NeurIPS 2025 Papers

Neural fields have emerged as a powerful representation for 3D geometry, enabling compact and continuous modeling of complex shapes. Despite their expressive power, manipulating neural fields in a controlled and accurate manner -- particularly under spatial constraints -- remains an open challenge, as existing approaches struggle to balance surface quality, robustness, and efficiency. We address this by introducing a novel method for handle-guided neural field deformation, which leverages discrete local surface representations to optimize the As-Rigid-As-Possible deformation energy. To this end, we propose the local patch mesh representation, which discretizes level sets of a neural signed distance field by projecting and deforming flat mesh patches guided solely by the SDF and its gradient. We conduct a comprehensive evaluation showing that our method consistently outperforms baselines in deformation quality, robustness, and computational efficiency. We also present experiments that motivate our choice of discretization over marching cubes. By bridging classical geometry processing and neural representations through local patch meshing, our work enables scalable, high-quality deformation of neural fields and paves the way for extending other geometric tasks to neural domains.

How precisely does circuit wiring specify function? This fundamental question is particularly relevant for modern neuroscience, as large-scale electron microscopy now enables the reconstruction of neural circuits at single-synapse resolution across many organisms. To interpret circuit function from such datasets, we must understand the extent to which [measured] structure constrains dynamics. We investigate this question in the drosophila head direction (HD) circuit, which maintains an internal heading estimate through attractor dynamics that integrate self-motion velocity cues. This circuit serves as a sensitive assay for functional specification: continuous attractor networks are theoretically known to require finely tuned wiring, whereas connectomes reveal that biological wiring can be variable and omit key cellular parameters such as synaptic gains, neuronal thresholds, and time constants. We introduce a method that combines self-supervised and unsupervised learning objectives to estimate unknown parameters at the level of cell types, rather than individual neurons and synapses. Given the raw connectivity matrix, our approach recovers a network that robustly exhibits continuous attractor dynamics and accurately integrates a range of velocity inputs, despite minimal parameter tuning on a connectome which notably departs from the symmetric regularity of an idealized ring attractor. We characterize how deviations from the original connectome shape the space of viable solutions. We also perform in-silico ablation experiments to probe the distinct functional roles of specific cell types in the circuit, demonstrating how connectome-derived structure, when augmented with minimal, biologically grounded tuning, can replicate known physiology and elucidate circuit function.

While sparse coding plays an important role in promoting the efficiency of biological neural systems, it has not been fully utilized by artificial models as the activation sparsity is not well suited to the current structure of deep networks. Spiking Neural Networks (SNNs), with their event-driven characteristics, offer a more natural platform for leveraging activation sparsity. In this work, we specifically target the reduction of neuronal activity, which directly leads to lower computational cost and facilitates efficient SNN deployment on Neuromorphic hardware. We begin by analyzing the limitations of existing activity regularization methods and identifying critical challenges in training sparse SNNs. To address these issues, we propose a modified neuron model, AT-LIF, coupled with a threshold adaptation technique that stabilizes training and effectively suppresses spike activity. Through extensive experiments on multiple datasets, we demonstrate that our approach achieves significant reductions in average firing rates and synaptic operations without sacrificing much accuracy. Furthermore, we show that our method complements weight-based pruning techniques and successfully trains an SNN with only 0.06 average firing rate and 2.22M parameters on ImageNet, highlighting its potential for building highly efficient and scalable SNN models. Code is available at https://github.com/putshua/Activity-Pruning-SNN.

The explosive growth in sequence length has intensified the demand for effective and efficient long sequence modeling. Benefiting from intrinsic oscillatory membrane dynamics, Resonate-and-Fire (RF) neurons can efficiently extract frequency components from input signals and encode them into spatiotemporal spike trains, making them well-suited for long sequence modeling. However, RF neurons exhibit limited effective memory capacity and a trade-off between energy efficiency and training speed on complex temporal tasks. Inspired by the dendritic structure of biological neurons, we propose a Dendritic Resonate-and-Fire (D-RF) model, which explicitly incorporates a multi-dendritic and soma architecture. Each dendritic branch encodes specific frequency bands by utilizing the intrinsic oscillatory dynamics of RF neurons, thereby collectively achieving comprehensive frequency representation. Furthermore, we introduce an adaptive threshold mechanism into the soma structure. his mechanism adjusts the firing threshold according to historical spiking activity, thereby reducing redundant spikes while maintaining training efficiency in long-sequence tasks. Extensive experiments demonstrate that our method maintains competitive accuracy while substantially ensuring sparse spikes without compromising computational efficiency during training. These results underscore its potential as an effective and efficient solution for long sequence modeling on edge platforms.

