM, an approach that enables conditional flow matching (CFM) on matrix manifolds by exploiting pullback metrics induced by global diffeomorphisms on Euclidean spaces. We show that Riemannian CFM with such metrics is equivalent to applying standard CFM after data transformation. This equivalence allows efficient vector field learning, and fast sampling with standard ODE solvers. We instantiate DiffeoCFM with two different settings: the matrix logarithm for covariance matrices and the normalized Cholesky decomposition for correlation matrices. We evaluate DiffeoCFM on three large-scale fMRI datasets with more than 4600 scans from 2800 subjects (ADNI, ABIDE, OASIS-3) and two EEG motor imagery datasets with over 30000 trials from 26 subjects (BNCI2014-002 and BNCI2015-001). It enables fast training and achieves state-of-the-art performance, all while preserving manifold constraints. Code: https://github.com/antoinecollas/DiffeoCFM
HoPE: Hybrid of Position Embedding for Long Context Vision-Language Models
Venue: Conference NeurIPS 2025
Year: 2025

Vision-Language Models (VLMs) have made significant progress in multimodal tasks. However, their performance often deteriorates in long-context scenarios, particularly long videos. While Rotary Position Embedding (RoPE) has been widely adopted for length generalization in Large Language Models (LLMs), extending vanilla RoPE to capture the intricate spatial-temporal dependencies in videos remains an unsolved challenge. Existing methods typically allocate different frequencies within RoPE to encode 3D positional information. However, these allocation strategies mainly rely on heuristics, lacking in-depth theoretical analysis. In this paper, we first study how different allocation strategies impact the long-context capabilities of VLMs. Our analysis reveals that current multimodal RoPEs fail to reliably capture semantic similarities over extended contexts. To address this issue, we propose HoPE, a Hybrid of Position Embedding designed to improve the long-context capabilities of VLMs. HoPE introduces a hybrid frequency allocation strategy for reliable semantic modeling over arbitrarily long contexts, and a dynamic temporal scaling mechanism to facilitate robust learning and flexible inference across diverse context lengths. Extensive experiments across four video benchmarks on long video understanding and retrieval tasks demonstrate that HoPE consistently outperforms existing methods, confirming its effectiveness. Our code is available at https://github.com/hrlics/HoPE.
GUI-Rise: Structured Reasoning and History Summarization for GUI Navigation
Venue: Conference NeurIPS 2025
Year: 2025

While Multimodal Large Language Models (MLLMs) have advanced GUI navigation agents, current approaches face limitations in cross-domain generalization and effective history utilization. We present a reasoning-enhanced framework that systematically integrates structured reasoning, action prediction, and history summarization. The structured reasoning component generates coherent Chain-of-Thought analyses combining progress estimation and decision reasoning, which inform both immediate action predictions and compact history summaries for future steps. Based on this framework, we train a GUI agent, \textbf{GUI-Rise}, through supervised fine-tuning on pseudo-labeled trajectories and reinforcement learning with Group Relative Policy Optimization (GRPO). This framework employs specialized rewards, including a history-aware objective, directly linking summary quality to subsequent action performance. Comprehensive evaluations on standard benchmarks demonstrate state-of-the-art results under identical training data conditions, with particularly strong performance in out-of-domain scenarios. These findings validate our framework's ability to maintain robust reasoning and generalization across diverse GUI navigation tasks. Code is available at https://leon022.github.io/GUI-Rise.
FALCON: Fine-grained Activation Manipulation by Contrastive Orthogonal Unalignment for Large Language Model
Venue: Conference NeurIPS 2025
Year: 2025

