NeurIPS 2025 Papers

Recent advances in 3D Gaussian Splatting (3DGS) have improved the visual fidelity of dynamic avatar reconstruction. However, existing methods often overlook the inherent chromatic similarity of human skin tones, leading to poor capture of intricate facial geometry under subtle appearance changes. This is caused by the affine approximation of Gaussian projection, which fails to be perspective-aware to depth-induced shear effects. To this end, we propose True-to-Geometry Avatar Dynamic Reconstruction (TGA), a perspective-aware 4D Gaussian avatar framework that sensitively captures fine-grained facial variations for accurate 3D geometry reconstruction. Specifically, to enable color-sensitive and geometry-consistent Gaussian representations under dynamic conditions, we introduce Perspective-Aware Gaussian Transformation that jointly models temporal deformations and spatial projection by integrating Jacobian-guided adaptive deformation into the homogeneous formulation. Furthermore, we develop Incremental BVH Tree Pivoting to enable fast frame-by-frame mesh extraction for 4D Gaussian representations. A dynamic Gaussian Bounding Volume Hierarchy (BVH) tree is used to model the topological relationships among points, where active ones are filtered out by BVH pivoting and subsequently re-triangulated for surface reconstruction. Extensive experiments demonstrate that TGA achieves superior geometric accuracy.

Reconstructing accurate surfaces with radiance fields has achieved remarkable progress in recent years. However, prevailing approaches, primarily based on Gaussian Splatting, are increasingly constrained by representational bottlenecks. In this paper, we introduce GeoSVR, an explicit voxel-based framework that explores and extends the under-investigated potential of sparse voxels for achieving accurate, detailed, and complete surface reconstruction. As strengths, sparse voxels support preserving the coverage completeness and geometric clarity, while corresponding challenges also arise from absent scene constraints and locality in surface refinement. To ensure correct scene convergence, we first propose a Voxel-Uncertainty Depth Constraint that maximizes the effect of monocular depth cues while presenting a voxel-oriented uncertainty to avoid quality degradation, enabling effective and robust scene constraints yet preserving highly accurate geometries. Subsequently, Sparse Voxel Surface Regularization is designed to enhance geometric consistency for tiny voxels and facilitate the voxel-based formation of sharp and accurate surfaces. Extensive experiments demonstrate our superior performance compared to existing methods across diverse challenging scenarios, excelling in geometric accuracy, detail preservation, and reconstruction completeness while maintaining high efficiency. Code is available at https://github.com/Fictionarry/GeoSVR.

Oligonucleotide therapeutics offer great potential to address previously undruggable targets and enable personalized medicine. However, their progress is often hindered by insufficient safety and efficacy profiles. Predictive modeling and machine learning could significantly accelerate oligonucleotide drug discovery by identifying suboptimal compounds early on, but their application in this area lags behind other modalities. A key obstacle to the adoption of machine learning in the field is the scarcity of readily accessible and standardized datasets for model development, as data are often scattered across diverse experiments with inconsistent molecular representations. To overcome this challenge, we introduce OligoGym, a curated collection of standardized, machine learning-ready datasets encompassing various oligonucleotide therapeutic modalities and endpoints. We used OligoGym to benchmark diverse classical and deep learning methods, establishing performance baselines for each dataset across different featurization techniques, model configurations, and splitting strategies. Our work represents a crucial first step in creating a more unified framework for oligonucleotide therapeutic dataset generation and model training.

Recent advances in generative models have achieved high-fidelity in 3D human reconstruction, yet their utility for specific tasks (e.g., human 3D segmentation) remains constrained. We propose HumanCrafter, a unified framework that enables the joint modeling of appearance and human-part semantics from a single image in a feed-forward manner. Specifically, we integrate human geometric priors in the reconstruction stage and self-supervised semantic priors in the segmentation stage. To address labeled 3D human datasets scarcity, we further develop an interactive annotation procedure for generating high-quality data-label pairs. Our pixel-aligned aggregation enables cross-task synergy, while the multi-task objective simultaneously optimizes texture modeling fidelity and semantic consistency. Extensive experiments demonstrate that HumanCrafter surpasses existing state-of-the-art methods in both 3D human-part segmentation and 3D human reconstruction **from a single image**.