Brain atlases are essential for reducing the dimensionality of neuroimaging data and enabling interpretable analysis. However, most existing atlases are predefined, group-level templates with limited flexibility and resolution. We present Deep Cluster Atlas (DCA), a graph-guided deep embedding clustering framework for generating individualized, voxel-wise brain parcellations. DCA combines a pretrained autoencoder with spatially regularized deep clustering to produce functionally coherent and spatially contiguous regions. Our method supports flexible control over resolution and anatomical scope, and generalizes to arbitrary brain structures. We further introduce a standardized benchmarking platform for atlas evaluation, using multiple large-scale fMRI datasets. Across multiple datasets and scales, DCA outperforms state-of-the-art atlases, improving functional homogeneity by 98.8% and silhouette coefficient by 29%, and achieves superior performance in downstream tasks such as autism diagnosis and cognitive decoding. We also observe that a fine-tuned pretrained model achieves superior results on the corresponding task. Codes and models are available at https://github.com/ncclab-sustech/DCA.

Learning a compact representation of history is critical for planning and generalization in partially observable environments. While meta-reinforcement learning (RL) agents can attain near Bayes-optimal policies, they often fail to learn the compact, interpretable Bayes-optimal belief states. This representational inefficiency potentially limits the agent's adaptability and generalization capacity. Inspired by predictive coding in neuroscience---which suggests that the brain predicts sensory inputs as a neural implementation of Bayesian inference---and by auxiliary predictive objectives in deep RL, we investigate whether integrating self-supervised predictive coding modules into meta-RL can facilitate learning of Bayes-optimal representations. Through state machine simulation, we show that meta-RL with predictive modules consistently generates more interpretable representations that better approximate Bayes-optimal belief states compared to conventional meta-RL across a wide variety of tasks, even when both achieve optimal policies. In challenging tasks requiring active information seeking, only meta-RL with predictive modules successfully learns optimal representations and policies, whereas conventional meta-RL struggles with inadequate representation learning. Finally, we demonstrate that better representation learning leads to improved generalization. Our results strongly suggest the role of predictive learning as a guiding principle for effective representation learning in agents navigating partial observability.

Many modeling tasks from disparate domains can be framed the same way, computing spherical signals from geometric inputs, for example, computing the radar response of different objects or navigating through an environment. This paper introduces G2Sphere, a general method for mapping object geometries to spherical signals. G2Sphere operates entirely in Fourier space, encoding geometric structure into latent Fourier features using equivariant neural networks and outputting the Fourier coefficients of the continuous target signal, which can be evaluated at any resolution. By utilizing a hybrid GNN-spherical CNN architecture, our method achieves much higher frequency output signal than comparable equivariant GNNs and avoids hand-engineered geometry features used previously by purely spherical methods. We perform experiments on various challenging domains including radar response modeling, aerodynamic drag prediction, and policy learning for manipulation and navigation. We find that G2Sphere outperforms competitive baselines in terms of accuracy and inference time, and we demonstrate that equivariance and Fourier features lead to improved sample efficiency and generalization.The source code is available at: https://github.com/ColinKohler/geometry2sphere.

Functional brain network (FBN) modeling often relies on local pairwise interactions, whose limitation in capturing high-order dependencies is theoretically analyzed in this paper. Meanwhile, the computational burden and heuristic nature of current hypergraph modeling approaches hinder end-to-end learning of FBN structures directly from data distributions. To address this, we propose to extract high-order FBN structures under global constraints, and implement this as a Global Constraints oriented Multi-resolution (GCM) FBN structure learning framework. It incorporates 4 types of global constraint (signal synchronization, subject identity, expected edge numbers, and data labels) to enable learning FBN structures for 4 distinct levels (sample/subject/group/project) of modeling resolution. Experimental results demonstrate that GCM achieves up to a 30.6% improvement in relative accuracy and a 96.3% reduction in computational time across 5 datasets and 2 task settings, compared to 9 baselines and 10 state-of-the-art methods. Extensive experiments validate the contributions of individual components and highlight the interpretability of GCM. This work offers a novel perspective on FBN structure learning and provides a foundation for interdisciplinary applications in cognitive neuroscience. Code is publicly available on https://github.com/lzhan94swu/GCM.

