NeurIPS 2025 Papers

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.

Multimodal representation learning is critical for a wide range of applications, such as multimodal sentiment analysis. Current multimodal representation learning methods mainly focus on the multimodal alignment or fusion strategies, such that the complementary and consistent information among heterogeneous modalities can be fully explored. However, they mistakenly treat the uncertainty noise within each modality as the complementary information, failing to simultaneously leverage both consistent and complementary information while eliminating the aleatoric uncertainty within each modality. To address this issue, we propose a plug-and-play feature causality decomposition method for multimodal representation learning from causality perspective, which can be integrated into existing models with no affects on the original model structures. Specifically, to deal with the heterogeneity and consistency, according to whether it can be aligned with other modalities, the unimodal feature is first disentangled into two parts: modality-invariant (the synergistic information shared by all heterogeneous modalities) and modality-specific part. To deal with complementarity and uncertainty, the modality-specific part is further decomposed into unique and redundant features, where the redundant feature is removed and the unique feature is reserved based on the backdoor-adjustment. The effectiveness of noise removal is supported by causality theory. Finally, the task-related information, including both synergistic and unique components, is further fed to the original fusion module to obtain the final multimodal representations. Extensive experiments show the effectiveness of our proposed strategies.

Blind Image Quality Assessment (BIQA) has advanced significantly through deep learning, but the scarcity of large-scale labeled datasets remains a challenge. While synthetic data offers a promising solution, models trained on existing synthetic datasets often show limited generalization ability. In this work, we make a key observation that representations learned from synthetic datasets often exhibit a discrete and clustered pattern that hinders regression performance: features of high-quality images cluster around reference images, while those of low-quality images cluster based on distortion types. Our analysis reveals that this issue stems from the distribution of synthetic data rather than model architecture. Consequently, we introduce a novel framework SynDR-IQA, which reshapes synthetic data distribution to enhance BIQA generalization. Based on theoretical derivations of sample diversity and redundancy's impact on generalization error, SynDR-IQA employs two strategies: distribution-aware diverse content upsampling, which enhances visual diversity while preserving content distribution, and density-aware redundant cluster downsampling, which balances samples by reducing the density of densely clustered areas. Extensive experiments across three cross-dataset settings (synthetic-to-authentic, synthetic-to-algorithmic, and synthetic-to-synthetic) demonstrate the effectiveness of our method. The code is available at https://github.com/Li-aobo/SynDR-IQA.

Table Question Answering (TableQA) combines natural language understanding and structured data reasoning, posing challenges in semantic interpretation and logical inference. Recent advances in Large Language Models (LLMs) have improved TableQA performance through Direct Prompting and Agent paradigms. However, these models often rely on spurious correlations, as they tend to overfit to token co-occurrence patterns in pretraining corpora, rather than perform genuine reasoning. To address this issue, we propose Causal Intervention TableQA (CIT), which is based on a structural causal graph and applies front-door adjustment to eliminate bias caused by token co-occurrence. CIT formalizes TableQA as a causal graph and identifies token co-occurrence patterns as confounders. By applying front-door adjustment, CIT guides question variant generation and reasoning to reduce confounding effects. Experiments on multiple benchmarks show that CIT achieves state-of-the-art performance, demonstrating its effectiveness in mitigating bias. Consistent gains across various LLMs further confirm its generalizability.

Plug-and-play (PnP) methods with deep denoisers have shown impressive results in imaging problems. They typically require strong convexity or smoothness of the fidelity term and a (residual) non-expansive denoiser for convergence. These assumptions, however, are violated in Poisson inverse problems, and non-expansiveness can hinder denoising performance. To address these challenges, we propose a cocoercive conservative (CoCo) denoiser, which may be (residual) expansive, leading to improved denoising performance. By leveraging the generalized Helmholtz decomposition, we introduce a novel training strategy that combines Hamiltonian regularization to promote conservativeness and spectral regularization to ensure cocoerciveness. We prove that CoCo denoiser is a proximal operator of a weakly convex function, enabling a restoration model with an implicit weakly convex prior. The global convergence of PnP methods to a stationary point of this restoration model is established. Extensive experimental results demonstrate that our approach outperforms closely related methods in both visual quality and quantitative metrics.