Diffusion models have advanced rapidly in recent years, producing high-fidelity images while raising concerns about intellectual property protection and the misuse of generative AI. Image watermarking for diffusion models, particularly Noise-as-Watermark (NaW) methods, encode watermark as specific standard Gaussian noise vector for image generation, embedding the infomation seamlessly while maintaining image quality. For detection, the generation process is inverted to recover the initial noise vector containing the watermark before extraction. However, existing NaW methods struggle to balance watermark robustness with generation diversity. Some methods achieve strong robustness by heavily constraining initial noise sampling, which degrades user experience, while others preserve diversity but prove too fragile for real-world deployment. To address this issue, we propose T2SMark, a two-stage watermarking scheme based on Tail-Truncated Sampling (TTS). Unlike prior methods that simply map bits to positive or negative values, TTS enhances robustness by embedding bits exclusively in the reliable tail regions while randomly sampling the central zone to preserve the latent distribution. Our two-stage framework then ensures sampling diversity by integrating a randomly generated session key into both encryption pipelines. We evaluate T2SMark on diffusion models with both U-Net and DiT backbones. Extensive experiments show that it achieves an optimal balance between robustness and diversity.

Recently, reasoning-based MLLMs have achieved a degree of success in generating long-form textual reasoning chains. However, they still struggle with complex tasks that necessitate dynamic and iterative focusing on and revisiting of visual regions to achieve precise grounding of textual reasoning in visual evidence. We introduce VLM-R³ (Visual Language Model with Region Recognition, Reasoning, and Refinement ), a framework that equips an MLLM with the ability to (i) decide when additional visual evidence is needed, (ii) determine where to ground within the image, and (iii) seamlessly weave the relevant sub-image content back into an interleaved chain-of-thought. The core of our method is \textbf{Region-Conditioned Reinforcement Policy Optimization (R-GRPO)}, a training paradigm that rewards the model for selecting informative regions, formulating appropriate transformations (e.g. crop, zoom), and integrating the resulting visual context into subsequent reasoning steps. To bootstrap this policy, we compile a modest but carefully curated Visuo-Lingual Interleaved Rationale (VLIR) corpus that provides step-level supervision on region selection and textual justification. Extensive experiments on MathVista, ScienceQA, and other benchmarks show that VLM-R$^3$ sets a new state of the art in zero-shot and few-shot settings, with the largest gains appearing on questions demanding subtle spatial reasoning or fine-grained visual cue extraction.

As large language models (LLMs) are increasingly deployed in real-world applications, ensuring the safety of their outputs during decoding has become a critical challenge. However, existing decoding-time interventions, such as Contrastive Decoding, often force a severe trade-off between safety and response quality. In this work, we propose **CARE**, a novel framework for decoding-time safety alignment that integrates three key components: (1) a guard model for real-time safety monitoring, enabling detection of potentially unsafe content; (2) a rollback mechanism with a token buffer to correct unsafe outputs efficiently at an earlier stage without disrupting the user experience; and (3) a novel introspection-based intervention strategy, where the model generates self-reflective critiques of its previous outputs and incorporates these reflections into the context to guide subsequent decoding steps. The framework achieves a superior safety-quality trade-off by using its guard model for precise interventions, its rollback mechanism for timely corrections, and our novel introspection method for effective self-correction. Experimental results demonstrate that our framework achieves a superior balance of safety, quality, and efficiency, attaining a **low harmful response rate** and **minimal disruption to the user experience** while **maintaining high response quality**.

We present PBR-SR, a novel method for physically based rendering (PBR) texture super resolution (SR). It outputs high-resolution, high-quality PBR textures from low-resolution (LR) PBR input in a zero-shot manner. PBR-SR leverages an off-the-shelf super-resolution model trained on natural images, and iteratively minimizes the deviations between super-resolution priors and differentiable renderings. These enhancements are then back-projected into the PBR map space in a differentiable manner to produce refined, high-resolution textures. To mitigate the effects of view inconsistency and lighting sensitivity inherent to view-based super-resolution, our approach incorporates 2D prior constraints across multi-view renderings, enabling iterative refinement of shared upscaled textures. In parallel, we incorporate identity constraints directly in the PBR texture domain to ensure the upscaled textures remain faithful to the LR input. PBR-SR operates without any additional training or data requirements, relying entirely on pretrained image priors. We demonstrate that our approach produces high-fidelity PBR textures for both artist-designed and AI-generated meshes, outperforming both direct SR models application and prior texture optimization methods. Our results show high-quality outputs in both PBR and rendering evaluations, supporting advanced applications such as relighting.