Large language models have been widely applied, but can inadvertently encode sensitive or harmful information, raising significant safety concerns. Machine unlearning has emerged to alleviate this concern; however, existing training-time unlearning approaches, relying on coarse-grained loss combinations, have limitations in precisely separating knowledge and balancing removal effectiveness with model utility. In contrast, we propose Fine-grained Activation manipuLation by Contrastive Orthogonal uNalignment (FALCON), a novel representation-guided unlearning approach that leverages information-theoretic guidance for efficient parameter selection, employs contrastive mechanisms to enhance representation separation, and projects conflict gradients onto orthogonal subspaces to resolve conflicts between forgetting and retention objectives. Extensive experiments demonstrate that FALCON achieves superior unlearning effectiveness while maintaining model utility, exhibiting robust resistance against knowledge recovery attempts.
ADG: Ambient Diffusion-Guided Dataset Recovery for Corruption-Robust Offline Reinforcement Learning
Venue: Conference NeurIPS 2025
Year: 2025

Real-world datasets collected from sensors or human inputs are prone to noise and errors, posing significant challenges for applying offline reinforcement learning (RL). While existing methods have made progress in addressing corrupted actions and rewards, they remain insufficient for handling corruption in high-dimensional state spaces and for cases where multiple elements in the dataset are corrupted simultaneously. Diffusion models, known for their strong denoising capabilities, offer a promising direction for this problem-but their tendency to overfit noisy samples limits their direct applicability. To overcome this, we propose Ambient Diffusion-Guided Dataset Recovery (ADG), a novel approach that pioneers the use of diffusion models to tackle data corruption in offline RL. First, we introduce Ambient Denoising Diffusion Probabilistic Models (DDPM) from approximated distributions, which enable learning on partially corrupted datasets with theoretical guarantees. Second, we use the noise-prediction property of Ambient DDPM to distinguish between clean and corrupted data, and then use the clean subset to train a standard DDPM. Third, we employ the trained standard DDPM to refine the previously identified corrupted data, enhancing data quality for subsequent offline RL training. A notable strength of ADG is its versatility-it can be seamlessly integrated with any offline RL algorithm. Experiments on a range of benchmarks, including MuJoCo, Kitchen, and Adroit, demonstrate that ADG effectively mitigates the impact of corrupted data and improves the robustness of offline RL under various noise settings, achieving state-of-the-art results.
Watermarking Autoregressive Image Generation
Venue: Conference NeurIPS 2025
Year: 2025

Watermarking the outputs of generative models has emerged as a promising approach for tracking their provenance. Despite significant interest in autoregressive image generation models and their potential for misuse, no prior work has attempted to watermark their outputs at the token level. In this work, we present the first such approach by adapting language model watermarking techniques to this setting. We identify a key challenge: the lack of reverse cycle-consistency (RCC), wherein re-tokenizing generated image tokens significantly alters the token sequence, effectively erasing the watermark. To address this and to make our method robust to common image transformations, neural compression, and removal attacks, we introduce (i) a custom tokenizer-detokenizer finetuning procedure that improves RCC, and (ii) a complementary watermark synchronization layer. As our experiments demonstrate, our approach enables reliable and robust watermark detection with theoretically grounded p-values. Code and models are available at https://github.com/facebookresearch/wmar.
CPPO: Accelerating the Training of Group Relative Policy Optimization-Based Reasoning Models
Venue: Conference NeurIPS 2025
Year: 2025

This paper introduces Completion Pruning Policy Optimization (CPPO) to accelerate the training of reasoning models based on Group Relative Policy Optimization (GRPO). GRPO, while effective, incurs high training costs due to the need to sample multiple completions for each question. Our experiment and theoretical analysis reveal that the number of completions impacts model accuracy yet increases training time multiplicatively, and not all completions contribute equally to policy training -- their contribution depends on their relative advantage. To address these issues, we propose CPPO, which prunes completions with low absolute advantages, significantly reducing the number needed for gradient calculation and updates. Additionally, we introduce a dynamic completion allocation strategy to maximize GPU utilization by incorporating additional questions, further enhancing training efficiency. Experiments show that CPPO achieves up to $7.98\times$ speedup on GSM8K and $3.48\times$ on Math while preserving or even enhancing the accuracy compared to the original GRPO. We release our code at \href{https://github.com/lzhxmu/CPPO}{https://github.com/lzhxmu/CPPO}.
Recursive Inference Scaling: A Winning Path to Scalable Inference in Language and Multimodal Systems
Venue: Conference NeurIPS 2025
Year: 2025