Temporal graph link prediction aims to predict future interactions between nodes in a graph based on their historical interactions, which are encoded in node embeddings. We observe that heterogeneity naturally appears in temporal interactions, e.g., a few node pairs can make most interaction events, and interaction events happen at varying intervals. This leads to the problems of ineffective temporal information encoding and forgetting of past interactions for a pair of nodes that interact intermittently for their link prediction. Existing methods, however, do not consider such heterogeneity in their learning process, and thus their learned temporal node embeddings are less effective, especially when predicting the links for infrequently interacting node pairs. To cope with the heterogeneity, we propose a novel framework called TAMI, which contains two effective components, namely log time encoding function (LTE) and link history aggregation (LHA). LTE better encodes the temporal information through transforming interaction intervals into more balanced ones, and LHA prevents the historical interactions for each target node pair from being forgotten. State-of-the-art temporal graph neural networks can be seamlessly and readily integrated into TAMI to improve their effectiveness. Experiment results on 13 classic datasets and three newest temporal graph benchmark (TGB) datasets show that TAMI consistently improves the link prediction performance of the underlying models in both transductive and inductive settings. Our code is available at https://github.com/Alleinx/TAMI_temporal_graph.

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.

In-context Ranking (ICR) is an emerging paradigm for Information Retrieval (IR), which leverages contextual understanding of LLMs by directly incorporating the task description, candidate documents, and the query into the model's input prompt and tasking the LLM to identify relevant document(s). While it is effective, efficiency is a significant challenge in this paradigm, especially as the candidate list grows due to quadratic/super-linear scaling of attention operation with context length. To this end, this paper first identifies inherent and exploitable structures in the attention of LLMs finetuned for ICR: (1) inter-document block sparsity: attention is dense within each document block but sparse across different documents in the context; and (2) query-document block relevance: the attention scores from certain query tokens to a document block in middle layers strongly correlate with that document's actual relevance. Motivated by these observations, we introduce BlockRank (Blockwise In-context Ranking), a novel method that adapts the attention operation in an LLM by (a) architecturally enforcing the observed inter-document block sparsity, reducing attention complexity from quadratic to linear without loss in performance, and (b) optimizing query-document block relevance for true relevant documents during fine-tuning using an auxiliary contrastive training objective, improving retrieval in attention. Experiments on BEIR, MSMarco and NQ with Mistral-7B demonstrate that BlockRank Mistral matches or outperforms existing SOTA listwise rankers and controlled fine-tuned baseline while being significantly more efficient at inference (4.7x for 100 MSMarco documents in context) and scaling gracefully to long-context shortlists, around 500 documents in-context (approximately 100K context length) within a second, presenting a scalable and effective solution for ICR.

The weighted controlled direct effect (WCDE) generalizes the standard controlled direct effect (CDE) by averaging over the mediator distribution, providing a robust estimate when treatment effects vary across mediator levels. This makes the WCDE especially relevant in fairness analysis, where it isolates the direct effect of an exposure on an outcome, independent of mediating pathways. In this work, we first establish necessary and sufficient conditions for the unique identifiability of the WCDE, clarifying when it diverges from the CDE. Next, we derive the efficient influence function for the WCDE and consider the class of regular and asymptotically linear estimators. We characterize the optimal covariate adjustment set that minimizes asymptotic variance, demonstrating how mediator-confounder interactions introduce distinct requirements compared to average treatment effect estimation. Our results offer a principled framework for efficient estimation of direct effects in complex causal systems, with practical applications in fairness and mediation analysis.

Tools from control and dynamical systems have proven valuable for analyzing and developing optimization methods. In this paper, we establish rigorous theoretical foundations for using feedback linearization—a well-established nonlinear control technique—to solve constrained optimization problems. For equality-constrained optimization, we establish global convergence rates to first-order Karush-Kuhn-Tucker (KKT) points and uncover the close connection between the FL method and the Sequential Quadratic Programming (SQP) algorithm. Building on this relationship, we extend the FL approach to handle inequality-constrained problems. Furthermore, we introduce a momentum-accelerated feedback linearization algorithm and provide a rigorous convergence guarantee.

Recent advances in language modeling and vision stem from training large models on diverse, multi‑task data. This paradigm has had limited impact in value-based reinforcement learning (RL), where improvements are often driven by small models trained in a single-task context. This is because in multi-task RL sparse rewards and gradient conflicts make optimization of temporal difference brittle. Practical workflows for generalist policies therefore avoid online training, instead cloning expert trajectories or distilling collections of single‑task policies into one agent. In this work, we show that the use of high-capacity value models trained via cross-entropy and conditioned on learnable task embeddings addresses the problem of task interference in online RL, allowing for robust and scalable multi‑task training. We test our approach on 7 multi-task benchmarks with over 280 unique tasks, spanning high degree-of-freedom humanoid control and discrete vision-based RL. We find that, despite its simplicity, the proposed approach leads to state-of-the-art single and multi-task performance, as well as sample-efficient transfer to new tasks.