Resolution of complex SQL issues persists as a significant bottleneck in real-world database applications. Current Large Language Models (LLMs), while adept at text-to-SQL translation, have not been rigorously evaluated on the more challenging task of debugging on SQL issues. In order to address this gap, we introduce **BIRD-CRITIC**, a new SQL issue debugging benchmark comprising 530 carefully curated PostgreSQL tasks (**BIRD-CRITIC-PG**) and 570 multi-dialect tasks (**BIRD-CRITIC-Multi**), which are distilled from authentic user issues and replayed within new environments to facilitate rigorous and contamination-free evaluation. Baseline evaluations on BIRD-CRITIC underscore the task's complexity, with the leading reasoning model **O3-Mini** achieving only 38.87% success rate on **BIRD-CRITIC-PG** and 33.33% on **BIRD-CRITIC-Multi**. Meanwhile, realizing open-source models for database tasks is crucial which can empower local development while safeguarding data privacy. Therefore, we present **Six-Gym** (**S**ql-f**IX**-Gym), a training environment for elevating the capabilities of open-source models specifically for SQL issue debugging. This environment leverages **SQL-Rewind** strategy, which automatically generates executable issue-solution datasets by reverse-engineering issues from verified SQLs. However, popular trajectory-based fine-tuning methods do not explore substantial supervisory signals. We further propose *f*-Plan Boosting, which extracts high-level debugging plans automatically from SQL solutions, enabling the teacher LLMs to harvest and produce 73.7% more successful trajectories for training. We integrate these components into an open-source agent, **BIRD-Fixer**. Based on Qwen-2.5-Coder-14B, **BIRD-Fixer** raises its success rate to 38.11% on **BIRD-CRITIC-PG** and 29.65% on **BIRD-CRITIC-Multi**, surpassing many leading proprietary models such as Claude-3.7-Sonnet and GPT-4.1, marking a significant step toward democratizing sophisticated SQL-debugging capabilities for both research and industry.

We propose a novel two-stage framework, Coarse-to-Fine Part Assembly (CFPA), for 3D shape assembly from basic parts. Effective part assembly demands precise local geometric reasoning for accurate component assembly, as well as global structural understanding to ensure semantic coherence and plausible configurations. CFPA addresses this challenge by integrating semantic abstraction and symmetry-aware reasoning into a unified pose prediction process. In the first stage, semantic super-parts are constructed via an optimal transport formulation to capture high-level object structure, which is then propagated to individual parts through a dual-range feature propagation mechanism. The second stage refines part poses via cross-stage feature interaction and instance-level geometric encoding, improving spatial precision and coherence. To enable diverse yet valid assemblies, we introduce a symmetry-aware loss that jointly models both self-symmetry and inter-part geometric similarity, allowing for diverse but structurally consistent assemblies. Extensive experiments on the PartNet benchmark demonstrate that CFPA achieves state-of-the-art performance in assembly accuracy, structural consistency, and diversity across multiple categories.

We present DyMU, an efficient, training-free framework that dynamically reduces the computational burden of vision-language models (VLMs) while maintaining high task performance. Our approach comprises two key components. First, Dynamic Token Merging (DToMe) reduces the number of visual token embeddings by merging similar tokens based on image complexity, addressing the inherent inefficiency of fixed-length outputs in vision transformers. Second, Virtual Token Unmerging (VTU) simulates the expected token sequence for large language models (LLMs) by efficiently reconstructing the attention dynamics of a full sequence, thus preserving the downstream performance without additional fine-tuning. Unlike previous approaches, our method dynamically determines token length based on the *image content*—not just resolution—and operates completely training-free, making it readily applicable to most state-of-the-art VLM architectures. Extensive experiments on image and video understanding tasks, demonstrate that DyMU can reduce the average visual token count by 32%-85% while achieving comparable performance to full-length models, across diverse VLM architectures. Furthermore, qualitative analyses show that the adaptive token reduction from DToMe aligns well with human perception and enables users to better control computational costs through flexible integration with additional vision tools and models.