Retrieval-Augmented Generation (RAG) enhances Large Language Models by grounding their outputs in external documents. These systems, however, remain vulnerable to attacks on the retrieval corpus, such as prompt injection. RAG-based search systems (e.g., Google’s Search AI Overview) present an interesting setting for studying and protecting against such threats, as defense algorithms can benefit from built-in reliability signals—like document ranking—and represent a non-LLM challenge for the adversary due to decades of work to thwart SEO. Motivated by, but not limited to, this scenario, this work introduces ReliabilityRAG, a framework for adversarial robustness that explicitly leverages reliability information of retrieved documents. Our first contribution adopts a graph-theoretic perspective to identify a ``consistent majority'' among retrieved documents to filter out malicious ones. We introduce a novel algorithm based on finding a Maximum Independent Set (MIS) on a document graph where edges encode contradiction. Our MIS variant explicitly prioritizes higher-reliability documents and provides provable robustness guarantees against bounded adversarial corruption under natural assumptions. Recognizing the computational cost of exact MIS for large retrieval sets, our second contribution is a scalable weighted sample and aggregate framework. It explicitly utilizes reliability information, preserving some robustness guarantees while efficiently handling many documents. We present empirical results showing ReliabilityRAG provides superior robustness against adversarial attacks compared to prior methods, maintains high benign accuracy, and excels in long-form generation tasks where prior robustness-focused methods struggled. Our work is a significant step towards more effective, provably robust defenses against retrieved corpus corruption in RAG.

Visual navigation is essential for robotics and embodied AI. However, existing foundation models, particularly those with transformer decoders, suffer from high computational overhead and lack interpretability, limiting their deployment on edge devices. To address this, we propose DynaNav, a Dynamic Visual Navigation framework that adapts feature and layer selection based on scene complexity. It employs a trainable hard feature selector for sparse operations, enhancing efficiency and interpretability. Additionally, we integrate feature selection into an early-exit mechanism, with Bayesian Optimization determining optimal exit thresholds to reduce computational cost. Extensive experiments in real-world-based datasets and simulated environments demonstrate the effectiveness of DynaNav. Compared to ViNT, DynaNav achieves a $2.6\times$ reduction in FLOPs, 42.3% lower inference time, and 32.8% lower memory usage while improving navigation performance across four public datasets.

Stylizing 3D scenes instantly while maintaining multi-view consistency and faithfully resembling a style image remains a significant challenge. Current state-of-the-art 3D stylization methods typically involve computationally intensive test-time optimization to transfer artistic features into a pretrained 3D representation, often requiring dense posed input images. In contrast, leveraging recent advances in feed-forward reconstruction models, we demonstrate a novel approach to achieve direct 3D stylization in less than a second using unposed sparse-view scene images and an arbitrary style image. To address the inherent decoupling between reconstruction and stylization, we introduce a branched architecture that separates structure modeling and appearance shading, effectively preventing stylistic transfer from distorting the underlying 3D scene structure. Furthermore, we adapt an identity loss to facilitate pre-training our stylization model through the novel view synthesis task. This strategy also allows our model to retain its original reconstruction capabilities while being fine-tuned for stylization. Comprehensive evaluations, using both in-domain and out-of-domain datasets, demonstrate that our approach produces high-quality stylized 3D content that achieve a superior blend of style and scene appearance, while also outperforming existing methods in terms of multi-view consistency and efficiency.