Accurate estimation of background error (i.e., forecast error) distribution is critical for effective data assimilation (DA) in numerical weather prediction (NWP). In state-of-the-art operational DA systems, it is common to account for the temporal evolution of background errors by employing hybrid methods, which blend a static climatological covariance with a flow-dependent ensemble-derived component. While effective to some extent, these methods typically assume Gaussian-distributed errors and rely heavily on hand-crafted covariance structures and domain expertise, limiting their ability to capture the complex, non-Gaussian nature of atmospheric dynamics. In this work, we propose LoRA-EnVar, a novel hybrid ensemble variational DA algorithm that integrates low-rank adaptation (LoRA) into a deep generative modeling framework. We first learn a climatological background error distribution using a variational autoencoder (VAE) trained on historical data. To incorporate flow-dependent uncertainty, we introduce LoRA modules that efficiently adapt the learned distribution in response to flow-dependent ensemble perturbations. Our approach supports online finetuning, enabling dynamic updates of the background error distribution without catastrophic forgetting. We validate LoRA-EnVar in high-resolution assimilation settings using the FengWu forecast model and simulated observations from ERA5 reanalysis. Experimental results show that LoRA-EnVar significantly improves assimilation accuracy over models assuming static background error distribution and achieves comparable or better performance than full finetuning while reducing the number of trainable parameters by three orders of magnitude. This demonstrates the potential of parameter-efficient adaptation for scalable, non-Gaussian DA in operational meteorology.

Motivated by the success of general‑purpose large language models (LLMs) in software patching, recent works started to train specialized patching models. Most works trained one model to handle the end‑to‑end patching pipeline (including issue localization, patch generation, and patch validation). However, it is hard for a small model to handle all tasks, as different sub-tasks have different workflows and require different expertise. As such, by using a 70 billion model, SOTA methods can only reach up to 41% resolved rate on SWE-bench-Verified. Motivated by the collaborative nature, we propose Co-PatcheR, the first collaborative patching system with small and specialized reasoning models for individual components. Our key technique novelties are the specific task designs and training recipes. First, we train a model for localization and patch generation. Our localization pinpoints the suspicious lines through a two-step procedure, and our generation combines patch generation and critique. We then propose a hybrid patch validation that includes two models for crafting issue-reproducing test cases with and without assertions and judging patch correctness, followed by a majority vote-based patch selection. Through extensive evaluation, we show that Co-PatcheR achieves 46% resolved rate on SWE-bench-Verified with only 3 x 14B models. This makes Co-PatcheR the best patcher with specialized models, requiring the least training resources and the smallest models. We conduct a comprehensive ablation study to validate our recipes, as well as our choice of training data number, model size, and testing-phase scaling strategy.

Adversarial attacks are widely used to evaluate model robustness, and in black-box scenarios, the transferability of these attacks becomes crucial. Existing generator-based attacks have excellent generalization and transferability due to their instance-agnostic nature. However, when training generators for multi-target tasks, the success rate of transfer attacks is relatively low due to the limitations of the model's capacity. To address these challenges, we propose a novel Dual-Flow framework for multi-target instance-agnostic adversarial attacks, utilizing Cascading Distribution Shift Training to develop an adversarial velocity function. Extensive experiments demonstrate that Dual-Flow significantly improves transferability over previous multi-target generative attacks. For example, it increases the success rate from Inception-v3 to ResNet-152 by 34.58%. Furthermore, our attack method shows substantially stronger robustness against defense mechanisms, such as adversarially trained models.

Evolutionary algorithms (EAs) have proven effective in exploring the vast solution spaces typical of graph-structured combinatorial problems. However, traditional encoding schemes, such as binary or numerical representations, often fail to straightforwardly capture the intricate structural properties of networks. Through employing the image-based encoding to preserve topological context, this study utilizes multimodal large language models (MLLMs) as evolutionary operators to facilitate structure-aware optimization over graph data. To address the visual clutter inherent in large-scale network visualizations, we leverage graph sparsification techniques to simplify structures while maintaining essential structural features. To further improve robustness and mitigate bias from different sparsification views, we propose a cooperative evolutionary optimization framework that facilitates cross-domain knowledge transfer and unifies multiple sparsified variants of diverse structures. Additionally, recognizing the sensitivity of MLLMs to network layout, we introduce an ensemble strategy that aggregates outputs from various layout configurations through consensus voting. Finally, experiments on real-world networks through various tasks demonstrate that our approach improves both the quality and reliability of solutions in MLLM-driven evolutionary optimization.