Text-to-image (T2I) diffusion models exhibit impressive photorealistic image generation capabilities, yet they struggle in compositional image generation. In this work, we introduce RoleBench, a benchmark focused on evaluating compositional generalization in action-based relations (e.g., "mouse chasing cat"). We show that state-of-the-art T2I models and compositional generation methods consistently default to frequent reversed relations (i.e., "cat chasing mouse"), a phenomenon we call role collapse. Related works attribute this to the model’s architectural limitation or underrepresentation in the data. Our key insight reveals that while models fail on rare compositions when their inversions are common, they can successfully generate similar intermediate compositions (e.g., "mouse chasing boy"), suggesting that this limitation is also due to the presence of frequent counterparts rather than just the absence of rare compositions. Motivated by this, we hypothesize that directional decomposition can gradually mitigate role collapse. We test this via ReBind, a lightweight framework that teaches role bindings using carefully selected active/passive intermediate compositions. Experiments suggest that intermediate compositions through simple fine-tuning can significantly reduce role collapse, with humans preferring ReBind more than 78% compared to state-of-the-art methods. Our findings highlight the role of distributional asymmetries in compositional failures and offer a simple, effective path for improving generalization.

Neural population activity exhibits complex, nonlinear dynamics, varying in time, over trials, and across experimental conditions. Here, we develop *Conditionally Linear Dynamical System* (CLDS) models as a general-purpose method to characterize these dynamics. These models use Gaussian Process priors to capture the nonlinear dependence of circuit dynamics on task and behavioral variables. Conditioned on these covariates, the data is modeled with linear dynamics. This allows for transparent interpretation and tractable Bayesian inference. We find that CLDS models can perform well even in severely data-limited regimes (e.g. one trial per condition) due to their Bayesian formulation and ability to share statistical power across nearby task conditions. In example applications, we apply CLDS to model thalamic neurons that nonlinearly encode heading direction and to model motor cortical neurons during a cued-reaching task.

Task-specific pre-training is essential when task representations diverge from generic pre-training features. Existing task-general pre-training EEG models struggle with complex tasks like emotion recognition due to mismatches between task-specific features and broad pre-training approaches. This work aims to develop a task-specific multi-dataset joint pre-training framework for cross-dataset emotion recognition, tackling problems of large inter-dataset distribution shifts, inconsistent emotion category definitions, and substantial inter-subject variability. We introduce a cross-dataset covariance alignment loss to align second-order statistical properties across datasets, enabling robust generalization without the need for extensive labels or per-subject calibration. To capture the long-term dependency and complex dynamics of EEG, we propose a hybrid encoder combining a Mamba-like linear attention channel encoder and a spatiotemporal dynamics model. Our method outperforms state-of-the-art large-scale EEG models by an average of 4.57% in AUROC for few-shot emotion recognition and 11.92% in accuracy for zero-shot generalization to a new dataset. Performance scales with the increase of datasets used in pre-training. Multi-dataset joint pre-training achieves a performance gain of 8.55\% over single-dataset training. This work provides a scalable framework for task-specific pre-training and highlights its benefit in generalizable affective computing. Our code is available at https://github.com/ncclab-sustech/mdJPT_nips2025.

How should feedback influence recurrent neural network (RNN) learning? One way to address the known limitations of backpropagation through time is to directly adjust neural activities during the learning process. However, it remains unclear how to effectively use feedback to shape RNN dynamics. Here, we introduce error forcing (EF), where the network activity is guided orthogonally toward the zero-error manifold during learning. This method contrasts with alternatives like teaching forcing, which impose stronger constraints on neural activity and thus induce larger feedback influence on circuit dynamics. Furthermore, EF can be understood from a Bayesian perspective as a form of approximate dynamic inference. Empirically, EF consistently outperforms other learning algorithms across several tasks and its benefits persist when additional biological constraints are taken into account. Overall, EF is a powerful temporal credit assignment mechanism and a promising candidate model for learning in biological systems.