Predicting changes in binding free energy ($\Delta\Delta G$) is essential for understanding protein-protein interactions, which are critical in drug design and protein engineering. However, existing methods often rely on pre-trained knowledge and heuristic features, limiting their ability to accurately model complex mutation effects, particularly higher-order and many-body interactions. To address these challenges, we propose H3-DDG, a Hypergraph-driven Hierarchical network to capture Higher-order many-body interactions across multiple scales. By introducing a hierarchical communication mechanism, H3-DDG effectively models both local and global mutational effects. Experimental results demonstrate state-of-the-art performance on multiple benchmarks. On the SKEMPI v2 dataset, H3-DDG achieves a Pearson correlation of 0.75, improving multi-point mutations prediction by 12.10%. On the challenging BindingGYM dataset, it outperforms Prompt-DDG and BA-DDG by 62.61% and 34.26%, respectively. Ablation and efficiency analyses demonstrate its robustness and scalability, while a case study on SARS-CoV-2 antibodies highlights its practical value in improving binding affinity for therapeutic design.

Cryo-EM is a transformational paradigm in molecular biology where computational methods are used to infer 3D molecular structure at atomic resolution from extremely noisy 2D electron microscope images. At the forefront of research is how to model the structure when the imaged particles exhibit non-rigid conformational flexibility and compositional variation where parts are sometimes missing. We introduce a novel 3D reconstruction framework with a hierarchical Gaussian mixture model, inspired in part by Gaussian Splatting for 4D scene reconstruction. In particular, the structure of the model is grounded in an initial process that infers a part-based segmentation of the particle, providing essential inductive bias in order to handle both conformational and compositional variability. The framework, called \methodName, is shown to reveal biologically meaningful structures on complex experimental datasets, and establishes a new state-of-the-art on CryoBench, a benchmark for cryo-EM heterogeneity methods.

Monitoring individual tree mortality at scale has been found to be crucial for understanding forest loss, ecosystem resilience, carbon fluxes, and climate-induced impacts. However, the fine-granularity monitoring faces major challenges on both the data and methodology sides because: (1) finding isolated individual-level tree deaths requires high-resolution remote sensing images with broad coverage, and (2) compared to regular geo-objects (e.g., buildings), dead trees often exhibit weaker contrast and high variability across tree types, landscapes and ecosystems. Existing datasets on tree mortality primarily rely on moderate-resolution satellite imagery (e.g., 30m resolution), which aims to detect large-patch wipe-outs but is unable to recognize individual-level tree mortality events. Several efforts have explored alternatives via very-high-resolution drone imagery. However, drone images are highly expensive and can only be collected at local scales, which are therefore not suitable for national-scale applications and beyond. To bridge the gaps, we introduce TreeFinder, the first high-resolution remote sensing benchmark dataset designed for individual-level tree mortality mapping across the Contiguous United States (CONUS). Specifically, the dataset uses NAIP imagery at 0.6m resolution that provides wall-to-wall coverage of the entire CONUS. TreeFinder contains images with pixel-level labels generated via extensive manual annotation that covers forested areas in 48 states with over 23,000 hectares. All annotations are rigorously validated using multi-temporal NAIP images and auxiliary vegetation indices from remote sensing imagery. Moreover, TreeFinder includes multiple evaluation scenarios to test the models' ability in generalizing across different geographic regions, climate zones, and forests with different plant function types. Finally, we develop benchmarks using a suite of semantic segmentation models, including both convolutional architectures and more recent foundation models based on vision transformers for general and remote sensing images. Our dataset and code are publicly available on Kaggle and GitHub: https://www.kaggle.com/datasets/zhihaow/tree-finder and https://github.com/zhwang0/treefinder.

The integration of big data, physical laws, and machine learning algorithms has shown potential to improve the estimation and understanding of complex real-world systems. However, effectively incorporating physical laws with uncertainties into machine learning algorithms remains understudied. In this work, we bridge this gap by developing the Partial Physics Informed Diffusion Model (PPIDM), a novel framework that integrates known physical principles through a physics operator while reducing the impact of unknown dynamics by minimizing related discrepancies. We showcase PPIDM’s capabilities using ocean surface chlorophyll concentration data, which are influenced by both physical and biological processes, while the latter is poorly constrained. Experimental results reveal that PPIDM achieves substantially improved prediction accuracy and stability, significantly outperforming baseline methods that either neglect physics entirely or impose incomplete physical constraints under the assumption of completeness.