Inspired by recent findings on the fractal geometry of language, we introduce Recursive INference Scaling (RINS) as a complementary, plug-in recipe for scaling inference time in language and multimodal systems. RINS is a particular form of recursive depth that significantly outperforms +55 other variants, including the recent "repeat-all-over" (RAO) strategy in Mobile LLM (Liu et al., 2024) and latent recurrent thinking (Geiping et al., 2025). Unlike prior works, we carry out our comparisons on a compute-matched regime, and demonstrate that for a fixed model size and training compute budget, RINS substantially improves language modeling performance. It also generalizes beyond pure language tasks, delivering gains in multimodal systems, including a +2% improvement in 0-shot ImageNet accuracy for SigLIP-B/16. Additionally, by deriving data scaling laws, we show that RINS improves both the asymptotic performance limits and the scaling exponents. More importantly, with light-weight (linear) adapters (comprising <1% of model parameters) and stochastic dropout, RINS offers a no-regret strategy, meaning that RINS-enabled pretraining improves performance in language modeling even when recursive depth is not applied at inference time. This corresponds to improving performance on a training compute-, parameter-, and inference-matched regime, suggesting its potential as a viable component of LLM pretraining!
Joint Velocity-Growth Flow Matching for Single-Cell Dynamics Modeling
Venue: Conference NeurIPS 2025
Year: 2025

Learning the underlying dynamics of single cells from snapshot data has gained increasing attention in scientific and machine learning research. The destructive measurement technique and cell proliferation/death result in unpaired and unbalanced data between snapshots, making the learning of the underlying dynamics challenging. In this paper, we propose joint Velocity-Growth Flow Matching (VGFM), a novel paradigm that jointly learns state transition and mass growth of single-cell populations via flow matching. VGFM builds an ideal single-cell dynamics containing velocity of state and growth of mass, driven by a presented two-period dynamic understanding of the static semi-relaxed optimal transport, a mathematical tool that seeks the coupling between unpaired and unbalanced data. To enable practical usage, we approximate the ideal dynamics using neural networks, forming our joint velocity and growth matching framework. A distribution fitting loss is also employed in VGFM to further improve the fitting performance for snapshot data. Extensive experimental results on both synthetic and real datasets demonstrate that VGFM can capture the underlying biological dynamics accounting for mass and state variations over time, outperforming existing approaches for single-cell dynamics modeling.
Rethinking Optimal Verification Granularity for Compute-Efficient Test-Time Scaling
Venue: Conference NeurIPS 2025
Year: 2025

Test-time scaling (TTS) has proven effective in enhancing the reasoning capabilities of large language models (LLMs). Verification plays a key role in TTS, simultaneously influencing (1) reasoning performance and (2) compute efficiency, due to the quality and computational cost of verification. In this work, we challenge the conventional paradigms of verification, and make the first attempt toward systematically investigating the impact of verification granularity-that is, how frequently the verifier is invoked during generation, beyond verifying only the final output or individual generation steps. To this end, we introduce Variable Granularity Search (VG-Search), a unified algorithm that generalizes beam search and Best-of-N sampling via a tunable granularity parameter g. Extensive experiments with VG-Search under varying compute budgets, generator-verifier configurations, and task attributes reveal that dynamically selecting g can improve the compute efficiency and scaling behavior. Building on these findings, we propose adaptive VG-Search strategies that achieve accuracy gains of up to 3.1\% over Beam Search and 3.6\% over Best-of-N, while reducing FLOPs by over 52\%. We will open-source the code to support future research.