Noisy labels often compel models to overfit, especially in multi-label classification tasks. Existing methods for noisy multi-label learning (NML) primarily follow a discriminative paradigm, which relies on noise transition matrix estimation or small-loss strategies to correct noisy labels. However, they remain substantial optimization difficulties compared to noisy single-label learning. In this paper, we propose a Co-Occurrence-Aware Diffusion (CAD) model, which reformulates NML from a generative perspective. We treat features as conditions and multi-labels as diffusion targets, optimizing the diffusion model for multi-label learning with theoretical guarantees. Benefiting from the diffusion model's strength in capturing multi-object semantics and structured label matrix representation, we can effectively learn the posterior mapping from features to true multi-labels. To mitigate the interference of noisy labels in the forward process, we guide generation using pseudo-clean labels reconstructed from the latent neighborhood space, replacing original point-wise estimates with neighborhood-based proxies. In the reverse process, we further incorporate label co-occurrence constraints to enhance the model's awareness of incorrect generation directions, thereby promoting robust optimization. Extensive experiments on both synthetic (Pascal-VOC, MS-COCO) and real-world (NUS-WIDE) noisy datasets demonstrate that our approach outperforms state-of-the-art methods.

Low-Rank Adaptation (LoRA) lowers the computational and memory overhead of fine-tuning large models by updating a low-dimensional subspace of the pre-trained weight matrix. Albeit efficient, LoRA exhibits suboptimal convergence and noticeable performance degradation, due to inconsistent and imbalanced weight updates induced by its nonunique low-rank factorizations. To overcome these limitations, this article identifies the optimal low-rank factorization per step that minimizes an upper bound on the loss. The resultant refactored low-rank adaptation (RefLoRA) method promotes a flatter loss landscape, along with consistent and balanced weight updates, thus speeding up stable convergence. Extensive experiments evaluate RefLoRA on natural language understanding, and commonsense reasoning tasks with popular large language models including DeBERTaV3, LLaMA-7B, LLaMA2-7B and LLaMA3-8B. The numerical tests corroborate that RefLoRA converges faster, outperforms various benchmarks, and enjoys negligible computational overhead compared to state-of-the-art LoRA variants.

Autoregressive models have emerged as a powerful framework for modeling exchangeable sequences---i.i.d. observations when conditioned on some latent factor---enabling direct modeling of uncertainty from missing data (rather than a latent). Motivated by the critical role posterior inference plays as a subroutine in decision-making (e.g., active learning, bandits), we study the inferential and architectural inductive biases that are most effective for exchangeable sequence modeling. For the inference stage, we highlight a fundamental limitation of the prevalent single-step generation approach: its inability to distinguish between epistemic and aleatoric uncertainty. Instead, a long line of works in Bayesian statistics advocates for multi-step autoregressive generation; we demonstrate this "correct approach" enables superior uncertainty quantification that translates into better performance on downstream decision-making tasks. This naturally leads to the next question: which architectures are best suited for multi-step inference? We identify a subtle yet important gap between recently proposed Transformer architectures for exchangeable sequences (Müller et al., 2022; Nguyen & Grover, 2022; Ye & Namkoong, 2024), and prove that they in fact cannot guarantee exchangeability despite introducing significant computational overhead. Through empirical evaluation, we find that these custom architectures can significantly underperform compared to standard causal masking, highlighting the need for new architectural innovations in Transformer-based modeling of exchangeable sequences.

Feed-forward 3D Gaussian Splatting (3DGS) models have recently emerged as a promising solution for novel view synthesis, enabling one-pass inference without the need for per-scene 3DGS optimization. However, their scalability is fundamentally constrained by the limited capacity of their encoders, leading to degraded performance or excessive memory consumption as the number of input views increases. In this work, we analyze feed-forward 3DGS frameworks through the lens of the Information Bottleneck principle and introduce ZPressor, a lightweight architecture-agnostic module that enables efficient compression of multi-view inputs into a compact latent state $Z$ that retains essential scene information while discarding redundancy. Concretely, ZPressor enables existing feed-forward 3DGS models to scale to over 100 input views at 480P resolution on an 80GB GPU, by partitioning the views into anchor and support sets and using cross attention to compress the information from the support views into anchor views, forming the compressed latent state $Z$. We show that integrating ZPressor into several state-of-the-art feed-forward 3DGS models consistently improves performance under moderate input views and enhances robustness under dense view settings on two large-scale benchmarks DL3DV-10K and RealEstate10K.