In coded aperture snapshot spectral imaging (CASSI), the captured measurement entangles spatial and spectral information, posing a severely ill-posed inverse problem for hyperspectral images (HSIs) reconstruction. Moreover, the captured radiance inherently depends on scene illumination, making it difficult to recover the intrinsic spectral reflectance that remains invariant to lighting conditions. To address these challenges, we propose a chromaticity-intensity decomposition framework, which disentangles an HSI into a spatially smooth intensity map and a spectrally variant chromaticity cube. The chromaticity encodes lighting-invariant reflectance, enriched with high-frequency spatial details and local spectral sparsity. Building on this decomposition, we develop CIDNet—a Chromaticity-Intensity Decomposition unfolding network within a dual-camera CASSI system. CIDNet integrates a hybrid spatial-spectral Transformer tailored to reconstruct fine-grained and sparse spectral chromaticity and a degradation-aware, spatially-adaptive noise estimation module that captures anisotropic noise across iterative stages. Extensive experiments on both synthetic and real-world CASSI datasets demonstrate that our method achieves superior performance in both spectral and chromaticity fidelity. Code is released at: \url{https://github.com/xiaodongwo/CIDNet}.

Analysing how neural networks represent data features in their activations can help interpret how they perform tasks. Hence, a long line of work has focused on mathematically characterising the geometry of such "neural representations." In parallel, machine learning has seen a surge of interest in understanding how dynamical systems perform computations on time-varying input data. Yet, the link between computation-through-dynamics and representational geometry remains poorly understood. Here, we hypothesise that recurrent neural networks (RNNs) perform computations by dynamically warping their representations of task variables. To test this hypothesis, we develop a Riemannian geometric framework that enables the derivation of the manifold topology and geometry of a dynamical system from the manifold of its inputs. By characterising the time-varying geometry of RNNs, we show that dynamic warping is a fundamental feature of their computations.

Indoor scene synthesis has become increasingly important with the rise of Embodied AI, which requires 3D environments that are not only visually realistic but also physically plausible and functionally diverse. While recent approaches have advanced visual fidelity, they often remain constrained to fixed scene categories, lack sufficient object-level detail and physical consistency, and struggle to align with complex user instructions. In this work, we present SceneWeaver, a reflective agentic framework that unifies diverse scene synthesis paradigms through tool-based iterative refinement. At its core, SceneWeaver employs a language model-based planner to select from a suite of extensible scene generation tools, ranging from data-driven generative models to visual- and LLM-based methods, guided by self-evaluation of physical plausibility, visual realism, and semantic alignment with user input. This closed-loop reason-act-reflect design enables the agent to identify semantic inconsistencies, invoke targeted tools, and update the environment over successive iterations. Extensive experiments on both common and open-vocabulary room types demonstrate that \model not only outperforms prior methods on physical, visual, and semantic metrics, but also generalizes effectively to complex scenes with diverse instructions, marking a step toward general-purpose 3D environment generation.

Existing infrared and visible image fusion methods often face the dilemma of balancing modal information. Generative fusion methods reconstruct fused images by learning from data distributions, but their generative capabilities remain limited. Moreover, the lack of interpretability in modal information selection further affects the reliability and consistency of fusion results in complex scenarios. This manuscript revisits the essence of generative image fusion under the inspiration of human cognitive laws and proposes a novel infrared and visible image fusion method, termed HCLFuse. First, HCLFuse investigates the quantification theory of information mapping in unsupervised fusion networks, which leads to the design of a multi-scale mask-regulated variational bottleneck encoder. This encoder applies posterior probability modeling and information decomposition to extract accurate and concise low-level modal information, thereby supporting the generation of high-fidelity structural details. Furthermore, the probabilistic generative capability of the diffusion model is integrated with physical laws, forming a time-varying physical guidance mechanism that adaptively regulates the generation process at different stages, thereby enhancing the ability of the model to perceive the intrinsic structure of data and reducing dependence on data quality. Experimental results show that the proposed method achieves state-of-the-art fusion performance in qualitative and quantitative evaluations across multiple datasets and significantly improves semantic segmentation metrics. This fully demonstrates the advantages of this generative image fusion method, drawing inspiration from human cognition, in enhancing structural consistency and detail quality.