Biomedical research data portals are essential resources for scientific inquiry, and interactive exploratory visualizations are an integral component for querying such data repositories. Increasingly, machine learning is being integrated into visualization systems to create natural language interfaces where questions about data can be answered with visualizations, and follow-up questions can build on the previous state. This paper introduces a framework that takes abstract low-level questions about data and a visualization grammar specification that can answer such a question, reifies them with data entities and fields that meet certain constraints, and paraphrases the question language to produce the final collection of realized data-question-visualization triplets. Furthermore, we can link these foundational elements together to construct chains of queries, visualizations, and follow-up queries. We developed an open-source review interface for evaluating the results of these datasets. We applied this framework to five biomedical research data repositories, resulting in DQVis, a dataset of 1.08 million data-question-visualization triplets and 11.4 thousand two-step question samples. Five visualization experts provided feedback on the generated dataset through our review interface. We present a summary of their input and publish the full reviews as an additional resource alongside the dataset. The DQVis dataset and generation code are available at https://huggingface.co/datasets/HIDIVE/DQVis and https://github.com/hms-dbmi/DQVis-Generation.

Spectral decomposition of linear operators plays a central role in many areas of machine learning and scientific computing. Recent work has explored training neural networks to approximate eigenfunctions of such operators, enabling scalable approaches to representation learning, dynamical systems, and partial differential equations (PDEs). In this paper, we revisit a classical optimization framework from the computational physics literature known as the *orbital minimization method* (OMM), originally proposed in the 1990s for solving eigenvalue problems in computational chemistry. We provide a simple linear-algebraic proof of the consistency of the OMM objective, and reveal connections between this method and several ideas that have appeared independently across different domains. Our primary goal is to justify its broader applicability in modern learning pipelines. We adapt this framework to train neural networks to decompose positive semidefinite operators, and demonstrate its practical advantages across a range of benchmark tasks. Our results highlight how revisiting classical numerical methods through the lens of modern theory and computation can provide not only a principled approach for deploying neural networks in numerical simulation, but also effective and scalable tools for machine learning.

Physics-Informed Neural Networks (PINNs) have emerged as a powerful frame- work for solving partial differential equations (PDEs). However, standard MLP- based PINNs often fail to converge when dealing with complex initial value problems, leading to solutions that violate causality and suffer from a spectral bias towards low-frequency components. To address these issues, we introduce NeuSA (Neuro-Spectral Architectures), a novel class of PINNs inspired by classi- cal spectral methods, designed to solve linear and nonlinear PDEs with variable coefficients. NeuSA learns a projection of the underlying PDE onto a spectral basis, leading to a finite-dimensional representation of the dynamics which is then integrated with an adapted Neural ODE (NODE). This allows us to overcome spectral bias, by leveraging the high-frequency components enabled by the spectral representation; to enforce causality, by inheriting the causal structure of NODEs, and to start training near the target solution, by means of an initialization scheme based on classical methods. We validate NeuSA on canonical benchmarks for lin- ear and nonlinear wave equations, demonstrating strong performance as compared to other architectures, with faster convergence, improved temporal consistency and superior predictive accuracy. Code and pretrained models are available in https://github.com/arthur-bizzi/neusa.

Large language models (LLMs) and vision-language models (LVLMs) have driven the paradigm shift towards general-purpose foundation models. However, both of them are prone to hallucinations, which compromise their factual accuracy and reliability. While existing research primarily focuses on isolated textual- or visual-centric errors, a critical yet underexplored phenomenon persists in LVLMs: Even neither of textual- or visual centric errors occur, LVLMs often struggle with a new and subtle hallucination mode that arising from composition of them. In this paper, we define this issue as Simple Compositional Hallucination (SCHall). Through an preliminary analysis, we present two key findings: (1) visual abstraction fails under compositional questioning, and (2) visual inputs induce degradation in language processing, leading to hallucinations. To facilitate future research on this phenomenon, we introduce a custom benchmark, SCBench, and propose a novel VLR-distillation method, which serves as the first baseline to effectively mitigate SCHall. Furthermore, experiment results on publicly available benchmarks, including both hallucination-specific and general-purpose ones, demonstrate the effectiveness of our VLR-distillation method.